2020��� 04��� 28��� ��������� 20:36:55 CST /home/web/freesurver/test/MRI/subjects02 /usr/local/freesurfer/bin/recon-all -all -s subjects02 subjid subjects02 setenv SUBJECTS_DIR /home/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux web-virtual-machine 4.15.0-96-generic #97~16.04.1-Ubuntu SMP Wed Apr 1 03:03:31 UTC 2020 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 257450 maxlocks unlimited maxsignal 257450 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 65968380 1950728 59509108 123516 4508544 63078404 Swap: 8386556 0 8386556 ######################################## 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: 2020/04/28-12:36:55-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:55-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:55-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/04/28-12:36:55-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:55-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:55-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/04/28-12:36:55-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/04/28-12:36:55-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/04/28-12:36:55-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/04/28-12:36:55-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/04/28-12:36:55-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/04/28-12:36:55-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:55-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:55-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/04/28-12:36:56-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: web Machine: web-virtual-machine Platform: Linux PlatformVersion: 4.15.0-96-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# MotionCor 2020��� 04��� 28��� ��������� 20:36:56 CST Found 1 runs /home/web/freesurver/test/MRI/subjects02/mri//002.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/web/freesurver/test/MRI/subjects02/mri//002.mgz /home/web/freesurver/test/MRI/subjects02/mri/rawavg.mgz /home/web/freesurver/test/MRI/subjects02 mri_convert /home/web/freesurver/test/MRI/subjects02/mri/rawavg.mgz /home/web/freesurver/test/MRI/subjects02/mri/orig.mgz --conform mri_convert.bin /home/web/freesurver/test/MRI/subjects02/mri/rawavg.mgz /home/web/freesurver/test/MRI/subjects02/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/web/freesurver/test/MRI/subjects02/mri/rawavg.mgz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/web/freesurver/test/MRI/subjects02/mri/orig.mgz... mri_add_xform_to_header -c /home/web/freesurver/test/MRI/subjects02/mri/transforms/talairach.xfm /home/web/freesurver/test/MRI/subjects02/mri/orig.mgz /home/web/freesurver/test/MRI/subjects02/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach 2020��� 04��� 28��� ��������� 20:37:05 CST /home/web/freesurver/test/MRI/subjects02/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/web/freesurver/test/MRI/subjects02/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux web-virtual-machine 4.15.0-96-generic #97~16.04.1-Ubuntu SMP Wed Apr 1 03:03:31 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 2020��� 04��� 28��� ��������� 20:37:06 CST 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.6686 /home/web/freesurver/test/MRI/subjects02/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.6686/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.6686/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.6686/nu0.mnc... -------------------------------------------------------- Iteration 1 2020��� 04��� 28��� ��������� 20:37:20 CST nu_correct -clobber ./tmp.mri_nu_correct.mni.6686/nu0.mnc ./tmp.mri_nu_correct.mni.6686/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.6686/0/ -iterations 1000 -distance 50 [web@web-virtual-machine:/home/web/freesurver/test/MRI/subjects02/mri/] [2020-04-28 20:37:21] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.6686/0/ ./tmp.mri_nu_correct.mni.6686/nu0.mnc ./tmp.mri_nu_correct.mni.6686/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 Number of iterations: 34 CV of field change: 0.000966133 mri_convert ./tmp.mri_nu_correct.mni.6686/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.6686/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.6686/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 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... 2020��� 04��� 28��� ��������� 20:38:32 CST mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at 2020��� 04��� 28��� ��������� 20:38:32 CST Ended at 2020��� 04��� 28��� ��������� 20:39:20 CST talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection 2020��� 04��� 28��� ��������� 20:39:22 CST /home/web/freesurver/test/MRI/subjects02/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6120, pval=0.2817 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /home/web/freesurver/test/MRI/subjects02/mri/transforms/talairach_avi.log tal_QC_AZS /home/web/freesurver/test/MRI/subjects02/mri/transforms/talairach_avi.log TalAviQA: 0.97417 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction 2020��� 04��� 28��� ��������� 20:39:22 CST mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home/web/freesurver/test/MRI/subjects02/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux web-virtual-machine 4.15.0-96-generic #97~16.04.1-Ubuntu SMP Wed Apr 1 03:03:31 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 2020��� 04��� 28��� ��������� 20:39:22 CST 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.9791 /home/web/freesurver/test/MRI/subjects02/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9791/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.9791/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.9791/nu0.mnc... -------------------------------------------------------- Iteration 1 2020��� 04��� 28��� ��������� 20:39:27 CST nu_correct -clobber ./tmp.mri_nu_correct.mni.9791/nu0.mnc ./tmp.mri_nu_correct.mni.9791/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9791/0/ [web@web-virtual-machine:/home/web/freesurver/test/MRI/subjects02/mri/] [2020-04-28 20:39:27] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.9791/0/ ./tmp.mri_nu_correct.mni.9791/nu0.mnc ./tmp.mri_nu_correct.mni.9791/nu1.imp Processing:.................................................................Done 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-------------------------------------------------------- Iteration 2 2020��� 04��� 28��� ��������� 20:40:13 CST nu_correct -clobber ./tmp.mri_nu_correct.mni.9791/nu1.mnc ./tmp.mri_nu_correct.mni.9791/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.9791/1/ [web@web-virtual-machine:/home/web/freesurver/test/MRI/subjects02/mri/] [2020-04-28 20:40:13] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.9791/1/ ./tmp.mri_nu_correct.mni.9791/nu1.mnc ./tmp.mri_nu_correct.mni.9791/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Number of iterations: 16 CV of field change: 0.000982944 mri_binarize --i ./tmp.mri_nu_correct.mni.9791/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9791/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /home/web/freesurver/test/MRI/subjects02/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.9791/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9791/ones.mgz sysname Linux hostname web-virtual-machine machine x86_64 user web input ./tmp.mri_nu_correct.mni.9791/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.9791/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.9791/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9791/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9791/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.9791/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9791/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9791/input.mean.dat sysname Linux hostname web-virtual-machine machine x86_64 user web UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9791/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.9791/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9791/ones.mgz --i ./tmp.mri_nu_correct.mni.9791/nu2.mnc --sum ./tmp.mri_nu_correct.mni.9791/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9791/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.9791/ones.mgz --i ./tmp.mri_nu_correct.mni.9791/nu2.mnc --sum ./tmp.mri_nu_correct.mni.9791/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9791/output.mean.dat sysname Linux hostname web-virtual-machine machine x86_64 user web UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9791/ones.mgz Loading ./tmp.mri_nu_correct.mni.9791/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.9791/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.9791/nu2.mnc ./tmp.mri_nu_correct.mni.9791/nu2.mnc mul .99922071276385840274 Saving result to './tmp.mri_nu_correct.mni.9791/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.9791/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.9791/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.9791/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 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 16 seconds. mapping ( 8, 167) to ( 3, 110) 2020��� 04��� 28��� ��������� 20:41:51 CST mri_nu_correct.mni done mri_add_xform_to_header -c /home/web/freesurver/test/MRI/subjects02/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization 2020��� 04��� 28��� ��������� 20:41:51 CST /home/web/freesurver/test/MRI/subjects02/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 1.07273 -0.09763 -0.03672 0.24467; 0.01505 1.18026 -0.02405 -50.17537; 0.03513 0.05982 1.10563 -18.22433; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 20 Starting OpenSpline(): npoints = 20 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 60 (60), valley at 30 (30) csf peak at 30, setting threshold to 50 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 60 (60), valley at 27 (27) csf peak at 31, setting threshold to 50 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 30 seconds. #-------------------------------------------- #@# Skull Stripping 2020��� 04��� 28��� ��������� 20:44:23 CST /home/web/freesurver/test/MRI/subjects02/mri mri_em_register -rusage /home/web/freesurver/test/MRI/subjects02/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=8.0 skull bounding box = (44, 44, 38) --> (208, 214, 217) using (99, 101, 128) as brain centroid... mean wm in atlas = 108, using box (79,80,106) --> (119, 121,150) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 107 +- 5.0 after smoothing, mri peak at 107, scaling input intensities by 1.009 scaling channel 0 by 1.00935 initial log_p = -4.379 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.381499 @ (0.000, 0.000, 0.000) max log p = -4.291744 @ (4.545, -4.545, -4.545) max log p = -4.219114 @ (-2.273, 2.273, -6.818) max log p = -4.177411 @ (-1.136, 3.409, 3.409) max log p = -4.177124 @ (0.568, -6.250, -3.977) max log p = -4.177124 @ (0.000, 0.000, 0.000) Found translation: (1.7, -5.1, -11.9): log p = -4.177 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.875, old_max_log_p =-4.177 (thresh=-4.2) 1.14016 0.00000 0.15011 -41.50042; 0.00000 1.15000 0.00000 -19.70681; -0.15011 0.00000 1.14016 -10.66281; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.827, old_max_log_p =-3.875 (thresh=-3.9) 1.05465 0.00000 0.13885 -29.02224; 0.02106 1.22567 -0.15998 -5.79869; -0.14882 0.15011 1.13041 -30.75235; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.827, old_max_log_p =-3.827 (thresh=-3.8) 1.05465 0.00000 0.13885 -29.02224; 0.02106 1.22567 -0.15998 -5.79869; -0.14882 0.15011 1.13041 -30.75235; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.720, old_max_log_p =-3.827 (thresh=-3.8) 1.03394 0.03955 0.13332 -28.91385; -0.02278 1.20824 -0.08845 -10.36870; -0.15269 0.07093 1.15980 -25.11539; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.720, old_max_log_p =-3.720 (thresh=-3.7) 1.03394 0.03955 0.13332 -28.91385; -0.02278 1.20824 -0.08845 -10.36870; -0.15269 0.07093 1.15980 -25.11539; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.702, old_max_log_p =-3.720 (thresh=-3.7) 1.03543 0.01979 0.13460 -27.00729; -0.00832 1.20547 -0.06703 -14.51726; -0.15176 0.05097 1.15701 -23.06865; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.695, old_max_log_p =-3.702 (thresh=-3.7) 1.03543 0.01979 0.13460 -27.00729; -0.00834 1.20830 -0.06719 -14.88451; -0.15123 0.05079 1.15295 -22.59795; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.695, old_max_log_p =-3.695 (thresh=-3.7) 1.03543 0.01979 0.13460 -27.00729; -0.00834 1.20830 -0.06719 -14.88451; -0.15123 0.05079 1.15295 -22.59795; 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 1.03543 0.01979 0.13460 -27.00729; -0.00834 1.20830 -0.06719 -14.88451; -0.15123 0.05079 1.15295 -22.59795; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.03543 0.01979 0.13460 -27.00729; -0.00834 1.20830 -0.06719 -14.88451; -0.15123 0.05079 1.15295 -22.59795; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03543 0.01979 0.13460 -27.00729; -0.00834 1.20830 -0.06719 -14.88451; -0.15123 0.05079 1.15295 -22.59795; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.695 (old=-4.379) transform before final EM align: 1.03543 0.01979 0.13460 -27.00729; -0.00834 1.20830 -0.06719 -14.88451; -0.15123 0.05079 1.15295 -22.59795; 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 1.03543 0.01979 0.13460 -27.00729; -0.00834 1.20830 -0.06719 -14.88451; -0.15123 0.05079 1.15295 -22.59795; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.03543 0.01979 0.13460 -27.00729; -0.00834 1.20830 -0.06719 -14.88451; -0.15123 0.05079 1.15295 -22.59795; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.1 tol 0.000000 final transform: 1.03543 0.01979 0.13460 -27.00729; -0.00834 1.20830 -0.06719 -14.88451; -0.15123 0.05079 1.15295 -22.59795; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1228.558975 mri_em_register stimesec 5.298688 mri_em_register ru_maxrss 614128 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 274121 mri_em_register ru_majflt 6 mri_em_register ru_nswap 0 mri_em_register ru_inblock 150296 mri_em_register ru_oublock 32 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 400 mri_em_register ru_nivcsw 1897 registration took 20 minutes and 35 seconds. mri_watershed -rusage /home/web/freesurver/test/MRI/subjects02/touch/rusage.mri_watershed.dat -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=128 y=117 z=128 r=71 first estimation of the main basin volume: 1556604 voxels Looking for seedpoints 2 found in the cerebellum 14 found in the rest of the brain global maximum in x=102, y=100, z=95, Imax=255 CSF=13, 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=409322401 voxels, voxel volume =1.000 = 409322401 mmm3 = 409322.400 cm3 done. PostAnalyze...Basin Prior 18 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=127,y=117, z=121, r=8853 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=6, CSF_MAX=28 , nb = 43496 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = -1039543888 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=25 , nb = 1103306992 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=6, CSF_MAX=27 , nb = 1080509693 LEFT_BRAIN CSF_MIN=0, CSF_intensity=6, CSF_MAX=29 , nb = 1072936312 OTHER CSF_MIN=0, CSF_intensity=9, CSF_MAX=35 , nb = 1076341494 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 28, 32, 37, 59 after analyzing : 28, 35, 37, 41 RIGHT_CER before analyzing : 24, 28, 35, 66 after analyzing : 24, 32, 35, 40 LEFT_CER before analyzing : 25, 30, 37, 61 after analyzing : 25, 34, 37, 40 RIGHT_BRAIN before analyzing : 27, 32, 37, 58 after analyzing : 27, 35, 37, 40 LEFT_BRAIN before analyzing : 29, 33, 37, 59 after analyzing : 29, 35, 37, 41 OTHER before analyzing : 35, 26, 12, 59 after analyzing : 21, 26, 26, 34 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...62 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 67.350, std = 5.801 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 8.28, sigma = 12.39 after rotation: sse = 8.28, sigma = 12.39 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 9.53, its var is 11.94 before Erosion-Dilatation 9.33% of inacurate vertices after Erosion-Dilatation 11.82% 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...42 iterations mri_strip_skull: done peeling brain Brain Size = 1527130 voxels, voxel volume = 1.000 mm3 = 1527130 mmm3 = 1527.130 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 23.386398 mri_watershed stimesec 1.374852 mri_watershed ru_maxrss 827476 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 242933 mri_watershed ru_majflt 9 mri_watershed ru_nswap 0 mri_watershed ru_inblock 9688 mri_watershed ru_oublock 2424 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 54 mri_watershed ru_nivcsw 30 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration 2020��� 04��� 28��� ��������� 21:05:25 CST /home/web/freesurver/test/MRI/subjects02/mri mri_em_register -rusage /home/web/freesurver/test/MRI/subjects02/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=25.0 skull bounding box = (58, 60, 50) --> (196, 168, 207) using (104, 96, 129) as brain centroid... mean wm in atlas = 107, using box (87,83,110) --> (120, 109,148) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 107 +- 4.2 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.057 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.056911 @ (0.000, 0.000, 0.000) max log p = -3.891417 @ (-4.545, -4.545, -13.636) max log p = -3.716679 @ (6.818, 2.273, -2.273) max log p = -3.716679 @ (0.000, 0.000, 0.000) max log p = -3.706585 @ (-1.705, -0.568, -0.568) max log p = -3.706585 @ (0.000, 0.000, 0.000) Found translation: (0.6, -2.8, -16.5): log p = -3.707 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.515, old_max_log_p =-3.707 (thresh=-3.7) 1.00000 0.00000 0.00000 0.56818; 0.00000 1.06580 -0.16136 16.29612; 0.00000 0.13053 1.14016 -49.50728; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.515, old_max_log_p =-3.515 (thresh=-3.5) 1.00000 0.00000 0.00000 0.56818; 0.00000 1.06580 -0.16136 16.29612; 0.00000 0.13053 1.14016 -49.50728; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.225, old_max_log_p =-3.515 (thresh=-3.5) 1.05469 0.00419 0.07938 -18.42992; 0.00000 1.13312 -0.09137 -3.86845; -0.06295 0.05814 1.10285 -26.77160; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.223, old_max_log_p =-3.225 (thresh=-3.2) 1.05413 -0.03289 0.08233 -14.32256; 0.03516 1.15388 -0.09039 -9.07426; -0.06295 0.05814 1.10285 -26.77160; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.182, old_max_log_p =-3.223 (thresh=-3.2) 1.05041 -0.00409 0.08883 -18.46064; 0.00925 1.15435 -0.09231 -6.51734; -0.07162 0.05817 1.10345 -26.20691; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.180, old_max_log_p =-3.182 (thresh=-3.2) 1.05165 -0.00410 0.08894 -18.16204; 0.00867 1.15614 -0.08338 -7.73887; -0.07161 0.04867 1.10288 -24.55144; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05165 -0.00410 0.08894 -18.16204; 0.00867 1.15614 -0.08338 -7.73887; -0.07161 0.04867 1.10288 -24.55144; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.05165 -0.00410 0.08894 -18.16204; 0.00867 1.15614 -0.08338 -7.73887; -0.07161 0.04867 1.10288 -24.55144; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.05165 -0.00410 0.08894 -18.16204; 0.00867 1.15614 -0.08338 -7.73887; -0.07161 0.04867 1.10288 -24.55144; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.180 (old=-4.057) transform before final EM align: 1.05165 -0.00410 0.08894 -18.16204; 0.00867 1.15614 -0.08338 -7.73887; -0.07161 0.04867 1.10288 -24.55144; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05165 -0.00410 0.08894 -18.16204; 0.00867 1.15614 -0.08338 -7.73887; -0.07161 0.04867 1.10288 -24.55144; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.05165 -0.00410 0.08894 -18.16204; 0.00867 1.15614 -0.08338 -7.73887; -0.07161 0.04867 1.10288 -24.55144; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 3.8 tol 0.000000 final transform: 1.05165 -0.00410 0.08894 -18.16204; 0.00867 1.15614 -0.08338 -7.73887; -0.07161 0.04867 1.10288 -24.55144; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 769.534887 mri_em_register stimesec 3.153899 mri_em_register ru_maxrss 603248 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 162492 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 140152 mri_em_register ru_oublock 32 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 230 mri_em_register ru_nivcsw 1308 registration took 12 minutes and 54 seconds. #-------------------------------------- #@# CA Normalize 2020��� 04��� 28��� ��������� 21:18:18 CST /home/web/freesurver/test/MRI/subjects02/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=25.0 skull bounding box = (58, 60, 50) --> (196, 168, 207) using (104, 96, 129) as brain centroid... mean wm in atlas = 107, using box (87,83,110) --> (120, 109,148) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 107 +- 4.2 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 using 246344 sample points... INFO: compute sample coordinates transform 1.05165 -0.00410 0.08894 -18.16204; 0.00867 1.15614 -0.08338 -7.73887; -0.07161 0.04867 1.10288 -24.55144; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (125, 58, 49) --> (191, 164, 202) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 1 of 5100 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 59, 48) --> (129, 165, 200) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 1 of 4878 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 132, 68) --> (177, 168, 118) Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 22 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (88, 132, 65) --> (131, 169, 117) Right_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 38 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 126, 98) --> (145, 186, 128) Brain_Stem: limiting intensities to 101.0 --> 132.0 13 of 32 (40.6%) samples deleted using 10070 total control points for intensity normalization... bias field = 0.970 +- 0.037 68 of 10055 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (125, 58, 49) --> (191, 164, 202) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 5754 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 59, 48) --> (129, 165, 200) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 3 of 5528 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 132, 68) --> (177, 168, 118) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 83 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (88, 132, 65) --> (131, 169, 117) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 99 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 126, 98) --> (145, 186, 128) Brain_Stem: limiting intensities to 88.0 --> 132.0 9 of 106 (8.5%) samples deleted using 11570 total control points for intensity normalization... bias field = 1.021 +- 0.037 73 of 11432 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (125, 58, 49) --> (191, 164, 202) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 5779 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 59, 48) --> (129, 165, 200) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 3 of 5613 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (131, 132, 68) --> (177, 168, 118) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 25 of 168 (14.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (88, 132, 65) --> (131, 169, 117) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 39 of 144 (27.1%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 126, 98) --> (145, 186, 128) Brain_Stem: limiting intensities to 88.0 --> 132.0 88 of 185 (47.6%) samples deleted using 11889 total control points for intensity normalization... bias field = 1.018 +- 0.034 44 of 11498 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 52 seconds. #-------------------------------------- #@# CA Reg 2020��� 04��� 28��� ��������� 21:20:10 CST /home/web/freesurver/test/MRI/subjects02/mri mri_ca_register -rusage /home/web/freesurver/test/MRI/subjects02/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.35 (predicted orig area = 5.9) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.776, neg=0, invalid=762 0001: dt=217.458996, rms=0.706 (9.004%), neg=0, invalid=762 0002: dt=175.532164, rms=0.686 (2.866%), neg=0, invalid=762 0003: dt=153.893130, rms=0.680 (0.932%), neg=0, invalid=762 0004: dt=295.936000, rms=0.674 (0.811%), neg=0, invalid=762 0005: dt=129.472000, rms=0.671 (0.392%), neg=0, invalid=762 0006: dt=517.888000, rms=0.668 (0.460%), neg=0, invalid=762 0007: dt=110.976000, rms=0.666 (0.343%), neg=0, invalid=762 0008: dt=2071.552000, rms=0.659 (1.017%), neg=0, invalid=762 0009: dt=110.976000, rms=0.656 (0.499%), neg=0, invalid=762 0010: dt=517.888000, rms=0.654 (0.238%), neg=0, invalid=762 0011: dt=517.888000, rms=0.654 (-0.461%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.655, neg=0, invalid=762 0012: dt=129.472000, rms=0.654 (0.211%), neg=0, invalid=762 0013: dt=517.888000, rms=0.652 (0.205%), neg=0, invalid=762 0014: dt=517.888000, rms=0.651 (0.186%), neg=0, invalid=762 0015: dt=517.888000, rms=0.649 (0.264%), neg=0, invalid=762 0016: dt=517.888000, rms=0.649 (-0.257%), neg=0, invalid=762 0017: dt=110.976000, rms=0.648 (0.189%), neg=0, invalid=762 0018: dt=517.888000, rms=0.647 (0.127%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.650, neg=0, invalid=762 0019: dt=203.122507, rms=0.636 (2.122%), neg=0, invalid=762 0020: dt=113.132743, rms=0.625 (1.714%), neg=0, invalid=762 0021: dt=87.208791, rms=0.620 (0.751%), neg=0, invalid=762 0022: dt=144.615385, rms=0.616 (0.666%), neg=0, invalid=762 0023: dt=69.539281, rms=0.612 (0.625%), neg=0, invalid=762 0024: dt=145.152000, rms=0.610 (0.459%), neg=0, invalid=762 0025: dt=76.585774, rms=0.607 (0.461%), neg=0, invalid=762 0026: dt=115.380282, rms=0.605 (0.301%), neg=0, invalid=762 0027: dt=76.962025, rms=0.603 (0.347%), neg=0, invalid=762 0028: dt=103.680000, rms=0.602 (0.221%), neg=0, invalid=762 0029: dt=103.680000, rms=0.600 (0.252%), neg=0, invalid=762 0030: dt=103.680000, rms=0.597 (0.540%), neg=0, invalid=762 0031: dt=103.680000, rms=0.594 (0.470%), neg=0, invalid=762 0032: dt=103.680000, rms=0.589 (0.825%), neg=0, invalid=762 0033: dt=103.680000, rms=0.586 (0.568%), neg=0, invalid=762 0034: dt=103.680000, rms=0.582 (0.656%), neg=0, invalid=762 0035: dt=103.680000, rms=0.579 (0.520%), neg=0, invalid=762 0036: dt=103.680000, rms=0.576 (0.455%), neg=0, invalid=762 0037: dt=103.680000, rms=0.574 (0.399%), neg=0, invalid=762 0038: dt=103.680000, rms=0.573 (0.231%), neg=0, invalid=762 0039: dt=103.680000, rms=0.571 (0.248%), neg=0, invalid=762 0040: dt=103.680000, rms=0.570 (0.196%), neg=0, invalid=762 0041: dt=103.680000, rms=0.569 (0.190%), neg=0, invalid=762 0042: dt=103.680000, rms=0.568 (0.131%), neg=0, invalid=762 0043: dt=103.680000, rms=0.568 (0.093%), neg=0, invalid=762 0044: dt=103.680000, rms=0.567 (0.190%), neg=0, invalid=762 0045: dt=103.680000, rms=0.566 (0.137%), neg=0, invalid=762 0046: dt=103.680000, rms=0.565 (0.104%), neg=0, invalid=762 0047: dt=103.680000, rms=0.565 (0.085%), neg=0, invalid=762 0048: dt=62.208000, rms=0.565 (0.038%), neg=0, invalid=762 0049: dt=62.208000, rms=0.564 (0.012%), neg=0, invalid=762 0050: dt=62.208000, rms=0.564 (0.005%), neg=0, invalid=762 0051: dt=62.208000, rms=0.564 (0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.565, neg=0, invalid=762 0052: dt=82.944000, rms=0.564 (0.250%), neg=0, invalid=762 0053: dt=145.152000, rms=0.563 (0.126%), neg=0, invalid=762 0054: dt=145.152000, rms=0.563 (-0.178%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.585, neg=0, invalid=762 0055: dt=0.100000, rms=0.585 (0.100%), neg=0, invalid=762 0056: dt=0.000000, rms=0.585 (0.001%), neg=0, invalid=762 0057: dt=0.250000, rms=0.585 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.585, neg=0, invalid=762 0058: dt=0.700000, rms=0.585 (0.103%), neg=0, invalid=762 0059: dt=0.400000, rms=0.585 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.650, neg=0, invalid=762 0060: dt=5.048406, rms=0.629 (3.245%), neg=0, invalid=762 0061: dt=1.852349, rms=0.629 (0.088%), neg=0, invalid=762 0062: dt=1.852349, rms=0.629 (-0.033%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.629, neg=0, invalid=762 0063: dt=0.036000, rms=0.629 (0.080%), neg=0, invalid=762 0064: dt=0.000176, rms=0.629 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.688, neg=0, invalid=762 0065: dt=1.536000, rms=0.682 (0.866%), neg=0, invalid=762 0066: dt=1.792000, rms=0.678 (0.708%), neg=0, invalid=762 0067: dt=0.448000, rms=0.677 (0.033%), neg=0, invalid=762 0068: dt=0.448000, rms=0.677 (0.025%), neg=0, invalid=762 0069: dt=0.448000, rms=0.677 (0.000%), neg=0, invalid=762 0070: dt=0.448000, rms=0.677 (-0.062%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.678, neg=0, invalid=762 0071: dt=1.536000, rms=0.676 (0.242%), neg=0, invalid=762 0072: dt=0.000000, rms=0.676 (-0.001%), 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=0.636, neg=0, invalid=762 0073: dt=0.884316, rms=0.617 (3.033%), neg=0, invalid=762 0074: dt=0.080000, rms=0.616 (0.163%), neg=0, invalid=762 0075: dt=0.080000, rms=0.616 (-0.090%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.616, neg=0, invalid=762 0076: dt=0.028000, rms=0.616 (0.088%), neg=0, invalid=762 0077: dt=0.000313, rms=0.616 (-0.000%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.18635 (10) Left_Lateral_Ventricle (4): linear fit = 0.41 x + 0.0 (800 voxels, overlap=0.005) Left_Lateral_Ventricle (4): linear fit = 0.41 x + 0.0 (800 voxels, peak = 8), gca=8.1 gca peak = 0.15565 (16) mri peak = 0.18297 ( 9) Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (898 voxels, overlap=0.043) Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (898 voxels, peak = 8), gca=8.2 gca peak = 0.26829 (96) mri peak = 0.11619 (97) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (809 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (809 voxels, peak = 96), gca=95.5 gca peak = 0.20183 (93) mri peak = 0.07698 (96) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (678 voxels, overlap=1.006) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (678 voxels, peak = 95), gca=95.3 gca peak = 0.21683 (55) mri peak = 0.10273 (56) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (785 voxels, overlap=0.997) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (785 voxels, peak = 55), gca=55.0 gca peak = 0.30730 (58) mri peak = 0.09399 (62) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (840 voxels, overlap=0.997) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (840 voxels, peak = 59), gca=59.4 gca peak = 0.11430 (101) mri peak = 0.10383 (105) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (52829 voxels, overlap=0.619) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (52829 voxels, peak = 106), gca=105.5 gca peak = 0.12076 (102) mri peak = 0.11416 (105) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (55181 voxels, overlap=0.587) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (55181 voxels, peak = 107), gca=106.6 gca peak = 0.14995 (59) mri peak = 0.04536 (56) Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (22027 voxels, overlap=0.971) Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (22027 voxels, peak = 57), gca=56.9 gca peak = 0.15082 (58) mri peak = 0.04724 (56) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (22830 voxels, overlap=0.980) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (22830 voxels, peak = 56), gca=56.0 gca peak = 0.14161 (67) mri peak = 0.10846 (70) Right_Caudate (50): linear fit = 1.03 x + 0.0 (397 voxels, overlap=0.752) Right_Caudate (50): linear fit = 1.03 x + 0.0 (397 voxels, peak = 69), gca=69.3 gca peak = 0.15243 (71) mri peak = 0.10133 (77) Left_Caudate (11): linear fit = 1.03 x + 0.0 (879 voxels, overlap=0.907) Left_Caudate (11): linear fit = 1.03 x + 0.0 (879 voxels, peak = 73), gca=73.5 gca peak = 0.13336 (57) mri peak = 0.04586 (60) Left_Cerebellum_Cortex (8): linear fit = 1.09 x + 0.0 (21690 voxels, overlap=0.809) Left_Cerebellum_Cortex (8): linear fit = 1.09 x + 0.0 (21690 voxels, peak = 62), gca=61.8 gca peak = 0.13252 (56) mri peak = 0.05102 (60) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (23346 voxels, overlap=0.886) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (23346 voxels, peak = 59), gca=58.5 gca peak = 0.18181 (84) mri peak = 0.08717 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (7316 voxels, overlap=0.526) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (7316 voxels, peak = 90), gca=90.3 gca peak = 0.20573 (83) mri peak = 0.09484 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (6800 voxels, overlap=0.581) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (6800 voxels, peak = 88), gca=87.6 gca peak = 0.21969 (57) mri peak = 0.10324 (63) Left_Amygdala (18): linear fit = 1.10 x + 0.0 (414 voxels, overlap=0.446) Left_Amygdala (18): linear fit = 1.10 x + 0.0 (414 voxels, peak = 62), gca=62.4 gca peak = 0.39313 (56) mri peak = 0.11465 (59) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (470 voxels, overlap=0.910) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (470 voxels, peak = 59), gca=58.5 gca peak = 0.14181 (85) mri peak = 0.05280 (89) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (4934 voxels, overlap=0.852) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (4934 voxels, peak = 91), gca=90.5 gca peak = 0.11978 (83) mri peak = 0.08399 (84) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3875 voxels, overlap=0.928) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3875 voxels, peak = 85), gca=85.1 gca peak = 0.13399 (79) mri peak = 0.08260 (84) Left_Putamen (12): linear fit = 1.05 x + 0.0 (1939 voxels, overlap=0.864) Left_Putamen (12): linear fit = 1.05 x + 0.0 (1939 voxels, peak = 83), gca=83.3 gca peak = 0.14159 (79) mri peak = 0.08593 (84) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2118 voxels, overlap=0.997) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2118 voxels, peak = 83), gca=82.6 gca peak = 0.10025 (80) mri peak = 0.09146 (85) Brain_Stem (16): linear fit = 1.10 x + 0.0 (10775 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (10775 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.07340 (93) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1170 voxels, overlap=0.555) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1170 voxels, peak = 97), gca=96.8 gca peak = 0.12801 (89) mri peak = 0.08053 (96) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1264 voxels, overlap=0.619) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1264 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) mri peak = 0.06427 (20) gca peak = 0.15061 (21) mri peak = 0.15068 (12) Fourth_Ventricle (15): linear fit = 0.54 x + 0.0 (245 voxels, overlap=0.285) Fourth_Ventricle (15): linear fit = 0.54 x + 0.0 (245 voxels, peak = 11), gca=11.2 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 1.02 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.46 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=0.639, neg=0, invalid=762 0078: dt=149.034965, rms=0.632 (1.085%), neg=0, invalid=762 0079: dt=295.936000, rms=0.628 (0.574%), neg=0, invalid=762 0080: dt=110.976000, rms=0.627 (0.156%), neg=0, invalid=762 0081: dt=295.936000, rms=0.626 (0.185%), neg=0, invalid=762 0082: dt=92.480000, rms=0.625 (0.123%), neg=0, invalid=762 0083: dt=369.920000, rms=0.625 (0.142%), neg=0, invalid=762 0084: dt=92.480000, rms=0.624 (0.118%), neg=0, invalid=762 0085: dt=295.936000, rms=0.623 (0.098%), neg=0, invalid=762 0086: dt=110.976000, rms=0.623 (0.086%), neg=0, invalid=762 0087: dt=129.472000, rms=0.622 (0.054%), neg=0, invalid=762 0088: dt=295.936000, rms=0.622 (0.080%), neg=0, invalid=762 0089: dt=92.480000, rms=0.621 (0.065%), neg=0, invalid=762 0090: dt=517.888000, rms=0.621 (0.130%), neg=0, invalid=762 0091: dt=73.984000, rms=0.620 (0.064%), neg=0, invalid=762 0092: dt=4734.976000, rms=0.617 (0.559%), neg=0, invalid=762 0093: dt=110.976000, rms=0.615 (0.244%), neg=0, invalid=762 0094: dt=73.984000, rms=0.615 (0.012%), neg=0, invalid=762 0095: dt=73.984000, rms=0.615 (0.010%), neg=0, invalid=762 0096: dt=73.984000, rms=0.615 (0.016%), neg=0, invalid=762 0097: dt=73.984000, rms=0.615 (0.023%), neg=0, invalid=762 0098: dt=73.984000, rms=0.615 (0.033%), neg=0, invalid=762 0099: dt=73.984000, rms=0.614 (0.038%), neg=0, invalid=762 0100: dt=73.984000, rms=0.614 (0.043%), neg=0, invalid=762 0101: dt=73.984000, rms=0.614 (0.042%), neg=0, invalid=762 0102: dt=73.984000, rms=0.614 (0.044%), neg=0, invalid=762 0103: dt=73.984000, rms=0.613 (0.047%), neg=0, invalid=762 0104: dt=73.984000, rms=0.613 (0.048%), neg=0, invalid=762 0105: dt=73.984000, rms=0.613 (0.048%), neg=0, invalid=762 0106: dt=73.984000, rms=0.613 (0.041%), neg=0, invalid=762 0107: dt=73.984000, rms=0.612 (0.038%), neg=0, invalid=762 0108: dt=73.984000, rms=0.612 (0.038%), neg=0, invalid=762 0109: dt=73.984000, rms=0.612 (0.033%), neg=0, invalid=762 0110: dt=73.984000, rms=0.612 (0.034%), neg=0, invalid=762 0111: dt=73.984000, rms=0.611 (0.034%), neg=0, invalid=762 0112: dt=73.984000, rms=0.611 (0.034%), neg=0, invalid=762 0113: dt=73.984000, rms=0.611 (0.031%), neg=0, invalid=762 0114: dt=73.984000, rms=0.611 (0.030%), neg=0, invalid=762 0115: dt=73.984000, rms=0.611 (0.030%), neg=0, invalid=762 0116: dt=73.984000, rms=0.610 (0.031%), neg=0, invalid=762 0117: dt=73.984000, rms=0.610 (0.029%), neg=0, invalid=762 0118: dt=73.984000, rms=0.610 (0.027%), neg=0, invalid=762 0119: dt=73.984000, rms=0.610 (0.026%), neg=0, invalid=762 0120: dt=73.984000, rms=0.610 (0.025%), neg=0, invalid=762 0121: dt=73.984000, rms=0.610 (0.021%), neg=0, invalid=762 0122: dt=73.984000, rms=0.610 (0.022%), neg=0, invalid=762 0123: dt=73.984000, rms=0.609 (0.021%), neg=0, invalid=762 0124: dt=2071.552000, rms=0.609 (0.044%), neg=0, invalid=762 0125: dt=55.488000, rms=0.609 (0.021%), neg=0, invalid=762 0126: dt=55.488000, rms=0.609 (0.002%), neg=0, invalid=762 0127: dt=55.488000, rms=0.609 (0.004%), neg=0, invalid=762 0128: dt=55.488000, rms=0.609 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.610, neg=0, invalid=762 0129: dt=129.472000, rms=0.609 (0.164%), neg=0, invalid=762 0130: dt=129.472000, rms=0.608 (0.031%), neg=0, invalid=762 0131: dt=129.472000, rms=0.608 (0.035%), neg=0, invalid=762 0132: dt=129.472000, rms=0.608 (0.035%), neg=0, invalid=762 0133: dt=129.472000, rms=0.608 (0.032%), neg=0, invalid=762 0134: dt=129.472000, rms=0.608 (0.028%), neg=0, invalid=762 0135: dt=129.472000, rms=0.607 (0.042%), neg=0, invalid=762 0136: dt=129.472000, rms=0.607 (0.037%), neg=0, invalid=762 0137: dt=129.472000, rms=0.607 (0.031%), neg=0, invalid=762 0138: dt=129.472000, rms=0.607 (0.021%), neg=0, invalid=762 0139: dt=129.472000, rms=0.607 (0.031%), neg=0, invalid=762 0140: dt=129.472000, rms=0.606 (0.035%), neg=0, invalid=762 0141: dt=129.472000, rms=0.606 (0.033%), neg=0, invalid=762 0142: dt=129.472000, rms=0.606 (0.026%), neg=0, invalid=762 0143: dt=129.472000, rms=0.606 (0.027%), neg=0, invalid=762 0144: dt=129.472000, rms=0.606 (0.032%), neg=0, invalid=762 0145: dt=129.472000, rms=0.606 (0.032%), neg=0, invalid=762 0146: dt=129.472000, rms=0.605 (0.023%), neg=0, invalid=762 0147: dt=129.472000, rms=0.605 (0.019%), neg=0, invalid=762 0148: dt=129.472000, rms=0.605 (0.004%), neg=0, invalid=762 0149: dt=129.472000, rms=0.605 (0.001%), neg=0, invalid=762 0150: dt=129.472000, rms=0.605 (0.002%), neg=0, invalid=762 0151: dt=129.472000, rms=0.605 (0.009%), neg=0, invalid=762 0152: dt=129.472000, rms=0.605 (0.017%), neg=0, invalid=762 0153: dt=129.472000, rms=0.605 (0.011%), neg=0, invalid=762 0154: dt=129.472000, rms=0.605 (0.011%), neg=0, invalid=762 0155: dt=129.472000, rms=0.605 (0.012%), neg=0, invalid=762 0156: dt=129.472000, rms=0.605 (0.016%), neg=0, invalid=762 0157: dt=129.472000, rms=0.605 (0.015%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.606, neg=0, invalid=762 0158: dt=147.582090, rms=0.600 (1.013%), neg=0, invalid=762 0159: dt=99.401802, rms=0.594 (0.854%), neg=0, invalid=762 0160: dt=90.666667, rms=0.592 (0.427%), neg=0, invalid=762 0161: dt=62.802139, rms=0.589 (0.568%), neg=0, invalid=762 0162: dt=123.108280, rms=0.586 (0.427%), neg=0, invalid=762 0163: dt=85.333333, rms=0.584 (0.351%), neg=0, invalid=762 0164: dt=36.288000, rms=0.582 (0.336%), neg=0, invalid=762 0165: dt=580.608000, rms=0.576 (1.105%), neg=0, invalid=762 0166: dt=68.800000, rms=0.572 (0.635%), neg=0, invalid=762 0167: dt=36.288000, rms=0.571 (0.177%), neg=0, invalid=762 0168: dt=497.664000, rms=0.568 (0.450%), neg=0, invalid=762 0169: dt=36.288000, rms=0.566 (0.327%), neg=0, invalid=762 0170: dt=145.152000, rms=0.565 (0.240%), neg=0, invalid=762 0171: dt=36.288000, rms=0.565 (0.075%), neg=0, invalid=762 0172: dt=414.720000, rms=0.563 (0.247%), neg=0, invalid=762 0173: dt=65.479769, rms=0.562 (0.258%), neg=0, invalid=762 0174: dt=82.944000, rms=0.562 (0.059%), neg=0, invalid=762 0175: dt=124.416000, rms=0.561 (0.115%), neg=0, invalid=762 0176: dt=36.288000, rms=0.561 (0.056%), neg=0, invalid=762 0177: dt=414.720000, rms=0.559 (0.196%), neg=0, invalid=762 0178: dt=36.288000, rms=0.559 (0.164%), neg=0, invalid=762 0179: dt=36.288000, rms=0.558 (0.036%), neg=0, invalid=762 0180: dt=36.288000, rms=0.558 (0.027%), neg=0, invalid=762 0181: dt=2.268000, rms=0.558 (0.003%), neg=0, invalid=762 0182: dt=1.134000, rms=0.558 (0.001%), neg=0, invalid=762 0183: dt=0.486000, rms=0.558 (0.000%), neg=0, invalid=762 0184: dt=0.007594, rms=0.558 (0.000%), neg=0, invalid=762 0185: dt=0.003797, rms=0.558 (0.000%), neg=0, invalid=762 0186: dt=0.001898, rms=0.558 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.559, neg=0, invalid=762 0187: dt=124.416000, rms=0.556 (0.475%), neg=0, invalid=762 0188: dt=73.050505, rms=0.555 (0.204%), neg=0, invalid=762 0189: dt=36.288000, rms=0.555 (0.061%), neg=0, invalid=762 0190: dt=580.608000, rms=0.553 (0.392%), neg=0, invalid=762 0191: dt=36.288000, rms=0.552 (0.189%), neg=0, invalid=762 0192: dt=145.152000, rms=0.551 (0.125%), neg=0, invalid=762 0193: dt=36.288000, rms=0.551 (0.028%), neg=0, invalid=762 0194: dt=36.288000, rms=0.551 (0.023%), neg=0, invalid=762 0195: dt=36.288000, rms=0.550 (0.042%), neg=0, invalid=762 0196: dt=36.288000, rms=0.550 (0.063%), neg=0, invalid=762 0197: dt=36.288000, rms=0.550 (0.081%), neg=0, invalid=762 0198: dt=36.288000, rms=0.549 (0.088%), neg=0, invalid=762 0199: dt=36.288000, rms=0.549 (0.018%), neg=0, invalid=762 0200: dt=36.288000, rms=0.549 (0.039%), neg=0, invalid=762 0201: dt=36.288000, rms=0.549 (0.020%), neg=0, invalid=762 0202: dt=36.288000, rms=0.549 (0.019%), neg=0, invalid=762 0203: dt=9.072000, rms=0.548 (0.006%), neg=0, invalid=762 0204: dt=9.072000, rms=0.548 (0.006%), neg=0, invalid=762 0205: dt=0.567000, rms=0.548 (-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=0.553, neg=0, invalid=762 0206: dt=94.680412, rms=0.540 (2.322%), neg=0, invalid=762 0207: dt=38.400000, rms=0.530 (1.827%), neg=0, invalid=762 0208: dt=9.600000, rms=0.529 (0.288%), neg=0, invalid=762 0209: dt=0.125000, rms=0.529 (-0.002%), neg=0, invalid=762 0210: dt=0.125000, rms=0.529 (0.003%), neg=0, invalid=762 0211: dt=0.015625, rms=0.529 (0.000%), neg=0, invalid=762 0212: dt=0.007812, rms=0.529 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.530, neg=0, invalid=762 0213: dt=0.000000, rms=0.529 (0.133%), neg=0, invalid=762 0214: dt=0.000000, rms=0.529 (0.000%), neg=0, invalid=762 0215: dt=0.000244, rms=0.529 (0.000%), neg=0, invalid=762 0216: dt=0.000061, rms=0.529 (0.000%), neg=0, invalid=762 0217: dt=0.000031, 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=0.544, neg=0, invalid=762 0218: dt=0.000000, rms=0.543 (0.126%), neg=0, invalid=762 0219: dt=0.000000, rms=0.543 (0.000%), neg=0, invalid=762 0220: dt=0.000002, rms=0.543 (0.000%), neg=0, invalid=762 0221: dt=0.000001, rms=0.543 (0.000%), neg=0, invalid=762 0222: dt=0.000001, rms=0.543 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.544, neg=0, invalid=762 0223: dt=0.000000, rms=0.543 (0.126%), neg=0, invalid=762 0224: dt=0.000000, rms=0.543 (0.000%), neg=0, invalid=762 0225: dt=0.000000, rms=0.543 (0.000%), neg=0, invalid=762 0226: dt=0.000000, rms=0.543 (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=0.573, neg=0, invalid=762 0227: dt=0.448000, rms=0.569 (0.571%), neg=0, invalid=762 0228: dt=0.448000, rms=0.567 (0.388%), neg=0, invalid=762 0229: dt=0.384000, rms=0.566 (0.277%), neg=0, invalid=762 0230: dt=0.080000, rms=0.565 (0.052%), neg=0, invalid=762 0231: dt=0.007000, rms=0.565 (0.004%), neg=0, invalid=762 0232: dt=0.000875, rms=0.565 (0.001%), neg=0, invalid=762 0233: dt=0.000219, rms=0.565 (0.000%), neg=0, invalid=762 0234: dt=0.000109, rms=0.565 (0.000%), neg=0, invalid=762 0235: dt=0.000000, rms=0.565 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.566, neg=0, invalid=762 0236: dt=0.000109, rms=0.565 (0.110%), neg=0, invalid=762 0237: dt=0.000000, rms=0.565 (0.000%), neg=0, invalid=762 0238: dt=0.000024, rms=0.565 (0.000%), neg=0, invalid=762 0239: dt=0.000012, rms=0.565 (0.000%), neg=0, invalid=762 0240: dt=0.000006, rms=0.565 (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=0.521, neg=0, invalid=762 0241: dt=0.448000, rms=0.506 (2.857%), neg=0, invalid=762 0242: dt=0.384000, rms=0.503 (0.571%), neg=0, invalid=762 0243: dt=0.384000, rms=0.502 (0.350%), neg=0, invalid=762 0244: dt=0.384000, rms=0.501 (0.222%), neg=0, invalid=762 0245: dt=0.384000, rms=0.500 (0.161%), neg=0, invalid=762 0246: dt=0.384000, rms=0.499 (0.111%), neg=0, invalid=762 0247: dt=0.384000, rms=0.499 (0.093%), neg=0, invalid=762 0248: dt=0.384000, rms=0.498 (0.067%), neg=0, invalid=762 0249: dt=0.384000, rms=0.498 (0.062%), neg=0, invalid=762 0250: dt=0.384000, rms=0.498 (0.041%), neg=0, invalid=762 0251: dt=0.384000, rms=0.498 (0.039%), neg=0, invalid=762 0252: dt=0.384000, rms=0.497 (0.067%), neg=0, invalid=762 0253: dt=0.384000, rms=0.497 (0.020%), neg=0, invalid=762 0254: dt=0.384000, rms=0.497 (0.039%), neg=0, invalid=762 0255: dt=0.384000, rms=0.497 (0.012%), neg=0, invalid=762 0256: dt=0.384000, rms=0.497 (0.023%), neg=0, invalid=762 0257: dt=0.384000, rms=0.497 (0.013%), neg=0, invalid=762 0258: dt=0.320000, rms=0.497 (0.005%), neg=0, invalid=762 0259: dt=0.320000, rms=0.497 (0.009%), neg=0, invalid=762 0260: dt=0.320000, rms=0.497 (0.010%), neg=0, invalid=762 0261: dt=0.160000, rms=0.497 (0.002%), neg=0, invalid=762 0262: dt=0.160000, rms=0.497 (0.004%), neg=0, invalid=762 0263: dt=0.160000, rms=0.497 (0.007%), neg=0, invalid=762 0264: dt=0.160000, rms=0.497 (0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.497, neg=0, invalid=762 0265: dt=0.320000, rms=0.494 (0.738%), neg=0, invalid=762 0266: dt=0.320000, rms=0.493 (0.219%), neg=0, invalid=762 0267: dt=0.320000, rms=0.492 (0.085%), neg=0, invalid=762 0268: dt=0.320000, rms=0.492 (0.036%), neg=0, invalid=762 0269: dt=0.320000, rms=0.492 (0.019%), neg=0, invalid=762 0270: dt=0.320000, rms=0.492 (0.026%), neg=0, invalid=762 0271: dt=0.160000, rms=0.492 (0.000%), neg=0, invalid=762 0272: dt=0.160000, rms=0.492 (0.005%), neg=0, invalid=762 0273: dt=0.160000, rms=0.492 (0.005%), neg=0, invalid=762 0274: dt=0.320000, rms=0.492 (0.002%), neg=0, invalid=762 0275: dt=0.320000, rms=0.492 (0.004%), neg=0, invalid=762 0276: dt=0.320000, rms=0.492 (0.007%), neg=0, invalid=762 0277: dt=0.320000, rms=0.492 (0.006%), neg=0, invalid=762 0278: dt=0.320000, rms=0.492 (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=0.490, neg=0, invalid=762 0279: dt=0.003387, rms=0.489 (0.142%), neg=0, invalid=762 0280: dt=0.000000, rms=0.489 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.490, neg=0, invalid=762 0281: dt=129.472000, rms=0.489 (0.158%), neg=0, invalid=762 0282: dt=295.936000, rms=0.489 (0.014%), neg=0, invalid=762 0283: dt=295.936000, rms=0.489 (-0.074%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.490, neg=0, invalid=762 0284: dt=20.736000, rms=0.489 (0.151%), neg=0, invalid=762 0285: dt=25.920000, rms=0.489 (0.002%), neg=0, invalid=762 0286: dt=25.920000, rms=0.489 (0.004%), neg=0, invalid=762 0287: dt=25.920000, rms=0.489 (0.000%), neg=0, invalid=762 0288: dt=25.920000, rms=0.489 (-0.015%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.490, neg=0, invalid=762 0289: dt=98.388060, rms=0.488 (0.389%), neg=0, invalid=762 0290: dt=36.288000, rms=0.487 (0.113%), neg=0, invalid=762 0291: dt=36.288000, rms=0.487 (0.043%), neg=0, invalid=762 0292: dt=36.288000, rms=0.487 (0.073%), neg=0, invalid=762 0293: dt=36.288000, rms=0.486 (0.101%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0294: dt=36.288000, rms=0.486 (0.100%), neg=0, invalid=762 0295: dt=36.288000, rms=0.485 (0.102%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0296: dt=36.288000, rms=0.485 (0.089%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0297: dt=145.152000, rms=0.485 (0.043%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.486, neg=0, invalid=762 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0298: dt=44.800000, rms=0.482 (0.699%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 1 iterations, nbhd size=0, neg = 0 0299: dt=64.680851, rms=0.478 (0.811%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0300: dt=21.314685, rms=0.476 (0.423%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 3 iterations, nbhd size=0, neg = 0 0301: dt=110.333333, rms=0.474 (0.547%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0302: dt=29.918699, rms=0.472 (0.448%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0303: dt=38.400000, rms=0.470 (0.299%), neg=0, invalid=762 0304: dt=25.600000, rms=0.469 (0.151%), neg=0, invalid=762 0305: dt=25.600000, rms=0.469 (0.138%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0306: dt=25.600000, rms=0.468 (0.209%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=0, neg = 0 0307: dt=25.600000, rms=0.467 (0.258%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 3 iterations, nbhd size=0, neg = 0 0308: dt=25.600000, rms=0.465 (0.289%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 3 iterations, nbhd size=0, neg = 0 0309: dt=25.600000, rms=0.464 (0.324%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 1 iterations, nbhd size=0, neg = 0 0310: dt=25.600000, rms=0.462 (0.325%), neg=0, invalid=762 iter 0, gcam->neg = 20 after 17 iterations, nbhd size=1, neg = 0 0311: dt=25.600000, rms=0.461 (0.268%), neg=0, invalid=762 iter 0, gcam->neg = 23 after 15 iterations, nbhd size=1, neg = 0 0312: dt=25.600000, rms=0.460 (0.254%), neg=0, invalid=762 iter 0, gcam->neg = 23 after 6 iterations, nbhd size=0, neg = 0 0313: dt=25.600000, rms=0.459 (0.216%), neg=0, invalid=762 iter 0, gcam->neg = 19 after 16 iterations, nbhd size=1, neg = 0 0314: dt=25.600000, rms=0.458 (0.196%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 3 iterations, nbhd size=0, neg = 0 0315: dt=25.600000, rms=0.457 (0.169%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0316: dt=25.600000, rms=0.456 (0.176%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0317: dt=25.600000, rms=0.456 (0.173%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 3 iterations, nbhd size=0, neg = 0 0318: dt=25.600000, rms=0.455 (0.146%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 10 iterations, nbhd size=1, neg = 0 0319: dt=25.600000, rms=0.454 (0.121%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 5 iterations, nbhd size=0, neg = 0 0320: dt=25.600000, rms=0.454 (0.107%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0321: dt=32.000000, rms=0.454 (0.046%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0322: dt=32.000000, rms=0.454 (0.013%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 3 iterations, nbhd size=0, neg = 0 0323: dt=32.000000, rms=0.453 (0.029%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 6 iterations, nbhd size=0, neg = 0 0324: dt=32.000000, rms=0.453 (-0.026%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.454, neg=0, invalid=762 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 0325: dt=66.093458, rms=0.451 (0.816%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 0326: dt=24.861538, rms=0.449 (0.259%), neg=0, invalid=762 0327: dt=38.400000, rms=0.449 (0.119%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 4 iterations, nbhd size=0, neg = 0 0328: dt=38.400000, rms=0.449 (0.030%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0329: dt=38.400000, rms=0.448 (0.170%), neg=0, invalid=762 0330: dt=38.400000, rms=0.448 (0.079%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0331: dt=38.400000, rms=0.447 (0.118%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 4 iterations, nbhd size=0, neg = 0 0332: dt=38.400000, rms=0.447 (-0.034%), neg=0, invalid=762 0333: dt=25.600000, rms=0.447 (0.028%), neg=0, invalid=762 0334: dt=25.600000, rms=0.447 (0.019%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.456, neg=0, invalid=762 0335: dt=0.000000, rms=0.455 (0.176%), neg=0, invalid=762 0336: dt=0.000000, rms=0.455 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.456, neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0337: dt=0.864000, rms=0.455 (0.180%), neg=0, invalid=762 0338: dt=0.180000, rms=0.455 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.472, neg=0, invalid=762 0339: dt=1.280000, rms=0.469 (0.599%), neg=0, invalid=762 0340: dt=0.320000, rms=0.469 (0.019%), neg=0, invalid=762 0341: dt=0.320000, rms=0.469 (-0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.469, neg=0, invalid=762 0342: dt=1.280000, rms=0.468 (0.307%), neg=0, invalid=762 0343: dt=0.320000, rms=0.468 (0.002%), neg=0, invalid=762 0344: dt=0.320000, rms=0.468 (0.002%), neg=0, invalid=762 0345: dt=0.320000, rms=0.468 (-0.028%), 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=0.457, neg=0, invalid=762 iter 0, gcam->neg = 953 after 13 iterations, nbhd size=1, neg = 0 0346: dt=2.270487, rms=0.424 (7.272%), neg=0, invalid=762 0347: dt=0.080000, rms=0.424 (0.045%), neg=0, invalid=762 0348: dt=0.080000, rms=0.424 (-0.063%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.424, neg=0, invalid=762 0349: dt=0.064000, rms=0.423 (0.225%), neg=0, invalid=762 0350: dt=-0.000031, rms=0.423 (0.002%), neg=0, invalid=762 0351: dt=-0.000031, rms=0.423 (0.000%), neg=0, invalid=762 0352: dt=-0.000031, rms=0.423 (0.000%), neg=0, invalid=762 0353: dt=-0.000031, rms=0.423 (0.000%), neg=0, invalid=762 0354: dt=-0.000031, rms=0.423 (0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0355: dt=1.445000, rms=0.408 (0.000%), neg=0, invalid=762 0356: dt=0.007902, rms=0.408 (0.000%), neg=0, invalid=762 0357: dt=0.007902, rms=0.408 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0358: dt=32.368000, rms=0.408 (0.005%), neg=0, invalid=762 0359: dt=32.368000, rms=0.408 (0.002%), neg=0, invalid=762 0360: dt=32.368000, rms=0.408 (0.001%), neg=0, invalid=762 0361: dt=32.368000, rms=0.408 (0.000%), neg=0, invalid=762 0362: dt=32.368000, rms=0.408 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0363: dt=0.000000, rms=0.408 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0364: dt=124.416000, rms=0.408 (0.068%), neg=0, invalid=762 0365: dt=82.944000, rms=0.408 (0.040%), neg=0, invalid=762 0366: dt=82.944000, rms=0.408 (0.019%), neg=0, invalid=762 0367: dt=82.944000, rms=0.408 (0.031%), neg=0, invalid=762 0368: dt=82.944000, rms=0.408 (0.033%), neg=0, invalid=762 0369: dt=82.944000, rms=0.407 (0.028%), neg=0, invalid=762 0370: dt=82.944000, rms=0.407 (0.017%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0371: dt=11.200000, rms=0.408 (0.085%), neg=0, invalid=762 0372: dt=11.200000, rms=0.408 (0.044%), neg=0, invalid=762 0373: dt=11.200000, rms=0.408 (0.034%), neg=0, invalid=762 0374: dt=11.200000, rms=0.407 (0.026%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0375: dt=11.200000, rms=0.407 (-0.011%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.407, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0376: dt=44.800000, rms=0.405 (0.634%), neg=0, invalid=762 0377: dt=32.000000, rms=0.404 (0.237%), neg=0, invalid=762 0378: dt=32.000000, rms=0.403 (0.211%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 9 iterations, nbhd size=1, neg = 0 0379: dt=32.000000, rms=0.402 (0.239%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 12 iterations, nbhd size=1, neg = 0 0380: dt=32.000000, rms=0.401 (0.327%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 2 iterations, nbhd size=0, neg = 0 0381: dt=32.000000, rms=0.400 (0.270%), neg=0, invalid=762 iter 0, gcam->neg = 27 after 17 iterations, nbhd size=1, neg = 0 0382: dt=32.000000, rms=0.399 (0.282%), neg=0, invalid=762 iter 0, gcam->neg = 20 after 15 iterations, nbhd size=1, neg = 0 0383: dt=32.000000, rms=0.398 (0.181%), neg=0, invalid=762 iter 0, gcam->neg = 27 after 10 iterations, nbhd size=1, neg = 0 0384: dt=32.000000, rms=0.397 (0.167%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 4 iterations, nbhd size=0, neg = 0 0385: dt=32.000000, rms=0.397 (0.141%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 10 iterations, nbhd size=1, neg = 0 0386: dt=32.000000, rms=0.396 (0.192%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 4 iterations, nbhd size=0, neg = 0 0387: dt=32.000000, rms=0.395 (0.158%), neg=0, invalid=762 iter 0, gcam->neg = 35 after 5 iterations, nbhd size=0, neg = 0 0388: dt=32.000000, rms=0.395 (0.114%), neg=0, invalid=762 iter 0, gcam->neg = 42 after 5 iterations, nbhd size=0, neg = 0 0389: dt=32.000000, rms=0.394 (0.081%), neg=0, invalid=762 0390: dt=38.400000, rms=0.394 (0.053%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0391: dt=38.400000, rms=0.394 (0.025%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 4 iterations, nbhd size=0, neg = 0 0392: dt=38.400000, rms=0.394 (0.029%), neg=0, invalid=762 iter 0, gcam->neg = 40 after 7 iterations, nbhd size=0, neg = 0 0393: dt=38.400000, rms=0.394 (-0.019%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.399, neg=0, invalid=762 0394: dt=0.000211, rms=0.399 (0.000%), neg=0, invalid=762 0395: dt=0.000000, rms=0.399 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.399, neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0396: dt=1.250000, rms=0.399 (0.006%), neg=0, invalid=762 0397: dt=0.576000, rms=0.399 (0.001%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0398: dt=0.576000, rms=0.399 (-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=0.410, neg=0, invalid=762 0399: dt=0.000000, rms=0.410 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.410, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0400: dt=0.080000, rms=0.410 (0.001%), neg=0, invalid=762 0401: dt=0.000050, rms=0.410 (0.000%), neg=0, invalid=762 0402: dt=0.000050, rms=0.410 (-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=0.392, neg=0, invalid=762 iter 0, gcam->neg = 686 after 17 iterations, nbhd size=1, neg = 0 0403: dt=1.155959, rms=0.383 (2.360%), neg=0, invalid=762 0404: dt=0.000023, rms=0.383 (0.000%), neg=0, invalid=762 0405: dt=0.000023, rms=0.383 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.383, neg=0, invalid=762 0406: dt=0.064000, rms=0.383 (0.021%), neg=0, invalid=762 0407: dt=0.028000, rms=0.383 (0.004%), neg=0, invalid=762 0408: dt=0.028000, rms=0.383 (0.002%), neg=0, invalid=762 0409: dt=0.028000, rms=0.383 (-0.005%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 29 minutes and 42 seconds. mri_ca_register utimesec 8958.723784 mri_ca_register stimesec 23.248758 mri_ca_register ru_maxrss 1336068 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4082703 mri_ca_register ru_majflt 8 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 1696 mri_ca_register ru_oublock 62808 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 10 mri_ca_register ru_nivcsw 3447 FSRUNTIME@ mri_ca_register 2.4951 hours 1 threads #-------------------------------------- #@# SubCort Seg 2020��� 04��� 28��� ��������� 23:49:53 CST mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname web-virtual-machine machine x86_64 setenv SUBJECTS_DIR /home/web/freesurver/test/MRI cd /home/web/freesurver/test/MRI/subjects02/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 5.91 Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.16118 (10) Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (848 voxels, overlap=0.004) Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (848 voxels, peak = 9), gca=8.9 gca peak = 0.17677 (13) mri peak = 0.21700 ( 9) Right_Lateral_Ventricle (43): linear fit = 0.56 x + 0.0 (1761 voxels, overlap=0.090) Right_Lateral_Ventricle (43): linear fit = 0.56 x + 0.0 (1761 voxels, peak = 7), gca=7.2 gca peak = 0.28129 (95) mri peak = 0.11809 (96) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (669 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (669 voxels, peak = 96), gca=96.4 gca peak = 0.16930 (96) mri peak = 0.14162 (101) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (692 voxels, overlap=0.743) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (692 voxels, peak = 99), gca=99.4 gca peak = 0.24553 (55) mri peak = 0.09822 (56) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (981 voxels, overlap=1.006) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (981 voxels, peak = 55), gca=55.0 gca peak = 0.30264 (59) mri peak = 0.09193 (60) Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (891 voxels, overlap=1.007) Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (891 voxels, peak = 62), gca=61.7 gca peak = 0.07580 (103) mri peak = 0.11300 (105) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (33309 voxels, overlap=0.597) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (33309 voxels, peak = 105), gca=104.5 gca peak = 0.07714 (104) mri peak = 0.10773 (105) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (35906 voxels, overlap=0.566) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (35906 voxels, peak = 107), gca=106.6 gca peak = 0.09712 (58) mri peak = 0.05040 (59) Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (28674 voxels, overlap=0.982) Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (28674 voxels, peak = 56), gca=56.0 gca peak = 0.11620 (58) mri peak = 0.05120 (56) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (28545 voxels, overlap=0.984) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (28545 voxels, peak = 56), gca=56.0 gca peak = 0.30970 (66) mri peak = 0.12078 (73) Right_Caudate (50): linear fit = 1.10 x + 0.0 (843 voxels, overlap=0.374) Right_Caudate (50): linear fit = 1.10 x + 0.0 (843 voxels, peak = 72), gca=72.3 gca peak = 0.15280 (69) mri peak = 0.12060 (77) Left_Caudate (11): linear fit = 1.01 x + 0.0 (794 voxels, overlap=0.922) Left_Caudate (11): linear fit = 1.01 x + 0.0 (794 voxels, peak = 70), gca=70.0 gca peak = 0.13902 (56) mri peak = 0.05786 (62) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (20170 voxels, overlap=0.864) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (20170 voxels, peak = 62), gca=62.4 gca peak = 0.14777 (55) mri peak = 0.06274 (60) Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (20774 voxels, overlap=0.940) Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (20774 voxels, peak = 59), gca=58.6 gca peak = 0.16765 (84) mri peak = 0.11268 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4913 voxels, overlap=0.637) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4913 voxels, peak = 89), gca=89.5 gca peak = 0.18739 (84) mri peak = 0.11802 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5256 voxels, overlap=0.671) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5256 voxels, peak = 89), gca=89.5 gca peak = 0.29869 (57) mri peak = 0.11091 (63) Left_Amygdala (18): linear fit = 1.10 x + 0.0 (556 voxels, overlap=0.791) Left_Amygdala (18): linear fit = 1.10 x + 0.0 (556 voxels, peak = 62), gca=62.4 gca peak = 0.33601 (57) mri peak = 0.15028 (61) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (573 voxels, overlap=1.012) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (573 voxels, peak = 60), gca=59.6 gca peak = 0.11131 (90) mri peak = 0.06623 (89) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4126 voxels, overlap=0.952) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4126 voxels, peak = 91), gca=91.3 gca peak = 0.11793 (83) mri peak = 0.08237 (84) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (3905 voxels, overlap=0.978) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (3905 voxels, peak = 87), gca=86.7 gca peak = 0.08324 (81) mri peak = 0.08909 (83) Left_Putamen (12): linear fit = 1.04 x + 0.0 (2464 voxels, overlap=0.757) Left_Putamen (12): linear fit = 1.04 x + 0.0 (2464 voxels, peak = 85), gca=84.6 gca peak = 0.10360 (77) mri peak = 0.08709 (84) Right_Putamen (51): linear fit = 1.03 x + 0.0 (2549 voxels, overlap=0.881) Right_Putamen (51): linear fit = 1.03 x + 0.0 (2549 voxels, peak = 80), gca=79.7 gca peak = 0.08424 (78) mri peak = 0.09325 (85) Brain_Stem (16): linear fit = 1.08 x + 0.0 (10413 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.08 x + 0.0 (10413 voxels, peak = 84), gca=83.9 gca peak = 0.12631 (89) mri peak = 0.07230 (97) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1201 voxels, overlap=0.492) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1201 voxels, peak = 97), gca=97.5 gca peak = 0.14500 (87) mri peak = 0.08347 (97) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1290 voxels, overlap=0.474) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1290 voxels, peak = 94), gca=93.5 gca peak = 0.14975 (24) mri peak = 0.28571 (10) gca peak = 0.19357 (14) mri peak = 0.16904 (12) Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (165 voxels, overlap=0.063) Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (165 voxels, peak = 10), gca=9.9 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 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 1.02 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.57 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.29485 ( 9) mri peak = 0.16118 (10) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (848 voxels, overlap=0.958) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (848 voxels, peak = 9), gca=9.5 gca peak = 0.25357 ( 7) mri peak = 0.21700 ( 9) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (1761 voxels, overlap=0.823) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (1761 voxels, peak = 8), gca=7.5 gca peak = 0.25980 (97) mri peak = 0.11809 (96) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (669 voxels, overlap=1.002) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (669 voxels, peak = 96), gca=95.5 gca peak = 0.16005 (100) mri peak = 0.14162 (101) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (692 voxels, overlap=1.000) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (692 voxels, peak = 100), gca=100.0 gca peak = 0.24552 (55) mri peak = 0.09822 (56) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (981 voxels, overlap=1.006) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (981 voxels, peak = 55), gca=55.0 gca peak = 0.28380 (59) mri peak = 0.09193 (60) Left_Hippocampus (17): linear fit = 0.96 x + 0.0 (891 voxels, overlap=1.006) Left_Hippocampus (17): linear fit = 0.96 x + 0.0 (891 voxels, peak = 57), gca=56.9 gca peak = 0.07772 (104) mri peak = 0.11300 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (33309 voxels, overlap=0.662) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (33309 voxels, peak = 104), gca=104.0 gca peak = 0.07686 (107) mri peak = 0.10773 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35906 voxels, overlap=0.677) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35906 voxels, peak = 107), gca=107.0 gca peak = 0.10081 (56) mri peak = 0.05040 (59) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (28674 voxels, overlap=0.969) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (28674 voxels, peak = 57), gca=57.4 gca peak = 0.11969 (56) mri peak = 0.05120 (56) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (28545 voxels, overlap=0.973) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (28545 voxels, peak = 57), gca=57.4 gca peak = 0.25612 (73) mri peak = 0.12078 (73) Right_Caudate (50): linear fit = 1.00 x + 0.0 (843 voxels, overlap=1.002) Right_Caudate (50): linear fit = 1.00 x + 0.0 (843 voxels, peak = 73), gca=73.0 gca peak = 0.15299 (70) mri peak = 0.12060 (77) Left_Caudate (11): linear fit = 1.00 x + 0.0 (794 voxels, overlap=0.997) Left_Caudate (11): linear fit = 1.00 x + 0.0 (794 voxels, peak = 70), gca=70.0 gca peak = 0.12492 (62) mri peak = 0.05786 (62) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (20170 voxels, overlap=0.998) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (20170 voxels, peak = 61), gca=61.1 gca peak = 0.13842 (58) mri peak = 0.06274 (60) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (20774 voxels, overlap=0.994) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (20774 voxels, peak = 59), gca=59.4 gca peak = 0.15873 (90) mri peak = 0.11268 (88) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (4913 voxels, overlap=0.936) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (4913 voxels, peak = 89), gca=88.7 gca peak = 0.15163 (90) mri peak = 0.11802 (87) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5256 voxels, overlap=0.940) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5256 voxels, peak = 89), gca=88.7 gca peak = 0.26595 (62) mri peak = 0.11091 (63) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (556 voxels, overlap=1.016) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (556 voxels, peak = 62), gca=62.0 gca peak = 0.30045 (60) mri peak = 0.15028 (61) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (573 voxels, overlap=1.007) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (573 voxels, peak = 62), gca=61.5 gca peak = 0.11191 (90) mri peak = 0.06623 (89) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4126 voxels, overlap=0.971) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4126 voxels, peak = 90), gca=89.6 gca peak = 0.09438 (90) mri peak = 0.08237 (84) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3905 voxels, overlap=0.982) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3905 voxels, peak = 89), gca=88.7 gca peak = 0.07460 (79) mri peak = 0.08909 (83) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2464 voxels, overlap=0.869) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2464 voxels, peak = 79), gca=79.0 gca peak = 0.10883 (78) mri peak = 0.08709 (84) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2549 voxels, overlap=0.987) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2549 voxels, peak = 78), gca=78.0 gca peak = 0.08832 (84) mri peak = 0.09325 (85) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10413 voxels, overlap=0.738) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10413 voxels, peak = 84), gca=83.6 gca peak = 0.11643 (92) mri peak = 0.07230 (97) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1201 voxels, overlap=0.827) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1201 voxels, peak = 92), gca=91.5 gca peak = 0.16884 (92) mri peak = 0.08347 (97) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1290 voxels, overlap=0.877) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1290 voxels, peak = 94), gca=94.3 gca peak = 0.25218 (15) mri peak = 0.28571 (10) gca peak = 0.26059 (10) mri peak = 0.16904 (12) Fourth_Ventricle (15): linear fit = 1.04 x + 0.0 (165 voxels, overlap=0.745) Fourth_Ventricle (15): linear fit = 1.04 x + 0.0 (165 voxels, peak = 10), gca=10.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.17867 (28) gca peak Left_Thalamus = 1.00000 (96) gca peak Third_Ventricle = 0.25218 (15) gca peak CSF = 0.26345 (21) gca peak Left_Accumbens_area = 0.79368 (63) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.26964 (23) gca peak Right_Accumbens_area = 0.29961 (71) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.89470 (18) gca peak WM_hypointensities = 0.07766 (78) gca peak non_WM_hypointensities = 0.08683 (44) gca peak Optic_Chiasm = 0.70795 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.06 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 44579 voxels changed in iteration 0 of unlikely voxel relabeling 145 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 25463 gm and wm labels changed (%25 to gray, %75 to white out of all changed labels) 326 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 54650 changed. image ll: -2.067, PF=0.500 pass 2: 14355 changed. image ll: -2.066, PF=0.500 pass 3: 4310 changed. 28682 voxels changed in iteration 0 of unlikely voxel relabeling 231 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5347 voxels changed in iteration 0 of unlikely voxel relabeling 95 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4162 voxels changed in iteration 0 of unlikely voxel relabeling 52 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 3522 voxels changed in iteration 0 of unlikely voxel relabeling 15 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 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 2968.190784 mri_ca_label stimesec 12.491049 mri_ca_label ru_maxrss 2121812 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 809135 mri_ca_label ru_majflt 8 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 1616 mri_ca_label ru_oublock 440 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 9 mri_ca_label ru_nivcsw 987 auto-labeling took 49 minutes and 41 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/web/freesurver/test/MRI/subjects02/mri/transforms/cc_up.lta subjects02 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/web/freesurver/test/MRI/subjects02/mri/transforms/cc_up.lta reading aseg from /home/web/freesurver/test/MRI/subjects02/mri/aseg.auto_noCCseg.mgz reading norm from /home/web/freesurver/test/MRI/subjects02/mri/norm.mgz 46932 voxels in left wm, 49692 in right wm, xrange [121, 133] searching rotation angles z=[-7 7], y=[-2 12] searching scale 1 Z rot -6.9 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 global minimum found at slice 127.2, rotations (4.59, 0.08) final transformation (x=127.2, yr=4.590, zr=0.079): 0.99679 -0.00137 0.08002 -8.50605; 0.00137 1.00000 0.00011 24.81229; -0.08002 0.00000 0.99679 15.57411; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 103 123 eigenvectors: 0.00116 -0.00010 1.00000; 0.17585 -0.98442 -0.00030; 0.98442 0.17585 -0.00113; writing aseg with callosum to /home/web/freesurver/test/MRI/subjects02/mri/aseg.auto.mgz... corpus callosum segmentation took 1.1 minutes #-------------------------------------- #@# Merge ASeg 2020��� 04��� 29��� ��������� 00:40:37 CST cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 2020��� 04��� 29��� ��������� 00:40:37 CST /home/web/freesurver/test/MRI/subjects02/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... 667 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 62 (62), valley at 37 (37) csf peak at 10, setting threshold to 44 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 64 (64), valley at 35 (35) csf peak at 10, setting threshold to 46 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 34 seconds. #-------------------------------------------- #@# Mask BFS 2020��� 04��� 29��� ��������� 00:44:14 CST /home/web/freesurver/test/MRI/subjects02/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1487613 voxels in mask (pct= 8.87) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation 2020��� 04��� 29��� ��������� 00:44:16 CST mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (105.0): 105.6 +- 5.4 [79.0 --> 125.0] GM (71.0) : 69.3 +- 9.6 [30.0 --> 95.0] setting bottom of white matter range to 78.9 setting top of gray matter range to 88.5 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 4058 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4221 filled 728 bright non-wm voxels segmented. 2010 diagonally connected voxels added... white matter segmentation took 1.5 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 0.53 minutes reading wm segmentation from wm.seg.mgz... 53 voxels added to wm to prevent paths from MTL structures to cortex 2486 additional wm voxels added 0 additional wm voxels added SEG EDIT: 38996 voxels turned on, 40310 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+): 13 found - 13 modified | TOTAL: 13 pass 2 (xy+): 0 found - 13 modified | TOTAL: 13 pass 1 (xy-): 5 found - 5 modified | TOTAL: 18 pass 2 (xy-): 0 found - 5 modified | TOTAL: 18 pass 1 (yz+): 22 found - 22 modified | TOTAL: 40 pass 2 (yz+): 0 found - 22 modified | TOTAL: 40 pass 1 (yz-): 17 found - 17 modified | TOTAL: 57 pass 2 (yz-): 0 found - 17 modified | TOTAL: 57 pass 1 (xz+): 9 found - 9 modified | TOTAL: 66 pass 2 (xz+): 0 found - 9 modified | TOTAL: 66 pass 1 (xz-): 7 found - 7 modified | TOTAL: 73 pass 2 (xz-): 0 found - 7 modified | TOTAL: 73 Iteration Number : 1 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 8 found - 8 modified | TOTAL: 12 pass 2 (+++): 0 found - 8 modified | TOTAL: 12 pass 1 (+++): 6 found - 6 modified | TOTAL: 18 pass 2 (+++): 0 found - 6 modified | TOTAL: 18 pass 1 (+++): 7 found - 7 modified | TOTAL: 25 pass 2 (+++): 0 found - 7 modified | TOTAL: 25 Iteration Number : 1 pass 1 (++): 85 found - 85 modified | TOTAL: 85 pass 2 (++): 0 found - 85 modified | TOTAL: 85 pass 1 (+-): 81 found - 81 modified | TOTAL: 166 pass 2 (+-): 0 found - 81 modified | TOTAL: 166 pass 1 (--): 59 found - 59 modified | TOTAL: 225 pass 2 (--): 0 found - 59 modified | TOTAL: 225 pass 1 (-+): 79 found - 79 modified | TOTAL: 304 pass 2 (-+): 0 found - 79 modified | TOTAL: 304 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 3 found - 3 modified | TOTAL: 4 pass 2 (xz+): 0 found - 3 modified | TOTAL: 4 pass 1 (xz-): 2 found - 2 modified | TOTAL: 6 pass 2 (xz-): 0 found - 2 modified | TOTAL: 6 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 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 409 (out of 506111: 0.080812) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill 2020��� 04��� 29��� ��������� 00:46:25 CST /home/web/freesurver/test/MRI/subjects02/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.05165 -0.00410 0.08894 -18.16203; 0.00867 1.15614 -0.08338 -7.73886; -0.07161 0.04867 1.10288 -24.55145; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.05165 -0.00410 0.08894 -18.16203; 0.00867 1.15614 -0.08338 -7.73886; -0.07161 0.04867 1.10288 -24.55145; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1356 (min = 350, max = 1400), aspect = 0.45 (min = 0.10, max = 0.75) no need to search using seed (125, 120, 148), TAL = (3.0, 20.0, 8.0) talairach voxel to voxel transform 0.94568 0.00654 -0.07577 15.36591; -0.00266 0.86219 0.06539 8.22960; 0.06152 -0.03762 0.89891 22.89581; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 120, 148) --> (3.0, 20.0, 8.0) done. writing output to filled.mgz... filling took 0.8 minutes talairach cc position changed to (3.00, 20.00, 8.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, 20.00, 8.00) SRC: (106.13, 121.09, 158.00) search lh wm seed point around talairach space (-15.00, 20.00, 8.00), SRC: (140.17, 120.99, 160.22) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh 2020��� 04��� 29��� ��������� 00:47:16 CST /home/web/freesurver/test/MRI/subjects02/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 1 found - 1 modified | TOTAL: 3 pass 2 (xz+): 0 found - 1 modified | TOTAL: 3 pass 1 (xz-): 1 found - 1 modified | TOTAL: 4 pass 2 (xz-): 0 found - 1 modified | TOTAL: 4 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 5 (out of 241241: 0.002073) 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: 2097 vertices, 2242 faces slice 70: 8657 vertices, 8906 faces slice 80: 16877 vertices, 17179 faces slice 90: 26563 vertices, 26926 faces slice 100: 37375 vertices, 37762 faces slice 110: 48737 vertices, 49130 faces slice 120: 60917 vertices, 61357 faces slice 130: 73539 vertices, 73959 faces slice 140: 85377 vertices, 85784 faces slice 150: 96157 vertices, 96517 faces slice 160: 104680 vertices, 104954 faces slice 170: 112426 vertices, 112706 faces slice 180: 119517 vertices, 119780 faces slice 190: 124975 vertices, 125207 faces slice 200: 128479 vertices, 128581 faces slice 210: 128856 vertices, 128890 faces slice 220: 128856 vertices, 128890 faces slice 230: 128856 vertices, 128890 faces slice 240: 128856 vertices, 128890 faces slice 250: 128856 vertices, 128890 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... 128856 voxel in cpt #1: X=-34 [v=128856,e=386670,f=257780] located at (-27.319117, -5.228705, 16.720301) For the whole surface: X=-34 [v=128856,e=386670,f=257780] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh 2020��� 04��� 29��� ��������� 00:47:39 CST /home/web/freesurver/test/MRI/subjects02/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-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 3 found - 3 modified | TOTAL: 5 pass 2 (yz+): 0 found - 3 modified | TOTAL: 5 pass 1 (yz-): 0 found - 0 modified | TOTAL: 5 pass 1 (xz+): 0 found - 0 modified | TOTAL: 5 pass 1 (xz-): 1 found - 1 modified | TOTAL: 6 pass 2 (xz-): 0 found - 1 modified | TOTAL: 6 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 2 found - 2 modified | TOTAL: 3 pass 2 (+-): 0 found - 2 modified | TOTAL: 3 pass 1 (--): 0 found - 0 modified | TOTAL: 3 pass 1 (-+): 0 found - 0 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 9 (out of 246985: 0.003644) 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: 1067 vertices, 1145 faces slice 70: 5841 vertices, 6089 faces slice 80: 14078 vertices, 14378 faces slice 90: 24874 vertices, 25285 faces slice 100: 37398 vertices, 37765 faces slice 110: 50147 vertices, 50549 faces slice 120: 63173 vertices, 63629 faces slice 130: 76419 vertices, 76860 faces slice 140: 88256 vertices, 88640 faces slice 150: 99293 vertices, 99626 faces slice 160: 107134 vertices, 107421 faces slice 170: 115017 vertices, 115286 faces slice 180: 121573 vertices, 121802 faces slice 190: 127375 vertices, 127588 faces slice 200: 130345 vertices, 130425 faces slice 210: 130634 vertices, 130660 faces slice 220: 130634 vertices, 130660 faces slice 230: 130634 vertices, 130660 faces slice 240: 130634 vertices, 130660 faces slice 250: 130634 vertices, 130660 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... 130634 voxel in cpt #1: X=-26 [v=130634,e=391980,f=261320] located at (28.962048, -5.296278, 16.199213) For the whole surface: X=-26 [v=130634,e=391980,f=261320] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh 2020��� 04��� 29��� ��������� 00:47:45 CST /home/web/freesurver/test/MRI/subjects02/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 2020��� 04��� 29��� ��������� 00:47:52 CST /home/web/freesurver/test/MRI/subjects02/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 2020��� 04��� 29��� ��������� 00:47:57 CST /home/web/freesurver/test/MRI/subjects02/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 44.4 mm, total surface area = 67856 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.6 minutes step 000: RMS=0.153 (target=0.015) step 005: RMS=0.115 (target=0.015) step 010: RMS=0.084 (target=0.015) step 015: RMS=0.069 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.042 (target=0.015) step 040: RMS=0.039 (target=0.015) step 045: RMS=0.036 (target=0.015) step 050: RMS=0.034 (target=0.015) step 055: RMS=0.033 (target=0.015) step 060: RMS=0.034 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 34.046779 mris_inflate stimesec 0.104008 mris_inflate ru_maxrss 169940 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 40910 mris_inflate ru_majflt 5 mris_inflate ru_nswap 0 mris_inflate ru_inblock 1048 mris_inflate ru_oublock 9072 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 5 mris_inflate ru_nivcsw 48 #-------------------------------------------- #@# Inflation1 rh 2020��� 04��� 29��� ��������� 00:48:32 CST /home/web/freesurver/test/MRI/subjects02/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 44.2 mm, total surface area = 69078 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.6 minutes step 000: RMS=0.152 (target=0.015) step 005: RMS=0.114 (target=0.015) step 010: RMS=0.084 (target=0.015) step 015: RMS=0.070 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.041 (target=0.015) step 040: RMS=0.037 (target=0.015) step 045: RMS=0.035 (target=0.015) step 050: RMS=0.034 (target=0.015) step 055: RMS=0.033 (target=0.015) step 060: RMS=0.034 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 36.641780 mris_inflate stimesec 0.092034 mris_inflate ru_maxrss 172056 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 41436 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9192 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 14 #-------------------------------------------- #@# QSphere lh 2020��� 04��� 29��� ��������� 00:49:09 CST /home/web/freesurver/test/MRI/subjects02/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.03 +- 0.55 (0.00-->6.63) (max @ vno 88515 --> 89763) face area 0.03 +- 0.03 (-0.09-->0.69) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.333... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.971, avgs=0 005/300: dt: 0.9000, rms radial error=175.714, avgs=0 010/300: dt: 0.9000, rms radial error=175.163, avgs=0 015/300: dt: 0.9000, rms radial error=174.439, avgs=0 020/300: dt: 0.9000, rms radial error=173.614, avgs=0 025/300: dt: 0.9000, rms radial error=172.731, avgs=0 030/300: dt: 0.9000, rms radial error=171.815, avgs=0 035/300: dt: 0.9000, rms radial error=170.881, avgs=0 040/300: dt: 0.9000, rms radial error=169.940, avgs=0 045/300: dt: 0.9000, rms radial error=168.996, avgs=0 050/300: dt: 0.9000, rms radial error=168.053, avgs=0 055/300: dt: 0.9000, rms radial error=167.115, avgs=0 060/300: dt: 0.9000, rms radial error=166.182, avgs=0 065/300: dt: 0.9000, rms radial error=165.253, avgs=0 070/300: dt: 0.9000, rms radial error=164.328, avgs=0 075/300: dt: 0.9000, rms radial error=163.407, avgs=0 080/300: dt: 0.9000, rms radial error=162.491, avgs=0 085/300: dt: 0.9000, rms radial error=161.580, avgs=0 090/300: dt: 0.9000, rms radial error=160.674, avgs=0 095/300: dt: 0.9000, rms radial error=159.772, avgs=0 100/300: dt: 0.9000, rms radial error=158.876, avgs=0 105/300: dt: 0.9000, rms radial error=157.984, avgs=0 110/300: dt: 0.9000, rms radial error=157.097, avgs=0 115/300: dt: 0.9000, rms radial error=156.215, avgs=0 120/300: dt: 0.9000, rms radial error=155.337, avgs=0 125/300: dt: 0.9000, rms radial error=154.464, avgs=0 130/300: dt: 0.9000, rms radial error=153.596, avgs=0 135/300: dt: 0.9000, rms radial error=152.733, avgs=0 140/300: dt: 0.9000, rms radial error=151.874, avgs=0 145/300: dt: 0.9000, rms radial error=151.020, avgs=0 150/300: dt: 0.9000, rms radial error=150.170, avgs=0 155/300: dt: 0.9000, rms radial error=149.325, avgs=0 160/300: dt: 0.9000, rms radial error=148.485, avgs=0 165/300: dt: 0.9000, rms radial error=147.649, avgs=0 170/300: dt: 0.9000, rms radial error=146.818, avgs=0 175/300: dt: 0.9000, rms radial error=145.992, avgs=0 180/300: dt: 0.9000, rms radial error=145.170, avgs=0 185/300: dt: 0.9000, rms radial error=144.353, avgs=0 190/300: dt: 0.9000, rms radial error=143.540, avgs=0 195/300: dt: 0.9000, rms radial error=142.732, avgs=0 200/300: dt: 0.9000, rms radial error=141.928, avgs=0 205/300: dt: 0.9000, rms radial error=141.129, avgs=0 210/300: dt: 0.9000, rms radial error=140.334, avgs=0 215/300: dt: 0.9000, rms radial error=139.544, avgs=0 220/300: dt: 0.9000, rms radial error=138.758, avgs=0 225/300: dt: 0.9000, rms radial error=137.976, avgs=0 230/300: dt: 0.9000, rms radial error=137.199, avgs=0 235/300: dt: 0.9000, rms radial error=136.426, avgs=0 240/300: dt: 0.9000, rms radial error=135.657, avgs=0 245/300: dt: 0.9000, rms radial error=134.893, avgs=0 250/300: dt: 0.9000, rms radial error=134.133, avgs=0 255/300: dt: 0.9000, rms radial error=133.377, avgs=0 260/300: dt: 0.9000, rms radial error=132.625, avgs=0 265/300: dt: 0.9000, rms radial error=131.877, avgs=0 270/300: dt: 0.9000, rms radial error=131.134, avgs=0 275/300: dt: 0.9000, rms radial error=130.395, avgs=0 280/300: dt: 0.9000, rms radial error=129.660, avgs=0 285/300: dt: 0.9000, rms radial error=128.929, avgs=0 290/300: dt: 0.9000, rms radial error=128.202, avgs=0 295/300: dt: 0.9000, rms radial error=127.479, avgs=0 300/300: dt: 0.9000, rms radial error=126.760, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14680.97 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 2281.90 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00021 epoch 3 (K=160.0), pass 1, starting sse = 192.50 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.14/12 = 0.01142 epoch 4 (K=640.0), pass 1, starting sse = 7.98 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/12 = 0.01030 final distance error %23.36 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.06 hours mris_sphere utimesec 231.580787 mris_sphere stimesec 0.115998 mris_sphere ru_maxrss 170080 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 40921 mris_sphere ru_majflt 7 mris_sphere ru_nswap 0 mris_sphere ru_inblock 1304 mris_sphere ru_oublock 9072 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 7 mris_sphere ru_nivcsw 240 FSRUNTIME@ mris_sphere 0.0644 hours 1 threads #-------------------------------------------- #@# QSphere rh 2020��� 04��� 29��� ��������� 00:53:00 CST /home/web/freesurver/test/MRI/subjects02/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.03 +- 0.55 (0.00-->7.29) (max @ vno 91534 --> 91557) face area 0.03 +- 0.03 (-0.32-->0.78) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.342... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.248, avgs=0 005/300: dt: 0.9000, rms radial error=174.992, avgs=0 010/300: dt: 0.9000, rms radial error=174.440, avgs=0 015/300: dt: 0.9000, rms radial error=173.716, avgs=0 020/300: dt: 0.9000, rms radial error=172.892, avgs=0 025/300: dt: 0.9000, rms radial error=172.010, avgs=0 030/300: dt: 0.9000, rms radial error=171.097, avgs=0 035/300: dt: 0.9000, rms radial error=170.166, avgs=0 040/300: dt: 0.9000, rms radial error=169.228, avgs=0 045/300: dt: 0.9000, rms radial error=168.287, avgs=0 050/300: dt: 0.9000, rms radial error=167.348, avgs=0 055/300: dt: 0.9000, rms radial error=166.411, avgs=0 060/300: dt: 0.9000, rms radial error=165.477, avgs=0 065/300: dt: 0.9000, rms radial error=164.548, avgs=0 070/300: dt: 0.9000, rms radial error=163.623, avgs=0 075/300: dt: 0.9000, rms radial error=162.703, avgs=0 080/300: dt: 0.9000, rms radial error=161.788, avgs=0 085/300: dt: 0.9000, rms radial error=160.878, avgs=0 090/300: dt: 0.9000, rms radial error=159.973, avgs=0 095/300: dt: 0.9000, rms radial error=159.073, avgs=0 100/300: dt: 0.9000, rms radial error=158.177, avgs=0 105/300: dt: 0.9000, rms radial error=157.287, avgs=0 110/300: dt: 0.9000, rms radial error=156.401, avgs=0 115/300: dt: 0.9000, rms radial error=155.521, avgs=0 120/300: dt: 0.9000, rms radial error=154.645, avgs=0 125/300: dt: 0.9000, rms radial error=153.773, avgs=0 130/300: dt: 0.9000, rms radial error=152.907, avgs=0 135/300: dt: 0.9000, rms radial error=152.045, avgs=0 140/300: dt: 0.9000, rms radial error=151.188, avgs=0 145/300: dt: 0.9000, rms radial error=150.336, avgs=0 150/300: dt: 0.9000, rms radial error=149.488, avgs=0 155/300: dt: 0.9000, rms radial error=148.646, avgs=0 160/300: dt: 0.9000, rms radial error=147.808, avgs=0 165/300: dt: 0.9000, rms radial error=146.974, avgs=0 170/300: dt: 0.9000, rms radial error=146.146, avgs=0 175/300: dt: 0.9000, rms radial error=145.321, avgs=0 180/300: dt: 0.9000, rms radial error=144.502, avgs=0 185/300: dt: 0.9000, rms radial error=143.687, avgs=0 190/300: dt: 0.9000, rms radial error=142.876, avgs=0 195/300: dt: 0.9000, rms radial error=142.070, avgs=0 200/300: dt: 0.9000, rms radial error=141.269, avgs=0 205/300: dt: 0.9000, rms radial error=140.472, avgs=0 210/300: dt: 0.9000, rms radial error=139.679, avgs=0 215/300: dt: 0.9000, rms radial error=138.891, avgs=0 220/300: dt: 0.9000, rms radial error=138.107, avgs=0 225/300: dt: 0.9000, rms radial error=137.328, avgs=0 230/300: dt: 0.9000, rms radial error=136.553, avgs=0 235/300: dt: 0.9000, rms radial error=135.782, avgs=0 240/300: dt: 0.9000, rms radial error=135.016, avgs=0 245/300: dt: 0.9000, rms radial error=134.254, avgs=0 250/300: dt: 0.9000, rms radial error=133.496, avgs=0 255/300: dt: 0.9000, rms radial error=132.743, avgs=0 260/300: dt: 0.9000, rms radial error=131.993, avgs=0 265/300: dt: 0.9000, rms radial error=131.248, avgs=0 270/300: dt: 0.9000, rms radial error=130.507, avgs=0 275/300: dt: 0.9000, rms radial error=129.771, avgs=0 280/300: dt: 0.9000, rms radial error=129.038, avgs=0 285/300: dt: 0.9000, rms radial error=128.310, avgs=0 290/300: dt: 0.9000, rms radial error=127.586, avgs=0 295/300: dt: 0.9000, rms radial error=126.866, avgs=0 300/300: dt: 0.9000, rms radial error=126.149, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14710.87 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 2 (K=40.0), pass 1, starting sse = 2226.50 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 3 (K=160.0), pass 1, starting sse = 180.35 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/11 = 0.01034 epoch 4 (K=640.0), pass 1, starting sse = 8.50 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/13 = 0.00885 final distance error %22.49 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.06 hours mris_sphere utimesec 231.879834 mris_sphere stimesec 0.275995 mris_sphere ru_maxrss 172752 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 82431 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9192 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 0 mris_sphere ru_nivcsw 79 FSRUNTIME@ mris_sphere 0.0645 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh 2020��� 04��� 29��� ��������� 00:56:53 CST /home/web/freesurver/test/MRI/subjects02/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh 2020��� 04��� 29��� ��������� 00:56:53 CST /home/web/freesurver/test/MRI/subjects02/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh 2020��� 04��� 29��� ��������� 00:56:53 CST mris_fix_topology -rusage /home/web/freesurver/test/MRI/subjects02/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 subjects02 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=-34 (nv=128856, nf=257780, ne=386670, g=18) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 1999 ambiguous faces found in tessellation segmenting defects... 29 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 29 defects to be corrected 0 vertices coincident reading input surface /home/web/freesurver/test/MRI/subjects02/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.3882 (-4.6941) -vertex loglikelihood: -6.3535 (-3.1767) -normal dot loglikelihood: -3.6237 (-3.6237) -quad curv loglikelihood: -6.4952 (-3.2476) Total Loglikelihood : -25.8606 CORRECTING DEFECT 0 (vertices=31, convex hull=63, v0=61) After retessellation of defect 0 (v0=61), euler #=-26 (127592,382219,254601) : difference with theory (-26) = 0 CORRECTING DEFECT 1 (vertices=19, convex hull=48, v0=1222) After retessellation of defect 1 (v0=1222), euler #=-25 (127602,382265,254638) : difference with theory (-25) = 0 CORRECTING DEFECT 2 (vertices=31, convex hull=58, v0=9857) After retessellation of defect 2 (v0=9857), euler #=-24 (127616,382327,254687) : difference with theory (-24) = 0 CORRECTING DEFECT 3 (vertices=62, convex hull=55, v0=14904) After retessellation of defect 3 (v0=14904), euler #=-23 (127634,382399,254742) : difference with theory (-23) = 0 CORRECTING DEFECT 4 (vertices=35, convex hull=36, v0=16567) After retessellation of defect 4 (v0=16567), euler #=-22 (127640,382428,254766) : difference with theory (-22) = 0 CORRECTING DEFECT 5 (vertices=36, convex hull=75, v0=18791) After retessellation of defect 5 (v0=18791), euler #=-21 (127658,382510,254831) : difference with theory (-21) = 0 CORRECTING DEFECT 6 (vertices=54, convex hull=115, v0=23770) After retessellation of defect 6 (v0=23770), euler #=-20 (127688,382651,254943) : difference with theory (-20) = 0 CORRECTING DEFECT 7 (vertices=57, convex hull=84, v0=28465) After retessellation of defect 7 (v0=28465), euler #=-19 (127702,382728,255007) : difference with theory (-19) = 0 CORRECTING DEFECT 8 (vertices=18, convex hull=63, v0=30455) After retessellation of defect 8 (v0=30455), euler #=-18 (127711,382778,255049) : difference with theory (-18) = 0 CORRECTING DEFECT 9 (vertices=39, convex hull=82, v0=37199) After retessellation of defect 9 (v0=37199), euler #=-17 (127736,382884,255131) : difference with theory (-17) = 0 CORRECTING DEFECT 10 (vertices=10, convex hull=16, v0=43879) After retessellation of defect 10 (v0=43879), euler #=-16 (127736,382887,255135) : difference with theory (-16) = 0 CORRECTING DEFECT 11 (vertices=8, convex hull=22, v0=49481) After retessellation of defect 11 (v0=49481), euler #=-15 (127738,382898,255145) : difference with theory (-15) = 0 CORRECTING DEFECT 12 (vertices=9, convex hull=19, v0=54033) After retessellation of defect 12 (v0=54033), euler #=-14 (127739,382907,255154) : difference with theory (-14) = 0 CORRECTING DEFECT 13 (vertices=17, convex hull=19, v0=61531) After retessellation of defect 13 (v0=61531), euler #=-13 (127744,382927,255170) : difference with theory (-13) = 0 CORRECTING DEFECT 14 (vertices=103, convex hull=45, v0=61812) After retessellation of defect 14 (v0=61812), euler #=-12 (127768,383018,255238) : difference with theory (-12) = 0 CORRECTING DEFECT 15 (vertices=33, convex hull=30, v0=62906) After retessellation of defect 15 (v0=62906), euler #=-11 (127777,383052,255264) : difference with theory (-11) = 0 CORRECTING DEFECT 16 (vertices=14, convex hull=41, v0=78877) After retessellation of defect 16 (v0=78877), euler #=-10 (127781,383077,255286) : difference with theory (-10) = 0 CORRECTING DEFECT 17 (vertices=244, convex hull=43, v0=83867) After retessellation of defect 17 (v0=83867), euler #=-9 (127790,383125,255326) : difference with theory (-9) = 0 CORRECTING DEFECT 18 (vertices=34, convex hull=55, v0=87327) After retessellation of defect 18 (v0=87327), euler #=-8 (127806,383194,255380) : difference with theory (-8) = 0 CORRECTING DEFECT 19 (vertices=32, convex hull=67, v0=88605) After retessellation of defect 19 (v0=88605), euler #=-7 (127815,383247,255425) : difference with theory (-7) = 0 CORRECTING DEFECT 20 (vertices=50, convex hull=39, v0=91899) After retessellation of defect 20 (v0=91899), euler #=-6 (127829,383302,255467) : difference with theory (-6) = 0 CORRECTING DEFECT 21 (vertices=116, convex hull=45, v0=94069) After retessellation of defect 21 (v0=94069), euler #=-5 (127842,383358,255511) : difference with theory (-5) = 0 CORRECTING DEFECT 22 (vertices=46, convex hull=95, v0=99799) After retessellation of defect 22 (v0=99799), euler #=-4 (127869,383480,255607) : difference with theory (-4) = 0 CORRECTING DEFECT 23 (vertices=21, convex hull=22, v0=102125) After retessellation of defect 23 (v0=102125), euler #=-3 (127873,383502,255626) : difference with theory (-3) = 0 CORRECTING DEFECT 24 (vertices=7, convex hull=39, v0=108950) After retessellation of defect 24 (v0=108950), euler #=-2 (127876,383521,255643) : difference with theory (-2) = 0 CORRECTING DEFECT 25 (vertices=94, convex hull=107, v0=110877) After retessellation of defect 25 (v0=110877), euler #=-1 (127894,383621,255726) : difference with theory (-1) = 0 CORRECTING DEFECT 26 (vertices=19, convex hull=64, v0=124812) After retessellation of defect 26 (v0=124812), euler #=0 (127905,383680,255775) : difference with theory (0) = 0 CORRECTING DEFECT 27 (vertices=22, convex hull=62, v0=125795) After retessellation of defect 27 (v0=125795), euler #=1 (127918,383741,255824) : difference with theory (1) = 0 CORRECTING DEFECT 28 (vertices=10, convex hull=23, v0=126023) After retessellation of defect 28 (v0=126023), euler #=2 (127920,383754,255836) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.21 (0.06-->7.96) (max @ vno 109756 --> 116317) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.21 (0.06-->7.96) (max @ vno 109756 --> 116317) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 110 mutations (35.3%), 202 crossovers (64.7%), 64 vertices were eliminated building final representation... 936 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=127920, nf=255836, ne=383754, g=0) writing corrected surface to /home/web/freesurver/test/MRI/subjects02/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 13.5 minutes 0 defective edges removing intersecting faces 000: 116 intersecting mris_fix_topology utimesec 809.177429 mris_fix_topology stimesec 2.571939 mris_fix_topology ru_maxrss 405112 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 158347 mris_fix_topology ru_majflt 8 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 1464 mris_fix_topology ru_oublock 12024 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 10 mris_fix_topology ru_nivcsw 487 FSRUNTIME@ mris_fix_topology lh 0.2256 hours 1 threads #@# Fix Topology rh 2020��� 04��� 29��� ��������� 01:10:25 CST mris_fix_topology -rusage /home/web/freesurver/test/MRI/subjects02/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 subjects02 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=-26 (nv=130634, nf=261320, ne=391980, g=14) 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... 2400 ambiguous faces found in tessellation segmenting defects... 21 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 19 into 18 20 defects to be corrected 0 vertices coincident reading input surface /home/web/freesurver/test/MRI/subjects02/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.3409 (-4.6705) -vertex loglikelihood: -6.3394 (-3.1697) -normal dot loglikelihood: -3.6237 (-3.6237) -quad curv loglikelihood: -6.5306 (-3.2653) Total Loglikelihood : -25.8345 CORRECTING DEFECT 0 (vertices=27, convex hull=68, v0=37) After retessellation of defect 0 (v0=37), euler #=-18 (129186,386968,257764) : difference with theory (-17) = 1 CORRECTING DEFECT 1 (vertices=7, convex hull=20, v0=9989) After retessellation of defect 1 (v0=9989), euler #=-17 (129187,386976,257772) : difference with theory (-16) = 1 CORRECTING DEFECT 2 (vertices=231, convex hull=105, v0=13711) After retessellation of defect 2 (v0=13711), euler #=-16 (129210,387087,257861) : difference with theory (-15) = 1 CORRECTING DEFECT 3 (vertices=18, convex hull=30, v0=16438) After retessellation of defect 3 (v0=16438), euler #=-15 (129212,387102,257875) : difference with theory (-14) = 1 CORRECTING DEFECT 4 (vertices=17, convex hull=63, v0=17812) After retessellation of defect 4 (v0=17812), euler #=-14 (129222,387154,257918) : difference with theory (-13) = 1 CORRECTING DEFECT 5 (vertices=35, convex hull=63, v0=24500) After retessellation of defect 5 (v0=24500), euler #=-13 (129241,387238,257984) : difference with theory (-12) = 1 CORRECTING DEFECT 6 (vertices=23, convex hull=60, v0=38537) After retessellation of defect 6 (v0=38537), euler #=-12 (129256,387307,258039) : difference with theory (-11) = 1 CORRECTING DEFECT 7 (vertices=307, convex hull=206, v0=43253) normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces normal vector of length zero at vertex 129801 with 3 faces After retessellation of defect 7 (v0=43253), euler #=-11 (129352,387694,258331) : difference with theory (-10) = 1 CORRECTING DEFECT 8 (vertices=11, convex hull=33, v0=73465) After retessellation of defect 8 (v0=73465), euler #=-10 (129356,387717,258351) : difference with theory (-9) = 1 CORRECTING DEFECT 9 (vertices=89, convex hull=58, v0=80156) After retessellation of defect 9 (v0=80156), euler #=-9 (129369,387780,258402) : difference with theory (-8) = 1 CORRECTING DEFECT 10 (vertices=23, convex hull=23, v0=85611) After retessellation of defect 10 (v0=85611), euler #=-8 (129374,387801,258419) : difference with theory (-7) = 1 CORRECTING DEFECT 11 (vertices=42, convex hull=70, v0=85766) After retessellation of defect 11 (v0=85766), euler #=-7 (129400,387909,258502) : difference with theory (-6) = 1 CORRECTING DEFECT 12 (vertices=7, convex hull=29, v0=86579) After retessellation of defect 12 (v0=86579), euler #=-6 (129401,387924,258517) : difference with theory (-5) = 1 CORRECTING DEFECT 13 (vertices=159, convex hull=86, v0=87077) After retessellation of defect 13 (v0=87077), euler #=-5 (129437,388077,258635) : difference with theory (-4) = 1 CORRECTING DEFECT 14 (vertices=84, convex hull=73, v0=87961) After retessellation of defect 14 (v0=87961), euler #=-4 (129443,388128,258681) : difference with theory (-3) = 1 CORRECTING DEFECT 15 (vertices=140, convex hull=95, v0=91449) After retessellation of defect 15 (v0=91449), euler #=-3 (129454,388204,258747) : difference with theory (-2) = 1 CORRECTING DEFECT 16 (vertices=41, convex hull=95, v0=100846) After retessellation of defect 16 (v0=100846), euler #=-2 (129479,388322,258841) : difference with theory (-1) = 1 CORRECTING DEFECT 17 (vertices=36, convex hull=73, v0=105442) After retessellation of defect 17 (v0=105442), euler #=-1 (129496,388408,258911) : difference with theory (0) = 1 CORRECTING DEFECT 18 (vertices=149, convex hull=125, v0=119178) After retessellation of defect 18 (v0=119178), euler #=1 (129532,388573,259042) : difference with theory (1) = 0 CORRECTING DEFECT 19 (vertices=18, convex hull=45, v0=124871) After retessellation of defect 19 (v0=124871), euler #=2 (129541,388617,259078) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.05-->8.01) (max @ vno 45456 --> 48109) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.05-->8.01) (max @ vno 45456 --> 48109) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 64 mutations (32.0%), 136 crossovers (68.0%), 55 vertices were eliminated building final representation... 1093 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=129541, nf=259078, ne=388617, g=0) writing corrected surface to /home/web/freesurver/test/MRI/subjects02/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 11.7 minutes 0 defective edges removing intersecting faces 000: 175 intersecting 001: 11 intersecting mris_fix_topology utimesec 701.816788 mris_fix_topology stimesec 1.249950 mris_fix_topology ru_maxrss 410448 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 101551 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 12184 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 1 mris_fix_topology ru_nivcsw 527 FSRUNTIME@ mris_fix_topology rh 0.1953 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 127920 - 383754 + 255836 = 2 --> 0 holes F =2V-4: 255836 = 255840-4 (0) 2E=3F: 767508 = 767508 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 129541 - 388617 + 259078 = 2 --> 0 holes F =2V-4: 259078 = 259082-4 (0) 2E=3F: 777234 = 777234 (0) total defect index = 0 /home/web/freesurver/test/MRI/subjects02/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 5 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /home/web/freesurver/test/MRI/subjects02/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 8 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh 2020��� 04��� 29��� ��������� 01:22:17 CST /home/web/freesurver/test/MRI/subjects02/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs subjects02 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/web/freesurver/test/MRI/subjects02/mri/filled.mgz... reading volume /home/web/freesurver/test/MRI/subjects02/mri/brain.finalsurfs.mgz... reading volume /home/web/freesurver/test/MRI/subjects02/mri/../mri/aseg.presurf.mgz... reading volume /home/web/freesurver/test/MRI/subjects02/mri/wm.mgz... 20105 bright wm thresholded. 867 bright non-wm voxels segmented. reading original surface position from /home/web/freesurver/test/MRI/subjects02/surf/lh.orig... computing class statistics... border white: 235147 voxels (1.40%) border gray 268831 voxels (1.60%) WM (98.0): 98.3 +- 8.7 [70.0 --> 110.0] GM (70.0) : 69.7 +- 10.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 54.0 (was 70) setting MAX_BORDER_WHITE to 111.7 (was 105) setting MIN_BORDER_WHITE to 64.0 (was 85) setting MAX_CSF to 43.9 (was 40) setting MAX_GRAY to 94.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 54.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 33.9 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.02-->3.02) (max @ vno 30389 --> 31458) face area 0.28 +- 0.12 (0.00-->1.87) mean absolute distance = 0.70 +- 0.85 3844 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-5.2, GM=64+-7.8 mean inside = 93.5, mean outside = 73.4 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=77.0, 59 (59) missing vertices, mean dist 0.4 [0.5 (%32.6)->0.8 (%67.4))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=web-v, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.25 (0.11-->3.81) (max @ vno 75968 --> 74847) face area 0.28 +- 0.13 (0.00-->1.82) mean absolute distance = 0.35 +- 0.55 2892 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3712717.2, rms=11.440 001: dt: 0.5000, sse=2160744.0, rms=8.239 (27.979%) 002: dt: 0.5000, sse=1446501.6, rms=6.231 (24.371%) 003: dt: 0.5000, sse=1088208.8, rms=4.918 (21.065%) 004: dt: 0.5000, sse=910999.1, rms=4.111 (16.410%) 005: dt: 0.5000, sse=837648.0, rms=3.725 (9.408%) 006: dt: 0.5000, sse=803882.9, rms=3.527 (5.302%) 007: dt: 0.5000, sse=793964.3, rms=3.465 (1.763%) 008: dt: 0.5000, sse=784954.4, rms=3.405 (1.743%) rms = 3.40, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=784125.7, rms=3.398 (0.195%) 010: dt: 0.2500, sse=612483.4, rms=2.013 (40.759%) 011: dt: 0.2500, sse=580346.3, rms=1.646 (18.252%) 012: dt: 0.2500, sse=573657.9, rms=1.549 (5.891%) 013: dt: 0.2500, sse=569434.1, rms=1.492 (3.680%) rms = 1.47, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=568333.6, rms=1.468 (1.614%) 015: dt: 0.1250, sse=563512.4, rms=1.398 (4.713%) rms = 1.39, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=563143.5, rms=1.391 (0.554%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=80.7, 77 (34) missing vertices, mean dist -0.2 [0.4 (%75.4)->0.2 (%24.6))] %79 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=web-v, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.24 (0.12-->3.65) (max @ vno 46866 --> 48070) face area 0.36 +- 0.16 (0.00-->2.41) mean absolute distance = 0.24 +- 0.38 2684 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1340343.4, rms=5.278 017: dt: 0.5000, sse=938007.6, rms=3.388 (35.811%) rms = 3.37, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=930988.8, rms=3.370 (0.546%) 019: dt: 0.2500, sse=745400.6, rms=1.890 (43.911%) 020: dt: 0.2500, sse=717130.0, rms=1.558 (17.557%) 021: dt: 0.2500, sse=706776.4, rms=1.411 (9.456%) 022: dt: 0.2500, sse=700719.8, rms=1.320 (6.399%) rms = 1.28, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=698537.4, rms=1.277 (3.297%) 024: dt: 0.1250, sse=695287.0, rms=1.201 (5.955%) rms = 1.19, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=695480.7, rms=1.193 (0.618%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=83.3, 60 (18) missing vertices, mean dist -0.1 [0.3 (%72.3)->0.2 (%27.7))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=web-v, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.24 (0.12-->3.77) (max @ vno 46866 --> 48070) face area 0.35 +- 0.16 (0.00-->2.51) mean absolute distance = 0.20 +- 0.31 2888 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=916075.4, rms=3.376 026: dt: 0.5000, sse=828682.4, rms=2.787 (17.455%) rms = 3.12, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=714583.0, rms=1.773 (36.389%) 028: dt: 0.2500, sse=679696.9, rms=1.313 (25.914%) 029: dt: 0.2500, sse=669269.4, rms=1.158 (11.816%) rms = 1.15, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=669060.6, rms=1.148 (0.882%) 031: dt: 0.1250, sse=664156.1, rms=1.066 (7.143%) rms = 1.06, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=663784.7, rms=1.064 (0.214%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=84.2, 55 (16) missing vertices, mean dist -0.0 [0.2 (%57.6)->0.2 (%42.4))] %89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=web-v, 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/web/freesurver/test/MRI/subjects02/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=684163.8, rms=1.566 rms = 1.77, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=651277.0, rms=1.046 (33.212%) 034: dt: 0.2500, sse=639542.4, rms=0.783 (25.186%) rms = 0.80, time step reduction 2 of 3 to 0.125... rms = 0.78, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=639249.3, rms=0.780 (0.301%) positioning took 0.4 minutes generating cortex label... 6 non-cortical segments detected only using segment with 7443 vertices erasing segment 1 (vno[0] = 84318) erasing segment 2 (vno[0] = 84350) erasing segment 3 (vno[0] = 84461) erasing segment 4 (vno[0] = 88971) erasing segment 5 (vno[0] = 90000) writing cortex label to /home/web/freesurver/test/MRI/subjects02/label/lh.cortex.label... writing curvature file /home/web/freesurver/test/MRI/subjects02/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/web/freesurver/test/MRI/subjects02/surf/lh.area vertex spacing 0.90 +- 0.25 (0.02-->3.83) (max @ vno 90062 --> 91122) face area 0.34 +- 0.15 (0.00-->2.52) refinement took 5.2 minutes #-------------------------------------------- #@# Make White Surf rh 2020��� 04��� 29��� ��������� 01:27:28 CST /home/web/freesurver/test/MRI/subjects02/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs subjects02 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/web/freesurver/test/MRI/subjects02/mri/filled.mgz... reading volume /home/web/freesurver/test/MRI/subjects02/mri/brain.finalsurfs.mgz... reading volume /home/web/freesurver/test/MRI/subjects02/mri/../mri/aseg.presurf.mgz... reading volume /home/web/freesurver/test/MRI/subjects02/mri/wm.mgz... 20105 bright wm thresholded. 867 bright non-wm voxels segmented. reading original surface position from /home/web/freesurver/test/MRI/subjects02/surf/rh.orig... computing class statistics... border white: 235147 voxels (1.40%) border gray 268831 voxels (1.60%) WM (98.0): 98.3 +- 8.7 [70.0 --> 110.0] GM (70.0) : 69.7 +- 10.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 54.0 (was 70) setting MAX_BORDER_WHITE to 111.7 (was 105) setting MIN_BORDER_WHITE to 64.0 (was 85) setting MAX_CSF to 43.9 (was 40) setting MAX_GRAY to 94.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 54.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 33.9 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->4.28) (max @ vno 52964 --> 129305) face area 0.28 +- 0.12 (0.00-->2.93) mean absolute distance = 0.70 +- 0.85 3987 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-6.1, GM=64+-8.7 mean inside = 93.3, mean outside = 73.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=77.2, 40 (40) missing vertices, mean dist 0.4 [0.5 (%33.0)->0.8 (%67.0))] %71 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=web-v, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.25 (0.06-->4.60) (max @ vno 45456 --> 46796) face area 0.28 +- 0.13 (0.00-->2.76) mean absolute distance = 0.35 +- 0.56 3032 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3740937.5, rms=11.377 001: dt: 0.5000, sse=2180707.8, rms=8.199 (27.936%) 002: dt: 0.5000, sse=1467641.0, rms=6.218 (24.157%) 003: dt: 0.5000, sse=1103869.1, rms=4.902 (21.160%) 004: dt: 0.5000, sse=924976.4, rms=4.100 (16.356%) 005: dt: 0.5000, sse=847083.0, rms=3.691 (9.975%) 006: dt: 0.5000, sse=815257.9, rms=3.503 (5.104%) 007: dt: 0.5000, sse=801679.3, rms=3.426 (2.208%) rms = 3.38, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=795019.2, rms=3.381 (1.317%) 009: dt: 0.2500, sse=625927.2, rms=2.016 (40.379%) 010: dt: 0.2500, sse=591759.4, rms=1.656 (17.838%) 011: dt: 0.2500, sse=585504.4, rms=1.568 (5.321%) 012: dt: 0.2500, sse=581652.4, rms=1.515 (3.350%) rms = 1.49, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=579878.6, rms=1.490 (1.676%) 014: dt: 0.1250, sse=575156.7, rms=1.414 (5.127%) rms = 1.40, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=574428.6, rms=1.403 (0.738%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.9, 39 (7) missing vertices, mean dist -0.2 [0.4 (%75.3)->0.2 (%24.7))] %79 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=web-v, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.24 (0.08-->5.04) (max @ vno 45456 --> 46796) face area 0.36 +- 0.16 (0.00-->4.13) mean absolute distance = 0.24 +- 0.37 2824 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1354528.8, rms=5.256 016: dt: 0.5000, sse=940595.3, rms=3.320 (36.833%) rms = 3.32, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=829625.4, rms=2.559 (22.940%) 018: dt: 0.2500, sse=758985.8, rms=1.917 (25.083%) 019: dt: 0.2500, sse=732115.9, rms=1.609 (16.044%) 020: dt: 0.2500, sse=728760.3, rms=1.477 (8.246%) 021: dt: 0.2500, sse=716617.7, rms=1.387 (6.040%) 022: dt: 0.2500, sse=712775.8, rms=1.325 (4.475%) rms = 1.28, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=713762.9, rms=1.283 (3.212%) 024: dt: 0.1250, sse=705163.8, rms=1.217 (5.121%) rms = 1.21, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=704350.2, rms=1.206 (0.946%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=83.3, 42 (6) missing vertices, mean dist -0.1 [0.3 (%72.1)->0.2 (%27.9))] %86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=web-v, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.24 (0.11-->5.23) (max @ vno 45456 --> 46796) face area 0.34 +- 0.16 (0.00-->4.23) mean absolute distance = 0.20 +- 0.31 2883 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=914103.4, rms=3.297 026: dt: 0.5000, sse=841700.3, rms=2.789 (15.414%) rms = 3.08, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=726622.3, rms=1.794 (35.654%) 028: dt: 0.2500, sse=689354.9, rms=1.324 (26.220%) 029: dt: 0.2500, sse=678997.0, rms=1.165 (12.022%) rms = 1.15, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=682984.5, rms=1.150 (1.257%) 031: dt: 0.1250, sse=673039.5, rms=1.066 (7.341%) rms = 1.06, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=673525.6, rms=1.065 (0.086%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=84.2, 52 (6) missing vertices, mean dist -0.0 [0.2 (%57.3)->0.2 (%42.7))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=web-v, 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/web/freesurver/test/MRI/subjects02/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=694889.4, rms=1.563 rms = 1.73, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=662204.6, rms=1.064 (31.944%) 034: dt: 0.2500, sse=649878.6, rms=0.792 (25.556%) rms = 0.81, time step reduction 2 of 3 to 0.125... rms = 0.79, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=649472.4, rms=0.789 (0.385%) positioning took 0.4 minutes generating cortex label... 14 non-cortical segments detected only using segment with 6900 vertices erasing segment 0 (vno[0] = 24239) erasing segment 1 (vno[0] = 25394) erasing segment 3 (vno[0] = 82773) erasing segment 4 (vno[0] = 82811) erasing segment 5 (vno[0] = 83846) erasing segment 6 (vno[0] = 87059) erasing segment 7 (vno[0] = 87107) erasing segment 8 (vno[0] = 89301) erasing segment 9 (vno[0] = 89339) erasing segment 10 (vno[0] = 89358) erasing segment 11 (vno[0] = 90534) erasing segment 12 (vno[0] = 95939) erasing segment 13 (vno[0] = 99527) writing cortex label to /home/web/freesurver/test/MRI/subjects02/label/rh.cortex.label... writing curvature file /home/web/freesurver/test/MRI/subjects02/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/web/freesurver/test/MRI/subjects02/surf/rh.area vertex spacing 0.90 +- 0.25 (0.02-->5.26) (max @ vno 45456 --> 46796) face area 0.34 +- 0.16 (0.00-->4.20) refinement took 5.3 minutes #-------------------------------------------- #@# Smooth2 lh 2020��� 04��� 29��� ��������� 01:32:43 CST /home/web/freesurver/test/MRI/subjects02/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 2020��� 04��� 29��� ��������� 01:32:50 CST /home/web/freesurver/test/MRI/subjects02/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 2020��� 04��� 29��� ��������� 01:32:56 CST /home/web/freesurver/test/MRI/subjects02/scripts mris_inflate -rusage /home/web/freesurver/test/MRI/subjects02/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 44.5 mm, total surface area = 78639 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.177 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.022 (target=0.015) step 060: RMS=0.021 (target=0.015) inflation complete. inflation took 0.6 minutes mris_inflate utimesec 33.659890 mris_inflate stimesec 0.275966 mris_inflate ru_maxrss 168952 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 80767 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 232 mris_inflate ru_oublock 10000 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 1 mris_inflate ru_nivcsw 49 #-------------------------------------------- #@# Inflation2 rh 2020��� 04��� 29��� ��������� 01:33:30 CST /home/web/freesurver/test/MRI/subjects02/scripts mris_inflate -rusage /home/web/freesurver/test/MRI/subjects02/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 44.3 mm, total surface area = 79673 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.176 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 0.6 minutes mris_inflate utimesec 34.493716 mris_inflate stimesec 0.092004 mris_inflate ru_maxrss 170744 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 41104 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10136 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 16 #-------------------------------------------- #@# Curv .H and .K lh 2020��� 04��� 29��� ��������� 01:34:04 CST /home/web/freesurver/test/MRI/subjects02/surf mris_curvature -w lh.white.preaparc total integrated curvature = 1.038*4pi (13.040) --> 0 handles ICI = 133.3, FI = 1558.9, variation=23986.783 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 208 vertices thresholded to be in k1 ~ [-0.21 0.41], k2 ~ [-0.10 0.04] total integrated curvature = 0.594*4pi (7.468) --> 0 handles ICI = 1.4, FI = 8.1, variation=141.930 114 vertices thresholded to be in [-0.01 0.01] 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 [-0.12 0.20] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.022 done. #-------------------------------------------- #@# Curv .H and .K rh 2020��� 04��� 29��� ��������� 01:35:19 CST /home/web/freesurver/test/MRI/subjects02/surf mris_curvature -w rh.white.preaparc total integrated curvature = 14.970*4pi (188.125) --> -14 handles ICI = 150.5, FI = 1575.0, variation=24561.621 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 143 vertices thresholded to be in k1 ~ [-0.18 2.13], k2 ~ [-0.08 0.05] total integrated curvature = 0.574*4pi (7.207) --> 0 handles ICI = 1.5, FI = 8.7, variation=151.109 101 vertices thresholded to be in [-0.03 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 90 vertices thresholded to be in [-0.12 0.49] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.023 done. #----------------------------------------- #@# Curvature Stats lh 2020��� 04��� 29��� ��������� 01:36:36 CST /home/web/freesurver/test/MRI/subjects02/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm subjects02 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 [ subjects02/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 [ 225 ] Gb_filter = 0 WARN: S lookup min: -0.003682 WARN: S explicit min: 0.000000 vertex = 298 #----------------------------------------- #@# Curvature Stats rh 2020��� 04��� 29��� ��������� 01:36:40 CST /home/web/freesurver/test/MRI/subjects02/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm subjects02 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 [ subjects02/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 [ 245 ] Gb_filter = 0 WARN: S lookup min: -0.307940 WARN: S explicit min: 0.000000 vertex = 122 #-------------------------------------------- #@# Sphere lh 2020��� 04��� 29��� ��������� 01:36:44 CST /home/web/freesurver/test/MRI/subjects02/scripts mris_sphere -rusage /home/web/freesurver/test/MRI/subjects02/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 0.310... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=web-v, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %18.98 pass 1: epoch 2 of 3 starting distance error %18.98 unfolding complete - removing small folds... starting distance error %18.96 removing remaining folds... final distance error %18.97 MRISunfold() return, current seed 1234 -01: dt=0.0000, 68 negative triangles 163: dt=0.9900, 68 negative triangles 164: dt=0.9900, 39 negative triangles 165: dt=0.9900, 20 negative triangles 166: dt=0.9900, 18 negative triangles 167: dt=0.9900, 11 negative triangles 168: dt=0.9900, 8 negative triangles 169: dt=0.9900, 3 negative triangles 170: dt=0.9900, 3 negative triangles 171: dt=0.9900, 2 negative triangles 172: dt=0.9900, 1 negative triangles 173: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.64 hours mris_sphere utimesec 2316.277271 mris_sphere stimesec 0.960007 mris_sphere ru_maxrss 230992 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 57560 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9000 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 0 mris_sphere ru_nivcsw 904 FSRUNTIME@ mris_sphere 0.6437 hours 1 threads #-------------------------------------------- #@# Sphere rh 2020��� 04��� 29��� ��������� 02:15:21 CST /home/web/freesurver/test/MRI/subjects02/scripts mris_sphere -rusage /home/web/freesurver/test/MRI/subjects02/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 0.318... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=web-v, 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 %38.12 pass 1: epoch 2 of 3 starting distance error %18.68 unfolding complete - removing small folds... starting distance error %18.59 removing remaining folds... final distance error %18.61 MRISunfold() return, current seed 1234 -01: dt=0.0000, 91 negative triangles 131: dt=0.9900, 91 negative triangles 132: dt=0.9900, 62 negative triangles 133: dt=0.9900, 67 negative triangles 134: dt=0.9900, 61 negative triangles 135: dt=0.9900, 58 negative triangles 136: dt=0.9900, 54 negative triangles 137: dt=0.9900, 54 negative triangles 138: dt=0.9900, 46 negative triangles 139: dt=0.9900, 48 negative triangles 140: dt=0.9900, 39 negative triangles 141: dt=0.9900, 49 negative triangles 142: dt=0.9900, 34 negative triangles 143: dt=0.9900, 43 negative triangles 144: dt=0.9900, 41 negative triangles 145: dt=0.9900, 42 negative triangles 146: dt=0.9900, 36 negative triangles 147: dt=0.9900, 46 negative triangles 148: dt=0.9900, 41 negative triangles 149: dt=0.9900, 44 negative triangles 150: dt=0.9900, 37 negative triangles 151: dt=0.9900, 38 negative triangles 152: dt=0.9405, 35 negative triangles 153: dt=0.9405, 40 negative triangles 154: dt=0.9405, 36 negative triangles 155: dt=0.9405, 38 negative triangles 156: dt=0.9405, 33 negative triangles 157: dt=0.9405, 40 negative triangles 158: dt=0.9405, 34 negative triangles 159: dt=0.9405, 34 negative triangles 160: dt=0.9405, 37 negative triangles 161: dt=0.9405, 37 negative triangles 162: dt=0.9405, 38 negative triangles 163: dt=0.9405, 35 negative triangles 164: dt=0.9405, 37 negative triangles 165: dt=0.9405, 35 negative triangles 166: dt=0.8935, 38 negative triangles 167: dt=0.8935, 35 negative triangles 168: dt=0.8935, 32 negative triangles 169: dt=0.8935, 37 negative triangles 170: dt=0.8935, 34 negative triangles 171: dt=0.8935, 38 negative triangles 172: dt=0.8935, 35 negative triangles 173: dt=0.8935, 33 negative triangles 174: dt=0.8935, 34 negative triangles 175: dt=0.8935, 36 negative triangles 176: dt=0.8935, 34 negative triangles 177: dt=0.8935, 35 negative triangles 178: dt=0.8488, 36 negative triangles 179: dt=0.8488, 35 negative triangles 180: dt=0.8488, 34 negative triangles 181: dt=0.8488, 32 negative triangles 182: dt=0.8488, 32 negative triangles 183: dt=0.8488, 32 negative triangles 184: dt=0.8488, 34 negative triangles 185: dt=0.8488, 35 negative triangles 186: dt=0.8488, 33 negative triangles 187: dt=0.8488, 33 negative triangles 188: dt=0.8488, 31 negative triangles 189: dt=0.8488, 35 negative triangles 190: dt=0.8488, 31 negative triangles 191: dt=0.8488, 30 negative triangles 192: dt=0.8488, 35 negative triangles 193: dt=0.8488, 31 negative triangles 194: dt=0.8488, 32 negative triangles 195: dt=0.8488, 36 negative triangles 196: dt=0.8488, 32 negative triangles 197: dt=0.8488, 30 negative triangles 198: dt=0.8488, 34 negative triangles 199: dt=0.8488, 31 negative triangles 200: dt=0.8488, 36 negative triangles 201: dt=0.8064, 37 negative triangles 202: dt=0.8064, 33 negative triangles 203: dt=0.8064, 31 negative triangles 204: dt=0.8064, 37 negative triangles 205: dt=0.8064, 32 negative triangles 206: dt=0.8064, 35 negative triangles 207: dt=0.8064, 35 negative triangles 208: dt=0.8064, 35 negative triangles 209: dt=0.8064, 37 negative triangles 210: dt=0.8064, 32 negative triangles 211: dt=0.7660, 34 negative triangles 212: dt=0.7660, 31 negative triangles 213: dt=0.7660, 35 negative triangles 214: dt=0.7660, 32 negative triangles 215: dt=0.7660, 29 negative triangles 216: dt=0.7660, 30 negative triangles 217: dt=0.7660, 28 negative triangles 218: dt=0.7660, 30 negative triangles 219: dt=0.7660, 32 negative triangles 220: dt=0.7660, 26 negative triangles 221: dt=0.7660, 29 negative triangles 222: dt=0.7660, 27 negative triangles 223: dt=0.7660, 31 negative triangles 224: dt=0.7660, 30 negative triangles 225: dt=0.7660, 27 negative triangles 226: dt=0.7660, 26 negative triangles 227: dt=0.7660, 26 negative triangles 228: dt=0.7660, 26 negative triangles 229: dt=0.7660, 24 negative triangles 230: dt=0.7660, 23 negative triangles 231: dt=0.7660, 22 negative triangles 232: dt=0.7660, 27 negative triangles 233: dt=0.7660, 23 negative triangles 234: dt=0.7660, 22 negative triangles 235: dt=0.7660, 25 negative triangles 236: dt=0.7660, 23 negative triangles 237: dt=0.7660, 25 negative triangles 238: dt=0.7660, 21 negative triangles 239: dt=0.7660, 22 negative triangles 240: dt=0.7660, 21 negative triangles 241: dt=0.7660, 22 negative triangles 242: dt=0.7660, 21 negative triangles 243: dt=0.7660, 20 negative triangles 244: dt=0.7660, 15 negative triangles 245: dt=0.7660, 19 negative triangles 246: dt=0.7660, 15 negative triangles 247: dt=0.7660, 11 negative triangles 248: dt=0.7660, 11 negative triangles 249: dt=0.7660, 9 negative triangles 250: dt=0.7660, 9 negative triangles 251: dt=0.7660, 5 negative triangles 252: dt=0.7660, 2 negative triangles 253: dt=0.7660, 3 negative triangles 254: dt=0.7660, 2 negative triangles 255: dt=0.7660, 4 negative triangles 256: dt=0.7660, 3 negative triangles 257: dt=0.7660, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.51 hours mris_sphere utimesec 1846.716869 mris_sphere stimesec 0.728085 mris_sphere ru_maxrss 233736 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 119807 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9120 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 0 mris_sphere ru_nivcsw 2260 FSRUNTIME@ mris_sphere 0.5132 hours 1 threads #-------------------------------------------- #@# Surf Reg lh 2020��� 04��� 29��� ��������� 02:46:09 CST /home/web/freesurver/test/MRI/subjects02/scripts mris_register -curv -rusage /home/web/freesurver/test/MRI/subjects02/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /home/web/freesurver/test/MRI/subjects02/scripts cmdline mris_register -curv -rusage /home/web/freesurver/test/MRI/subjects02/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /usr/local/freesurfer/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/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=web-v, 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=web-v, 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 = 5.649 curvature mean = 0.037, std = 0.811 curvature mean = 0.017, std = 0.871 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, 16.00) sse = 203542.2, tmin=1.1458 d=16.00 min @ (0.00, -4.00, 0.00) sse = 186862.1, tmin=3.4361 d=8.00 min @ (0.00, 0.00, 2.00) sse = 184238.5, tmin=4.6110 d=4.00 min @ (0.00, 1.00, -1.00) sse = 182498.5, tmin=5.7970 d=2.00 min @ (0.00, 0.00, 0.50) sse = 182457.6, tmin=6.9735 d=1.00 min @ (-0.25, -0.25, -0.25) sse = 182207.8, tmin=8.1207 d=0.50 min @ (0.12, 0.00, 0.00) sse = 182188.4, tmin=9.2778 tol=1.0e+00, sigma=0.5, host=web-v, 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 9.28 min curvature mean = 0.011, std = 0.836 curvature mean = 0.007, std = 0.952 curvature mean = 0.009, std = 0.847 curvature mean = 0.003, std = 0.981 curvature mean = 0.008, std = 0.850 curvature mean = 0.001, std = 0.993 2 Reading smoothwm curvature mean = -0.023, std = 0.287 curvature mean = 0.043, std = 0.250 curvature mean = 0.055, std = 0.356 curvature mean = 0.040, std = 0.308 curvature mean = 0.024, std = 0.556 curvature mean = 0.039, std = 0.335 curvature mean = 0.011, std = 0.697 curvature mean = 0.039, std = 0.346 curvature mean = 0.003, std = 0.799 MRISregister() return, current seed 0 -01: dt=0.0000, 6 negative triangles 110: dt=0.9900, 6 negative triangles expanding nbhd size to 1 111: dt=0.9900, 8 negative triangles 112: dt=0.9900, 5 negative triangles 113: dt=0.9900, 4 negative triangles 114: dt=0.9900, 4 negative triangles 115: dt=0.9900, 4 negative triangles 116: dt=0.9900, 3 negative triangles 117: dt=0.9900, 3 negative triangles 118: dt=0.9900, 3 negative triangles 119: dt=0.9900, 3 negative triangles 120: dt=0.9900, 2 negative triangles 121: dt=0.9900, 2 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.83 hours mris_register utimesec 2990.473972 mris_register stimesec 6.688600 mris_register ru_maxrss 222588 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 110891 mris_register ru_majflt 9 mris_register ru_nswap 0 mris_register ru_inblock 7208 mris_register ru_oublock 9008 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 24 mris_register ru_nivcsw 4607 FSRUNTIME@ mris_register 0.8327 hours 1 threads #-------------------------------------------- #@# Surf Reg rh 2020��� 04��� 29��� ��������� 03:36:06 CST /home/web/freesurver/test/MRI/subjects02/scripts mris_register -curv -rusage /home/web/freesurver/test/MRI/subjects02/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /home/web/freesurver/test/MRI/subjects02/scripts cmdline mris_register -curv -rusage /home/web/freesurver/test/MRI/subjects02/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /usr/local/freesurfer/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/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=web-v, 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=web-v, 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 = 5.652 curvature mean = 0.041, std = 0.803 curvature mean = 0.015, std = 0.868 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, 16.00) sse = 324709.3, tmin=1.1021 d=32.00 min @ (0.00, -8.00, 0.00) sse = 299663.2, tmin=2.2396 d=16.00 min @ (4.00, 4.00, 4.00) sse = 279622.6, tmin=3.3871 d=8.00 min @ (-2.00, 0.00, -2.00) sse = 274694.2, tmin=4.6145 d=2.00 min @ (0.50, 0.00, 0.00) sse = 274478.0, tmin=7.0752 d=1.00 min @ (0.00, -0.25, 0.00) sse = 274445.8, tmin=8.2864 d=0.50 min @ (-0.12, 0.12, 0.00) sse = 274431.6, tmin=9.4870 tol=1.0e+00, sigma=0.5, host=web-v, 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 9.49 min curvature mean = 0.009, std = 0.825 curvature mean = 0.006, std = 0.950 curvature mean = 0.006, std = 0.835 curvature mean = 0.002, std = 0.981 curvature mean = 0.006, std = 0.838 curvature mean = 0.001, std = 0.993 2 Reading smoothwm curvature mean = -0.024, std = 0.526 curvature mean = 0.037, std = 0.241 curvature mean = 0.030, std = 0.197 curvature mean = 0.031, std = 0.300 curvature mean = 0.016, std = 0.302 curvature mean = 0.031, std = 0.325 curvature mean = 0.008, std = 0.379 curvature mean = 0.031, std = 0.336 curvature mean = 0.002, std = 0.441 MRISregister() return, current seed 0 -01: dt=0.0000, 40 negative triangles 112: dt=0.9900, 40 negative triangles expanding nbhd size to 1 113: dt=0.9900, 56 negative triangles 114: dt=0.9900, 37 negative triangles 115: dt=0.9900, 36 negative triangles 116: dt=0.9900, 33 negative triangles 117: dt=0.9900, 32 negative triangles 118: dt=0.9900, 32 negative triangles 119: dt=0.9900, 28 negative triangles 120: dt=0.9900, 29 negative triangles 121: dt=0.9900, 28 negative triangles 122: dt=0.9900, 27 negative triangles 123: dt=0.9900, 26 negative triangles 124: dt=0.9900, 28 negative triangles 125: dt=0.9900, 26 negative triangles 126: dt=0.9900, 28 negative triangles 127: dt=0.9900, 25 negative triangles 128: dt=0.9900, 25 negative triangles 129: dt=0.9900, 26 negative triangles 130: dt=0.9900, 24 negative triangles 131: dt=0.9900, 27 negative triangles 132: dt=0.9900, 25 negative triangles 133: dt=0.9900, 26 negative triangles 134: dt=0.9900, 22 negative triangles 135: dt=0.9900, 24 negative triangles 136: dt=0.9900, 24 negative triangles 137: dt=0.9900, 24 negative triangles 138: dt=0.9900, 21 negative triangles 139: dt=0.9900, 23 negative triangles 140: dt=0.9900, 23 negative triangles 141: dt=0.9900, 25 negative triangles 142: dt=0.9900, 23 negative triangles 143: dt=0.9900, 25 negative triangles 144: dt=0.9900, 23 negative triangles 145: dt=0.9900, 26 negative triangles 146: dt=0.9900, 24 negative triangles 147: dt=0.9900, 26 negative triangles 148: dt=0.9405, 26 negative triangles 149: dt=0.9405, 24 negative triangles 150: dt=0.9405, 26 negative triangles 151: dt=0.9405, 27 negative triangles 152: dt=0.9405, 27 negative triangles 153: dt=0.9405, 27 negative triangles 154: dt=0.9405, 27 negative triangles 155: dt=0.9405, 27 negative triangles 156: dt=0.9405, 28 negative triangles 157: dt=0.9405, 27 negative triangles 158: dt=0.8935, 28 negative triangles 159: dt=0.8935, 22 negative triangles 160: dt=0.8935, 22 negative triangles 161: dt=0.8935, 20 negative triangles 162: dt=0.8935, 21 negative triangles 163: dt=0.8935, 20 negative triangles 164: dt=0.8935, 20 negative triangles 165: dt=0.8935, 22 negative triangles 166: dt=0.8935, 20 negative triangles 167: dt=0.8935, 22 negative triangles 168: dt=0.8935, 20 negative triangles 169: dt=0.8935, 21 negative triangles 170: dt=0.8935, 19 negative triangles 171: dt=0.8935, 19 negative triangles 172: dt=0.8935, 21 negative triangles 173: dt=0.8935, 19 negative triangles 174: dt=0.8935, 21 negative triangles 175: dt=0.8935, 18 negative triangles 176: dt=0.8935, 19 negative triangles 177: dt=0.8935, 18 negative triangles 178: dt=0.8935, 19 negative triangles 179: dt=0.8935, 17 negative triangles 180: dt=0.8935, 19 negative triangles 181: dt=0.8935, 17 negative triangles 182: dt=0.8935, 17 negative triangles 183: dt=0.8935, 14 negative triangles 184: dt=0.8935, 15 negative triangles 185: dt=0.8935, 13 negative triangles 186: dt=0.8935, 14 negative triangles 187: dt=0.8935, 15 negative triangles 188: dt=0.8935, 13 negative triangles 189: dt=0.8935, 15 negative triangles 190: dt=0.8935, 13 negative triangles 191: dt=0.8935, 15 negative triangles 192: dt=0.8935, 12 negative triangles 193: dt=0.8935, 13 negative triangles 194: dt=0.8935, 13 negative triangles 195: dt=0.8935, 12 negative triangles 196: dt=0.8935, 8 negative triangles 197: dt=0.8935, 7 negative triangles 198: dt=0.8935, 7 negative triangles 199: dt=0.8935, 8 negative triangles 200: dt=0.8935, 6 negative triangles 201: dt=0.8935, 8 negative triangles 202: dt=0.8935, 6 negative triangles 203: dt=0.8935, 4 negative triangles 204: dt=0.8935, 4 negative triangles 205: dt=0.8935, 5 negative triangles 206: dt=0.8935, 3 negative triangles 207: dt=0.8935, 3 negative triangles 208: dt=0.8935, 3 negative triangles 209: dt=0.8935, 2 negative triangles 210: dt=0.8935, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.95 hours mris_register utimesec 3432.363056 mris_register stimesec 1.824035 mris_register ru_maxrss 225632 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 92347 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 5584 mris_register ru_oublock 9120 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 13 mris_register ru_nivcsw 966 FSRUNTIME@ mris_register 0.9540 hours 1 threads #-------------------------------------------- #@# Jacobian white lh 2020��� 04��� 29��� ��������� 04:33:21 CST /home/web/freesurver/test/MRI/subjects02/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 2020��� 04��� 29��� ��������� 04:33:32 CST /home/web/freesurver/test/MRI/subjects02/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 2020��� 04��� 29��� ��������� 04:33:34 CST /home/web/freesurver/test/MRI/subjects02/scripts mrisp_paint -a 5 /usr/local/freesurfer/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/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh 2020��� 04��� 29��� ��������� 04:33:35 CST /home/web/freesurver/test/MRI/subjects02/scripts mrisp_paint -a 5 /usr/local/freesurfer/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/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh 2020��� 04��� 29��� ��������� 04:33:37 CST /home/web/freesurver/test/MRI/subjects02/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subjects02 lh ../surf/lh.sphere.reg /usr/local/freesurfer/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/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... 1287 labels changed using aseg relabeling using gibbs priors... 000: 2905 changed, 127920 examined... 001: 706 changed, 12477 examined... 002: 166 changed, 3929 examined... 003: 63 changed, 1024 examined... 004: 29 changed, 378 examined... 005: 18 changed, 174 examined... 006: 5 changed, 98 examined... 007: 1 changed, 32 examined... 008: 0 changed, 5 examined... 231 labels changed using aseg 000: 129 total segments, 84 labels (265 vertices) changed 001: 43 total segments, 3 labels (11 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 7 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1742 vertices marked for relabeling... 1742 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 14 seconds. #----------------------------------------- #@# Cortical Parc rh 2020��� 04��� 29��� ��������� 04:33:51 CST /home/web/freesurver/test/MRI/subjects02/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subjects02 rh ../surf/rh.sphere.reg /usr/local/freesurfer/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/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... 1063 labels changed using aseg relabeling using gibbs priors... 000: 2702 changed, 129541 examined... 001: 609 changed, 11676 examined... 002: 128 changed, 3472 examined... 003: 36 changed, 765 examined... 004: 6 changed, 196 examined... 005: 2 changed, 36 examined... 006: 0 changed, 13 examined... 146 labels changed using aseg 000: 84 total segments, 45 labels (156 vertices) changed 001: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 5 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1419 vertices marked for relabeling... 1419 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 13 seconds. #-------------------------------------------- #@# Make Pial Surf lh 2020��� 04��� 29��� ��������� 04:34:04 CST /home/web/freesurver/test/MRI/subjects02/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs subjects02 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/web/freesurver/test/MRI/subjects02/mri/filled.mgz... reading volume /home/web/freesurver/test/MRI/subjects02/mri/brain.finalsurfs.mgz... reading volume /home/web/freesurver/test/MRI/subjects02/mri/../mri/aseg.presurf.mgz... reading volume /home/web/freesurver/test/MRI/subjects02/mri/wm.mgz... 20105 bright wm thresholded. 867 bright non-wm voxels segmented. reading original surface position from /home/web/freesurver/test/MRI/subjects02/surf/lh.orig... computing class statistics... border white: 235147 voxels (1.40%) border gray 268831 voxels (1.60%) WM (98.0): 98.3 +- 8.7 [70.0 --> 110.0] GM (70.0) : 69.7 +- 10.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 54.0 (was 70) setting MAX_BORDER_WHITE to 111.7 (was 105) setting MIN_BORDER_WHITE to 64.0 (was 85) setting MAX_CSF to 43.9 (was 40) setting MAX_GRAY to 94.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 54.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 33.9 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-5.2, GM=64+-7.8 mean inside = 93.5, mean outside = 73.4 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 0.90 +- 0.25 (0.02-->3.83) (max @ vno 90062 --> 91122) face area 0.34 +- 0.15 (0.00-->2.51) mean absolute distance = 0.62 +- 0.83 2187 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 1 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 4 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown deleting segment 6 with 118 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 7 points - only 0.00% unknown mean border=76.7, 61 (61) missing vertices, mean dist 0.4 [0.9 (%11.6)->0.6 (%88.4))] %67 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=web-v, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.26 (0.06-->4.04) (max @ vno 46866 --> 48070) face area 0.34 +- 0.16 (0.00-->2.86) mean absolute distance = 0.35 +- 0.56 2780 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2659757.8, rms=9.142 001: dt: 0.5000, sse=1332595.6, rms=5.412 (40.803%) 002: dt: 0.5000, sse=973276.1, rms=3.837 (29.106%) 003: dt: 0.5000, sse=904103.2, rms=3.455 (9.951%) 004: dt: 0.5000, sse=859479.5, rms=3.189 (7.695%) rms = 3.29, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=735609.7, rms=2.196 (31.129%) 006: dt: 0.2500, sse=691660.3, rms=1.702 (22.512%) 007: dt: 0.2500, sse=677759.2, rms=1.523 (10.527%) 008: dt: 0.2500, sse=674563.0, rms=1.471 (3.397%) rms = 1.43, time step reduction 2 of 3 to 0.125... 009: dt: 0.2500, sse=671571.8, rms=1.426 (3.081%) 010: dt: 0.1250, sse=668832.2, rms=1.376 (3.510%) rms = 1.37, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=668312.3, rms=1.369 (0.485%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown deleting segment 2 with 54 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown mean border=80.5, 52 (24) missing vertices, mean dist -0.2 [0.4 (%75.9)->0.2 (%24.1))] %78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=web-v, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.10-->4.16) (max @ vno 91122 --> 90062) face area 0.36 +- 0.17 (0.00-->3.87) mean absolute distance = 0.24 +- 0.38 2724 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1353401.9, rms=5.287 012: dt: 0.5000, sse=939786.1, rms=3.327 (37.072%) 013: dt: 0.5000, sse=927603.8, rms=3.269 (1.755%) rms = 3.23, time step reduction 1 of 3 to 0.250... 014: dt: 0.5000, sse=916666.3, rms=3.226 (1.321%) 015: dt: 0.2500, sse=748563.6, rms=1.797 (44.297%) 016: dt: 0.2500, sse=718118.6, rms=1.377 (23.371%) 017: dt: 0.2500, sse=710156.0, rms=1.283 (6.827%) 018: dt: 0.2500, sse=705846.6, rms=1.211 (5.595%) rms = 1.20, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=705009.2, rms=1.201 (0.805%) 020: dt: 0.1250, sse=701341.4, rms=1.136 (5.432%) rms = 1.14, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=701405.9, rms=1.136 (0.001%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 66 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 2 with 5 points - only 0.00% unknown deleting segment 3 with 6 points - only 0.00% unknown mean border=83.2, 40 (17) missing vertices, mean dist -0.1 [0.3 (%72.9)->0.2 (%27.1))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=web-v, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.05-->4.22) (max @ vno 91122 --> 90062) face area 0.35 +- 0.16 (0.00-->4.03) mean absolute distance = 0.20 +- 0.31 2798 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=923663.6, rms=3.405 022: dt: 0.5000, sse=833447.8, rms=2.778 (18.426%) rms = 3.08, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=719479.8, rms=1.760 (36.638%) 024: dt: 0.2500, sse=683629.1, rms=1.286 (26.953%) 025: dt: 0.2500, sse=675901.9, rms=1.127 (12.324%) rms = 1.12, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=672839.4, rms=1.117 (0.910%) 027: dt: 0.1250, sse=668502.2, rms=1.039 (6.999%) rms = 1.04, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=669124.6, rms=1.038 (0.056%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown deleting segment 1 with 79 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 13 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown mean border=84.1, 54 (15) missing vertices, mean dist -0.0 [0.2 (%57.9)->0.2 (%42.1))] %89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=web-v, 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/web/freesurver/test/MRI/subjects02/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=690152.3, rms=1.565 rms = 1.78, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=656540.7, rms=1.038 (33.700%) 030: dt: 0.2500, sse=645575.7, rms=0.775 (25.339%) rms = 0.80, time step reduction 2 of 3 to 0.125... rms = 0.77, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=644668.4, rms=0.772 (0.325%) positioning took 0.4 minutes generating cortex label... 6 non-cortical segments detected only using segment with 7417 vertices erasing segment 1 (vno[0] = 84316) erasing segment 2 (vno[0] = 84350) erasing segment 3 (vno[0] = 86642) erasing segment 4 (vno[0] = 88971) erasing segment 5 (vno[0] = 90000) writing cortex label to /home/web/freesurver/test/MRI/subjects02/label/lh.cortex.label... writing curvature file /home/web/freesurver/test/MRI/subjects02/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/web/freesurver/test/MRI/subjects02/surf/lh.area vertex spacing 0.90 +- 0.26 (0.02-->4.22) (max @ vno 90062 --> 91122) face area 0.34 +- 0.16 (0.00-->4.02) 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 smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=52.2, 64 (64) missing vertices, mean dist 1.8 [0.0 (%0.0)->2.6 (%100.0))] %14 local maxima, %50 large gradients and %32 min vals, 270 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=web-v, 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=26275752.0, rms=32.413 001: dt: 0.0500, sse=23143008.0, rms=30.370 (6.304%) 002: dt: 0.0500, sse=20893462.0, rms=28.813 (5.126%) 003: dt: 0.0500, sse=19168768.0, rms=27.560 (4.349%) 004: dt: 0.0500, sse=17776978.0, rms=26.505 (3.826%) 005: dt: 0.0500, sse=16608578.0, rms=25.587 (3.467%) 006: dt: 0.0500, sse=15601031.0, rms=24.767 (3.204%) 007: dt: 0.0500, sse=14712981.0, rms=24.021 (3.011%) 008: dt: 0.0500, sse=13918406.0, rms=23.333 (2.862%) 009: dt: 0.0500, sse=13199346.0, rms=22.693 (2.744%) 010: dt: 0.0500, sse=12542999.0, rms=22.093 (2.647%) positioning took 0.9 minutes mean border=52.1, 52 (38) missing vertices, mean dist 1.4 [0.1 (%0.0)->2.1 (%100.0))] %15 local maxima, %49 large gradients and %31 min vals, 271 gradients ignored tol=1.0e-04, sigma=2.0, host=web-v, 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=13066942.0, rms=22.575 011: dt: 0.0500, sse=12461077.0, rms=22.019 (2.466%) 012: dt: 0.0500, sse=11901230.0, rms=21.491 (2.395%) 013: dt: 0.0500, sse=11382123.0, rms=20.990 (2.331%) 014: dt: 0.0500, sse=10899387.0, rms=20.513 (2.272%) 015: dt: 0.0500, sse=10449956.0, rms=20.059 (2.214%) 016: dt: 0.0500, sse=10030911.0, rms=19.626 (2.159%) 017: dt: 0.0500, sse=9639785.0, rms=19.213 (2.105%) 018: dt: 0.0500, sse=9274496.0, rms=18.819 (2.051%) 019: dt: 0.0500, sse=8932939.0, rms=18.443 (1.999%) 020: dt: 0.0500, sse=8613378.0, rms=18.084 (1.947%) positioning took 0.9 minutes mean border=52.0, 59 (30) missing vertices, mean dist 1.2 [0.1 (%0.5)->1.8 (%99.5))] %15 local maxima, %49 large gradients and %31 min vals, 278 gradients ignored tol=1.0e-04, sigma=2.0, host=web-v, 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=8674600.0, rms=18.160 021: dt: 0.0500, sse=8369980.5, rms=17.812 (1.915%) 022: dt: 0.0500, sse=8084788.0, rms=17.480 (1.863%) 023: dt: 0.0500, sse=7816296.0, rms=17.162 (1.821%) 024: dt: 0.0500, sse=7564735.0, rms=16.858 (1.771%) 025: dt: 0.0500, sse=7328782.5, rms=16.568 (1.721%) 026: dt: 0.0500, sse=7106940.5, rms=16.290 (1.676%) 027: dt: 0.0500, sse=6897041.5, rms=16.023 (1.641%) 028: dt: 0.0500, sse=6696486.0, rms=15.763 (1.621%) 029: dt: 0.0500, sse=6504898.5, rms=15.511 (1.600%) 030: dt: 0.0500, sse=6321392.5, rms=15.265 (1.583%) positioning took 0.9 minutes mean border=51.9, 64 (22) missing vertices, mean dist 1.0 [0.1 (%6.5)->1.6 (%93.5))] %16 local maxima, %50 large gradients and %30 min vals, 282 gradients ignored tol=1.0e-04, sigma=2.0, host=web-v, 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=6384545.0, rms=15.352 031: dt: 0.5000, sse=5087820.5, rms=13.501 (12.056%) 032: dt: 0.5000, sse=4126488.0, rms=11.939 (11.571%) 033: dt: 0.5000, sse=3342081.2, rms=10.496 (12.087%) 034: dt: 0.5000, sse=2721897.0, rms=9.189 (12.453%) 035: dt: 0.5000, sse=2249032.5, rms=8.053 (12.360%) 036: dt: 0.5000, sse=1888952.0, rms=7.062 (12.307%) 037: dt: 0.5000, sse=1616851.1, rms=6.214 (12.008%) 038: dt: 0.5000, sse=1424176.5, rms=5.531 (10.984%) 039: dt: 0.5000, sse=1297591.4, rms=5.037 (8.933%) 040: dt: 0.5000, sse=1219411.2, rms=4.702 (6.648%) 041: dt: 0.5000, sse=1174786.1, rms=4.504 (4.219%) 042: dt: 0.5000, sse=1148885.6, rms=4.382 (2.717%) 043: dt: 0.5000, sse=1132330.4, rms=4.304 (1.772%) 044: dt: 0.5000, sse=1122156.1, rms=4.253 (1.181%) rms = 4.22, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1115478.2, rms=4.221 (0.744%) 046: dt: 0.2500, sse=1013378.9, rms=3.622 (14.210%) 047: dt: 0.2500, sse=987269.5, rms=3.468 (4.244%) rms = 3.47, time step reduction 2 of 3 to 0.125... 048: dt: 0.2500, sse=987433.3, rms=3.465 (0.071%) 049: dt: 0.1250, sse=975470.9, rms=3.388 (2.245%) rms = 3.38, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=974975.5, rms=3.384 (0.105%) positioning took 2.2 minutes mean border=50.5, 1452 (3) missing vertices, mean dist 0.1 [0.1 (%47.0)->0.4 (%53.0))] %28 local maxima, %39 large gradients and %27 min vals, 156 gradients ignored tol=1.0e-04, sigma=1.0, host=web-v, 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=1284757.8, rms=4.149 051: dt: 0.5000, sse=1198561.2, rms=3.698 (10.869%) rms = 3.75, time step reduction 1 of 3 to 0.250... 052: dt: 0.2500, sse=1111536.0, rms=3.145 (14.956%) 053: dt: 0.2500, sse=1078606.4, rms=2.917 (7.266%) 054: dt: 0.2500, sse=1068301.2, rms=2.844 (2.508%) rms = 2.82, time step reduction 2 of 3 to 0.125... 055: dt: 0.2500, sse=1065021.9, rms=2.822 (0.753%) 056: dt: 0.1250, sse=1052836.2, rms=2.725 (3.445%) rms = 2.71, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1050194.2, rms=2.707 (0.662%) positioning took 1.0 minutes mean border=49.5, 1699 (1) missing vertices, mean dist 0.1 [0.1 (%47.2)->0.3 (%52.8))] %42 local maxima, %26 large gradients and %26 min vals, 147 gradients ignored tol=1.0e-04, sigma=0.5, host=web-v, 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=1117172.2, rms=3.157 rms = 3.43, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1080401.4, rms=2.898 (8.207%) 059: dt: 0.2500, sse=1065230.5, rms=2.788 (3.798%) rms = 2.76, time step reduction 2 of 3 to 0.125... 060: dt: 0.2500, sse=1059868.0, rms=2.758 (1.061%) 061: dt: 0.1250, sse=1050314.6, rms=2.680 (2.839%) rms = 2.66, time step reduction 3 of 3 to 0.062... 062: dt: 0.1250, sse=1047089.9, rms=2.659 (0.785%) positioning took 0.8 minutes mean border=48.9, 3121 (1) missing vertices, mean dist 0.0 [0.1 (%48.7)->0.3 (%51.3))] %47 local maxima, %21 large gradients and %25 min vals, 132 gradients ignored tol=1.0e-04, sigma=0.2, host=web-v, 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/web/freesurver/test/MRI/subjects02/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1068838.4, rms=2.811 rms = 3.11, time step reduction 1 of 3 to 0.250... 063: dt: 0.2500, sse=1053416.5, rms=2.690 (4.313%) 064: dt: 0.2500, sse=1043621.6, rms=2.626 (2.389%) rms = 2.60, time step reduction 2 of 3 to 0.125... 065: dt: 0.2500, sse=1038920.9, rms=2.598 (1.048%) 066: dt: 0.1250, sse=1029942.4, rms=2.522 (2.922%) rms = 2.50, time step reduction 3 of 3 to 0.062... 067: dt: 0.1250, sse=1026991.4, rms=2.503 (0.768%) positioning took 0.8 minutes writing curvature file /home/web/freesurver/test/MRI/subjects02/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/web/freesurver/test/MRI/subjects02/surf/lh.area.pial vertex spacing 1.02 +- 0.43 (0.10-->8.20) (max @ vno 78416 --> 78390) face area 0.41 +- 0.31 (0.00-->6.43) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 127920 vertices processed 25000 of 127920 vertices processed 50000 of 127920 vertices processed 75000 of 127920 vertices processed 100000 of 127920 vertices processed 125000 of 127920 vertices processed 0 of 127920 vertices processed 25000 of 127920 vertices processed 50000 of 127920 vertices processed 75000 of 127920 vertices processed 100000 of 127920 vertices processed 125000 of 127920 vertices processed thickness calculation complete, 278:782 truncations. 31440 vertices at 0 distance 96428 vertices at 1 distance 75669 vertices at 2 distance 28330 vertices at 3 distance 8572 vertices at 4 distance 2513 vertices at 5 distance 790 vertices at 6 distance 276 vertices at 7 distance 110 vertices at 8 distance 53 vertices at 9 distance 23 vertices at 10 distance 18 vertices at 11 distance 19 vertices at 12 distance 22 vertices at 13 distance 13 vertices at 14 distance 7 vertices at 15 distance 7 vertices at 16 distance 1 vertices at 17 distance 3 vertices at 18 distance 1 vertices at 19 distance 5 vertices at 20 distance writing curvature file /home/web/freesurver/test/MRI/subjects02/surf/lh.thickness positioning took 14.5 minutes #-------------------------------------------- #@# Make Pial Surf rh 2020��� 04��� 29��� ��������� 04:48:32 CST /home/web/freesurver/test/MRI/subjects02/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs subjects02 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/web/freesurver/test/MRI/subjects02/mri/filled.mgz... reading volume /home/web/freesurver/test/MRI/subjects02/mri/brain.finalsurfs.mgz... reading volume /home/web/freesurver/test/MRI/subjects02/mri/../mri/aseg.presurf.mgz... reading volume /home/web/freesurver/test/MRI/subjects02/mri/wm.mgz... 20105 bright wm thresholded. 867 bright non-wm voxels segmented. reading original surface position from /home/web/freesurver/test/MRI/subjects02/surf/rh.orig... computing class statistics... border white: 235147 voxels (1.40%) border gray 268831 voxels (1.60%) WM (98.0): 98.3 +- 8.7 [70.0 --> 110.0] GM (70.0) : 69.7 +- 10.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 54.0 (was 70) setting MAX_BORDER_WHITE to 111.7 (was 105) setting MIN_BORDER_WHITE to 64.0 (was 85) setting MAX_CSF to 43.9 (was 40) setting MAX_GRAY to 94.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 54.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 33.9 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-6.1, GM=64+-8.7 mean inside = 93.3, mean outside = 73.5 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.25 (0.02-->5.26) (max @ vno 45456 --> 46796) face area 0.34 +- 0.15 (0.00-->4.18) mean absolute distance = 0.61 +- 0.83 2181 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 203 points - only 0.00% unknown deleting segment 5 with 16 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown mean border=76.9, 49 (49) missing vertices, mean dist 0.4 [0.9 (%11.7)->0.6 (%88.3))] %67 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=web-v, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.26 (0.09-->5.36) (max @ vno 45456 --> 46796) face area 0.34 +- 0.16 (0.00-->4.11) mean absolute distance = 0.35 +- 0.55 2858 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2658592.2, rms=9.041 001: dt: 0.5000, sse=1351208.9, rms=5.398 (40.289%) 002: dt: 0.5000, sse=987548.0, rms=3.828 (29.095%) 003: dt: 0.5000, sse=918477.7, rms=3.453 (9.787%) 004: dt: 0.5000, sse=871864.1, rms=3.179 (7.932%) rms = 3.28, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=747504.4, rms=2.194 (30.977%) 006: dt: 0.2500, sse=703331.6, rms=1.707 (22.204%) 007: dt: 0.2500, sse=689547.8, rms=1.534 (10.140%) rms = 1.49, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=689129.1, rms=1.487 (3.044%) 009: dt: 0.1250, sse=684660.4, rms=1.419 (4.609%) rms = 1.40, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=681335.6, rms=1.403 (1.096%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 2 with 77 points - only 0.00% unknown deleting segment 3 with 22 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 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 11 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown deleting segment 8 with 9 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown mean border=80.7, 33 (11) missing vertices, mean dist -0.2 [0.4 (%75.9)->0.2 (%24.1))] %79 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=web-v, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.07-->5.64) (max @ vno 45456 --> 46796) face area 0.36 +- 0.17 (0.00-->4.86) mean absolute distance = 0.24 +- 0.37 2810 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1365957.0, rms=5.254 011: dt: 0.5000, sse=947407.2, rms=3.286 (37.459%) 012: dt: 0.5000, sse=936226.5, rms=3.233 (1.609%) rms = 3.19, time step reduction 1 of 3 to 0.250... 013: dt: 0.5000, sse=925992.5, rms=3.195 (1.182%) 014: dt: 0.2500, sse=759225.4, rms=1.792 (43.909%) 015: dt: 0.2500, sse=727230.6, rms=1.378 (23.070%) 016: dt: 0.2500, sse=722141.1, rms=1.283 (6.896%) 017: dt: 0.2500, sse=717043.1, rms=1.217 (5.169%) rms = 1.21, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=717573.8, rms=1.210 (0.572%) 019: dt: 0.1250, sse=712538.7, rms=1.140 (5.788%) rms = 1.14, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=712465.9, rms=1.138 (0.145%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 1 with 6 points - only 0.00% unknown deleting segment 2 with 77 points - only 0.00% unknown deleting segment 3 with 38 points - only 13.16% unknown deleting segment 4 with 24 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 20 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown deleting segment 8 with 9 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown mean border=83.3, 38 (9) missing vertices, mean dist -0.1 [0.3 (%72.4)->0.2 (%27.6))] %86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=web-v, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.09-->5.71) (max @ vno 45456 --> 46796) face area 0.35 +- 0.16 (0.00-->4.81) mean absolute distance = 0.20 +- 0.31 2794 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=924394.1, rms=3.327 021: dt: 0.5000, sse=847293.6, rms=2.775 (16.600%) rms = 3.05, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=731624.8, rms=1.775 (36.039%) 023: dt: 0.2500, sse=693049.4, rms=1.293 (27.168%) 024: dt: 0.2500, sse=683147.7, rms=1.132 (12.450%) rms = 1.12, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=682081.0, rms=1.119 (1.117%) 026: dt: 0.1250, sse=677656.4, rms=1.037 (7.340%) rms = 1.04, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=677326.1, rms=1.035 (0.142%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 130 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 25 points - only 0.00% unknown deleting segment 3 with 6 points - only 0.00% unknown deleting segment 4 with 9 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group mean border=84.2, 38 (7) missing vertices, mean dist -0.0 [0.2 (%57.5)->0.2 (%42.5))] %89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=web-v, 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/web/freesurver/test/MRI/subjects02/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=699585.6, rms=1.564 rms = 1.74, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=666673.7, rms=1.047 (33.018%) 029: dt: 0.2500, sse=654224.9, rms=0.765 (26.916%) rms = 0.78, time step reduction 2 of 3 to 0.125... rms = 0.76, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=653707.1, rms=0.762 (0.485%) positioning took 0.4 minutes generating cortex label... 9 non-cortical segments detected only using segment with 6897 vertices erasing segment 1 (vno[0] = 84870) erasing segment 2 (vno[0] = 87059) erasing segment 3 (vno[0] = 87107) erasing segment 4 (vno[0] = 89301) erasing segment 5 (vno[0] = 89339) erasing segment 6 (vno[0] = 89358) erasing segment 7 (vno[0] = 90534) erasing segment 8 (vno[0] = 99527) writing cortex label to /home/web/freesurver/test/MRI/subjects02/label/rh.cortex.label... writing curvature file /home/web/freesurver/test/MRI/subjects02/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/web/freesurver/test/MRI/subjects02/surf/rh.area vertex spacing 0.90 +- 0.26 (0.02-->5.72) (max @ vno 45456 --> 46796) face area 0.34 +- 0.16 (0.00-->4.78) 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 smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=52.4, 73 (73) missing vertices, mean dist 1.7 [2.6 (%0.0)->2.6 (%100.0))] %13 local maxima, %49 large gradients and %34 min vals, 253 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=web-v, 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=26553148.0, rms=32.329 001: dt: 0.0500, sse=23390182.0, rms=30.293 (6.299%) 002: dt: 0.0500, sse=21124818.0, rms=28.746 (5.108%) 003: dt: 0.0500, sse=19388372.0, rms=27.501 (4.331%) 004: dt: 0.0500, sse=17986804.0, rms=26.453 (3.810%) 005: dt: 0.0500, sse=16810352.0, rms=25.540 (3.450%) 006: dt: 0.0500, sse=15794546.0, rms=24.725 (3.192%) 007: dt: 0.0500, sse=14898766.0, rms=23.983 (3.001%) 008: dt: 0.0500, sse=14095763.0, rms=23.298 (2.857%) 009: dt: 0.0500, sse=13368307.0, rms=22.659 (2.741%) 010: dt: 0.0500, sse=12704091.0, rms=22.060 (2.645%) positioning took 0.9 minutes mean border=52.2, 56 (43) missing vertices, mean dist 1.4 [0.1 (%0.0)->2.1 (%100.0))] %14 local maxima, %49 large gradients and %33 min vals, 243 gradients ignored tol=1.0e-04, sigma=2.0, host=web-v, 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=13267735.0, rms=22.570 011: dt: 0.0500, sse=12654194.0, rms=22.015 (2.460%) 012: dt: 0.0500, sse=12086974.0, rms=21.489 (2.390%) 013: dt: 0.0500, sse=11560975.0, rms=20.989 (2.326%) 014: dt: 0.0500, sse=11071878.0, rms=20.513 (2.266%) 015: dt: 0.0500, sse=10616125.0, rms=20.060 (2.211%) 016: dt: 0.0500, sse=10191534.0, rms=19.628 (2.153%) 017: dt: 0.0500, sse=9795434.0, rms=19.216 (2.098%) 018: dt: 0.0500, sse=9425920.0, rms=18.824 (2.042%) 019: dt: 0.0500, sse=9080629.0, rms=18.449 (1.988%) 020: dt: 0.0500, sse=8757644.0, rms=18.092 (1.936%) positioning took 0.9 minutes mean border=52.1, 76 (32) missing vertices, mean dist 1.2 [0.1 (%0.6)->1.8 (%99.4))] %15 local maxima, %48 large gradients and %33 min vals, 223 gradients ignored tol=1.0e-04, sigma=2.0, host=web-v, 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=8834070.0, rms=18.183 021: dt: 0.0500, sse=8526004.0, rms=17.837 (1.901%) 022: dt: 0.0500, sse=8237827.5, rms=17.507 (1.848%) 023: dt: 0.0500, sse=7966334.5, rms=17.191 (1.808%) 024: dt: 0.0500, sse=7712120.5, rms=16.889 (1.755%) 025: dt: 0.0500, sse=7473566.5, rms=16.601 (1.707%) 026: dt: 0.0500, sse=7248786.5, rms=16.325 (1.665%) 027: dt: 0.0500, sse=7035439.0, rms=16.058 (1.635%) 028: dt: 0.0500, sse=6831365.0, rms=15.798 (1.616%) 029: dt: 0.0500, sse=6636015.5, rms=15.546 (1.599%) 030: dt: 0.0500, sse=6448911.0, rms=15.300 (1.582%) positioning took 0.9 minutes mean border=52.0, 105 (30) missing vertices, mean dist 1.0 [0.1 (%7.5)->1.6 (%92.5))] %15 local maxima, %48 large gradients and %32 min vals, 212 gradients ignored tol=1.0e-04, sigma=2.0, host=web-v, 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=6520461.5, rms=15.395 031: dt: 0.5000, sse=5198914.5, rms=13.544 (12.024%) 032: dt: 0.5000, sse=4221143.5, rms=11.985 (11.509%) 033: dt: 0.5000, sse=3435489.2, rms=10.570 (11.805%) 034: dt: 0.5000, sse=2814161.5, rms=9.292 (12.088%) 035: dt: 0.5000, sse=2333287.2, rms=8.170 (12.076%) 036: dt: 0.5000, sse=1968504.8, rms=7.199 (11.890%) 037: dt: 0.5000, sse=1693695.6, rms=6.374 (11.461%) 038: dt: 0.5000, sse=1504710.8, rms=5.734 (10.031%) 039: dt: 0.5000, sse=1378352.2, rms=5.268 (8.133%) 040: dt: 0.5000, sse=1299440.9, rms=4.949 (6.065%) 041: dt: 0.5000, sse=1250079.1, rms=4.743 (4.156%) 042: dt: 0.5000, sse=1219284.4, rms=4.606 (2.892%) 043: dt: 0.5000, sse=1199724.8, rms=4.521 (1.846%) 044: dt: 0.5000, sse=1187681.0, rms=4.463 (1.284%) rms = 4.42, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1178619.9, rms=4.424 (0.865%) 046: dt: 0.2500, sse=1080494.2, rms=3.886 (12.174%) 047: dt: 0.2500, sse=1055544.9, rms=3.750 (3.478%) rms = 3.74, time step reduction 2 of 3 to 0.125... 048: dt: 0.2500, sse=1054722.4, rms=3.742 (0.225%) 049: dt: 0.1250, sse=1043705.9, rms=3.677 (1.744%) rms = 3.67, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1042900.2, rms=3.672 (0.133%) positioning took 2.3 minutes mean border=50.8, 1726 (18) missing vertices, mean dist 0.1 [0.2 (%47.2)->0.5 (%52.8))] %27 local maxima, %39 large gradients and %29 min vals, 91 gradients ignored tol=1.0e-04, sigma=1.0, host=web-v, 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=1308107.6, rms=4.145 051: dt: 0.5000, sse=1221887.8, rms=3.704 (10.642%) rms = 3.76, time step reduction 1 of 3 to 0.250... 052: dt: 0.2500, sse=1139906.2, rms=3.192 (13.810%) 053: dt: 0.2500, sse=1109135.4, rms=2.985 (6.494%) 054: dt: 0.2500, sse=1100929.2, rms=2.926 (1.961%) rms = 2.90, time step reduction 2 of 3 to 0.125... 055: dt: 0.2500, sse=1097098.8, rms=2.903 (0.809%) 056: dt: 0.1250, sse=1086174.9, rms=2.818 (2.938%) rms = 2.81, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1084500.8, rms=2.807 (0.375%) positioning took 1.0 minutes mean border=49.9, 1755 (14) missing vertices, mean dist 0.1 [0.1 (%46.9)->0.3 (%53.1))] %41 local maxima, %26 large gradients and %28 min vals, 99 gradients ignored tol=1.0e-04, sigma=0.5, host=web-v, 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=1143602.6, rms=3.180 rms = 3.41, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1110294.9, rms=2.951 (7.204%) 059: dt: 0.2500, sse=1097546.2, rms=2.863 (2.981%) rms = 2.84, time step reduction 2 of 3 to 0.125... 060: dt: 0.2500, sse=1093658.5, rms=2.844 (0.640%) 061: dt: 0.1250, sse=1085817.9, rms=2.783 (2.174%) rms = 2.77, time step reduction 3 of 3 to 0.062... 062: dt: 0.1250, sse=1084036.9, rms=2.773 (0.357%) positioning took 0.8 minutes mean border=49.3, 3471 (13) missing vertices, mean dist 0.0 [0.1 (%48.3)->0.3 (%51.7))] %45 local maxima, %21 large gradients and %27 min vals, 102 gradients ignored tol=1.0e-04, sigma=0.2, host=web-v, 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/web/freesurver/test/MRI/subjects02/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1104608.5, rms=2.902 rms = 3.14, time step reduction 1 of 3 to 0.250... 063: dt: 0.2500, sse=1089156.9, rms=2.786 (3.988%) 064: dt: 0.2500, sse=1079433.0, rms=2.727 (2.136%) rms = 2.70, time step reduction 2 of 3 to 0.125... 065: dt: 0.2500, sse=1075172.1, rms=2.704 (0.822%) 066: dt: 0.1250, sse=1066779.5, rms=2.637 (2.471%) rms = 2.62, time step reduction 3 of 3 to 0.062... 067: dt: 0.1250, sse=1064142.2, rms=2.622 (0.603%) positioning took 0.8 minutes writing curvature file /home/web/freesurver/test/MRI/subjects02/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/web/freesurver/test/MRI/subjects02/surf/rh.area.pial vertex spacing 1.02 +- 0.44 (0.10-->6.82) (max @ vno 82789 --> 81685) face area 0.41 +- 0.32 (0.00-->6.28) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 129541 vertices processed 25000 of 129541 vertices processed 50000 of 129541 vertices processed 75000 of 129541 vertices processed 100000 of 129541 vertices processed 125000 of 129541 vertices processed 0 of 129541 vertices processed 25000 of 129541 vertices processed 50000 of 129541 vertices processed 75000 of 129541 vertices processed 100000 of 129541 vertices processed 125000 of 129541 vertices processed thickness calculation complete, 288:732 truncations. 33090 vertices at 0 distance 98482 vertices at 1 distance 76056 vertices at 2 distance 28177 vertices at 3 distance 8503 vertices at 4 distance 2486 vertices at 5 distance 785 vertices at 6 distance 232 vertices at 7 distance 96 vertices at 8 distance 56 vertices at 9 distance 48 vertices at 10 distance 30 vertices at 11 distance 26 vertices at 12 distance 25 vertices at 13 distance 16 vertices at 14 distance 7 vertices at 15 distance 12 vertices at 16 distance 5 vertices at 17 distance 7 vertices at 18 distance 8 vertices at 19 distance 3 vertices at 20 distance writing curvature file /home/web/freesurver/test/MRI/subjects02/surf/rh.thickness positioning took 14.6 minutes #-------------------------------------------- #@# Surf Volume lh 2020��� 04��� 29��� ��������� 05:03:07 CST /home/web/freesurver/test/MRI/subjects02/surf /home/web/freesurver/test/MRI/subjects02/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 subjects02 lh /home/web/freesurver/test/MRI/subjects02/surf/lh.volume masking with /home/web/freesurver/test/MRI/subjects02/label/lh.cortex.label Total face volume 237539 Total vertex volume 233281 (mask=0) #@# subjects02 lh 233281 vertexvol Done #-------------------------------------------- #@# Surf Volume rh 2020��� 04��� 29��� ��������� 05:03:11 CST /home/web/freesurver/test/MRI/subjects02/surf /home/web/freesurver/test/MRI/subjects02/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 subjects02 rh /home/web/freesurver/test/MRI/subjects02/surf/rh.volume masking with /home/web/freesurver/test/MRI/subjects02/label/rh.cortex.label Total face volume 241163 Total vertex volume 237018 (mask=0) #@# subjects02 rh 237018 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask 2020��� 04��� 29��� ��������� 05:03:14 CST /home/web/freesurver/test/MRI/subjects02/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 subjects02 SUBJECTS_DIR is /home/web/freesurver/test/MRI 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 = 76 writing volume /home/web/freesurver/test/MRI/subjects02/mri/ribbon.mgz mris_volmask took 9.87 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh 2020��� 04��� 29��� ��������� 05:13:06 CST /home/web/freesurver/test/MRI/subjects02/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 subjects02 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/web/freesurver/test/MRI/subjects02/mri/wm.mgz... reading input surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white... reading input pial surface /home/web/freesurver/test/MRI/subjects02/surf/lh.pial... reading input white surface /home/web/freesurver/test/MRI/subjects02/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 237539 Total vertex volume 233281 (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) = 1386977 mm^3 (det: 1.404569 ) lhCtxGM: 233522.426 233230.000 diff= 292.4 pctdiff= 0.125 rhCtxGM: 237118.332 237065.000 diff= 53.3 pctdiff= 0.022 lhCtxWM: 212468.541 212507.000 diff= -38.5 pctdiff=-0.018 rhCtxWM: 216002.146 216507.000 diff= -504.9 pctdiff=-0.234 SubCortGMVol 56659.000 SupraTentVol 971298.444 (970013.000) diff=1285.444 pctdiff=0.132 SupraTentVolNotVent 957286.444 (956001.000) diff=1285.444 pctdiff=0.134 BrainSegVol 1096253.000 (1094128.000) diff=2125.000 pctdiff=0.194 BrainSegVolNotVent 1079201.000 (1078896.444) diff=304.556 pctdiff=0.028 BrainSegVolNotVent 1079201.000 CerebellumVol 123093.000 VentChorVol 14012.000 3rd4th5thCSF 3040.000 CSFVol 915.000, OptChiasmVol 107.000 MaskVol 1523756.000 1437 1034 2560 2.526 0.418 0.096 0.016 7 0.9 bankssts 884 597 1840 2.817 0.583 0.124 0.025 13 0.9 caudalanteriorcingulate 3153 2148 6354 2.628 0.512 0.118 0.020 31 2.4 caudalmiddlefrontal 2076 1424 2717 1.875 0.430 0.156 0.033 33 2.8 cuneus 787 539 2696 3.733 0.766 0.108 0.025 6 0.8 entorhinal 4749 3203 10766 2.886 0.661 0.131 0.026 59 4.9 fusiform 6820 4689 12468 2.367 0.510 0.128 0.025 88 7.0 inferiorparietal 4928 3427 10684 2.702 0.545 0.119 0.024 62 4.8 inferiortemporal 1542 995 2695 2.429 0.862 0.127 0.029 23 1.6 isthmuscingulate 7055 4656 10921 2.190 0.616 0.143 0.032 97 9.1 lateraloccipital 3648 2542 7710 2.748 0.631 0.138 0.032 56 4.7 lateralorbitofrontal 4111 2800 6157 2.105 0.544 0.149 0.035 60 6.1 lingual 2224 1573 4619 2.585 0.718 0.134 0.029 33 2.6 medialorbitofrontal 4719 3209 11656 2.961 0.608 0.132 0.027 76 5.0 middletemporal 1111 718 2579 3.123 0.773 0.109 0.019 11 0.7 parahippocampal 2106 1366 3751 2.573 0.601 0.108 0.020 17 1.8 paracentral 2268 1605 4745 2.611 0.470 0.127 0.023 27 2.0 parsopercularis 870 600 1992 2.518 0.565 0.129 0.026 13 0.9 parsorbitalis 1857 1237 4035 2.711 0.550 0.117 0.021 20 1.5 parstriangularis 1720 1221 1751 1.618 0.427 0.163 0.044 25 3.1 pericalcarine 6494 4250 10060 2.116 0.632 0.118 0.023 71 5.9 postcentral 1709 1144 3475 2.794 0.557 0.120 0.021 19 1.5 posteriorcingulate 7126 4394 12834 2.664 0.557 0.099 0.018 55 5.2 precentral 4965 3433 9033 2.421 0.584 0.128 0.026 61 5.2 precuneus 1144 784 2417 2.702 0.614 0.145 0.053 37 2.8 rostralanteriorcingulate 7682 5403 14934 2.398 0.533 0.133 0.029 104 8.9 rostralmiddlefrontal 10026 6831 23123 2.910 0.618 0.116 0.022 100 9.0 superiorfrontal 7452 5037 11262 2.082 0.471 0.128 0.024 89 7.0 superiorparietal 4919 3355 10895 2.822 0.634 0.104 0.019 47 3.7 superiortemporal 5246 3613 10435 2.566 0.582 0.138 0.027 76 5.8 supramarginal 394 273 1009 2.775 0.744 0.183 0.052 11 1.0 frontalpole 774 535 2762 3.729 0.653 0.126 0.025 11 0.8 temporalpole 608 412 1020 2.482 0.447 0.155 0.025 9 0.5 transversetemporal 3531 2347 7284 3.074 0.795 0.123 0.034 39 4.3 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 subjects02 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/web/freesurver/test/MRI/subjects02/mri/wm.mgz... reading input surface /home/web/freesurver/test/MRI/subjects02/surf/lh.pial... reading input pial surface /home/web/freesurver/test/MRI/subjects02/surf/lh.pial... reading input white surface /home/web/freesurver/test/MRI/subjects02/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 237539 Total vertex volume 233281 (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) = 1386977 mm^3 (det: 1.404569 ) lhCtxGM: 233522.426 233230.000 diff= 292.4 pctdiff= 0.125 rhCtxGM: 237118.332 237065.000 diff= 53.3 pctdiff= 0.022 lhCtxWM: 212468.541 212507.000 diff= -38.5 pctdiff=-0.018 rhCtxWM: 216002.146 216507.000 diff= -504.9 pctdiff=-0.234 SubCortGMVol 56659.000 SupraTentVol 971298.444 (970013.000) diff=1285.444 pctdiff=0.132 SupraTentVolNotVent 957286.444 (956001.000) diff=1285.444 pctdiff=0.134 BrainSegVol 1096253.000 (1094128.000) diff=2125.000 pctdiff=0.194 BrainSegVolNotVent 1079201.000 (1078896.444) diff=304.556 pctdiff=0.028 BrainSegVolNotVent 1079201.000 CerebellumVol 123093.000 VentChorVol 14012.000 3rd4th5thCSF 3040.000 CSFVol 915.000, OptChiasmVol 107.000 MaskVol 1523756.000 1437 972 2560 2.526 0.418 0.131 0.032 23 2.1 bankssts 884 703 1840 2.817 0.583 0.145 0.036 17 1.2 caudalanteriorcingulate 3153 2591 6354 2.628 0.512 0.135 0.025 33 3.4 caudalmiddlefrontal 2076 1619 2717 1.875 0.430 0.141 0.031 25 3.1 cuneus 787 899 2696 3.733 0.766 0.184 0.040 14 1.5 entorhinal 4749 4120 10766 2.886 0.661 0.151 0.037 61 7.7 fusiform 6820 5679 12468 2.367 0.510 0.146 0.030 79 8.9 inferiorparietal 4928 4310 10684 2.702 0.545 0.151 0.032 66 7.3 inferiortemporal 1542 1199 2695 2.429 0.862 0.149 0.038 27 2.4 isthmuscingulate 7055 5388 10921 2.190 0.616 0.137 0.030 99 9.3 lateraloccipital 3648 3121 7710 2.748 0.631 0.155 0.037 55 6.1 lateralorbitofrontal 4111 3235 6157 2.105 0.544 0.147 0.039 58 7.1 lingual 2224 2027 4619 2.585 0.718 0.178 0.041 36 4.5 medialorbitofrontal 4719 4499 11656 2.961 0.608 0.153 0.030 53 6.0 middletemporal 1111 947 2579 3.123 0.773 0.143 0.034 13 1.7 parahippocampal 2106 1588 3751 2.573 0.601 0.118 0.025 23 2.4 paracentral 2268 2019 4745 2.611 0.470 0.152 0.030 26 3.0 parsopercularis 870 955 1992 2.518 0.565 0.181 0.033 11 1.4 parsorbitalis 1857 1660 4035 2.711 0.550 0.145 0.028 22 2.4 parstriangularis 1720 1037 1751 1.618 0.427 0.142 0.046 32 3.2 pericalcarine 6494 5241 10060 2.116 0.632 0.134 0.027 64 7.3 postcentral 1709 1341 3475 2.794 0.557 0.141 0.033 34 2.4 posteriorcingulate 7126 5133 12834 2.664 0.557 0.111 0.023 65 6.9 precentral 4965 3993 9033 2.421 0.584 0.147 0.035 69 7.7 precuneus 1144 1034 2417 2.702 0.614 0.172 0.048 30 2.7 rostralanteriorcingulate 7682 6690 14934 2.398 0.533 0.158 0.031 101 11.0 rostralmiddlefrontal 10026 8665 23123 2.910 0.618 0.136 0.029 109 12.8 superiorfrontal 7452 5871 11262 2.082 0.471 0.139 0.028 89 9.0 superiorparietal 4919 4263 10895 2.822 0.634 0.138 0.028 57 6.2 superiortemporal 5246 4508 10435 2.566 0.582 0.153 0.031 67 7.2 supramarginal 394 452 1009 2.775 0.744 0.198 0.035 6 0.6 frontalpole 774 956 2762 3.729 0.653 0.185 0.037 14 1.3 temporalpole 608 448 1020 2.482 0.447 0.132 0.040 6 1.1 transversetemporal 3531 2299 7284 3.074 0.795 0.145 0.045 69 6.7 insula #----------------------------------------- #@# Parcellation Stats rh 2020��� 04��� 29��� ��������� 05:14:18 CST /home/web/freesurver/test/MRI/subjects02/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 subjects02 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/web/freesurver/test/MRI/subjects02/mri/wm.mgz... reading input surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white... reading input pial surface /home/web/freesurver/test/MRI/subjects02/surf/rh.pial... reading input white surface /home/web/freesurver/test/MRI/subjects02/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 241163 Total vertex volume 237018 (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) = 1386977 mm^3 (det: 1.404569 ) lhCtxGM: 233522.426 233230.000 diff= 292.4 pctdiff= 0.125 rhCtxGM: 237118.332 237065.000 diff= 53.3 pctdiff= 0.022 lhCtxWM: 212468.541 212507.000 diff= -38.5 pctdiff=-0.018 rhCtxWM: 216002.146 216507.000 diff= -504.9 pctdiff=-0.234 SubCortGMVol 56659.000 SupraTentVol 971298.444 (970013.000) diff=1285.444 pctdiff=0.132 SupraTentVolNotVent 957286.444 (956001.000) diff=1285.444 pctdiff=0.134 BrainSegVol 1096253.000 (1094128.000) diff=2125.000 pctdiff=0.194 BrainSegVolNotVent 1079201.000 (1078896.444) diff=304.556 pctdiff=0.028 BrainSegVolNotVent 1079201.000 CerebellumVol 123093.000 VentChorVol 14012.000 3rd4th5thCSF 3040.000 CSFVol 915.000, OptChiasmVol 107.000 MaskVol 1523756.000 1410 984 2615 2.801 0.423 0.112 0.018 10 1.1 bankssts 957 618 1869 2.533 0.760 0.119 0.019 13 0.8 caudalanteriorcingulate 2705 1821 5359 2.615 0.449 0.110 0.019 23 2.1 caudalmiddlefrontal 2163 1469 3199 2.009 0.510 0.146 0.035 30 3.2 cuneus 652 434 2431 4.053 0.773 0.096 0.019 4 0.5 entorhinal 4198 2896 9777 2.928 0.692 0.132 0.030 58 5.1 fusiform 7804 5290 14650 2.454 0.525 0.126 0.027 97 8.5 inferiorparietal 4736 3270 11067 2.830 0.724 0.128 0.030 62 5.8 inferiortemporal 1229 767 2079 2.320 0.909 0.124 0.023 18 1.1 isthmuscingulate 6591 4408 10562 2.233 0.502 0.143 0.032 90 8.6 lateraloccipital 3385 2348 7145 2.694 0.597 0.139 0.032 53 4.2 lateralorbitofrontal 4299 2938 6229 2.037 0.615 0.148 0.032 65 5.8 lingual 2804 1902 5352 2.422 0.655 0.124 0.029 42 3.2 medialorbitofrontal 5269 3710 13772 3.001 0.620 0.124 0.026 71 5.9 middletemporal 1018 674 2355 2.941 0.686 0.096 0.016 7 0.5 parahippocampal 2743 1711 5132 2.672 0.531 0.101 0.020 20 2.0 paracentral 1861 1276 4117 2.819 0.557 0.130 0.023 23 1.8 parsopercularis 1155 811 2764 2.614 0.564 0.160 0.044 23 2.2 parsorbitalis 1874 1313 4042 2.596 0.715 0.109 0.021 17 1.4 parstriangularis 1967 1333 1793 1.553 0.407 0.151 0.036 30 3.0 pericalcarine 6336 4191 9424 1.984 0.628 0.116 0.024 69 6.5 postcentral 1518 1012 3030 2.607 0.723 0.125 0.024 20 1.4 posteriorcingulate 7072 4460 12895 2.640 0.578 0.105 0.021 55 5.8 precentral 4932 3291 8260 2.397 0.562 0.126 0.026 58 5.1 precuneus 826 548 1651 2.645 0.765 0.152 0.035 17 1.2 rostralanteriorcingulate 9149 6426 16997 2.336 0.563 0.132 0.029 122 11.0 rostralmiddlefrontal 9175 6249 20920 2.872 0.578 0.122 0.024 98 8.7 superiorfrontal 8067 5437 12928 2.143 0.540 0.123 0.024 92 7.3 superiorparietal 5285 3520 11456 2.859 0.593 0.101 0.017 48 3.8 superiortemporal 5916 4127 11514 2.542 0.619 0.132 0.027 74 6.4 supramarginal 450 308 1237 2.724 0.617 0.149 0.032 9 0.7 frontalpole 641 452 2543 4.075 0.600 0.140 0.036 9 1.1 temporalpole 521 322 852 2.420 0.472 0.119 0.020 6 0.3 transversetemporal 3390 2316 6966 2.950 0.737 0.123 0.061 61 3.6 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 subjects02 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/web/freesurver/test/MRI/subjects02/mri/wm.mgz... reading input surface /home/web/freesurver/test/MRI/subjects02/surf/rh.pial... reading input pial surface /home/web/freesurver/test/MRI/subjects02/surf/rh.pial... reading input white surface /home/web/freesurver/test/MRI/subjects02/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 241163 Total vertex volume 237018 (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) = 1386977 mm^3 (det: 1.404569 ) lhCtxGM: 233522.426 233230.000 diff= 292.4 pctdiff= 0.125 rhCtxGM: 237118.332 237065.000 diff= 53.3 pctdiff= 0.022 lhCtxWM: 212468.541 212507.000 diff= -38.5 pctdiff=-0.018 rhCtxWM: 216002.146 216507.000 diff= -504.9 pctdiff=-0.234 SubCortGMVol 56659.000 SupraTentVol 971298.444 (970013.000) diff=1285.444 pctdiff=0.132 SupraTentVolNotVent 957286.444 (956001.000) diff=1285.444 pctdiff=0.134 BrainSegVol 1096253.000 (1094128.000) diff=2125.000 pctdiff=0.194 BrainSegVolNotVent 1079201.000 (1078896.444) diff=304.556 pctdiff=0.028 BrainSegVolNotVent 1079201.000 CerebellumVol 123093.000 VentChorVol 14012.000 3rd4th5thCSF 3040.000 CSFVol 915.000, OptChiasmVol 107.000 MaskVol 1523756.000 1410 867 2615 2.801 0.423 0.114 0.029 14 1.7 bankssts 957 824 1869 2.533 0.760 0.183 0.054 46 2.6 caudalanteriorcingulate 2705 2239 5359 2.615 0.449 0.126 0.023 25 2.7 caudalmiddlefrontal 2163 1811 3199 2.009 0.510 0.154 0.038 29 3.8 cuneus 652 759 2431 4.053 0.773 0.180 0.035 9 1.1 entorhinal 4198 3680 9777 2.928 0.692 0.153 0.038 68 7.5 fusiform 7804 6525 14650 2.454 0.525 0.150 0.032 97 11.3 inferiorparietal 4736 4347 11067 2.830 0.724 0.161 0.038 70 8.2 inferiortemporal 1229 962 2079 2.320 0.909 0.150 0.034 29 1.8 isthmuscingulate 6591 5121 10562 2.233 0.502 0.139 0.030 93 9.2 lateraloccipital 3385 2966 7145 2.694 0.597 0.171 0.043 61 6.7 lateralorbitofrontal 4299 3449 6229 2.037 0.615 0.146 0.037 62 7.2 lingual 2804 2461 5352 2.422 0.655 0.158 0.036 38 4.7 medialorbitofrontal 5269 5371 13772 3.001 0.620 0.157 0.030 59 7.5 middletemporal 1018 888 2355 2.941 0.686 0.133 0.033 9 1.5 parahippocampal 2743 2119 5132 2.672 0.531 0.124 0.026 28 3.3 paracentral 1861 1602 4117 2.819 0.557 0.144 0.027 21 2.4 parsopercularis 1155 1321 2764 2.614 0.564 0.198 0.038 18 2.1 parsorbitalis 1874 1746 4042 2.596 0.715 0.153 0.031 32 2.8 parstriangularis 1967 1116 1793 1.553 0.407 0.116 0.033 38 2.5 pericalcarine 6336 5184 9424 1.984 0.628 0.132 0.028 65 8.1 postcentral 1518 1248 3030 2.607 0.723 0.151 0.037 26 2.5 posteriorcingulate 7072 5186 12895 2.640 0.578 0.114 0.023 77 7.0 precentral 4932 3634 8260 2.397 0.562 0.140 0.032 70 6.8 precuneus 826 670 1651 2.645 0.765 0.181 0.052 21 1.8 rostralanteriorcingulate 9149 7925 16997 2.336 0.563 0.156 0.032 130 13.7 rostralmiddlefrontal 9175 7940 20920 2.872 0.578 0.141 0.029 112 11.5 superiorfrontal 8067 6555 12928 2.143 0.540 0.139 0.029 95 9.7 superiorparietal 5285 4504 11456 2.859 0.593 0.139 0.029 55 7.3 superiortemporal 5916 4827 11514 2.542 0.619 0.147 0.034 127 8.9 supramarginal 450 606 1237 2.724 0.617 0.217 0.035 5 0.9 frontalpole 641 825 2543 4.075 0.600 0.204 0.042 10 1.3 temporalpole 521 405 852 2.420 0.472 0.132 0.034 4 0.8 transversetemporal 3390 2295 6966 2.950 0.737 0.149 0.041 63 5.9 insula #----------------------------------------- #@# Cortical Parc 2 lh 2020��� 04��� 29��� ��������� 05:15:33 CST /home/web/freesurver/test/MRI/subjects02/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subjects02 lh ../surf/lh.sphere.reg /usr/local/freesurfer/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/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... 21 labels changed using aseg relabeling using gibbs priors... 000: 8100 changed, 127920 examined... 001: 1854 changed, 31681 examined... 002: 572 changed, 9762 examined... 003: 248 changed, 3250 examined... 004: 111 changed, 1422 examined... 005: 43 changed, 646 examined... 006: 28 changed, 267 examined... 007: 12 changed, 146 examined... 008: 4 changed, 76 examined... 009: 1 changed, 32 examined... 010: 0 changed, 6 examined... 4 labels changed using aseg 000: 220 total segments, 136 labels (1220 vertices) changed 001: 84 total segments, 1 labels (2 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 26 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1114 vertices marked for relabeling... 1114 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 17 seconds. #----------------------------------------- #@# Cortical Parc 2 rh 2020��� 04��� 29��� ��������� 05:15:51 CST /home/web/freesurver/test/MRI/subjects02/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subjects02 rh ../surf/rh.sphere.reg /usr/local/freesurfer/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/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... 0 labels changed using aseg relabeling using gibbs priors... 000: 8486 changed, 129541 examined... 001: 1838 changed, 33175 examined... 002: 513 changed, 9863 examined... 003: 199 changed, 2945 examined... 004: 96 changed, 1195 examined... 005: 50 changed, 528 examined... 006: 23 changed, 279 examined... 007: 16 changed, 146 examined... 008: 9 changed, 80 examined... 009: 5 changed, 40 examined... 010: 5 changed, 28 examined... 011: 3 changed, 23 examined... 012: 2 changed, 18 examined... 013: 2 changed, 13 examined... 014: 1 changed, 9 examined... 015: 0 changed, 5 examined... 0 labels changed using aseg 000: 217 total segments, 134 labels (1706 vertices) changed 001: 88 total segments, 6 labels (19 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 25 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 996 vertices marked for relabeling... 996 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 18 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh 2020��� 04��� 29��� ��������� 05:16:08 CST /home/web/freesurver/test/MRI/subjects02/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 subjects02 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/web/freesurver/test/MRI/subjects02/mri/wm.mgz... reading input surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white... reading input pial surface /home/web/freesurver/test/MRI/subjects02/surf/lh.pial... reading input white surface /home/web/freesurver/test/MRI/subjects02/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 237539 Total vertex volume 233281 (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) = 1386977 mm^3 (det: 1.404569 ) lhCtxGM: 233522.426 233230.000 diff= 292.4 pctdiff= 0.125 rhCtxGM: 237118.332 237065.000 diff= 53.3 pctdiff= 0.022 lhCtxWM: 212468.541 212507.000 diff= -38.5 pctdiff=-0.018 rhCtxWM: 216002.146 216507.000 diff= -504.9 pctdiff=-0.234 SubCortGMVol 56659.000 SupraTentVol 971298.444 (970013.000) diff=1285.444 pctdiff=0.132 SupraTentVolNotVent 957286.444 (956001.000) diff=1285.444 pctdiff=0.134 BrainSegVol 1096253.000 (1094128.000) diff=2125.000 pctdiff=0.194 BrainSegVolNotVent 1079201.000 (1078896.444) diff=304.556 pctdiff=0.028 BrainSegVolNotVent 1079201.000 CerebellumVol 123093.000 VentChorVol 14012.000 3rd4th5thCSF 3040.000 CSFVol 915.000, OptChiasmVol 107.000 MaskVol 1523756.000 1332 953 2454 2.258 0.529 0.144 0.033 22 1.8 G&S_frontomargin 1613 1131 3412 2.619 0.635 0.152 0.029 25 2.0 G&S_occipital_inf 1710 1049 2991 2.381 0.655 0.116 0.023 18 1.6 G&S_paracentral 1341 929 2925 2.683 0.461 0.136 0.028 19 1.5 G&S_subcentral 825 586 2209 2.779 0.661 0.169 0.043 18 1.7 G&S_transv_frontopol 1834 1296 3781 2.711 0.489 0.127 0.025 26 2.0 G&S_cingul-Ant 1237 862 2564 2.856 0.481 0.122 0.026 15 1.3 G&S_cingul-Mid-Ant 1385 949 2651 2.803 0.527 0.120 0.023 12 1.3 G&S_cingul-Mid-Post 656 454 1912 3.116 0.444 0.155 0.036 12 1.0 G_cingul-Post-dorsal 324 206 624 2.674 0.756 0.135 0.031 5 0.3 G_cingul-Post-ventral 1912 1273 2546 1.802 0.468 0.167 0.041 36 3.1 G_cuneus 1431 990 3539 2.717 0.516 0.153 0.032 26 1.8 G_front_inf-Opercular 395 252 1094 2.894 0.533 0.146 0.031 8 0.5 G_front_inf-Orbital 979 640 2605 2.932 0.524 0.129 0.026 15 1.0 G_front_inf-Triangul 4058 2782 9765 2.639 0.560 0.142 0.032 71 5.0 G_front_middle 6676 4477 17741 3.098 0.618 0.127 0.026 83 7.0 G_front_sup 694 479 1556 3.230 0.675 0.147 0.044 11 1.2 G_Ins_lg&S_cent_ins 856 537 2495 3.700 0.651 0.136 0.039 13 1.3 G_insular_short 2220 1427 4971 2.646 0.545 0.151 0.035 43 3.1 G_occipital_middle 1488 980 2297 2.082 0.493 0.148 0.031 23 1.8 G_occipital_sup 1740 1116 4377 3.099 0.551 0.141 0.030 29 1.8 G_oc-temp_lat-fusifor 2887 1927 4508 2.025 0.577 0.169 0.046 53 5.5 G_oc-temp_med-Lingual 1625 1050 4771 3.502 0.768 0.115 0.024 17 1.4 G_oc-temp_med-Parahip 2077 1431 5567 2.867 0.657 0.136 0.032 34 2.4 G_orbital 2599 1742 6080 2.618 0.532 0.144 0.031 47 3.4 G_pariet_inf-Angular 2565 1751 6059 2.741 0.564 0.147 0.030 44 3.1 G_pariet_inf-Supramar 2550 1714 4726 2.250 0.480 0.133 0.027 38 2.7 G_parietal_sup 2668 1646 4657 2.253 0.546 0.125 0.027 34 2.8 G_postcentral 2650 1486 5637 2.920 0.514 0.096 0.019 23 1.9 G_precentral 2538 1734 5583 2.530 0.626 0.143 0.030 44 3.2 G_precuneus 998 693 2452 2.748 0.723 0.165 0.045 25 1.9 G_rectus 600 360 1101 2.642 1.012 0.112 0.085 21 1.9 G_subcallosal 424 274 836 2.668 0.476 0.133 0.021 5 0.3 G_temp_sup-G_T_transv 1709 1128 5046 3.051 0.611 0.122 0.026 28 1.9 G_temp_sup-Lateral 747 532 2043 3.414 0.783 0.069 0.011 2 0.3 G_temp_sup-Plan_polar 884 611 1757 2.620 0.519 0.112 0.027 10 0.8 G_temp_sup-Plan_tempo 2240 1584 6323 2.920 0.554 0.134 0.032 43 3.0 G_temporal_inf 2963 1987 8145 3.067 0.580 0.147 0.033 62 3.8 G_temporal_middle 342 229 475 2.325 0.354 0.086 0.012 2 0.1 Lat_Fis-ant-Horizont 329 241 500 2.337 0.480 0.093 0.011 1 0.1 Lat_Fis-ant-Vertical 1030 701 1307 2.258 0.499 0.114 0.019 8 0.7 Lat_Fis-post 1794 1120 2139 1.827 0.457 0.152 0.038 29 2.7 Pole_occipital 1859 1270 6286 3.469 0.711 0.134 0.027 28 1.9 Pole_temporal 2072 1492 2501 1.929 0.598 0.145 0.035 25 3.0 S_calcarine 3119 2082 3559 1.923 0.615 0.099 0.017 18 2.2 S_central 1186 811 1679 2.325 0.387 0.094 0.015 6 0.7 S_cingul-Marginalis 479 336 847 2.982 0.531 0.086 0.012 1 0.3 S_circular_insula_ant 1217 824 1783 2.611 0.604 0.091 0.014 5 0.7 S_circular_insula_inf 1518 1032 2316 2.769 0.479 0.112 0.020 9 1.3 S_circular_insula_sup 1353 960 2186 2.423 0.505 0.098 0.012 8 0.8 S_collat_transv_ant 571 395 674 2.086 0.531 0.130 0.020 6 0.5 S_collat_transv_post 2145 1490 3444 2.385 0.381 0.112 0.018 17 1.6 S_front_inf 1335 964 2214 2.174 0.492 0.131 0.028 13 1.6 S_front_middle 3009 2067 4945 2.486 0.488 0.092 0.014 16 1.6 S_front_sup 315 235 467 2.420 0.534 0.139 0.023 3 0.4 S_interm_prim-Jensen 2905 1985 3311 1.931 0.406 0.116 0.017 23 2.1 S_intrapariet&P_trans 1106 772 1311 1.954 0.390 0.115 0.023 7 1.1 S_oc_middle&Lunatus 1270 870 1571 2.015 0.380 0.108 0.019 8 1.0 S_oc_sup&transversal 633 441 901 2.299 0.365 0.115 0.028 4 0.6 S_occipital_ant 751 524 1266 2.472 0.419 0.118 0.021 7 0.7 S_oc-temp_lat 2230 1533 3385 2.434 0.493 0.110 0.021 16 2.0 S_oc-temp_med&Lingual 366 262 577 2.369 0.431 0.122 0.024 3 0.4 S_orbital_lateral 582 410 855 2.563 0.785 0.126 0.023 6 0.5 S_orbital_med-olfact 1490 1067 2686 2.516 0.529 0.140 0.031 23 2.0 S_orbital-H_Shaped 1710 1185 2301 2.157 0.457 0.114 0.019 13 1.4 S_parieto_occipital 1339 802 1312 2.177 0.735 0.110 0.019 17 0.8 S_pericallosal 2819 1970 3775 2.129 0.458 0.114 0.019 22 2.2 S_postcentral 1318 909 2075 2.549 0.312 0.087 0.011 5 0.6 S_precentral-inf-part 1347 949 2145 2.501 0.543 0.100 0.015 8 0.9 S_precentral-sup-part 694 505 1065 2.231 0.517 0.102 0.011 4 0.3 S_suborbital 931 657 1466 2.383 0.496 0.113 0.020 6 0.7 S_subparietal 1651 1155 2460 2.436 0.387 0.104 0.016 8 1.2 S_temporal_inf 5677 3978 9327 2.486 0.512 0.112 0.019 46 4.3 S_temporal_sup 232 167 368 2.438 0.442 0.141 0.017 2 0.2 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh 2020��� 04��� 29��� ��������� 05:16:44 CST /home/web/freesurver/test/MRI/subjects02/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 subjects02 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/web/freesurver/test/MRI/subjects02/mri/wm.mgz... reading input surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white... reading input pial surface /home/web/freesurver/test/MRI/subjects02/surf/rh.pial... reading input white surface /home/web/freesurver/test/MRI/subjects02/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 241163 Total vertex volume 237018 (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) = 1386977 mm^3 (det: 1.404569 ) lhCtxGM: 233522.426 233230.000 diff= 292.4 pctdiff= 0.125 rhCtxGM: 237118.332 237065.000 diff= 53.3 pctdiff= 0.022 lhCtxWM: 212468.541 212507.000 diff= -38.5 pctdiff=-0.018 rhCtxWM: 216002.146 216507.000 diff= -504.9 pctdiff=-0.234 SubCortGMVol 56659.000 SupraTentVol 971298.444 (970013.000) diff=1285.444 pctdiff=0.132 SupraTentVolNotVent 957286.444 (956001.000) diff=1285.444 pctdiff=0.134 BrainSegVol 1096253.000 (1094128.000) diff=2125.000 pctdiff=0.194 BrainSegVolNotVent 1079201.000 (1078896.444) diff=304.556 pctdiff=0.028 BrainSegVolNotVent 1079201.000 CerebellumVol 123093.000 VentChorVol 14012.000 3rd4th5thCSF 3040.000 CSFVol 915.000, OptChiasmVol 107.000 MaskVol 1523756.000 1066 732 2083 2.330 0.646 0.141 0.031 17 1.5 G&S_frontomargin 984 689 2212 2.630 0.442 0.148 0.028 15 1.2 G&S_occipital_inf 1701 1021 3162 2.534 0.587 0.114 0.023 17 1.5 G&S_paracentral 1510 1087 3296 2.577 0.492 0.164 0.032 26 1.9 G&S_subcentral 1104 757 2684 2.703 0.620 0.158 0.043 23 1.7 G&S_transv_frontopol 2855 1983 5366 2.519 0.599 0.125 0.025 37 3.0 G&S_cingul-Ant 1195 814 2482 2.770 0.539 0.106 0.022 9 1.0 G&S_cingul-Mid-Ant 1446 985 2826 2.671 0.550 0.115 0.026 14 1.3 G&S_cingul-Mid-Post 376 241 1123 3.105 0.604 0.141 0.028 7 0.4 G_cingul-Post-dorsal 317 186 651 2.534 0.810 0.139 0.028 6 0.3 G_cingul-Post-ventral 2030 1369 2988 1.967 0.552 0.150 0.038 29 3.1 G_cuneus 1228 847 3365 2.914 0.581 0.146 0.030 20 1.7 G_front_inf-Opercular 319 215 807 2.926 0.567 0.128 0.022 4 0.2 G_front_inf-Orbital 821 580 2344 2.863 0.724 0.131 0.028 11 0.9 G_front_inf-Triangul 4165 2818 9287 2.568 0.537 0.140 0.031 68 5.9 G_front_middle 6412 4257 16466 3.043 0.562 0.128 0.026 79 6.9 G_front_sup 658 460 1441 3.038 0.729 0.136 0.199 33 0.7 G_Ins_lg&S_cent_ins 535 352 1806 3.419 0.745 0.140 0.041 11 0.9 G_insular_short 2370 1571 5095 2.558 0.483 0.158 0.040 46 3.9 G_occipital_middle 1628 1070 3010 2.270 0.538 0.139 0.031 23 1.9 G_occipital_sup 1936 1285 5108 2.980 0.651 0.145 0.037 39 2.9 G_oc-temp_lat-fusifor 2718 1845 4359 2.043 0.668 0.162 0.037 51 4.3 G_oc-temp_med-Lingual 1184 774 3885 3.687 0.875 0.104 0.022 10 0.8 G_oc-temp_med-Parahip 2733 1928 6985 2.758 0.626 0.163 0.046 62 5.1 G_orbital 2706 1801 6624 2.725 0.522 0.141 0.031 45 3.4 G_pariet_inf-Angular 2653 1860 6433 2.840 0.563 0.147 0.031 42 3.2 G_pariet_inf-Supramar 2278 1511 4644 2.367 0.568 0.138 0.030 34 2.6 G_parietal_sup 2284 1399 3779 2.125 0.606 0.113 0.028 25 2.8 G_postcentral 2923 1705 6642 2.950 0.502 0.110 0.024 28 2.8 G_precentral 2234 1501 4460 2.404 0.576 0.141 0.033 38 2.8 G_precuneus 798 516 1722 2.343 0.677 0.140 0.040 16 1.2 G_rectus 330 215 641 2.890 0.856 0.121 0.042 4 0.5 G_subcallosal 335 198 662 2.579 0.423 0.131 0.022 5 0.2 G_temp_sup-G_T_transv 1738 1137 4959 3.185 0.513 0.129 0.024 27 1.8 G_temp_sup-Lateral 780 514 1800 3.263 0.730 0.064 0.010 2 0.3 G_temp_sup-Plan_polar 1017 719 2042 2.477 0.578 0.117 0.022 14 0.9 G_temp_sup-Plan_tempo 2373 1653 7081 3.000 0.773 0.148 0.040 46 4.0 G_temporal_inf 3310 2334 9897 3.081 0.642 0.142 0.033 65 4.7 G_temporal_middle 284 191 446 2.496 0.602 0.079 0.013 1 0.1 Lat_Fis-ant-Horizont 304 221 391 2.139 0.513 0.096 0.015 2 0.1 Lat_Fis-ant-Vertical 1302 900 1942 2.625 0.564 0.104 0.018 8 0.9 Lat_Fis-post 2945 1929 3847 1.884 0.518 0.140 0.033 38 4.1 Pole_occipital 1821 1249 6671 3.738 0.719 0.142 0.035 27 2.9 Pole_temporal 1930 1292 2047 1.845 0.600 0.132 0.029 23 2.3 S_calcarine 3200 2114 3550 1.911 0.632 0.093 0.017 23 2.2 S_central 1296 860 1933 2.362 0.446 0.089 0.012 6 0.7 S_cingul-Marginalis 526 358 851 2.976 0.535 0.111 0.020 3 0.4 S_circular_insula_ant 1213 780 1740 2.477 0.573 0.075 0.008 4 0.5 S_circular_insula_inf 1226 859 2111 2.730 0.495 0.117 0.020 7 1.1 S_circular_insula_sup 1045 741 1849 2.680 0.522 0.102 0.018 6 0.6 S_collat_transv_ant 437 298 402 1.883 0.294 0.157 0.034 6 0.6 S_collat_transv_post 1885 1331 2887 2.369 0.368 0.102 0.017 12 1.2 S_front_inf 2960 2118 4913 2.175 0.529 0.128 0.024 32 3.0 S_front_middle 2032 1425 3319 2.467 0.489 0.092 0.015 10 1.1 S_front_sup 483 342 715 2.316 0.438 0.102 0.020 2 0.5 S_interm_prim-Jensen 3636 2483 4765 2.017 0.487 0.112 0.020 31 2.9 S_intrapariet&P_trans 808 572 1163 2.270 0.355 0.140 0.036 9 1.2 S_oc_middle&Lunatus 1554 1061 1979 2.095 0.377 0.116 0.020 12 1.2 S_oc_sup&transversal 723 508 1063 2.300 0.376 0.117 0.026 5 0.6 S_occipital_ant 1003 708 1521 2.422 0.367 0.110 0.019 7 0.8 S_oc-temp_lat 2319 1621 3546 2.550 0.502 0.112 0.018 15 1.8 S_oc-temp_med&Lingual 283 204 422 2.119 0.457 0.104 0.016 1 0.2 S_orbital_lateral 650 451 939 2.184 0.736 0.103 0.014 4 0.4 S_orbital_med-olfact 1395 978 2468 2.485 0.542 0.133 0.030 18 1.6 S_orbital-H_Shaped 1991 1321 2706 2.300 0.535 0.120 0.022 18 1.9 S_parieto_occipital 1405 845 1161 1.826 0.609 0.123 0.016 23 0.7 S_pericallosal 2915 2028 3282 1.877 0.440 0.112 0.019 20 2.3 S_postcentral 1411 964 2072 2.358 0.451 0.093 0.013 7 0.7 S_precentral-inf-part 1018 690 1585 2.572 0.416 0.097 0.015 6 0.6 S_precentral-sup-part 274 199 536 2.707 0.577 0.106 0.018 2 0.2 S_suborbital 986 681 1551 2.405 0.650 0.123 0.022 8 0.9 S_subparietal 1456 1015 2125 2.557 0.510 0.111 0.022 8 1.4 S_temporal_inf 6031 4156 9789 2.561 0.480 0.099 0.016 35 4.0 S_temporal_sup 304 213 511 2.817 0.467 0.116 0.014 2 0.2 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh 2020��� 04��� 29��� ��������� 05:17:20 CST /home/web/freesurver/test/MRI/subjects02/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subjects02 lh ../surf/lh.sphere.reg /usr/local/freesurfer/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/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... 1408 labels changed using aseg relabeling using gibbs priors... 000: 1974 changed, 127920 examined... 001: 467 changed, 9069 examined... 002: 143 changed, 2644 examined... 003: 65 changed, 759 examined... 004: 38 changed, 376 examined... 005: 27 changed, 212 examined... 006: 12 changed, 136 examined... 007: 5 changed, 73 examined... 008: 1 changed, 28 examined... 009: 1 changed, 7 examined... 010: 0 changed, 7 examined... 259 labels changed using aseg 000: 57 total segments, 24 labels (211 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 826 vertices marked for relabeling... 826 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 15 seconds. #----------------------------------------- #@# Cortical Parc 3 rh 2020��� 04��� 29��� ��������� 05:17:35 CST /home/web/freesurver/test/MRI/subjects02/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subjects02 rh ../surf/rh.sphere.reg /usr/local/freesurfer/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/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... 1229 labels changed using aseg relabeling using gibbs priors... 000: 1884 changed, 129541 examined... 001: 431 changed, 8847 examined... 002: 115 changed, 2478 examined... 003: 37 changed, 745 examined... 004: 13 changed, 235 examined... 005: 7 changed, 87 examined... 006: 4 changed, 46 examined... 007: 2 changed, 20 examined... 008: 2 changed, 14 examined... 009: 0 changed, 12 examined... 155 labels changed using aseg 000: 43 total segments, 10 labels (49 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 11 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 869 vertices marked for relabeling... 869 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 14 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh 2020��� 04��� 29��� ��������� 05:17:49 CST /home/web/freesurver/test/MRI/subjects02/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 subjects02 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /home/web/freesurver/test/MRI/subjects02/mri/wm.mgz... reading input surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white... reading input pial surface /home/web/freesurver/test/MRI/subjects02/surf/lh.pial... reading input white surface /home/web/freesurver/test/MRI/subjects02/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 237539 Total vertex volume 233281 (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) = 1386977 mm^3 (det: 1.404569 ) lhCtxGM: 233522.426 233230.000 diff= 292.4 pctdiff= 0.125 rhCtxGM: 237118.332 237065.000 diff= 53.3 pctdiff= 0.022 lhCtxWM: 212468.541 212507.000 diff= -38.5 pctdiff=-0.018 rhCtxWM: 216002.146 216507.000 diff= -504.9 pctdiff=-0.234 SubCortGMVol 56659.000 SupraTentVol 971298.444 (970013.000) diff=1285.444 pctdiff=0.132 SupraTentVolNotVent 957286.444 (956001.000) diff=1285.444 pctdiff=0.134 BrainSegVol 1096253.000 (1094128.000) diff=2125.000 pctdiff=0.194 BrainSegVolNotVent 1079201.000 (1078896.444) diff=304.556 pctdiff=0.028 BrainSegVolNotVent 1079201.000 CerebellumVol 123093.000 VentChorVol 14012.000 3rd4th5thCSF 3040.000 CSFVol 915.000, OptChiasmVol 107.000 MaskVol 1523756.000 1355 928 2684 2.778 0.515 0.121 0.023 18 1.2 caudalanteriorcingulate 3337 2283 6801 2.634 0.519 0.116 0.020 32 2.4 caudalmiddlefrontal 2749 1875 3763 1.924 0.441 0.145 0.030 40 3.3 cuneus 658 456 2207 3.658 0.795 0.099 0.020 4 0.5 entorhinal 4389 2964 9264 2.792 0.621 0.130 0.025 54 4.4 fusiform 6806 4662 12610 2.386 0.531 0.129 0.026 89 7.2 inferiorparietal 4917 3415 11550 2.798 0.647 0.123 0.025 66 5.1 inferiortemporal 1537 995 2713 2.446 0.851 0.127 0.029 23 1.6 isthmuscingulate 7008 4616 10936 2.201 0.610 0.144 0.031 98 8.9 lateraloccipital 4132 2871 8839 2.755 0.688 0.140 0.034 67 5.6 lateralorbitofrontal 4216 2878 6249 2.090 0.542 0.148 0.036 61 6.4 lingual 2158 1493 4690 2.630 0.777 0.131 0.034 35 2.9 medialorbitofrontal 6278 4300 14292 2.849 0.599 0.127 0.025 87 6.1 middletemporal 1192 771 2777 3.135 0.777 0.109 0.020 11 0.8 parahippocampal 2468 1604 4462 2.605 0.591 0.107 0.020 19 2.1 paracentral 2175 1530 4490 2.621 0.461 0.130 0.024 27 2.0 parsopercularis 837 573 1810 2.587 0.541 0.124 0.023 12 0.7 parsorbitalis 2175 1473 4655 2.661 0.547 0.114 0.020 22 1.8 parstriangularis 1715 1213 1743 1.619 0.425 0.166 0.046 26 3.2 pericalcarine 7458 4924 11535 2.127 0.622 0.120 0.023 80 7.1 postcentral 1844 1233 3618 2.761 0.575 0.119 0.022 20 1.7 posteriorcingulate 7029 4336 12676 2.666 0.550 0.099 0.019 55 5.2 precentral 4857 3347 8957 2.436 0.580 0.131 0.027 62 5.2 precuneus 1548 1070 2953 2.608 0.605 0.144 0.045 42 3.1 rostralanteriorcingulate 5374 3752 10505 2.403 0.530 0.133 0.028 73 6.2 rostralmiddlefrontal 11305 7730 25877 2.834 0.656 0.121 0.024 127 11.3 superiorfrontal 5871 3976 8829 2.070 0.474 0.124 0.023 67 5.3 superiorparietal 6745 4631 15758 2.919 0.696 0.108 0.021 67 5.7 superiortemporal 4744 3290 9275 2.542 0.580 0.137 0.027 68 5.3 supramarginal 611 413 1005 2.460 0.442 0.154 0.025 9 0.5 transversetemporal 2666 1801 5758 3.128 0.736 0.120 0.026 26 2.7 insula #----------------------------------------- #@# Parcellation Stats 3 rh 2020��� 04��� 29��� ��������� 05:18:24 CST /home/web/freesurver/test/MRI/subjects02/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 subjects02 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /home/web/freesurver/test/MRI/subjects02/mri/wm.mgz... reading input surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white... reading input pial surface /home/web/freesurver/test/MRI/subjects02/surf/rh.pial... reading input white surface /home/web/freesurver/test/MRI/subjects02/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 241163 Total vertex volume 237018 (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) = 1386977 mm^3 (det: 1.404569 ) lhCtxGM: 233522.426 233230.000 diff= 292.4 pctdiff= 0.125 rhCtxGM: 237118.332 237065.000 diff= 53.3 pctdiff= 0.022 lhCtxWM: 212468.541 212507.000 diff= -38.5 pctdiff=-0.018 rhCtxWM: 216002.146 216507.000 diff= -504.9 pctdiff=-0.234 SubCortGMVol 56659.000 SupraTentVol 971298.444 (970013.000) diff=1285.444 pctdiff=0.132 SupraTentVolNotVent 957286.444 (956001.000) diff=1285.444 pctdiff=0.134 BrainSegVol 1096253.000 (1094128.000) diff=2125.000 pctdiff=0.194 BrainSegVolNotVent 1079201.000 (1078896.444) diff=304.556 pctdiff=0.028 BrainSegVolNotVent 1079201.000 CerebellumVol 123093.000 VentChorVol 14012.000 3rd4th5thCSF 3040.000 CSFVol 915.000, OptChiasmVol 107.000 MaskVol 1523756.000 1031 672 2019 2.524 0.750 0.121 0.019 13 0.8 caudalanteriorcingulate 2829 1904 5587 2.631 0.452 0.112 0.020 25 2.3 caudalmiddlefrontal 2555 1743 3841 2.058 0.533 0.143 0.034 34 3.6 cuneus 548 355 2072 4.092 0.762 0.088 0.018 3 0.3 entorhinal 3866 2657 8308 2.809 0.597 0.130 0.028 52 4.5 fusiform 7649 5195 14546 2.465 0.534 0.127 0.027 96 8.3 inferiorparietal 5078 3519 12642 2.927 0.801 0.129 0.031 67 6.5 inferiortemporal 1218 760 2025 2.296 0.884 0.124 0.023 18 1.0 isthmuscingulate 6695 4477 10848 2.232 0.504 0.144 0.033 92 8.8 lateraloccipital 4196 2905 8770 2.626 0.634 0.145 0.063 97 6.3 lateralorbitofrontal 4286 2925 6170 2.035 0.614 0.149 0.033 65 6.0 lingual 2032 1358 4059 2.467 0.713 0.127 0.033 30 2.7 medialorbitofrontal 6484 4534 15778 2.932 0.613 0.120 0.025 79 7.0 middletemporal 1069 709 2491 2.948 0.681 0.096 0.017 9 0.6 parahippocampal 2799 1745 5337 2.700 0.543 0.101 0.019 20 2.0 paracentral 2051 1416 4361 2.756 0.575 0.127 0.021 23 1.9 parsopercularis 890 610 1943 2.569 0.519 0.135 0.029 12 1.1 parsorbitalis 1925 1333 4217 2.631 0.710 0.112 0.021 18 1.6 parstriangularis 1889 1289 1747 1.563 0.404 0.151 0.035 27 2.6 pericalcarine 7044 4647 10203 1.990 0.610 0.120 0.025 80 7.2 postcentral 1606 1073 3125 2.613 0.716 0.126 0.025 22 1.5 posteriorcingulate 6707 4221 12440 2.648 0.584 0.106 0.021 54 5.6 precentral 5243 3490 8865 2.378 0.571 0.128 0.026 63 5.7 precuneus 1069 721 2085 2.620 0.730 0.138 0.031 18 1.3 rostralanteriorcingulate 6526 4620 12680 2.384 0.549 0.136 0.031 94 8.7 rostralmiddlefrontal 12509 8559 26730 2.711 0.636 0.123 0.024 142 11.9 superiorfrontal 6522 4419 10528 2.129 0.552 0.119 0.023 70 5.6 superiorparietal 6828 4595 15768 2.975 0.688 0.108 0.020 65 5.6 superiortemporal 5706 3979 11108 2.556 0.624 0.130 0.026 71 6.1 supramarginal 524 328 873 2.433 0.493 0.122 0.020 6 0.3 transversetemporal 2727 1875 5853 3.010 0.674 0.117 0.024 26 2.5 insula #----------------------------------------- #@# WM/GM Contrast lh 2020��� 04��� 29��� ��������� 05:19:00 CST /home/web/freesurver/test/MRI/subjects02/scripts pctsurfcon --s subjects02 --lh-only Log file is /home/web/freesurver/test/MRI/subjects02/scripts/pctsurfcon.log 2020��� 04��� 29��� ��������� 05:19:00 CST setenv SUBJECTS_DIR /home/web/freesurver/test/MRI cd /home/web/freesurver/test/MRI/subjects02/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux web-virtual-machine 4.15.0-96-generic #97~16.04.1-Ubuntu SMP Wed Apr 1 03:03:31 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /home/web/freesurver/test/MRI/subjects02/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/web/freesurver/test/MRI/subjects02/surf/tmp.pctsurfcon.8839/lh.wm.mgh --regheader subjects02 --cortex srcvol = /home/web/freesurver/test/MRI/subjects02/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/web/freesurver/test/MRI/subjects02/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/web/freesurver/test/MRI/subjects02/label/lh.cortex.label Reading surface /home/web/freesurver/test/MRI/subjects02/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 = 63350 Masking with /home/web/freesurver/test/MRI/subjects02/label/lh.cortex.label Writing to /home/web/freesurver/test/MRI/subjects02/surf/tmp.pctsurfcon.8839/lh.wm.mgh Dim: 127920 1 1 mri_vol2surf --mov /home/web/freesurver/test/MRI/subjects02/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/web/freesurver/test/MRI/subjects02/surf/tmp.pctsurfcon.8839/lh.gm.mgh --projfrac 0.3 --regheader subjects02 --cortex srcvol = /home/web/freesurver/test/MRI/subjects02/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/web/freesurver/test/MRI/subjects02/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/web/freesurver/test/MRI/subjects02/label/lh.cortex.label Reading surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Done reading source surface Reading thickness /home/web/freesurver/test/MRI/subjects02/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 = 75463 Masking with /home/web/freesurver/test/MRI/subjects02/label/lh.cortex.label Writing to /home/web/freesurver/test/MRI/subjects02/surf/tmp.pctsurfcon.8839/lh.gm.mgh Dim: 127920 1 1 mri_concat /home/web/freesurver/test/MRI/subjects02/surf/tmp.pctsurfcon.8839/lh.wm.mgh /home/web/freesurver/test/MRI/subjects02/surf/tmp.pctsurfcon.8839/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/web/freesurver/test/MRI/subjects02/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/web/freesurver/test/MRI/subjects02/surf/lh.w-g.pct.mgh mri_segstats --in /home/web/freesurver/test/MRI/subjects02/surf/lh.w-g.pct.mgh --annot subjects02 lh aparc --sum /home/web/freesurver/test/MRI/subjects02/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/web/freesurver/test/MRI/subjects02/surf/lh.w-g.pct.mgh --annot subjects02 lh aparc --sum /home/web/freesurver/test/MRI/subjects02/stats/lh.w-g.pct.stats --snr sysname Linux hostname web-virtual-machine machine x86_64 user web UseRobust 0 Constructing seg from annotation Reading annotation /home/web/freesurver/test/MRI/subjects02/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/web/freesurver/test/MRI/subjects02/surf/lh.w-g.pct.mgh Vertex Area is 0.675646 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 2020��� 04��� 29��� ��������� 05:19:06 CST /home/web/freesurver/test/MRI/subjects02/scripts pctsurfcon --s subjects02 --rh-only Log file is /home/web/freesurver/test/MRI/subjects02/scripts/pctsurfcon.log 2020��� 04��� 29��� ��������� 05:19:06 CST setenv SUBJECTS_DIR /home/web/freesurver/test/MRI cd /home/web/freesurver/test/MRI/subjects02/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux web-virtual-machine 4.15.0-96-generic #97~16.04.1-Ubuntu SMP Wed Apr 1 03:03:31 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /home/web/freesurver/test/MRI/subjects02/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/web/freesurver/test/MRI/subjects02/surf/tmp.pctsurfcon.9007/rh.wm.mgh --regheader subjects02 --cortex srcvol = /home/web/freesurver/test/MRI/subjects02/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/web/freesurver/test/MRI/subjects02/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/web/freesurver/test/MRI/subjects02/label/rh.cortex.label Reading surface /home/web/freesurver/test/MRI/subjects02/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 = 63761 Masking with /home/web/freesurver/test/MRI/subjects02/label/rh.cortex.label Writing to /home/web/freesurver/test/MRI/subjects02/surf/tmp.pctsurfcon.9007/rh.wm.mgh Dim: 129541 1 1 mri_vol2surf --mov /home/web/freesurver/test/MRI/subjects02/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/web/freesurver/test/MRI/subjects02/surf/tmp.pctsurfcon.9007/rh.gm.mgh --projfrac 0.3 --regheader subjects02 --cortex srcvol = /home/web/freesurver/test/MRI/subjects02/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/web/freesurver/test/MRI/subjects02/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/web/freesurver/test/MRI/subjects02/label/rh.cortex.label Reading surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Done reading source surface Reading thickness /home/web/freesurver/test/MRI/subjects02/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 = 76315 Masking with /home/web/freesurver/test/MRI/subjects02/label/rh.cortex.label Writing to /home/web/freesurver/test/MRI/subjects02/surf/tmp.pctsurfcon.9007/rh.gm.mgh Dim: 129541 1 1 mri_concat /home/web/freesurver/test/MRI/subjects02/surf/tmp.pctsurfcon.9007/rh.wm.mgh /home/web/freesurver/test/MRI/subjects02/surf/tmp.pctsurfcon.9007/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/web/freesurver/test/MRI/subjects02/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/web/freesurver/test/MRI/subjects02/surf/rh.w-g.pct.mgh mri_segstats --in /home/web/freesurver/test/MRI/subjects02/surf/rh.w-g.pct.mgh --annot subjects02 rh aparc --sum /home/web/freesurver/test/MRI/subjects02/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/web/freesurver/test/MRI/subjects02/surf/rh.w-g.pct.mgh --annot subjects02 rh aparc --sum /home/web/freesurver/test/MRI/subjects02/stats/rh.w-g.pct.stats --snr sysname Linux hostname web-virtual-machine machine x86_64 user web UseRobust 0 Constructing seg from annotation Reading annotation /home/web/freesurver/test/MRI/subjects02/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/web/freesurver/test/MRI/subjects02/surf/rh.w-g.pct.mgh Vertex Area is 0.675821 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 2020��� 04��� 29��� ��������� 05:19:11 CST /home/web/freesurver/test/MRI/subjects02/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 977 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 1273 voxels changed to hypointensity... 2253 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc 2020��� 04��� 29��� ��������� 05:19:34 CST /home/web/freesurver/test/MRI/subjects02 mri_aparc2aseg --s subjects02 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/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/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/web/freesurver/test/MRI subject subjects02 outvol /home/web/freesurver/test/MRI/subjects02/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading lh pial surface /home/web/freesurver/test/MRI/subjects02/surf/lh.pial Loading lh annotations from /home/web/freesurver/test/MRI/subjects02/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/web/freesurver/test/MRI/subjects02/surf/rh.white Reading rh pial surface /home/web/freesurver/test/MRI/subjects02/surf/rh.pial Loading rh annotations from /home/web/freesurver/test/MRI/subjects02/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/web/freesurver/test/MRI/subjects02/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/web/freesurver/test/MRI/subjects02/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 5.91 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 107 rescaling Left_Cerebral_Cortex from 61 --> 57 rescaling Left_Lateral_Ventricle from 13 --> 9 rescaling Left_Inf_Lat_Vent from 34 --> 27 rescaling Left_Cerebellum_White_Matter from 86 --> 89 rescaling Left_Cerebellum_Cortex from 60 --> 61 rescaling Left_Thalamus from 94 --> 97 rescaling Left_Thalamus_Proper from 84 --> 90 rescaling Left_Caudate from 75 --> 70 rescaling Left_Putamen from 80 --> 79 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 16 rescaling Fourth_Ventricle from 22 --> 10 rescaling Brain_Stem from 81 --> 84 rescaling Left_Hippocampus from 57 --> 57 rescaling Left_Amygdala from 56 --> 62 rescaling CSF from 32 --> 22 rescaling Left_Accumbens_area from 62 --> 63 rescaling Left_VentralDC from 87 --> 94 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 57 rescaling Right_Lateral_Ventricle from 13 --> 8 rescaling Right_Inf_Lat_Vent from 25 --> 23 rescaling Right_Cerebellum_White_Matter from 87 --> 89 rescaling Right_Cerebellum_Cortex from 59 --> 59 rescaling Right_Thalamus_Proper from 85 --> 89 rescaling Right_Caudate from 62 --> 73 rescaling Right_Putamen from 80 --> 78 rescaling Right_Pallidum from 97 --> 96 rescaling Right_Hippocampus from 53 --> 55 rescaling Right_Amygdala from 55 --> 62 rescaling Right_Accumbens_area from 65 --> 71 rescaling Right_VentralDC from 86 --> 92 rescaling Fifth_Ventricle from 40 --> 19 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 44 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 = 468453 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 119 changed. pass 2: 9 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /home/web/freesurver/test/MRI/subjects02/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s 2020��� 04��� 29��� ��������� 05:25:28 CST /home/web/freesurver/test/MRI/subjects02 mri_aparc2aseg --s subjects02 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/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/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/web/freesurver/test/MRI subject subjects02 outvol /home/web/freesurver/test/MRI/subjects02/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading lh pial surface /home/web/freesurver/test/MRI/subjects02/surf/lh.pial Loading lh annotations from /home/web/freesurver/test/MRI/subjects02/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/web/freesurver/test/MRI/subjects02/surf/rh.white Reading rh pial surface /home/web/freesurver/test/MRI/subjects02/surf/rh.pial Loading rh annotations from /home/web/freesurver/test/MRI/subjects02/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/web/freesurver/test/MRI/subjects02/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/web/freesurver/test/MRI/subjects02/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 5.91 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 107 rescaling Left_Cerebral_Cortex from 61 --> 57 rescaling Left_Lateral_Ventricle from 13 --> 9 rescaling Left_Inf_Lat_Vent from 34 --> 27 rescaling Left_Cerebellum_White_Matter from 86 --> 89 rescaling Left_Cerebellum_Cortex from 60 --> 61 rescaling Left_Thalamus from 94 --> 97 rescaling Left_Thalamus_Proper from 84 --> 90 rescaling Left_Caudate from 75 --> 70 rescaling Left_Putamen from 80 --> 79 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 16 rescaling Fourth_Ventricle from 22 --> 10 rescaling Brain_Stem from 81 --> 84 rescaling Left_Hippocampus from 57 --> 57 rescaling Left_Amygdala from 56 --> 62 rescaling CSF from 32 --> 22 rescaling Left_Accumbens_area from 62 --> 63 rescaling Left_VentralDC from 87 --> 94 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 57 rescaling Right_Lateral_Ventricle from 13 --> 8 rescaling Right_Inf_Lat_Vent from 25 --> 23 rescaling Right_Cerebellum_White_Matter from 87 --> 89 rescaling Right_Cerebellum_Cortex from 59 --> 59 rescaling Right_Thalamus_Proper from 85 --> 89 rescaling Right_Caudate from 62 --> 73 rescaling Right_Putamen from 80 --> 78 rescaling Right_Pallidum from 97 --> 96 rescaling Right_Hippocampus from 53 --> 55 rescaling Right_Amygdala from 55 --> 62 rescaling Right_Accumbens_area from 65 --> 71 rescaling Right_VentralDC from 86 --> 92 rescaling Fifth_Ventricle from 40 --> 19 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 44 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 = 468457 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 119 changed. pass 2: 9 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /home/web/freesurver/test/MRI/subjects02/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas 2020��� 04��� 29��� ��������� 05:31:03 CST /home/web/freesurver/test/MRI/subjects02 mri_aparc2aseg --s subjects02 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/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/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/web/freesurver/test/MRI subject subjects02 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading lh pial surface /home/web/freesurver/test/MRI/subjects02/surf/lh.pial Loading lh annotations from /home/web/freesurver/test/MRI/subjects02/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/web/freesurver/test/MRI/subjects02/surf/rh.white Reading rh pial surface /home/web/freesurver/test/MRI/subjects02/surf/rh.pial Loading rh annotations from /home/web/freesurver/test/MRI/subjects02/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/web/freesurver/test/MRI/subjects02/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/web/freesurver/test/MRI/subjects02/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 5.91 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 107 rescaling Left_Cerebral_Cortex from 61 --> 57 rescaling Left_Lateral_Ventricle from 13 --> 9 rescaling Left_Inf_Lat_Vent from 34 --> 27 rescaling Left_Cerebellum_White_Matter from 86 --> 89 rescaling Left_Cerebellum_Cortex from 60 --> 61 rescaling Left_Thalamus from 94 --> 97 rescaling Left_Thalamus_Proper from 84 --> 90 rescaling Left_Caudate from 75 --> 70 rescaling Left_Putamen from 80 --> 79 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 16 rescaling Fourth_Ventricle from 22 --> 10 rescaling Brain_Stem from 81 --> 84 rescaling Left_Hippocampus from 57 --> 57 rescaling Left_Amygdala from 56 --> 62 rescaling CSF from 32 --> 22 rescaling Left_Accumbens_area from 62 --> 63 rescaling Left_VentralDC from 87 --> 94 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 57 rescaling Right_Lateral_Ventricle from 13 --> 8 rescaling Right_Inf_Lat_Vent from 25 --> 23 rescaling Right_Cerebellum_White_Matter from 87 --> 89 rescaling Right_Cerebellum_Cortex from 59 --> 59 rescaling Right_Thalamus_Proper from 85 --> 89 rescaling Right_Caudate from 62 --> 73 rescaling Right_Putamen from 80 --> 78 rescaling Right_Pallidum from 97 --> 96 rescaling Right_Hippocampus from 53 --> 55 rescaling Right_Amygdala from 55 --> 62 rescaling Right_Accumbens_area from 65 --> 71 rescaling Right_VentralDC from 86 --> 92 rescaling Fifth_Ventricle from 40 --> 19 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 44 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 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zkaufman Exp $ Linux web-virtual-machine 4.15.0-96-generic #97~16.04.1-Ubuntu SMP Wed Apr 1 03:03:31 UTC 2020 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/web/freesurver/test/MRI/subjects02/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 web-virtual-machine machine x86_64 user web 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 2020��� 04��� 29��� ��������� 05:35:58 CST Ended at 2020��� 04��� 29��� ��������� 05:36:05 CST Apas2aseg-Run-Time-Sec 7 apas2aseg Done #-------------------------------------------- #@# ASeg Stats 2020��� 04��� 29��� ��������� 05:36:05 CST /home/web/freesurver/test/MRI/subjects02 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/ASegStatsLUT.txt --subject subjects02 $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/ASegStatsLUT.txt --subject subjects02 sysname Linux hostname web-virtual-machine machine x86_64 user web UseRobust 0 atlas_icv (eTIV) = 1386977 mm^3 (det: 1.404569 ) Computing euler number orig.nofix lheno = -34, rheno = -26 orig.nofix lhholes = 18, rhholes = 14 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 233522.426 233230.000 diff= 292.4 pctdiff= 0.125 rhCtxGM: 237118.332 237065.000 diff= 53.3 pctdiff= 0.022 lhCtxWM: 212468.541 212507.000 diff= -38.5 pctdiff=-0.018 rhCtxWM: 216002.146 216507.000 diff= -504.9 pctdiff=-0.234 SubCortGMVol 56659.000 SupraTentVol 971298.444 (970013.000) diff=1285.444 pctdiff=0.132 SupraTentVolNotVent 957286.444 (956001.000) diff=1285.444 pctdiff=0.134 BrainSegVol 1096253.000 (1094128.000) diff=2125.000 pctdiff=0.194 BrainSegVolNotVent 1079201.000 (1078896.444) diff=304.556 pctdiff=0.028 BrainSegVolNotVent 1079201.000 CerebellumVol 123093.000 VentChorVol 14012.000 3rd4th5thCSF 3040.000 CSFVol 915.000, OptChiasmVol 107.000 MaskVol 1523756.000 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 2020��� 04��� 29��� ��������� 05:39:31 CST /home/web/freesurver/test/MRI/subjects02 mri_aparc2aseg --s subjects02 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /home/web/freesurver/test/MRI subject subjects02 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /home/web/freesurver/test/MRI/subjects02/mri/aparc+aseg.mgz Reading lh white surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading lh pial surface /home/web/freesurver/test/MRI/subjects02/surf/lh.pial Loading lh annotations from /home/web/freesurver/test/MRI/subjects02/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/web/freesurver/test/MRI/subjects02/surf/rh.white Reading rh pial surface /home/web/freesurver/test/MRI/subjects02/surf/rh.pial Loading rh annotations from /home/web/freesurver/test/MRI/subjects02/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/web/freesurver/test/MRI/subjects02/mri/ribbon.mgz Loading filled from /home/web/freesurver/test/MRI/subjects02/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 7785 vertices from left hemi Ripped 7443 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/web/freesurver/test/MRI/subjects02/mri/aseg.mgz Loading Ctx Seg File /home/web/freesurver/test/MRI/subjects02/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 = 895619 Used brute-force search on 301 voxels Fixing Parahip LH WM Found 4 clusters 0 k 29.000000 1 k 1.000000 2 k 1712.000000 3 k 1.000000 Fixing Parahip RH WM Found 8 clusters 0 k 2.000000 1 k 1.000000 2 k 1.000000 3 k 3.000000 4 k 2.000000 5 k 1634.000000 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 subjects02 --surf-wm-vol --ctab /usr/local/freesurfer/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 subjects02 --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname web-virtual-machine machine x86_64 user web UseRobust 0 atlas_icv (eTIV) = 1386977 mm^3 (det: 1.404569 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 233522.426 233230.000 diff= 292.4 pctdiff= 0.125 rhCtxGM: 237118.332 237065.000 diff= 53.3 pctdiff= 0.022 lhCtxWM: 212468.541 212507.000 diff= -38.5 pctdiff=-0.018 rhCtxWM: 216002.146 216507.000 diff= -504.9 pctdiff=-0.234 SubCortGMVol 56659.000 SupraTentVol 971298.444 (970013.000) diff=1285.444 pctdiff=0.132 SupraTentVolNotVent 957286.444 (956001.000) diff=1285.444 pctdiff=0.134 BrainSegVol 1096253.000 (1094128.000) diff=2125.000 pctdiff=0.194 BrainSegVolNotVent 1079201.000 (1078896.444) diff=304.556 pctdiff=0.028 BrainSegVolNotVent 1079201.000 CerebellumVol 123093.000 VentChorVol 14012.000 3rd4th5thCSF 3040.000 CSFVol 915.000, OptChiasmVol 107.000 MaskVol 1523756.000 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/web/freesurver/test/MRI/subjects02/label #-------------------------------------------- #@# BA_exvivo Labels lh 2020��� 04��� 29��� ��������� 05:50:45 CST mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.BA1_exvivo.label --trgsubject subjects02 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 300 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4429 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.BA2_exvivo.label --trgsubject subjects02 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 458 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8367 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.BA3a_exvivo.label --trgsubject subjects02 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 123 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4200 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.BA3b_exvivo.label --trgsubject subjects02 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 299 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6282 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.BA4a_exvivo.label --trgsubject subjects02 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 327 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6111 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.BA4p_exvivo.label --trgsubject subjects02 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 209 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4279 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.BA6_exvivo.label --trgsubject subjects02 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 871 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14460 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.BA44_exvivo.label --trgsubject subjects02 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 237 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4418 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.BA45_exvivo.label --trgsubject subjects02 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 412 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3834 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.V1_exvivo.label --trgsubject subjects02 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 954 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5595 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.V2_exvivo.label --trgsubject subjects02 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 1973 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 10087 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.MT_exvivo.label --trgsubject subjects02 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 369 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2387 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject subjects02 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 225 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1515 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject subjects02 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 238 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1437 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject subjects02 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 69 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1083 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject subjects02 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 205 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2297 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject subjects02 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 36 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1540 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject subjects02 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 134 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2130 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject subjects02 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 127 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2446 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject subjects02 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 56 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1605 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject subjects02 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 410 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7445 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject subjects02 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 119 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2031 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject subjects02 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 198 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1349 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject subjects02 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 682 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4087 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject subjects02 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 883 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4217 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject subjects02 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 85 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 598 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject subjects02 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 98 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 568 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject subjects02 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 127920 Number of reverse mapping hits = 98 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 548 mri_label2label: Done mris_label2annot --s subjects02 --hemi lh --ctab /usr/local/freesurfer/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/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/web/freesurver/test/MRI/subjects02/label cmdline mris_label2annot --s subjects02 --hemi lh --ctab /usr/local/freesurfer/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 web-virtual-machine machine x86_64 user web subject subjects02 hemi lh SUBJECTS_DIR /home/web/freesurver/test/MRI ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /home/web/freesurver/test/MRI/subjects02/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 88785 unhit vertices Writing annot to /home/web/freesurver/test/MRI/subjects02/label/lh.BA_exvivo.annot mris_label2annot --s subjects02 --hemi lh --ctab /usr/local/freesurfer/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/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/web/freesurver/test/MRI/subjects02/label cmdline mris_label2annot --s subjects02 --hemi lh --ctab /usr/local/freesurfer/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 web-virtual-machine machine x86_64 user web subject subjects02 hemi lh SUBJECTS_DIR /home/web/freesurver/test/MRI ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /home/web/freesurver/test/MRI/subjects02/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 104526 unhit vertices Writing annot to /home/web/freesurver/test/MRI/subjects02/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 subjects02 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /home/web/freesurver/test/MRI/subjects02/mri/wm.mgz... reading input surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white... reading input pial surface /home/web/freesurver/test/MRI/subjects02/surf/lh.pial... reading input white surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 237539 Total vertex volume 233281 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/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) = 1386977 mm^3 (det: 1.404569 ) lhCtxGM: 233522.426 233230.000 diff= 292.4 pctdiff= 0.125 rhCtxGM: 237118.332 237065.000 diff= 53.3 pctdiff= 0.022 lhCtxWM: 212468.541 212507.000 diff= -38.5 pctdiff=-0.018 rhCtxWM: 216002.146 216507.000 diff= -504.9 pctdiff=-0.234 SubCortGMVol 56659.000 SupraTentVol 971298.444 (970013.000) diff=1285.444 pctdiff=0.132 SupraTentVolNotVent 957286.444 (956001.000) diff=1285.444 pctdiff=0.134 BrainSegVol 1096253.000 (1094128.000) diff=2125.000 pctdiff=0.194 BrainSegVolNotVent 1079201.000 (1078896.444) diff=304.556 pctdiff=0.028 BrainSegVolNotVent 1079201.000 CerebellumVol 123093.000 VentChorVol 14012.000 3rd4th5thCSF 3040.000 CSFVol 915.000, OptChiasmVol 107.000 MaskVol 1523756.000 1166 717 2128 2.348 0.438 0.130 0.029 16 1.3 BA1_exvivo 4003 2710 6214 2.249 0.526 0.123 0.023 40 3.8 BA2_exvivo 1061 704 1009 1.713 0.418 0.131 0.025 10 1.0 BA3a_exvivo 2351 1560 3263 1.811 0.624 0.113 0.021 26 2.1 BA3b_exvivo 1631 921 3301 2.985 0.489 0.084 0.016 10 0.9 BA4a_exvivo 1260 777 1986 2.595 0.464 0.081 0.019 6 1.0 BA4p_exvivo 8908 5817 19979 2.911 0.592 0.107 0.019 74 6.7 BA6_exvivo 2209 1522 4482 2.595 0.416 0.127 0.023 28 2.1 BA44_exvivo 2698 1838 5949 2.650 0.556 0.123 0.024 33 2.4 BA45_exvivo 3070 2123 3311 1.618 0.426 0.161 0.044 49 5.7 V1_exvivo 7166 4808 10075 2.015 0.490 0.152 0.035 109 9.9 V2_exvivo 1961 1312 3704 2.600 0.574 0.138 0.031 29 2.4 MT_exvivo 758 461 2207 3.693 0.737 0.092 0.021 7 0.5 perirhinal_exvivo 893 643 3021 3.584 0.668 0.147 0.032 13 1.2 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab subjects02 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /home/web/freesurver/test/MRI/subjects02/mri/wm.mgz... reading input surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white... reading input pial surface /home/web/freesurver/test/MRI/subjects02/surf/lh.pial... reading input white surface /home/web/freesurver/test/MRI/subjects02/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 237539 Total vertex volume 233281 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/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) = 1386977 mm^3 (det: 1.404569 ) lhCtxGM: 233522.426 233230.000 diff= 292.4 pctdiff= 0.125 rhCtxGM: 237118.332 237065.000 diff= 53.3 pctdiff= 0.022 lhCtxWM: 212468.541 212507.000 diff= -38.5 pctdiff=-0.018 rhCtxWM: 216002.146 216507.000 diff= -504.9 pctdiff=-0.234 SubCortGMVol 56659.000 SupraTentVol 971298.444 (970013.000) diff=1285.444 pctdiff=0.132 SupraTentVolNotVent 957286.444 (956001.000) diff=1285.444 pctdiff=0.134 BrainSegVol 1096253.000 (1094128.000) diff=2125.000 pctdiff=0.194 BrainSegVolNotVent 1079201.000 (1078896.444) diff=304.556 pctdiff=0.028 BrainSegVolNotVent 1079201.000 CerebellumVol 123093.000 VentChorVol 14012.000 3rd4th5thCSF 3040.000 CSFVol 915.000, OptChiasmVol 107.000 MaskVol 1523756.000 740 445 1256 2.246 0.452 0.138 0.035 12 1.0 BA1_exvivo 1737 1141 2770 2.252 0.519 0.116 0.022 16 1.6 BA2_exvivo 888 592 799 1.701 0.393 0.130 0.026 8 0.9 BA3a_exvivo 1536 1015 1655 1.558 0.380 0.102 0.016 14 1.1 BA3b_exvivo 1591 903 3185 3.022 0.438 0.071 0.013 6 0.8 BA4a_exvivo 1027 654 1555 2.472 0.435 0.088 0.020 5 0.8 BA4p_exvivo 5042 3213 11092 2.906 0.601 0.112 0.021 44 4.1 BA6_exvivo 1408 976 2935 2.563 0.458 0.130 0.025 20 1.4 BA44_exvivo 1146 763 2812 2.743 0.634 0.131 0.026 16 1.0 BA45_exvivo 3249 2238 3562 1.628 0.435 0.159 0.043 50 6.0 V1_exvivo 3636 2412 4692 1.934 0.446 0.164 0.042 64 5.9 V2_exvivo 503 359 823 2.461 0.425 0.142 0.029 7 0.6 MT_exvivo 397 244 1349 3.789 0.682 0.073 0.016 2 0.2 perirhinal_exvivo 494 353 1472 3.507 0.751 0.138 0.023 6 0.4 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh 2020��� 04��� 29��� ��������� 05:55:58 CST mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.BA1_exvivo.label --trgsubject subjects02 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 321 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4283 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.BA2_exvivo.label --trgsubject subjects02 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 442 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7129 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.BA3a_exvivo.label --trgsubject subjects02 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 129 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4109 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.BA3b_exvivo.label --trgsubject subjects02 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 317 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4839 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.BA4a_exvivo.label --trgsubject subjects02 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 485 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6232 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.BA4p_exvivo.label --trgsubject subjects02 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 240 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4713 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.BA6_exvivo.label --trgsubject subjects02 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 707 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12963 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.BA44_exvivo.label --trgsubject subjects02 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 401 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7313 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.BA45_exvivo.label --trgsubject subjects02 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 469 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 5824 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.V1_exvivo.label --trgsubject subjects02 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 1040 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5767 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.V2_exvivo.label --trgsubject subjects02 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 1986 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10002 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.MT_exvivo.label --trgsubject subjects02 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 392 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2324 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject subjects02 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 119 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1157 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject subjects02 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 61 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 813 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject subjects02 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 103 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 979 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject subjects02 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 141 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2829 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject subjects02 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 45 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1743 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject subjects02 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 152 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2335 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject subjects02 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 192 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1580 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject subjects02 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 60 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1549 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject subjects02 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 328 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7287 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject subjects02 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 122 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1134 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject subjects02 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 78 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1256 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject subjects02 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 661 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 3893 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject subjects02 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 981 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4418 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject subjects02 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 46 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 314 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject subjects02 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 72 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 766 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/web/freesurver/test/MRI/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject subjects02 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/web/freesurver/test/MRI/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = subjects02 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/web/freesurver/test/MRI FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /home/web/freesurver/test/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white Reading target registration /home/web/freesurver/test/MRI/subjects02/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 129541 Number of reverse mapping hits = 26 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 317 mri_label2label: Done mris_label2annot --s subjects02 --hemi rh --ctab /usr/local/freesurfer/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/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/web/freesurver/test/MRI/subjects02/label cmdline mris_label2annot --s subjects02 --hemi rh --ctab /usr/local/freesurfer/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 web-virtual-machine machine x86_64 user web subject subjects02 hemi rh SUBJECTS_DIR /home/web/freesurver/test/MRI ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /home/web/freesurver/test/MRI/subjects02/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 91322 unhit vertices Writing annot to /home/web/freesurver/test/MRI/subjects02/label/rh.BA_exvivo.annot mris_label2annot --s subjects02 --hemi rh --ctab /usr/local/freesurfer/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/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/web/freesurver/test/MRI/subjects02/label cmdline mris_label2annot --s subjects02 --hemi rh --ctab /usr/local/freesurfer/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 web-virtual-machine machine x86_64 user web subject subjects02 hemi rh SUBJECTS_DIR /home/web/freesurver/test/MRI ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /home/web/freesurver/test/MRI/subjects02/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 107942 unhit vertices Writing annot to /home/web/freesurver/test/MRI/subjects02/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 subjects02 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /home/web/freesurver/test/MRI/subjects02/mri/wm.mgz... reading input surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white... reading input pial surface /home/web/freesurver/test/MRI/subjects02/surf/rh.pial... reading input white surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 241163 Total vertex volume 237018 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/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) = 1386977 mm^3 (det: 1.404569 ) lhCtxGM: 233522.426 233230.000 diff= 292.4 pctdiff= 0.125 rhCtxGM: 237118.332 237065.000 diff= 53.3 pctdiff= 0.022 lhCtxWM: 212468.541 212507.000 diff= -38.5 pctdiff=-0.018 rhCtxWM: 216002.146 216507.000 diff= -504.9 pctdiff=-0.234 SubCortGMVol 56659.000 SupraTentVol 971298.444 (970013.000) diff=1285.444 pctdiff=0.132 SupraTentVolNotVent 957286.444 (956001.000) diff=1285.444 pctdiff=0.134 BrainSegVol 1096253.000 (1094128.000) diff=2125.000 pctdiff=0.194 BrainSegVolNotVent 1079201.000 (1078896.444) diff=304.556 pctdiff=0.028 BrainSegVolNotVent 1079201.000 CerebellumVol 123093.000 VentChorVol 14012.000 3rd4th5thCSF 3040.000 CSFVol 915.000, OptChiasmVol 107.000 MaskVol 1523756.000 1026 569 1847 2.370 0.596 0.139 0.039 18 1.7 BA1_exvivo 3379 2307 4390 1.967 0.454 0.109 0.019 24 2.5 BA2_exvivo 1089 727 1047 1.794 0.434 0.124 0.025 10 0.9 BA3a_exvivo 2091 1397 2951 1.757 0.667 0.103 0.022 22 2.1 BA3b_exvivo 1766 978 3181 2.843 0.549 0.079 0.015 8 1.0 BA4a_exvivo 1298 837 2025 2.493 0.472 0.095 0.018 7 1.0 BA4p_exvivo 7098 4610 15910 2.913 0.541 0.112 0.021 63 6.0 BA6_exvivo 3241 2222 6360 2.627 0.558 0.118 0.021 33 2.8 BA44_exvivo 3505 2432 7425 2.569 0.639 0.118 0.023 38 3.2 BA45_exvivo 3362 2285 3946 1.700 0.467 0.148 0.036 47 5.1 V1_exvivo 7345 4912 10413 2.031 0.542 0.148 0.035 107 10.4 V2_exvivo 2011 1397 3573 2.389 0.406 0.126 0.025 22 2.1 MT_exvivo 652 416 2303 4.123 0.702 0.100 0.025 6 0.6 perirhinal_exvivo 356 256 1202 3.562 0.724 0.099 0.016 2 0.2 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 subjects02 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /home/web/freesurver/test/MRI/subjects02/mri/wm.mgz... reading input surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white... reading input pial surface /home/web/freesurver/test/MRI/subjects02/surf/rh.pial... reading input white surface /home/web/freesurver/test/MRI/subjects02/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 241163 Total vertex volume 237018 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/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) = 1386977 mm^3 (det: 1.404569 ) lhCtxGM: 233522.426 233230.000 diff= 292.4 pctdiff= 0.125 rhCtxGM: 237118.332 237065.000 diff= 53.3 pctdiff= 0.022 lhCtxWM: 212468.541 212507.000 diff= -38.5 pctdiff=-0.018 rhCtxWM: 216002.146 216507.000 diff= -504.9 pctdiff=-0.234 SubCortGMVol 56659.000 SupraTentVol 971298.444 (970013.000) diff=1285.444 pctdiff=0.132 SupraTentVolNotVent 957286.444 (956001.000) diff=1285.444 pctdiff=0.134 BrainSegVol 1096253.000 (1094128.000) diff=2125.000 pctdiff=0.194 BrainSegVolNotVent 1079201.000 (1078896.444) diff=304.556 pctdiff=0.028 BrainSegVolNotVent 1079201.000 CerebellumVol 123093.000 VentChorVol 14012.000 3rd4th5thCSF 3040.000 CSFVol 915.000, OptChiasmVol 107.000 MaskVol 1523756.000 701 380 1231 2.345 0.589 0.130 0.031 10 0.8 BA1_exvivo 1843 1248 2444 1.923 0.483 0.102 0.021 13 1.8 BA2_exvivo 960 649 831 1.746 0.374 0.129 0.024 8 0.9 BA3a_exvivo 1640 1094 1751 1.510 0.446 0.093 0.017 16 1.3 BA3b_exvivo 1165 574 2270 3.125 0.547 0.077 0.016 6 0.7 BA4a_exvivo 1022 670 1584 2.509 0.496 0.090 0.019 4 0.8 BA4p_exvivo 4501 2904 9910 2.865 0.532 0.114 0.022 40 4.1 BA6_exvivo 876 606 2148 2.903 0.561 0.137 0.028 13 1.1 BA44_exvivo 883 631 2259 2.706 0.783 0.123 0.026 9 1.0 BA45_exvivo 3195 2156 3607 1.669 0.470 0.146 0.036 46 4.8 V1_exvivo 3894 2599 5518 1.972 0.536 0.155 0.037 59 6.1 V2_exvivo 285 202 580 2.423 0.338 0.124 0.023 3 0.4 MT_exvivo 384 251 1502 4.280 0.629 0.068 0.012 2 0.1 perirhinal_exvivo 250 170 852 3.651 0.655 0.105 0.020 2 0.2 entorhinal_exvivo Started at 2020��� 04��� 28��� ��������� 20:36:55 CST Ended at 2020��� 04��� 29��� ��������� 06:01:19 CST #@#%# recon-all-run-time-hours 9.407 recon-all -s subjects02 finished without error at 2020��� 04��� 29��� ��������� 06:01:19 CST