Tue Feb 5 10:05:20 EST 2019 /users/zli/test/fs/a003 /users/zli/Applications/freesurfer/bin/recon-all -i /users/zli/test/T1/a003.nii.gz -s a003 -sd /users/zli/test/fs -all subjid a003 setenv SUBJECTS_DIR /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Actual FREESURFER_HOME /users/zli/Applications/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux compute-104 2.6.32-696.18.7.el6.x86_64 #1 SMP Thu Dec 28 20:15:47 EST 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize 10485760 kbytes datasize unlimited stacksize 262144 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse 4194304 kbytes descriptors 65536 memorylocked unlimited maxproc 514939 total used free shared buffers cached Mem: 131852184 84664284 47187900 8 463268 54145776 -/+ buffers/cache: 30055240 101796944 Swap: 11999228 4407824 7591404 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:20-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:20-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/02/05-15:05:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/02/05-15:05:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/02/05-15:05:22-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/02/05-15:05:22-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/02/05-15:05:22-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/02/05-15:05:22-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/02/05-15:05:22-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:22-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:22-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/02/05-15:05:22-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:23-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:23-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:23-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:23-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:23-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:23-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/02/05-15:05:23-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:23-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:24-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:24-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/02/05-15:05:24-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:24-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/02/05-15:05:24-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:24-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:24-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:24-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:25-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:25-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:25-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:25-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:25-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:25-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:25-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/02/05-15:05:25-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: zli Machine: compute-104 Platform: Linux PlatformVersion: 2.6.32-696.18.7.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /users/zli/Applications/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 /users/zli/Applications/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /users/zli/test/fs/a003 mri_convert /users/zli/test/T1/a003.nii.gz /users/zli/test/fs/a003/mri/orig/001.mgz mri_convert.bin /users/zli/test/T1/a003.nii.gz /users/zli/test/fs/a003/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /users/zli/test/T1/a003.nii.gz... WARNING: hdr.dim[4] = 0 (nframes), setting to 1 TR=6.66, 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) writing to /users/zli/test/fs/a003/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Tue Feb 5 10:05:39 EST 2019 Found 1 runs /users/zli/test/fs/a003/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /users/zli/test/fs/a003/mri/orig/001.mgz /users/zli/test/fs/a003/mri/rawavg.mgz /users/zli/test/fs/a003 mri_convert /users/zli/test/fs/a003/mri/rawavg.mgz /users/zli/test/fs/a003/mri/orig.mgz --conform mri_convert.bin /users/zli/test/fs/a003/mri/rawavg.mgz /users/zli/test/fs/a003/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /users/zli/test/fs/a003/mri/rawavg.mgz... TR=6.66, 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 /users/zli/test/fs/a003/mri/orig.mgz... mri_add_xform_to_header -c /users/zli/test/fs/a003/mri/transforms/talairach.xfm /users/zli/test/fs/a003/mri/orig.mgz /users/zli/test/fs/a003/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Feb 5 10:05:48 EST 2019 /users/zli/test/fs/a003/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /users/zli/test/fs/a003/mri /users/zli/Applications/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 compute-104 2.6.32-696.18.7.el6.x86_64 #1 SMP Thu Dec 28 20:15:47 EST 2017 x86_64 x86_64 x86_64 GNU/Linux Tue Feb 5 10:05:48 EST 2019 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.12111 /users/zli/test/fs/a003/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12111/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.12111/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=6.66, 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.12111/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Feb 5 10:05:50 EST 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.12111/nu0.mnc ./tmp.mri_nu_correct.mni.12111/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12111/0/ -iterations 1000 -distance 50 [zli@compute-104:/users/zli/test/fs/a003/mri/] [2019-02-05 10:05:50] running: /users/zli/Applications/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.12111/0/ ./tmp.mri_nu_correct.mni.12111/nu0.mnc ./tmp.mri_nu_correct.mni.12111/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 Number of iterations: 31 CV of field change: 0.000986727 mri_convert ./tmp.mri_nu_correct.mni.12111/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.12111/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.12111/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... Tue Feb 5 10:06:53 EST 2019 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Tue Feb 5 10:06:53 EST 2019 Ended at Tue Feb 5 10:07:27 EST 2019 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue Feb 5 10:07:29 EST 2019 /users/zli/test/fs/a003/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6878, pval=0.4932 >= threshold=0.0050) awk -f /users/zli/Applications/freesurfer/bin/extract_talairach_avi_QA.awk /users/zli/test/fs/a003/mri/transforms/talairach_avi.log tal_QC_AZS /users/zli/test/fs/a003/mri/transforms/talairach_avi.log TalAviQA: 0.98091 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Tue Feb 5 10:07:29 EST 2019 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /users/zli/test/fs/a003/mri /users/zli/Applications/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 compute-104 2.6.32-696.18.7.el6.x86_64 #1 SMP Thu Dec 28 20:15:47 EST 2017 x86_64 x86_64 x86_64 GNU/Linux Tue Feb 5 10:07:29 EST 2019 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.12845 /users/zli/test/fs/a003/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12845/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.12845/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=6.66, 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.12845/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Feb 5 10:07:32 EST 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.12845/nu0.mnc ./tmp.mri_nu_correct.mni.12845/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12845/0/ [zli@compute-104:/users/zli/test/fs/a003/mri/] [2019-02-05 10:07:32] running: /users/zli/Applications/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.12845/0/ ./tmp.mri_nu_correct.mni.12845/nu0.mnc ./tmp.mri_nu_correct.mni.12845/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 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./tmp.mri_nu_correct.mni.12845/nu1.mnc ./tmp.mri_nu_correct.mni.12845/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.12845/1/ [zli@compute-104:/users/zli/test/fs/a003/mri/] [2019-02-05 10:08:15] running: /users/zli/Applications/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.12845/1/ ./tmp.mri_nu_correct.mni.12845/nu1.mnc ./tmp.mri_nu_correct.mni.12845/nu2.imp 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: 11 CV of field change: 0.000919272 mri_binarize --i ./tmp.mri_nu_correct.mni.12845/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.12845/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /users/zli/test/fs/a003/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.12845/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.12845/ones.mgz sysname Linux hostname compute-104 machine x86_64 user zli input ./tmp.mri_nu_correct.mni.12845/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.12845/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.12845/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.12845/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12845/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.12845/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.12845/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12845/input.mean.dat sysname Linux hostname compute-104 machine x86_64 user zli UseRobust 0 Loading ./tmp.mri_nu_correct.mni.12845/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.12845/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.12845/ones.mgz --i ./tmp.mri_nu_correct.mni.12845/nu2.mnc --sum ./tmp.mri_nu_correct.mni.12845/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12845/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.12845/ones.mgz --i ./tmp.mri_nu_correct.mni.12845/nu2.mnc --sum ./tmp.mri_nu_correct.mni.12845/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12845/output.mean.dat sysname Linux hostname compute-104 machine x86_64 user zli UseRobust 0 Loading ./tmp.mri_nu_correct.mni.12845/ones.mgz Loading ./tmp.mri_nu_correct.mni.12845/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.12845/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.12845/nu2.mnc ./tmp.mri_nu_correct.mni.12845/nu2.mnc mul .99924267605650951586 Saving result to './tmp.mri_nu_correct.mni.12845/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.12845/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.12845/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.12845/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 8 seconds. mapping ( 7, 113) to ( 3, 110) Tue Feb 5 10:09:28 EST 2019 mri_nu_correct.mni done mri_add_xform_to_header -c /users/zli/test/fs/a003/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue Feb 5 10:09:30 EST 2019 /users/zli/test/fs/a003/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 1.01219 -0.03394 -0.03995 1.39548; 0.01518 1.12741 0.05866 -46.93456; 0.05701 0.02874 1.12004 -3.98128; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 20 Starting OpenSpline(): npoints = 20 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 72 (72), valley at 37 (37) csf peak at 37, setting threshold to 60 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 74 (74), valley at 37 (37) csf peak at 38, setting threshold to 62 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 56 seconds. #-------------------------------------------- #@# Skull Stripping Tue Feb 5 10:11:26 EST 2019 /users/zli/test/fs/a003/mri mri_em_register -rusage /users/zli/test/fs/a003/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /users/zli/Applications/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 '/users/zli/Applications/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=10.0 skull bounding box = (46, 41, 29) --> (214, 215, 215) using (102, 99, 122) as brain centroid... mean wm in atlas = 108, using box (81,78,99) --> (122, 120,144) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 107 +- 5.2 after smoothing, mri peak at 108, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.440 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.428126 @ (-9.091, 9.091, -9.091) max log p = -4.262265 @ (4.545, -13.636, -4.545) max log p = -4.239851 @ (2.273, 2.273, 2.273) max log p = -4.217765 @ (-3.409, 3.409, 5.682) max log p = -4.185891 @ (1.705, -0.568, -2.841) max log p = -4.180317 @ (-0.284, 0.284, 0.284) Found translation: (-4.3, 0.9, -8.2): log p = -4.180 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.980, old_max_log_p =-4.180 (thresh=-4.2) 1.00000 0.00000 0.00000 -4.26137; 0.00000 1.23625 0.00000 -25.03503; 0.00000 0.00000 1.15000 -26.11291; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.972, old_max_log_p =-3.980 (thresh=-4.0) 1.00000 0.00000 0.00000 -4.26137; 0.00000 1.32897 0.00000 -37.57573; 0.00000 0.00000 1.15000 -26.11291; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.972, old_max_log_p =-3.972 (thresh=-4.0) 1.00000 0.00000 0.00000 -4.26137; 0.00000 1.32897 0.00000 -37.57573; 0.00000 0.00000 1.15000 -26.11291; 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=-3.877, old_max_log_p =-3.972 (thresh=-4.0) 1.01766 0.03965 0.04064 -16.99769; -0.03209 1.25188 0.06979 -33.12091; -0.03272 -0.08687 1.14692 -11.64412; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.877, old_max_log_p =-3.877 (thresh=-3.9) 1.01766 0.03965 0.04064 -16.99769; -0.03209 1.25188 0.06979 -33.12091; -0.03272 -0.08687 1.14692 -11.64412; 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=-3.841, old_max_log_p =-3.877 (thresh=-3.9) 1.01894 0.01856 0.04890 -15.74711; -0.01522 1.25744 0.06132 -35.50480; -0.04107 -0.07646 1.14307 -11.04515; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.841, old_max_log_p =-3.841 (thresh=-3.8) 1.01894 0.01856 0.04890 -15.74711; -0.01522 1.25744 0.06132 -35.50480; -0.04107 -0.07646 1.14307 -11.04515; 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 1.01894 0.01856 0.04890 -15.74711; -0.01522 1.25744 0.06132 -35.50480; -0.04107 -0.07646 1.14307 -11.04515; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.01894 0.01856 0.04890 -15.74711; -0.01522 1.25744 0.06132 -35.50480; -0.04107 -0.07646 1.14307 -11.04515; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.01894 0.01856 0.04890 -15.74711; -0.01522 1.25744 0.06132 -35.50480; -0.04107 -0.07646 1.14307 -11.04515; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.841 (old=-4.440) transform before final EM align: 1.01894 0.01856 0.04890 -15.74711; -0.01522 1.25744 0.06132 -35.50480; -0.04107 -0.07646 1.14307 -11.04515; 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 1.01894 0.01856 0.04890 -15.74711; -0.01522 1.25744 0.06132 -35.50480; -0.04107 -0.07646 1.14307 -11.04515; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.01894 0.01856 0.04890 -15.74711; -0.01522 1.25744 0.06132 -35.50480; -0.04107 -0.07646 1.14307 -11.04515; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.3 tol 0.000000 final transform: 1.01894 0.01856 0.04890 -15.74711; -0.01522 1.25744 0.06132 -35.50480; -0.04107 -0.07646 1.14307 -11.04515; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1097.597139 mri_em_register stimesec 1.829721 mri_em_register ru_maxrss 611760 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157544 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 148912 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 39 mri_em_register ru_nivcsw 110918 registration took 18 minutes and 21 seconds. mri_watershed -rusage /users/zli/test/fs/a003/touch/rusage.mri_watershed.dat -T1 -brain_atlas /users/zli/Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=130 y=116 z=122 r=73 first estimation of the main basin volume: 1671683 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=110, y=100, z=87, Imax=255 CSF=20, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=7845934313 voxels, voxel volume =1.000 = 7845934313 mmm3 = 7845934.080 cm3 done. PostAnalyze...Basin Prior 3 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=130,y=120, z=117, r=8861 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=5, CSF_MAX=22 , nb = 45422 RIGHT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=19 , nb = -1036494832 LEFT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=21 , nb = 1101214415 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=23 , nb = 1061074913 LEFT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=22 , nb = 1074085204 OTHER CSF_MIN=0, CSF_intensity=4, CSF_MAX=22 , nb = 1071846592 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 22, 36, 50, 65 after analyzing : 22, 45, 50, 50 RIGHT_CER before analyzing : 19, 25, 42, 82 after analyzing : 19, 36, 42, 47 LEFT_CER before analyzing : 21, 29, 44, 75 after analyzing : 21, 39, 44, 48 RIGHT_BRAIN before analyzing : 23, 37, 50, 65 after analyzing : 23, 45, 50, 50 LEFT_BRAIN before analyzing : 22, 35, 49, 66 after analyzing : 22, 44, 49, 49 OTHER before analyzing : 22, 18, 0, 93 after analyzing : 18, 22, 25, 39 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...65 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.010 curvature mean = 69.852, std = 5.474 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 6.76, sigma = 9.29 after rotation: sse = 6.76, sigma = 9.29 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 6.92, its var is 7.19 before Erosion-Dilatation 3.67% of inacurate vertices after Erosion-Dilatation 3.96% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...43 iterations mri_strip_skull: done peeling brain Brain Size = 1624227 voxels, voxel volume = 1.000 mm3 = 1624227 mmm3 = 1624.227 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 19.967964 mri_watershed stimesec 0.434933 mri_watershed ru_maxrss 825184 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 212272 mri_watershed ru_majflt 2 mri_watershed ru_nswap 0 mri_watershed ru_inblock 8040 mri_watershed ru_oublock 2584 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 123 mri_watershed ru_nivcsw 2118 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Tue Feb 5 10:30:10 EST 2019 /users/zli/test/fs/a003/mri mri_em_register -rusage /users/zli/test/fs/a003/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /users/zli/Applications/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 '/users/zli/Applications/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=19.1 skull bounding box = (59, 60, 45) --> (202, 173, 201) using (107, 98, 123) as brain centroid... mean wm in atlas = 107, using box (89,84,104) --> (124, 111,142) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 4.5 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -3.993 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.939226 @ (-9.091, -9.091, -9.091) max log p = -3.649076 @ (4.545, 4.545, -4.545) max log p = -3.649076 @ (0.000, 0.000, 0.000) max log p = -3.634938 @ (-1.136, 3.409, 5.682) max log p = -3.616741 @ (0.568, -0.568, -0.568) max log p = -3.605603 @ (-0.852, -0.284, 0.284) Found translation: (-6.0, -2.0, -8.2): log p = -3.606 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.548, old_max_log_p =-3.606 (thresh=-3.6) 1.00000 0.00000 0.00000 -5.96591; 0.00000 1.07500 0.00000 -11.08454; 0.00000 0.00000 1.07500 -16.76487; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.548, old_max_log_p =-3.548 (thresh=-3.5) 1.00000 0.00000 0.00000 -5.96591; 0.00000 1.07500 0.00000 -11.08454; 0.00000 0.00000 1.07500 -16.76487; 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=-3.343, old_max_log_p =-3.548 (thresh=-3.5) 0.99732 -0.07027 0.03517 0.66518; 0.06786 1.11292 0.00000 -22.81364; -0.03326 0.00234 1.09457 -18.67825; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.342, old_max_log_p =-3.343 (thresh=-3.3) 1.01602 -0.07159 0.03583 -1.69866; 0.06548 1.09155 0.03514 -24.05957; -0.03546 -0.03407 1.09398 -12.08729; 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=-3.310, old_max_log_p =-3.342 (thresh=-3.3) 1.01747 -0.07139 0.02693 -1.82302; 0.06556 1.09283 0.03518 -25.16615; -0.02710 -0.03462 1.09296 -13.00497; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.310, old_max_log_p =-3.310 (thresh=-3.3) 1.01747 -0.07139 0.02693 -1.82302; 0.06556 1.09283 0.03518 -25.16615; -0.02710 -0.03462 1.09296 -13.00497; 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 1.01747 -0.07139 0.02693 -1.82302; 0.06556 1.09283 0.03518 -25.16615; -0.02710 -0.03462 1.09296 -13.00497; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.01747 -0.07139 0.02693 -1.82302; 0.06556 1.09283 0.03518 -25.16615; -0.02710 -0.03462 1.09296 -13.00497; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.01747 -0.07139 0.02693 -1.82302; 0.06556 1.09283 0.03518 -25.16615; -0.02710 -0.03462 1.09296 -13.00497; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.310 (old=-3.993) transform before final EM align: 1.01747 -0.07139 0.02693 -1.82302; 0.06556 1.09283 0.03518 -25.16615; -0.02710 -0.03462 1.09296 -13.00497; 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 1.01747 -0.07139 0.02693 -1.82302; 0.06556 1.09283 0.03518 -25.16615; -0.02710 -0.03462 1.09296 -13.00497; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.01747 -0.07139 0.02693 -1.82302; 0.06556 1.09283 0.03518 -25.16615; -0.02710 -0.03462 1.09296 -13.00497; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 009: -log(p) = 3.9 after pass:transform: ( 1.02, -0.07, 0.03, -1.82) ( 0.07, 1.09, 0.04, -25.17) ( -0.03, -0.03, 1.09, -13.00) dfp_em_step_func: 010: -log(p) = 3.9 after pass:transform: ( 1.02, -0.07, 0.03, -1.82) ( 0.07, 1.09, 0.04, -25.17) ( -0.03, -0.03, 1.09, -13.00) pass 2 through quasi-newton minimization... outof QuasiNewtonEMA: 012: -log(p) = 3.9 tol 0.000000 final transform: 1.01777 -0.07100 0.02736 -1.82302; 0.06603 1.09319 0.03558 -25.16615; -0.02713 -0.03469 1.09286 -13.00497; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 828.515046 mri_em_register stimesec 1.456778 mri_em_register ru_maxrss 601008 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 159307 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 140152 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 41 mri_em_register ru_nivcsw 84091 registration took 13 minutes and 51 seconds. #-------------------------------------- #@# CA Normalize Tue Feb 5 10:44:02 EST 2019 /users/zli/test/fs/a003/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /users/zli/Applications/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 '/users/zli/Applications/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=21.1 skull bounding box = (59, 60, 45) --> (202, 173, 200) using (107, 98, 123) as brain centroid... mean wm in atlas = 107, using box (89,84,104) --> (124, 111,142) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 4.5 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 using 246344 sample points... INFO: compute sample coordinates transform 1.01777 -0.07100 0.02736 -1.82302; 0.06603 1.09319 0.03558 -25.16615; -0.02713 -0.03469 1.09286 -13.00497; 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 (131, 58, 43) --> (197, 166, 197) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 0 of 582 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (67, 60, 43) --> (132, 170, 197) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 566 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (135, 138, 65) --> (184, 175, 114) Left_Cerebellum_White_Matter: limiting intensities to 93.0 --> 132.0 0 of 9 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (92, 138, 62) --> (135, 178, 115) Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 12 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (117, 130, 96) --> (152, 194, 125) Brain_Stem: limiting intensities to 89.0 --> 132.0 0 of 14 (0.0%) samples deleted using 1183 total control points for intensity normalization... bias field = 0.980 +- 0.048 11 of 1183 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (131, 58, 43) --> (197, 166, 197) Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 0 of 803 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (67, 60, 43) --> (132, 170, 197) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 132.0 0 of 743 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (135, 138, 65) --> (184, 175, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 77 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (92, 138, 62) --> (135, 178, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 64 (1.6%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (117, 130, 96) --> (152, 194, 125) Brain_Stem: limiting intensities to 88.0 --> 132.0 23 of 141 (16.3%) samples deleted using 1828 total control points for intensity normalization... bias field = 1.001 +- 0.061 3 of 1773 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (131, 58, 43) --> (197, 166, 197) Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 0 of 845 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (67, 60, 43) --> (132, 170, 197) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 1 of 806 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (135, 138, 65) --> (184, 175, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 38 of 90 (42.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (92, 138, 62) --> (135, 178, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 15 of 49 (30.6%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (117, 130, 96) --> (152, 194, 125) Brain_Stem: limiting intensities to 88.0 --> 132.0 59 of 121 (48.8%) samples deleted using 1911 total control points for intensity normalization... bias field = 1.010 +- 0.043 5 of 1768 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 34 seconds. #-------------------------------------- #@# CA Reg Tue Feb 5 10:45:36 EST 2019 /users/zli/test/fs/a003/mri mri_ca_register -rusage /users/zli/test/fs/a003/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /users/zli/Applications/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 '/users/zli/Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.22 (predicted orig area = 6.5) 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=0.833, neg=0, invalid=762 0001: dt=254.539597, rms=0.753 (9.601%), neg=0, invalid=762 0002: dt=165.431933, rms=0.724 (3.863%), neg=0, invalid=762 0003: dt=417.056311, rms=0.705 (2.662%), neg=0, invalid=762 0004: dt=110.976000, rms=0.699 (0.818%), neg=0, invalid=762 0005: dt=887.808000, rms=0.690 (1.294%), neg=0, invalid=762 0006: dt=443.904000, rms=0.686 (0.578%), neg=0, invalid=762 0007: dt=129.472000, rms=0.685 (0.141%), neg=0, invalid=762 0008: dt=129.472000, rms=0.685 (0.065%), neg=0, invalid=762 0009: dt=129.472000, rms=0.684 (0.103%), neg=0, invalid=762 0010: dt=129.472000, rms=0.683 (0.160%), neg=0, invalid=762 0011: dt=129.472000, rms=0.682 (0.218%), neg=0, invalid=762 0012: dt=129.472000, rms=0.680 (0.275%), neg=0, invalid=762 0013: dt=129.472000, rms=0.678 (0.268%), neg=0, invalid=762 0014: dt=129.472000, rms=0.676 (0.222%), neg=0, invalid=762 0015: dt=129.472000, rms=0.675 (0.184%), neg=0, invalid=762 0016: dt=129.472000, rms=0.674 (0.162%), neg=0, invalid=762 0017: dt=129.472000, rms=0.673 (0.127%), neg=0, invalid=762 0018: dt=129.472000, rms=0.672 (0.147%), neg=0, invalid=762 0019: dt=129.472000, rms=0.671 (0.157%), neg=0, invalid=762 0020: dt=129.472000, rms=0.670 (0.140%), neg=0, invalid=762 0021: dt=129.472000, rms=0.669 (0.138%), neg=0, invalid=762 0022: dt=129.472000, rms=0.668 (0.114%), neg=0, invalid=762 0023: dt=129.472000, rms=0.668 (0.107%), neg=0, invalid=762 0024: dt=369.920000, rms=0.668 (0.014%), neg=0, invalid=762 0025: dt=369.920000, rms=0.667 (0.093%), neg=0, invalid=762 0026: dt=369.920000, rms=0.667 (0.000%), neg=0, invalid=762 0027: dt=369.920000, rms=0.666 (0.140%), neg=0, invalid=762 0028: dt=369.920000, rms=0.665 (0.116%), neg=0, invalid=762 0029: dt=369.920000, rms=0.665 (0.103%), neg=0, invalid=762 0030: dt=295.936000, rms=0.664 (0.028%), neg=0, invalid=762 0031: dt=295.936000, rms=0.664 (-0.067%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.665, neg=0, invalid=762 0032: dt=295.936000, rms=0.662 (0.440%), neg=0, invalid=762 0033: dt=129.472000, rms=0.662 (0.047%), neg=0, invalid=762 0034: dt=129.472000, rms=0.662 (0.036%), neg=0, invalid=762 0035: dt=129.472000, rms=0.661 (0.056%), neg=0, invalid=762 0036: dt=129.472000, rms=0.661 (0.062%), neg=0, invalid=762 0037: dt=129.472000, rms=0.661 (0.062%), neg=0, invalid=762 0038: dt=129.472000, rms=0.660 (0.075%), neg=0, invalid=762 0039: dt=129.472000, rms=0.659 (0.085%), neg=0, invalid=762 0040: dt=129.472000, rms=0.659 (0.087%), neg=0, invalid=762 0041: dt=129.472000, rms=0.658 (0.079%), neg=0, invalid=762 0042: dt=129.472000, rms=0.658 (0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.664, neg=0, invalid=762 0043: dt=79.183183, rms=0.661 (0.459%), neg=0, invalid=762 0044: dt=497.664000, rms=0.646 (2.216%), neg=0, invalid=762 0045: dt=70.780842, rms=0.643 (0.572%), neg=0, invalid=762 0046: dt=331.776000, rms=0.635 (1.186%), neg=0, invalid=762 0047: dt=36.288000, rms=0.633 (0.243%), neg=0, invalid=762 0048: dt=36.288000, rms=0.633 (0.044%), neg=0, invalid=762 0049: dt=36.288000, rms=0.633 (-0.012%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.634, neg=0, invalid=762 0050: dt=145.152000, rms=0.630 (0.683%), neg=0, invalid=762 0051: dt=82.944000, rms=0.629 (0.153%), neg=0, invalid=762 0052: dt=82.944000, rms=0.628 (0.180%), neg=0, invalid=762 0053: dt=82.944000, rms=0.626 (0.251%), neg=0, invalid=762 0054: dt=82.944000, rms=0.624 (0.286%), neg=0, invalid=762 0055: dt=82.944000, rms=0.622 (0.306%), neg=0, invalid=762 0056: dt=82.944000, rms=0.620 (0.361%), neg=0, invalid=762 0057: dt=82.944000, rms=0.618 (0.364%), neg=0, invalid=762 0058: dt=82.944000, rms=0.616 (0.340%), neg=0, invalid=762 0059: dt=82.944000, rms=0.614 (0.276%), neg=0, invalid=762 0060: dt=82.944000, rms=0.612 (0.323%), neg=0, invalid=762 0061: dt=82.944000, rms=0.610 (0.296%), neg=0, invalid=762 0062: dt=82.944000, rms=0.609 (0.226%), neg=0, invalid=762 0063: dt=82.944000, rms=0.608 (0.198%), neg=0, invalid=762 0064: dt=82.944000, rms=0.606 (0.185%), neg=0, invalid=762 0065: dt=82.944000, rms=0.605 (0.229%), neg=0, invalid=762 0066: dt=82.944000, rms=0.604 (0.184%), neg=0, invalid=762 0067: dt=82.944000, rms=0.603 (0.140%), neg=0, invalid=762 0068: dt=82.944000, rms=0.602 (0.122%), neg=0, invalid=762 0069: dt=82.944000, rms=0.602 (0.128%), neg=0, invalid=762 0070: dt=82.944000, rms=0.601 (0.123%), neg=0, invalid=762 0071: dt=82.944000, rms=0.600 (0.120%), neg=0, invalid=762 0072: dt=20.736000, rms=0.600 (0.001%), neg=0, invalid=762 0073: dt=20.736000, rms=0.600 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.622, neg=0, invalid=762 0074: dt=0.000000, rms=0.621 (0.107%), neg=0, invalid=762 0075: dt=0.000000, rms=0.621 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.622, neg=0, invalid=762 0076: dt=0.000000, rms=0.621 (0.107%), neg=0, invalid=762 0077: dt=0.000000, rms=0.621 (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=0.686, neg=0, invalid=762 0078: dt=5.152542, rms=0.667 (2.741%), neg=0, invalid=762 0079: dt=2.304000, rms=0.666 (0.101%), neg=0, invalid=762 0080: dt=2.304000, rms=0.666 (-0.036%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.667, neg=0, invalid=762 0081: dt=0.000703, rms=0.666 (0.102%), neg=0, invalid=762 0082: dt=0.000000, rms=0.666 (0.000%), neg=0, invalid=762 0083: dt=0.150000, rms=0.666 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.730, neg=0, invalid=762 0084: dt=1.536000, rms=0.723 (0.865%), neg=0, invalid=762 0085: dt=2.069767, rms=0.717 (0.903%), neg=0, invalid=762 0086: dt=0.448000, rms=0.717 (0.049%), neg=0, invalid=762 0087: dt=0.448000, rms=0.716 (0.029%), neg=0, invalid=762 0088: dt=0.448000, rms=0.716 (0.015%), neg=0, invalid=762 0089: dt=0.448000, rms=0.716 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.717, neg=0, invalid=762 0090: dt=1.792000, rms=0.714 (0.407%), neg=0, invalid=762 0091: dt=0.080000, rms=0.714 (0.004%), neg=0, invalid=762 0092: dt=0.080000, rms=0.714 (-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=0.670, neg=0, invalid=762 0093: dt=0.824398, rms=0.653 (2.587%), neg=0, invalid=762 0094: dt=0.080000, rms=0.652 (0.135%), neg=0, invalid=762 0095: dt=0.080000, rms=0.652 (-0.086%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.652, neg=0, invalid=762 0096: dt=0.028000, rms=0.652 (0.123%), neg=0, invalid=762 0097: dt=0.005000, rms=0.652 (0.001%), neg=0, invalid=762 0098: dt=0.005000, rms=0.652 (-0.002%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.12478 (25) Left_Lateral_Ventricle (4): linear fit = 1.33 x + 0.0 (1406 voxels, overlap=0.577) Left_Lateral_Ventricle (4): linear fit = 1.33 x + 0.0 (1406 voxels, peak = 26), gca=26.5 gca peak = 0.15565 (16) mri peak = 0.10832 (27) Right_Lateral_Ventricle (43): linear fit = 1.59 x + 0.0 (1080 voxels, overlap=0.386) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1080 voxels, peak = 25), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.12124 (101) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (961 voxels, overlap=0.988) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (961 voxels, peak = 100), gca=100.3 gca peak = 0.20183 (93) mri peak = 0.08813 (100) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (818 voxels, overlap=1.004) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (818 voxels, peak = 97), gca=97.2 gca peak = 0.21683 (55) mri peak = 0.07974 (69) Right_Hippocampus (53): linear fit = 1.25 x + 0.0 (698 voxels, overlap=0.025) Right_Hippocampus (53): linear fit = 1.25 x + 0.0 (698 voxels, peak = 68), gca=68.5 gca peak = 0.30730 (58) mri peak = 0.09855 (69) Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (658 voxels, overlap=0.097) Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (658 voxels, peak = 68), gca=67.6 gca peak = 0.11430 (101) mri peak = 0.11505 (105) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (61876 voxels, overlap=0.549) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (61876 voxels, peak = 107), gca=106.6 gca peak = 0.12076 (102) mri peak = 0.11280 (106) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (65719 voxels, overlap=0.656) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (65719 voxels, peak = 106), gca=105.6 gca peak = 0.14995 (59) mri peak = 0.05569 (68) Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (23476 voxels, overlap=0.434) Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (23476 voxels, peak = 68), gca=67.6 gca peak = 0.15082 (58) mri peak = 0.05370 (66) Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (23322 voxels, overlap=0.385) Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (23322 voxels, peak = 66), gca=66.4 gca peak = 0.14161 (67) mri peak = 0.10519 (76) Right_Caudate (50): linear fit = 1.12 x + 0.0 (578 voxels, overlap=0.202) Right_Caudate (50): linear fit = 1.12 x + 0.0 (578 voxels, peak = 75), gca=74.7 gca peak = 0.15243 (71) mri peak = 0.10377 (79) Left_Caudate (11): linear fit = 1.09 x + 0.0 (1064 voxels, overlap=0.652) Left_Caudate (11): linear fit = 1.09 x + 0.0 (1064 voxels, peak = 77), gca=77.0 gca peak = 0.13336 (57) mri peak = 0.05035 (67) Left_Cerebellum_Cortex (8): linear fit = 1.22 x + 0.0 (12730 voxels, overlap=0.319) Left_Cerebellum_Cortex (8): linear fit = 1.22 x + 0.0 (12730 voxels, peak = 69), gca=69.3 gca peak = 0.13252 (56) mri peak = 0.03837 (68) Right_Cerebellum_Cortex (47): linear fit = 1.24 x + 0.0 (14673 voxels, overlap=0.013) Right_Cerebellum_Cortex (47): linear fit = 1.24 x + 0.0 (14673 voxels, peak = 69), gca=69.2 gca peak = 0.18181 (84) mri peak = 0.07837 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (7529 voxels, overlap=0.633) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (7529 voxels, peak = 89), gca=88.6 gca peak = 0.20573 (83) mri peak = 0.04870 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (6438 voxels, overlap=0.543) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (6438 voxels, peak = 88), gca=87.6 gca peak = 0.21969 (57) mri peak = 0.09510 (67) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (370 voxels, overlap=0.062) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (370 voxels, peak = 66), gca=66.4 gca peak = 0.39313 (56) mri peak = 0.08961 (69) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (492 voxels, overlap=0.056) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (492 voxels, peak = 67), gca=67.5 gca peak = 0.14181 (85) mri peak = 0.05162 (101) Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (5431 voxels, overlap=0.764) Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (5431 voxels, peak = 93), gca=93.1 gca peak = 0.11978 (83) mri peak = 0.04761 (85) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (4166 voxels, overlap=0.838) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (4166 voxels, peak = 90), gca=90.1 gca peak = 0.13399 (79) mri peak = 0.06396 (86) Left_Putamen (12): linear fit = 1.11 x + 0.0 (2436 voxels, overlap=0.603) Left_Putamen (12): linear fit = 1.11 x + 0.0 (2436 voxels, peak = 87), gca=87.3 gca peak = 0.14159 (79) mri peak = 0.05542 (89) Right_Putamen (51): linear fit = 1.14 x + 0.0 (2421 voxels, overlap=0.652) Right_Putamen (51): linear fit = 1.14 x + 0.0 (2421 voxels, peak = 90), gca=90.5 gca peak = 0.10025 (80) mri peak = 0.08944 (88) Brain_Stem (16): linear fit = 1.10 x + 0.0 (11079 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (11079 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.08395 (94) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1240 voxels, overlap=0.536) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1240 voxels, peak = 93), gca=93.3 gca peak = 0.12801 (89) mri peak = 0.08373 (90) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1393 voxels, overlap=0.668) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1393 voxels, peak = 93), gca=93.0 gca peak = 0.20494 (23) mri peak = 0.44444 (27) gca peak = 0.15061 (21) mri peak = 0.12503 (25) Fourth_Ventricle (15): linear fit = 1.41 x + 0.0 (317 voxels, overlap=0.635) Fourth_Ventricle (15): linear fit = 1.41 x + 0.0 (317 voxels, peak = 30), gca=29.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.18 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 1.41 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=0.652, neg=0, invalid=762 0099: dt=103.990794, rms=0.641 (1.637%), neg=0, invalid=762 0100: dt=295.936000, rms=0.636 (0.820%), neg=0, invalid=762 0101: dt=295.936000, rms=0.633 (0.521%), neg=0, invalid=762 0102: dt=110.976000, rms=0.631 (0.271%), neg=0, invalid=762 0103: dt=295.936000, rms=0.630 (0.164%), neg=0, invalid=762 0104: dt=129.472000, rms=0.629 (0.156%), neg=0, invalid=762 0105: dt=369.920000, rms=0.628 (0.163%), neg=0, invalid=762 0106: dt=129.472000, rms=0.627 (0.134%), neg=0, invalid=762 0107: dt=129.472000, rms=0.627 (0.067%), neg=0, invalid=762 0108: dt=517.888000, rms=0.625 (0.178%), neg=0, invalid=762 0109: dt=110.976000, rms=0.625 (0.102%), neg=0, invalid=762 0110: dt=443.904000, rms=0.624 (0.125%), neg=0, invalid=762 0111: dt=92.480000, rms=0.623 (0.079%), neg=0, invalid=762 0112: dt=3551.232000, rms=0.620 (0.566%), neg=0, invalid=762 0113: dt=110.976000, rms=0.619 (0.124%), neg=0, invalid=762 0114: dt=221.952000, rms=0.619 (0.040%), neg=0, invalid=762 0115: dt=221.952000, rms=0.619 (0.028%), neg=0, invalid=762 0116: dt=221.952000, rms=0.618 (0.084%), neg=0, invalid=762 0117: dt=221.952000, rms=0.618 (0.058%), neg=0, invalid=762 0118: dt=221.952000, rms=0.617 (0.110%), neg=0, invalid=762 0119: dt=221.952000, rms=0.617 (0.094%), neg=0, invalid=762 0120: dt=221.952000, rms=0.616 (0.077%), neg=0, invalid=762 0121: dt=221.952000, rms=0.616 (0.101%), neg=0, invalid=762 0122: dt=221.952000, rms=0.615 (0.061%), neg=0, invalid=762 0123: dt=221.952000, rms=0.615 (0.072%), neg=0, invalid=762 0124: dt=221.952000, rms=0.614 (0.066%), neg=0, invalid=762 0125: dt=221.952000, rms=0.614 (0.058%), neg=0, invalid=762 0126: dt=221.952000, rms=0.614 (0.064%), neg=0, invalid=762 0127: dt=221.952000, rms=0.613 (0.052%), neg=0, invalid=762 0128: dt=221.952000, rms=0.613 (0.071%), neg=0, invalid=762 0129: dt=221.952000, rms=0.612 (0.065%), neg=0, invalid=762 0130: dt=221.952000, rms=0.612 (0.049%), neg=0, invalid=762 0131: dt=221.952000, rms=0.612 (0.051%), neg=0, invalid=762 0132: dt=221.952000, rms=0.612 (0.046%), neg=0, invalid=762 0133: dt=221.952000, rms=0.611 (0.055%), neg=0, invalid=762 0134: dt=221.952000, rms=0.611 (0.043%), neg=0, invalid=762 0135: dt=221.952000, rms=0.611 (0.039%), neg=0, invalid=762 0136: dt=221.952000, rms=0.610 (0.043%), neg=0, invalid=762 0137: dt=221.952000, rms=0.610 (0.033%), neg=0, invalid=762 0138: dt=221.952000, rms=0.610 (0.042%), neg=0, invalid=762 0139: dt=221.952000, rms=0.610 (0.036%), neg=0, invalid=762 0140: dt=221.952000, rms=0.610 (0.032%), neg=0, invalid=762 0141: dt=221.952000, rms=0.609 (0.033%), neg=0, invalid=762 0142: dt=221.952000, rms=0.609 (0.035%), neg=0, invalid=762 0143: dt=221.952000, rms=0.609 (0.035%), neg=0, invalid=762 0144: dt=221.952000, rms=0.609 (0.032%), neg=0, invalid=762 0145: dt=221.952000, rms=0.608 (0.035%), neg=0, invalid=762 0146: dt=221.952000, rms=0.608 (0.032%), neg=0, invalid=762 0147: dt=221.952000, rms=0.608 (0.027%), neg=0, invalid=762 0148: dt=221.952000, rms=0.608 (0.034%), neg=0, invalid=762 0149: dt=221.952000, rms=0.608 (0.030%), neg=0, invalid=762 0150: dt=221.952000, rms=0.608 (0.026%), neg=0, invalid=762 0151: dt=221.952000, rms=0.607 (0.034%), neg=0, invalid=762 0152: dt=221.952000, rms=0.607 (0.028%), neg=0, invalid=762 0153: dt=221.952000, rms=0.607 (0.016%), neg=0, invalid=762 0154: dt=221.952000, rms=0.607 (0.024%), neg=0, invalid=762 0155: dt=221.952000, rms=0.607 (0.029%), neg=0, invalid=762 0156: dt=221.952000, rms=0.607 (0.021%), neg=0, invalid=762 0157: dt=221.952000, rms=0.607 (0.021%), neg=0, invalid=762 0158: dt=129.472000, rms=0.606 (0.007%), neg=0, invalid=762 0159: dt=129.472000, rms=0.606 (0.000%), neg=0, invalid=762 0160: dt=129.472000, rms=0.606 (0.002%), neg=0, invalid=762 0161: dt=129.472000, rms=0.606 (0.005%), neg=0, invalid=762 0162: dt=129.472000, rms=0.606 (0.005%), neg=0, invalid=762 0163: dt=129.472000, rms=0.606 (0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.607, neg=0, invalid=762 0164: dt=443.904000, rms=0.605 (0.339%), neg=0, invalid=762 0165: dt=92.480000, rms=0.604 (0.050%), neg=0, invalid=762 0166: dt=92.480000, rms=0.604 (0.006%), neg=0, invalid=762 0167: dt=92.480000, rms=0.604 (-0.006%), 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 0168: dt=121.263158, rms=0.604 (0.405%), neg=0, invalid=762 0169: dt=248.832000, rms=0.595 (1.384%), neg=0, invalid=762 0170: dt=56.347826, rms=0.593 (0.336%), neg=0, invalid=762 0171: dt=497.664000, rms=0.589 (0.718%), neg=0, invalid=762 0172: dt=79.728199, rms=0.584 (0.886%), neg=0, invalid=762 0173: dt=65.488372, rms=0.583 (0.193%), neg=0, invalid=762 0174: dt=145.152000, rms=0.581 (0.252%), neg=0, invalid=762 0175: dt=77.986755, rms=0.580 (0.169%), neg=0, invalid=762 0176: dt=103.680000, rms=0.579 (0.163%), neg=0, invalid=762 0177: dt=82.944000, rms=0.578 (0.138%), neg=0, invalid=762 0178: dt=103.680000, rms=0.578 (0.134%), neg=0, invalid=762 0179: dt=82.944000, rms=0.577 (0.135%), neg=0, invalid=762 0180: dt=82.944000, rms=0.576 (0.113%), neg=0, invalid=762 0181: dt=103.680000, rms=0.575 (0.126%), neg=0, invalid=762 0182: dt=82.944000, rms=0.575 (0.111%), neg=0, invalid=762 0183: dt=82.944000, rms=0.574 (0.112%), neg=0, invalid=762 0184: dt=103.680000, rms=0.574 (0.098%), neg=0, invalid=762 0185: dt=82.944000, rms=0.573 (0.114%), neg=0, invalid=762 0186: dt=82.944000, rms=0.572 (0.091%), neg=0, invalid=762 0187: dt=82.944000, rms=0.572 (0.102%), neg=0, invalid=762 0188: dt=82.944000, rms=0.571 (0.082%), neg=0, invalid=762 0189: dt=124.416000, rms=0.571 (0.112%), neg=0, invalid=762 0190: dt=36.288000, rms=0.570 (0.065%), neg=0, invalid=762 0191: dt=580.608000, rms=0.569 (0.325%), neg=0, invalid=762 0192: dt=36.288000, rms=0.567 (0.216%), neg=0, invalid=762 0193: dt=124.416000, rms=0.567 (0.078%), neg=0, invalid=762 0194: dt=36.288000, rms=0.567 (0.051%), neg=0, invalid=762 0195: dt=580.608000, rms=0.565 (0.215%), neg=0, invalid=762 0196: dt=36.288000, rms=0.564 (0.169%), neg=0, invalid=762 0197: dt=124.416000, rms=0.564 (0.072%), neg=0, invalid=762 0198: dt=36.288000, rms=0.564 (0.044%), neg=0, invalid=762 0199: dt=36.288000, rms=0.564 (0.022%), neg=0, invalid=762 0200: dt=36.288000, rms=0.563 (0.037%), neg=0, invalid=762 0201: dt=36.288000, rms=0.563 (0.051%), neg=0, invalid=762 0202: dt=36.288000, rms=0.563 (0.070%), neg=0, invalid=762 0203: dt=36.288000, rms=0.562 (0.082%), neg=0, invalid=762 0204: dt=36.288000, rms=0.562 (0.088%), neg=0, invalid=762 0205: dt=36.288000, rms=0.561 (0.092%), neg=0, invalid=762 0206: dt=36.288000, rms=0.561 (0.098%), neg=0, invalid=762 0207: dt=36.288000, rms=0.560 (0.094%), neg=0, invalid=762 0208: dt=36.288000, rms=0.560 (0.102%), neg=0, invalid=762 0209: dt=36.288000, rms=0.559 (0.107%), neg=0, invalid=762 0210: dt=36.288000, rms=0.558 (0.103%), neg=0, invalid=762 0211: dt=36.288000, rms=0.558 (0.101%), neg=0, invalid=762 0212: dt=36.288000, rms=0.557 (0.103%), neg=0, invalid=762 0213: dt=36.288000, rms=0.557 (0.098%), neg=0, invalid=762 0214: dt=36.288000, rms=0.556 (0.093%), neg=0, invalid=762 0215: dt=36.288000, rms=0.556 (0.094%), neg=0, invalid=762 0216: dt=36.288000, rms=0.555 (0.092%), neg=0, invalid=762 0217: dt=36.288000, rms=0.555 (0.088%), neg=0, invalid=762 0218: dt=36.288000, rms=0.554 (0.084%), neg=0, invalid=762 0219: dt=36.288000, rms=0.554 (0.084%), neg=0, invalid=762 0220: dt=36.288000, rms=0.553 (0.079%), neg=0, invalid=762 0221: dt=36.288000, rms=0.553 (0.072%), neg=0, invalid=762 0222: dt=36.288000, rms=0.553 (0.070%), neg=0, invalid=762 0223: dt=36.288000, rms=0.552 (0.073%), neg=0, invalid=762 0224: dt=36.288000, rms=0.552 (0.074%), neg=0, invalid=762 0225: dt=36.288000, rms=0.551 (0.071%), neg=0, invalid=762 0226: dt=36.288000, rms=0.551 (0.067%), neg=0, invalid=762 0227: dt=36.288000, rms=0.551 (0.066%), neg=0, invalid=762 0228: dt=36.288000, rms=0.550 (0.065%), neg=0, invalid=762 0229: dt=36.288000, rms=0.550 (0.062%), neg=0, invalid=762 0230: dt=36.288000, rms=0.550 (0.007%), neg=0, invalid=762 0231: dt=36.288000, rms=0.550 (0.012%), neg=0, invalid=762 0232: dt=36.288000, rms=0.550 (0.012%), neg=0, invalid=762 0233: dt=36.288000, rms=0.550 (0.017%), neg=0, invalid=762 0234: dt=36.288000, rms=0.550 (0.022%), neg=0, invalid=762 0235: dt=36.288000, rms=0.549 (0.024%), neg=0, invalid=762 0236: dt=36.288000, rms=0.549 (0.027%), neg=0, invalid=762 0237: dt=36.288000, rms=0.549 (0.029%), neg=0, invalid=762 0238: dt=36.288000, rms=0.549 (0.032%), neg=0, invalid=762 0239: dt=36.288000, rms=0.549 (0.033%), neg=0, invalid=762 0240: dt=36.288000, rms=0.549 (0.035%), neg=0, invalid=762 0241: dt=36.288000, rms=0.548 (0.037%), neg=0, invalid=762 0242: dt=36.288000, rms=0.548 (0.039%), neg=0, invalid=762 0243: dt=36.288000, rms=0.548 (0.038%), neg=0, invalid=762 0244: dt=36.288000, rms=0.548 (0.036%), neg=0, invalid=762 0245: dt=36.288000, rms=0.548 (0.039%), neg=0, invalid=762 0246: dt=36.288000, rms=0.547 (0.040%), neg=0, invalid=762 0247: dt=36.288000, rms=0.547 (0.042%), neg=0, invalid=762 0248: dt=36.288000, rms=0.547 (0.006%), neg=0, invalid=762 0249: dt=36.288000, rms=0.547 (0.010%), neg=0, invalid=762 0250: dt=36.288000, rms=0.547 (0.011%), neg=0, invalid=762 0251: dt=36.288000, rms=0.547 (0.016%), neg=0, invalid=762 0252: dt=36.288000, rms=0.547 (0.005%), neg=0, invalid=762 0253: dt=0.567000, rms=0.547 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.547, neg=0, invalid=762 0254: dt=145.152000, rms=0.544 (0.628%), neg=0, invalid=762 0255: dt=36.288000, rms=0.544 (0.063%), neg=0, invalid=762 0256: dt=124.416000, rms=0.543 (0.055%), neg=0, invalid=762 0257: dt=145.152000, rms=0.543 (0.112%), neg=0, invalid=762 0258: dt=36.288000, rms=0.542 (0.024%), neg=0, invalid=762 0259: dt=36.288000, rms=0.542 (0.015%), neg=0, invalid=762 0260: dt=36.288000, rms=0.542 (0.021%), neg=0, invalid=762 0261: dt=36.288000, rms=0.542 (0.035%), neg=0, invalid=762 0262: dt=36.288000, rms=0.542 (0.048%), neg=0, invalid=762 0263: dt=36.288000, rms=0.542 (0.060%), neg=0, invalid=762 0264: dt=36.288000, rms=0.541 (0.057%), neg=0, invalid=762 0265: dt=36.288000, rms=0.541 (0.054%), neg=0, invalid=762 0266: dt=36.288000, rms=0.541 (0.048%), neg=0, invalid=762 0267: dt=36.288000, rms=0.540 (0.040%), neg=0, invalid=762 0268: dt=36.288000, rms=0.540 (0.040%), neg=0, invalid=762 0269: dt=36.288000, rms=0.540 (0.045%), neg=0, invalid=762 0270: dt=36.288000, rms=0.540 (0.052%), neg=0, invalid=762 0271: dt=36.288000, rms=0.539 (0.050%), neg=0, invalid=762 0272: dt=36.288000, rms=0.539 (0.045%), neg=0, invalid=762 0273: dt=36.288000, rms=0.539 (0.046%), neg=0, invalid=762 0274: dt=36.288000, rms=0.539 (0.035%), neg=0, invalid=762 0275: dt=36.288000, rms=0.539 (0.039%), neg=0, invalid=762 0276: dt=36.288000, rms=0.538 (0.044%), neg=0, invalid=762 0277: dt=36.288000, rms=0.538 (0.047%), neg=0, invalid=762 0278: dt=36.288000, rms=0.538 (0.048%), neg=0, invalid=762 0279: dt=36.288000, rms=0.538 (0.045%), neg=0, invalid=762 0280: dt=36.288000, rms=0.537 (0.043%), neg=0, invalid=762 0281: dt=36.288000, rms=0.537 (0.038%), neg=0, invalid=762 0282: dt=36.288000, rms=0.537 (0.031%), neg=0, invalid=762 0283: dt=36.288000, rms=0.537 (0.038%), neg=0, invalid=762 0284: dt=36.288000, rms=0.537 (0.040%), neg=0, invalid=762 0285: dt=36.288000, rms=0.536 (0.038%), neg=0, invalid=762 0286: dt=36.288000, rms=0.536 (0.027%), neg=0, invalid=762 0287: dt=36.288000, rms=0.536 (0.025%), neg=0, invalid=762 0288: dt=36.288000, rms=0.536 (0.034%), neg=0, invalid=762 0289: dt=36.288000, rms=0.536 (0.032%), neg=0, invalid=762 0290: dt=36.288000, rms=0.535 (0.036%), neg=0, invalid=762 0291: dt=36.288000, rms=0.535 (0.031%), neg=0, invalid=762 0292: dt=36.288000, rms=0.535 (0.035%), neg=0, invalid=762 0293: dt=36.288000, rms=0.535 (0.031%), neg=0, invalid=762 0294: dt=36.288000, rms=0.535 (0.033%), neg=0, invalid=762 0295: dt=36.288000, rms=0.535 (0.031%), neg=0, invalid=762 0296: dt=36.288000, rms=0.534 (0.029%), neg=0, invalid=762 0297: dt=36.288000, rms=0.534 (0.027%), neg=0, invalid=762 0298: dt=36.288000, rms=0.534 (0.027%), neg=0, invalid=762 0299: dt=36.288000, rms=0.534 (0.027%), neg=0, invalid=762 0300: dt=36.288000, rms=0.534 (0.028%), neg=0, invalid=762 0301: dt=36.288000, rms=0.534 (0.028%), neg=0, invalid=762 0302: dt=36.288000, rms=0.534 (0.024%), neg=0, invalid=762 0303: dt=36.288000, rms=0.533 (0.024%), neg=0, invalid=762 0304: dt=497.664000, rms=0.533 (0.035%), neg=0, invalid=762 0305: dt=36.288000, rms=0.533 (0.012%), neg=0, invalid=762 0306: dt=36.288000, rms=0.533 (0.003%), neg=0, invalid=762 0307: dt=36.288000, rms=0.533 (0.001%), neg=0, invalid=762 0308: dt=36.288000, rms=0.533 (0.002%), neg=0, invalid=762 0309: dt=36.288000, rms=0.533 (0.008%), neg=0, invalid=762 0310: dt=36.288000, rms=0.533 (0.012%), neg=0, invalid=762 0311: dt=36.288000, rms=0.533 (0.016%), neg=0, invalid=762 0312: dt=36.288000, rms=0.533 (0.015%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.542, neg=0, invalid=762 0313: dt=11.200000, rms=0.541 (0.185%), neg=0, invalid=762 0314: dt=25.600000, rms=0.540 (0.116%), neg=0, invalid=762 0315: dt=44.800000, rms=0.538 (0.361%), neg=0, invalid=762 0316: dt=128.000000, rms=0.533 (0.934%), neg=0, invalid=762 0317: dt=57.791045, rms=0.530 (0.521%), neg=0, invalid=762 0318: dt=30.924370, rms=0.528 (0.313%), neg=0, invalid=762 0319: dt=94.577778, rms=0.526 (0.419%), neg=0, invalid=762 0320: dt=19.936795, rms=0.525 (0.297%), neg=0, invalid=762 0321: dt=44.800000, rms=0.524 (0.188%), neg=0, invalid=762 0322: dt=38.400000, rms=0.523 (0.199%), neg=0, invalid=762 0323: dt=32.000000, rms=0.522 (0.129%), neg=0, invalid=762 0324: dt=38.400000, rms=0.521 (0.150%), neg=0, invalid=762 0325: dt=32.000000, rms=0.521 (0.115%), neg=0, invalid=762 0326: dt=38.400000, rms=0.520 (0.154%), neg=0, invalid=762 0327: dt=25.600000, rms=0.519 (0.092%), neg=0, invalid=762 0328: dt=44.800000, rms=0.519 (0.132%), neg=0, invalid=762 0329: dt=25.600000, rms=0.518 (0.077%), neg=0, invalid=762 0330: dt=44.800000, rms=0.518 (0.117%), neg=0, invalid=762 0331: dt=25.600000, rms=0.517 (0.079%), neg=0, invalid=762 0332: dt=44.800000, rms=0.517 (0.111%), neg=0, invalid=762 0333: dt=25.600000, rms=0.516 (0.063%), neg=0, invalid=762 0334: dt=44.800000, rms=0.516 (0.101%), neg=0, invalid=762 0335: dt=25.600000, rms=0.515 (0.065%), neg=0, invalid=762 0336: dt=44.800000, rms=0.515 (0.103%), neg=0, invalid=762 0337: dt=32.000000, rms=0.515 (0.048%), neg=0, invalid=762 0338: dt=32.000000, rms=0.514 (0.088%), neg=0, invalid=762 0339: dt=32.000000, rms=0.514 (0.124%), neg=0, invalid=762 0340: dt=32.000000, rms=0.513 (0.043%), neg=0, invalid=762 0341: dt=16.000000, rms=0.513 (0.042%), neg=0, invalid=762 0342: dt=2.000000, rms=0.513 (0.007%), neg=0, invalid=762 0343: dt=0.250000, rms=0.513 (0.000%), neg=0, invalid=762 0344: dt=0.043750, rms=0.513 (0.001%), neg=0, invalid=762 0345: dt=0.002734, rms=0.513 (0.000%), neg=0, invalid=762 0346: dt=0.001367, rms=0.513 (0.000%), neg=0, invalid=762 0347: dt=0.000684, rms=0.513 (0.000%), neg=0, invalid=762 0348: dt=0.000342, rms=0.513 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.514, neg=0, invalid=762 0349: dt=67.200000, rms=0.510 (0.746%), neg=0, invalid=762 0350: dt=19.200000, rms=0.509 (0.119%), neg=0, invalid=762 0351: dt=44.800000, rms=0.509 (0.072%), neg=0, invalid=762 0352: dt=25.600000, rms=0.508 (0.055%), neg=0, invalid=762 0353: dt=32.000000, rms=0.508 (0.088%), neg=0, invalid=762 0354: dt=11.200000, rms=0.508 (0.025%), neg=0, invalid=762 0355: dt=11.200000, rms=0.508 (0.033%), neg=0, invalid=762 0356: dt=11.200000, rms=0.508 (0.035%), neg=0, invalid=762 0357: dt=11.200000, rms=0.507 (0.054%), neg=0, invalid=762 0358: dt=11.200000, rms=0.507 (0.066%), neg=0, invalid=762 0359: dt=11.200000, rms=0.507 (0.068%), neg=0, invalid=762 0360: dt=11.200000, rms=0.506 (0.071%), neg=0, invalid=762 0361: dt=11.200000, rms=0.506 (0.070%), neg=0, invalid=762 0362: dt=11.200000, rms=0.506 (0.071%), neg=0, invalid=762 0363: dt=11.200000, rms=0.505 (0.074%), neg=0, invalid=762 0364: dt=11.200000, rms=0.505 (0.079%), neg=0, invalid=762 0365: dt=11.200000, rms=0.504 (0.088%), neg=0, invalid=762 0366: dt=11.200000, rms=0.504 (0.093%), neg=0, invalid=762 0367: dt=11.200000, rms=0.503 (0.094%), neg=0, invalid=762 0368: dt=11.200000, rms=0.503 (0.102%), neg=0, invalid=762 0369: dt=11.200000, rms=0.502 (0.099%), neg=0, invalid=762 0370: dt=11.200000, rms=0.502 (0.097%), neg=0, invalid=762 0371: dt=11.200000, rms=0.501 (0.095%), neg=0, invalid=762 0372: dt=11.200000, rms=0.501 (0.096%), neg=0, invalid=762 0373: dt=11.200000, rms=0.500 (0.093%), neg=0, invalid=762 0374: dt=11.200000, rms=0.500 (0.094%), neg=0, invalid=762 0375: dt=11.200000, rms=0.500 (0.093%), neg=0, invalid=762 0376: dt=11.200000, rms=0.499 (0.091%), neg=0, invalid=762 0377: dt=11.200000, rms=0.499 (0.087%), neg=0, invalid=762 0378: dt=11.200000, rms=0.498 (0.086%), neg=0, invalid=762 0379: dt=11.200000, rms=0.498 (0.078%), neg=0, invalid=762 0380: dt=11.200000, rms=0.497 (0.074%), neg=0, invalid=762 0381: dt=11.200000, rms=0.497 (0.068%), neg=0, invalid=762 0382: dt=11.200000, rms=0.497 (0.063%), neg=0, invalid=762 0383: dt=11.200000, rms=0.497 (0.060%), neg=0, invalid=762 0384: dt=11.200000, rms=0.496 (0.054%), neg=0, invalid=762 0385: dt=11.200000, rms=0.496 (0.049%), neg=0, invalid=762 0386: dt=11.200000, rms=0.496 (0.053%), neg=0, invalid=762 0387: dt=11.200000, rms=0.495 (0.049%), neg=0, invalid=762 0388: dt=11.200000, rms=0.495 (0.047%), neg=0, invalid=762 0389: dt=11.200000, rms=0.495 (0.045%), neg=0, invalid=762 0390: dt=11.200000, rms=0.495 (0.043%), neg=0, invalid=762 0391: dt=11.200000, rms=0.495 (0.038%), neg=0, invalid=762 0392: dt=11.200000, rms=0.494 (0.041%), neg=0, invalid=762 0393: dt=11.200000, rms=0.494 (0.042%), neg=0, invalid=762 0394: dt=11.200000, rms=0.494 (0.035%), neg=0, invalid=762 0395: dt=11.200000, rms=0.494 (0.036%), neg=0, invalid=762 0396: dt=11.200000, rms=0.494 (0.031%), neg=0, invalid=762 0397: dt=11.200000, rms=0.494 (0.026%), neg=0, invalid=762 0398: dt=11.200000, rms=0.493 (0.035%), neg=0, invalid=762 0399: dt=11.200000, rms=0.493 (0.031%), neg=0, invalid=762 0400: dt=11.200000, rms=0.493 (0.034%), neg=0, invalid=762 0401: dt=11.200000, rms=0.493 (0.029%), neg=0, invalid=762 0402: dt=11.200000, rms=0.493 (0.030%), neg=0, invalid=762 0403: dt=11.200000, rms=0.493 (0.029%), neg=0, invalid=762 0404: dt=11.200000, rms=0.493 (0.027%), neg=0, invalid=762 0405: dt=11.200000, rms=0.492 (0.029%), neg=0, invalid=762 0406: dt=11.200000, rms=0.492 (0.026%), neg=0, invalid=762 0407: dt=11.200000, rms=0.492 (0.024%), neg=0, invalid=762 0408: dt=11.200000, rms=0.492 (0.025%), neg=0, invalid=762 0409: dt=11.200000, rms=0.492 (0.021%), neg=0, invalid=762 0410: dt=11.200000, rms=0.492 (0.023%), neg=0, invalid=762 0411: dt=11.200000, rms=0.492 (0.027%), neg=0, invalid=762 0412: dt=11.200000, rms=0.492 (0.019%), neg=0, invalid=762 0413: dt=11.200000, rms=0.491 (0.020%), neg=0, invalid=762 0414: dt=11.200000, rms=0.491 (0.018%), neg=0, invalid=762 0415: dt=44.800000, rms=0.491 (0.006%), neg=0, invalid=762 0416: dt=44.800000, rms=0.491 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.511, neg=0, invalid=762 0417: dt=0.000000, rms=0.510 (0.076%), neg=0, invalid=762 0418: dt=0.000000, rms=0.510 (0.000%), neg=0, invalid=762 0419: dt=0.150000, rms=0.510 (-0.023%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.511, neg=0, invalid=762 0420: dt=0.000000, rms=0.510 (0.076%), neg=0, invalid=762 0421: dt=0.000000, rms=0.510 (0.000%), neg=0, invalid=762 0422: dt=0.150000, rms=0.510 (-0.023%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.549, neg=0, invalid=762 0423: dt=0.768000, rms=0.547 (0.315%), neg=0, invalid=762 0424: dt=0.112000, rms=0.547 (0.008%), neg=0, invalid=762 0425: dt=0.112000, rms=0.547 (0.002%), neg=0, invalid=762 0426: dt=0.112000, rms=0.547 (-0.011%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.548, neg=0, invalid=762 0427: dt=0.448000, rms=0.547 (0.128%), neg=0, invalid=762 0428: dt=0.112000, rms=0.547 (0.004%), neg=0, invalid=762 0429: dt=0.112000, rms=0.547 (0.003%), neg=0, invalid=762 0430: dt=0.112000, rms=0.547 (-0.007%), 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=0.499, neg=0, invalid=762 0431: dt=0.448000, rms=0.485 (2.683%), neg=0, invalid=762 0432: dt=0.448000, rms=0.483 (0.485%), neg=0, invalid=762 0433: dt=0.448000, rms=0.481 (0.297%), neg=0, invalid=762 0434: dt=0.384000, rms=0.481 (0.144%), neg=0, invalid=762 0435: dt=0.448000, rms=0.480 (0.136%), neg=0, invalid=762 0436: dt=0.448000, rms=0.480 (0.095%), neg=0, invalid=762 0437: dt=0.448000, rms=0.479 (0.075%), neg=0, invalid=762 0438: dt=0.448000, rms=0.479 (0.057%), neg=0, invalid=762 0439: dt=0.448000, rms=0.479 (0.046%), neg=0, invalid=762 0440: dt=0.448000, rms=0.479 (0.038%), neg=0, invalid=762 0441: dt=0.448000, rms=0.478 (0.064%), neg=0, invalid=762 0442: dt=0.448000, rms=0.478 (0.074%), neg=0, invalid=762 0443: dt=0.448000, rms=0.478 (0.069%), neg=0, invalid=762 0444: dt=0.448000, rms=0.477 (0.051%), neg=0, invalid=762 0445: dt=0.448000, rms=0.477 (0.028%), neg=0, invalid=762 0446: dt=0.448000, rms=0.477 (0.008%), neg=0, invalid=762 0447: dt=0.448000, rms=0.477 (-0.007%), neg=0, invalid=762 0448: dt=0.028000, rms=0.477 (0.000%), neg=0, invalid=762 0449: dt=0.000438, rms=0.477 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.478, neg=0, invalid=762 0450: dt=0.448000, rms=0.472 (1.160%), neg=0, invalid=762 0451: dt=0.448000, rms=0.471 (0.160%), neg=0, invalid=762 0452: dt=0.448000, rms=0.471 (0.053%), neg=0, invalid=762 0453: dt=0.448000, rms=0.471 (0.015%), neg=0, invalid=762 0454: dt=0.448000, rms=0.471 (0.008%), neg=0, invalid=762 0455: dt=0.448000, rms=0.471 (0.009%), neg=0, invalid=762 0456: dt=0.448000, rms=0.471 (-0.005%), 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=0.469, neg=0, invalid=762 0457: dt=0.000000, rms=0.469 (0.094%), neg=0, invalid=762 0458: dt=0.000000, rms=0.469 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.469, neg=0, invalid=762 0459: dt=129.472000, rms=0.469 (0.128%), neg=0, invalid=762 0460: dt=73.984000, rms=0.469 (0.005%), neg=0, invalid=762 0461: dt=73.984000, rms=0.469 (0.009%), neg=0, invalid=762 0462: dt=73.984000, rms=0.469 (0.011%), neg=0, invalid=762 0463: dt=73.984000, rms=0.469 (0.010%), neg=0, invalid=762 0464: dt=73.984000, rms=0.468 (0.013%), neg=0, invalid=762 0465: dt=73.984000, rms=0.468 (0.011%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.469, neg=0, invalid=762 0466: dt=0.000000, rms=0.468 (0.093%), neg=0, invalid=762 0467: dt=0.000000, rms=0.468 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.469, neg=0, invalid=762 0468: dt=248.832000, rms=0.467 (0.475%), neg=0, invalid=762 0469: dt=36.288000, rms=0.466 (0.056%), neg=0, invalid=762 0470: dt=36.288000, rms=0.466 (0.035%), neg=0, invalid=762 0471: dt=36.288000, rms=0.466 (0.054%), neg=0, invalid=762 0472: dt=36.288000, rms=0.466 (0.059%), neg=0, invalid=762 0473: dt=36.288000, rms=0.465 (0.068%), neg=0, invalid=762 0474: dt=36.288000, rms=0.465 (0.077%), neg=0, invalid=762 0475: dt=36.288000, rms=0.465 (0.076%), neg=0, invalid=762 0476: dt=36.288000, rms=0.464 (0.064%), neg=0, invalid=762 0477: dt=36.288000, rms=0.464 (0.005%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.465, neg=0, invalid=762 0478: dt=11.200000, rms=0.464 (0.217%), neg=0, invalid=762 0479: dt=11.200000, rms=0.464 (0.069%), neg=0, invalid=762 0480: dt=11.200000, rms=0.463 (0.043%), neg=0, invalid=762 0481: dt=11.200000, rms=0.463 (0.005%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0482: dt=11.200000, rms=0.463 (-0.076%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.464, neg=0, invalid=762 0483: dt=55.490637, rms=0.458 (1.327%), neg=0, invalid=762 0484: dt=20.465116, rms=0.456 (0.301%), neg=0, invalid=762 0485: dt=38.400000, rms=0.455 (0.211%), neg=0, invalid=762 0486: dt=38.400000, rms=0.455 (0.009%), neg=0, invalid=762 0487: dt=38.400000, rms=0.453 (0.533%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0488: dt=38.400000, rms=0.452 (0.153%), neg=0, invalid=762 0489: dt=38.400000, rms=0.450 (0.587%), neg=0, invalid=762 0490: dt=38.400000, rms=0.449 (0.039%), neg=0, invalid=762 0491: dt=38.400000, rms=0.447 (0.568%), neg=0, invalid=762 0492: dt=38.400000, rms=0.447 (0.039%), neg=0, invalid=762 0493: dt=38.400000, rms=0.445 (0.382%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0494: dt=38.400000, rms=0.445 (0.004%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0495: dt=38.400000, rms=0.444 (0.251%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0496: dt=38.400000, rms=0.443 (0.116%), neg=0, invalid=762 0497: dt=38.400000, rms=0.443 (0.158%), neg=0, invalid=762 0498: dt=38.400000, rms=0.442 (0.055%), neg=0, invalid=762 0499: dt=38.400000, rms=0.442 (0.127%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0500: dt=38.400000, rms=0.442 (0.047%), neg=0, invalid=762 0501: dt=38.400000, rms=0.441 (0.061%), neg=0, invalid=762 0502: dt=38.400000, rms=0.441 (0.062%), neg=0, invalid=762 0503: dt=38.400000, rms=0.441 (0.074%), neg=0, invalid=762 0504: dt=38.400000, rms=0.440 (0.082%), neg=0, invalid=762 0505: dt=38.400000, rms=0.440 (-0.077%), neg=0, invalid=762 0506: dt=11.200000, rms=0.440 (0.139%), neg=0, invalid=762 0507: dt=11.200000, rms=0.440 (0.052%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.445, neg=0, invalid=762 0508: dt=0.000000, rms=0.444 (0.094%), neg=0, invalid=762 0509: dt=0.000000, rms=0.444 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.445, neg=0, invalid=762 0510: dt=0.000000, rms=0.444 (0.094%), neg=0, invalid=762 0511: dt=0.000000, rms=0.444 (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=0.455, neg=0, invalid=762 0512: dt=1.024000, rms=0.454 (0.278%), neg=0, invalid=762 0513: dt=0.112000, rms=0.454 (0.004%), neg=0, invalid=762 0514: dt=0.112000, rms=0.454 (0.001%), neg=0, invalid=762 0515: dt=0.112000, rms=0.454 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.454, neg=0, invalid=762 0516: dt=1.536000, rms=0.453 (0.286%), neg=0, invalid=762 0517: dt=0.448000, rms=0.453 (0.012%), neg=0, invalid=762 0518: dt=0.448000, rms=0.453 (0.010%), neg=0, invalid=762 0519: dt=0.448000, rms=0.453 (-0.024%), 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=0.446, neg=0, invalid=762 iter 0, gcam->neg = 502 after 12 iterations, nbhd size=1, neg = 0 0520: dt=2.123602, rms=0.417 (6.433%), neg=0, invalid=762 0521: dt=0.048000, rms=0.417 (0.031%), neg=0, invalid=762 0522: dt=0.048000, rms=0.417 (-0.020%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.417, neg=0, invalid=762 0523: dt=0.080000, rms=0.417 (0.185%), neg=0, invalid=762 0524: dt=0.001750, rms=0.416 (0.004%), neg=0, invalid=762 0525: dt=0.001750, rms=0.417 (-0.001%), 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=0.403, neg=0, invalid=762 0526: dt=0.000000, rms=0.403 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.403, neg=0, invalid=762 0527: dt=18.496000, rms=0.403 (0.001%), neg=0, invalid=762 0528: dt=2.023000, rms=0.403 (0.000%), neg=0, invalid=762 0529: dt=2.023000, rms=0.403 (0.000%), neg=0, invalid=762 0530: dt=2.023000, rms=0.403 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.403, neg=0, invalid=762 0531: dt=0.000000, rms=0.403 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.403, neg=0, invalid=762 0532: dt=31.104000, rms=0.403 (0.010%), neg=0, invalid=762 0533: dt=36.288000, rms=0.403 (0.004%), neg=0, invalid=762 0534: dt=36.288000, rms=0.403 (0.004%), neg=0, invalid=762 0535: dt=36.288000, rms=0.403 (0.001%), neg=0, invalid=762 0536: dt=36.288000, rms=0.403 (-0.005%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.404, neg=0, invalid=762 0537: dt=2.800000, rms=0.404 (0.007%), neg=0, invalid=762 0538: dt=0.600000, rms=0.404 (0.000%), neg=0, invalid=762 0539: dt=0.600000, rms=0.404 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.404, neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0540: dt=85.618729, rms=0.402 (0.539%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0541: dt=25.600000, rms=0.401 (0.160%), neg=0, invalid=762 0542: dt=25.600000, rms=0.401 (0.083%), neg=0, invalid=762 0543: dt=25.600000, rms=0.400 (0.108%), neg=0, invalid=762 0544: dt=25.600000, rms=0.400 (0.151%), neg=0, invalid=762 0545: dt=25.600000, rms=0.399 (0.133%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0546: dt=25.600000, rms=0.399 (0.140%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0547: dt=25.600000, rms=0.398 (0.114%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0548: dt=25.600000, rms=0.398 (0.109%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0549: dt=32.000000, rms=0.398 (0.023%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0550: dt=32.000000, rms=0.398 (0.020%), neg=0, invalid=762 0551: dt=32.000000, rms=0.397 (0.036%), neg=0, invalid=762 0552: dt=32.000000, rms=0.397 (0.038%), neg=0, invalid=762 0553: dt=32.000000, rms=0.397 (0.048%), neg=0, invalid=762 0554: dt=32.000000, rms=0.397 (0.047%), neg=0, invalid=762 0555: dt=32.000000, rms=0.397 (0.050%), neg=0, invalid=762 0556: dt=32.000000, rms=0.396 (0.058%), neg=0, invalid=762 0557: dt=32.000000, rms=0.396 (0.060%), neg=0, invalid=762 0558: dt=32.000000, rms=0.396 (0.063%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0559: dt=32.000000, rms=0.396 (0.056%), 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 0560: dt=0.000246, rms=0.399 (0.000%), neg=0, invalid=762 0561: 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 0562: dt=4.857143, rms=0.399 (0.031%), neg=0, invalid=762 0563: dt=4.400000, rms=0.399 (0.014%), neg=0, invalid=762 0564: dt=4.400000, rms=0.399 (0.011%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0565: dt=4.400000, rms=0.399 (-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=0.405, neg=0, invalid=762 0566: dt=0.000000, rms=0.405 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.405, neg=0, invalid=762 0567: dt=0.000000, rms=0.405 (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=0.395, neg=0, invalid=762 iter 0, gcam->neg = 304 after 17 iterations, nbhd size=1, neg = 0 0568: dt=1.176471, rms=0.388 (1.722%), neg=0, invalid=762 0569: dt=0.000027, rms=0.388 (0.000%), neg=0, invalid=762 0570: dt=0.000027, rms=0.388 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.388, neg=0, invalid=762 0571: dt=0.192000, rms=0.388 (0.166%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0572: dt=0.320000, rms=0.387 (0.138%), neg=0, invalid=762 0573: dt=0.320000, rms=0.386 (0.215%), neg=0, invalid=762 iter 0, gcam->neg = 76 after 11 iterations, nbhd size=1, neg = 0 0574: dt=0.320000, rms=0.386 (0.078%), neg=0, invalid=762 iter 0, gcam->neg = 181 after 11 iterations, nbhd size=1, neg = 0 0575: dt=0.320000, rms=0.386 (-0.283%), neg=0, invalid=762 0576: dt=0.256000, rms=0.386 (0.055%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0577: dt=0.384000, rms=0.385 (0.044%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 20 minutes and 24 seconds. mri_ca_register utimesec 8402.280659 mri_ca_register stimesec 9.174605 mri_ca_register ru_maxrss 1336060 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 5003064 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 65912 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 1826 mri_ca_register ru_nivcsw 851610 FSRUNTIME@ mri_ca_register 2.3401 hours 1 threads #-------------------------------------- #@# SubCort Seg Tue Feb 5 13:06:01 EST 2019 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /users/zli/Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname compute-104 machine x86_64 setenv SUBJECTS_DIR /users/zli/test/fs cd /users/zli/test/fs/a003/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /users/zli/Applications/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 /users/zli/Applications/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 6.54 Atlas used for the 3D morph was /users/zli/Applications/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 = 0.11952 (25) Left_Lateral_Ventricle (4): linear fit = 1.30 x + 0.0 (1987 voxels, overlap=0.601) Left_Lateral_Ventricle (4): linear fit = 1.30 x + 0.0 (1987 voxels, peak = 26), gca=26.1 gca peak = 0.17677 (13) mri peak = 0.11010 (27) Right_Lateral_Ventricle (43): linear fit = 1.83 x + 0.0 (1658 voxels, overlap=0.335) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1658 voxels, peak = 24), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.12632 (101) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (665 voxels, overlap=0.961) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (665 voxels, peak = 100), gca=100.2 gca peak = 0.16930 (96) mri peak = 0.12709 (101) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (716 voxels, overlap=0.750) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (716 voxels, peak = 101), gca=101.3 gca peak = 0.24553 (55) mri peak = 0.09600 (72) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (810 voxels, overlap=0.023) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (810 voxels, peak = 67), gca=67.4 gca peak = 0.30264 (59) mri peak = 0.09882 (70) Left_Hippocampus (17): linear fit = 1.21 x + 0.0 (927 voxels, overlap=0.021) Left_Hippocampus (17): linear fit = 1.21 x + 0.0 (927 voxels, peak = 71), gca=71.1 gca peak = 0.07580 (103) mri peak = 0.12328 (105) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (43091 voxels, overlap=0.548) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (43091 voxels, peak = 106), gca=105.6 gca peak = 0.07714 (104) mri peak = 0.12280 (106) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (47803 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (47803 voxels, peak = 106), gca=105.6 gca peak = 0.09712 (58) mri peak = 0.06025 (68) Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (29188 voxels, overlap=0.447) Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (29188 voxels, peak = 66), gca=65.8 gca peak = 0.11620 (58) mri peak = 0.05763 (67) Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (28405 voxels, overlap=0.548) Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (28405 voxels, peak = 66), gca=66.4 gca peak = 0.30970 (66) mri peak = 0.10957 (79) Right_Caudate (50): linear fit = 1.17 x + 0.0 (1062 voxels, overlap=0.018) Right_Caudate (50): linear fit = 1.17 x + 0.0 (1062 voxels, peak = 78), gca=77.5 gca peak = 0.15280 (69) mri peak = 0.09945 (79) Left_Caudate (11): linear fit = 1.07 x + 0.0 (1094 voxels, overlap=0.599) Left_Caudate (11): linear fit = 1.07 x + 0.0 (1094 voxels, peak = 73), gca=73.5 gca peak = 0.13902 (56) mri peak = 0.06498 (68) Left_Cerebellum_Cortex (8): linear fit = 1.21 x + 0.0 (16288 voxels, overlap=0.331) Left_Cerebellum_Cortex (8): linear fit = 1.21 x + 0.0 (16288 voxels, peak = 67), gca=67.5 gca peak = 0.14777 (55) mri peak = 0.05816 (67) Right_Cerebellum_Cortex (47): linear fit = 1.25 x + 0.0 (16677 voxels, overlap=0.227) Right_Cerebellum_Cortex (47): linear fit = 1.25 x + 0.0 (16677 voxels, peak = 68), gca=68.5 gca peak = 0.16765 (84) mri peak = 0.12379 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (4707 voxels, overlap=0.729) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (4707 voxels, peak = 89), gca=88.6 gca peak = 0.18739 (84) mri peak = 0.11746 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (4844 voxels, overlap=0.556) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (4844 voxels, peak = 90), gca=90.3 gca peak = 0.29869 (57) mri peak = 0.11268 (71) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (448 voxels, overlap=0.057) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (448 voxels, peak = 68), gca=67.5 gca peak = 0.33601 (57) mri peak = 0.12526 (69) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (487 voxels, overlap=0.049) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (487 voxels, peak = 68), gca=67.5 gca peak = 0.11131 (90) mri peak = 0.05849 (94) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (4515 voxels, overlap=0.869) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (4515 voxels, peak = 96), gca=95.9 gca peak = 0.11793 (83) mri peak = 0.05624 (88) Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (3785 voxels, overlap=0.822) Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (3785 voxels, peak = 92), gca=91.7 gca peak = 0.08324 (81) mri peak = 0.07588 (85) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1845 voxels, overlap=0.501) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1845 voxels, peak = 90), gca=90.3 gca peak = 0.10360 (77) mri peak = 0.06483 (89) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2067 voxels, overlap=0.600) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2067 voxels, peak = 87), gca=86.6 gca peak = 0.08424 (78) mri peak = 0.08438 (84) Brain_Stem (16): linear fit = 1.07 x + 0.0 (11805 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.07 x + 0.0 (11805 voxels, peak = 83), gca=83.1 gca peak = 0.12631 (89) mri peak = 0.08120 (96) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1452 voxels, overlap=0.618) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1452 voxels, peak = 97), gca=97.5 gca peak = 0.14500 (87) mri peak = 0.07682 (96) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1500 voxels, overlap=0.843) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1500 voxels, peak = 93), gca=92.7 gca peak = 0.14975 (24) mri peak = 0.13169 (32) Third_Ventricle (14): linear fit = 1.27 x + 0.0 (120 voxels, overlap=0.570) Third_Ventricle (14): linear fit = 1.27 x + 0.0 (120 voxels, peak = 31), gca=30.6 gca peak = 0.19357 (14) mri peak = 0.15278 (24) Fourth_Ventricle (15): linear fit = 1.54 x + 0.0 (432 voxels, overlap=0.210) Fourth_Ventricle (15): linear fit = 1.54 x + 0.0 (432 voxels, peak = 22), gca=21.6 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Fourth_Ventricle = 0.19357 (14) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.18 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.36 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15813 (24) mri peak = 0.11952 (25) Left_Lateral_Ventricle (4): linear fit = 0.99 x + 0.0 (1987 voxels, overlap=0.849) Left_Lateral_Ventricle (4): linear fit = 0.99 x + 0.0 (1987 voxels, peak = 24), gca=23.6 gca peak = 0.14041 (19) mri peak = 0.11010 (27) Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (1658 voxels, overlap=0.693) Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (1658 voxels, peak = 23), gca=22.5 gca peak = 0.27131 (101) mri peak = 0.12632 (101) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (665 voxels, overlap=1.013) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (665 voxels, peak = 101), gca=101.0 gca peak = 0.15758 (101) mri peak = 0.12709 (101) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (716 voxels, overlap=1.002) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (716 voxels, peak = 100), gca=100.5 gca peak = 0.25346 (68) mri peak = 0.09600 (72) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (810 voxels, overlap=1.003) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (810 voxels, peak = 68), gca=68.0 gca peak = 0.27033 (68) mri peak = 0.09882 (70) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (927 voxels, overlap=1.003) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (927 voxels, peak = 68), gca=68.0 gca peak = 0.07610 (105) mri peak = 0.12328 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (43091 voxels, overlap=0.658) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (43091 voxels, peak = 105), gca=105.0 gca peak = 0.07820 (106) mri peak = 0.12280 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (47803 voxels, overlap=0.679) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (47803 voxels, peak = 106), gca=106.0 gca peak = 0.08623 (66) mri peak = 0.06025 (68) Left_Cerebral_Cortex (3): linear fit = 1.03 x + 0.0 (29188 voxels, overlap=0.939) Left_Cerebral_Cortex (3): linear fit = 1.03 x + 0.0 (29188 voxels, peak = 68), gca=68.3 gca peak = 0.10279 (66) mri peak = 0.05763 (67) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (28405 voxels, overlap=0.960) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (28405 voxels, peak = 66), gca=66.0 gca peak = 0.23090 (78) mri peak = 0.10957 (79) Right_Caudate (50): linear fit = 0.99 x + 0.0 (1062 voxels, overlap=1.000) Right_Caudate (50): linear fit = 0.99 x + 0.0 (1062 voxels, peak = 77), gca=76.8 gca peak = 0.12687 (73) mri peak = 0.09945 (79) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1094 voxels, overlap=1.000) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1094 voxels, peak = 73), gca=73.0 gca peak = 0.12012 (67) mri peak = 0.06498 (68) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (16288 voxels, overlap=0.973) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (16288 voxels, peak = 66), gca=66.0 gca peak = 0.12473 (68) mri peak = 0.05816 (67) Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (16677 voxels, overlap=0.985) Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (16677 voxels, peak = 66), gca=66.3 gca peak = 0.16035 (89) mri peak = 0.12379 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4707 voxels, overlap=0.946) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4707 voxels, peak = 89), gca=89.0 gca peak = 0.14974 (90) mri peak = 0.11746 (88) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4844 voxels, overlap=0.934) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4844 voxels, peak = 89), gca=88.7 gca peak = 0.28055 (69) mri peak = 0.11268 (71) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (448 voxels, overlap=1.012) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (448 voxels, peak = 69), gca=69.0 gca peak = 0.31334 (68) mri peak = 0.12526 (69) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (487 voxels, overlap=1.007) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (487 voxels, peak = 69), gca=69.0 gca peak = 0.11504 (94) mri peak = 0.05849 (94) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (4515 voxels, overlap=0.998) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (4515 voxels, peak = 93), gca=92.6 gca peak = 0.09654 (89) mri peak = 0.05624 (88) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3785 voxels, overlap=0.970) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3785 voxels, peak = 88), gca=87.7 gca peak = 0.07894 (84) mri peak = 0.07588 (85) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1845 voxels, overlap=0.890) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1845 voxels, peak = 83), gca=82.7 gca peak = 0.09171 (88) mri peak = 0.06483 (89) Right_Putamen (51): linear fit = 0.96 x + 0.0 (2067 voxels, overlap=0.964) Right_Putamen (51): linear fit = 0.96 x + 0.0 (2067 voxels, peak = 85), gca=84.9 gca peak = 0.07297 (83) mri peak = 0.08438 (84) Brain_Stem (16): linear fit = 1.02 x + 0.0 (11805 voxels, overlap=0.728) Brain_Stem (16): linear fit = 1.02 x + 0.0 (11805 voxels, peak = 85), gca=85.1 gca peak = 0.12865 (92) mri peak = 0.08120 (96) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1452 voxels, overlap=0.846) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1452 voxels, peak = 92), gca=91.5 gca peak = 0.14400 (91) mri peak = 0.07682 (96) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1500 voxels, overlap=0.932) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1500 voxels, peak = 91), gca=90.5 gca peak = 0.16783 (33) mri peak = 0.13169 (32) Third_Ventricle (14): linear fit = 0.94 x + 0.0 (120 voxels, overlap=0.901) Third_Ventricle (14): linear fit = 0.94 x + 0.0 (120 voxels, peak = 31), gca=31.2 gca peak = 0.15125 (20) mri peak = 0.15278 (24) Fourth_Ventricle (15): linear fit = 1.13 x + 0.0 (432 voxels, overlap=0.620) Fourth_Ventricle (15): linear fit = 1.13 x + 0.0 (432 voxels, peak = 23), gca=22.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.14879 (39) gca peak Left_Thalamus = 0.36646 (103) gca peak CSF = 0.15453 (50) gca peak Left_Accumbens_area = 0.61670 (66) gca peak Left_undetermined = 0.96707 (30) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.12577 (35) gca peak Right_Inf_Lat_Vent = 0.20093 (28) gca peak Right_Accumbens_area = 0.31829 (76) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14507 (37) gca peak Fifth_Ventricle = 0.75707 (42) gca peak WM_hypointensities = 0.07560 (78) gca peak non_WM_hypointensities = 0.08683 (44) gca peak Optic_Chiasm = 0.70863 (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 72471 voxels changed in iteration 0 of unlikely voxel relabeling 379 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 43419 gm and wm labels changed (%30 to gray, %70 to white out of all changed labels) 279 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 70663 changed. image ll: -2.102, PF=0.500 pass 2: 18442 changed. image ll: -2.101, PF=0.500 pass 3: 4642 changed. 49272 voxels changed in iteration 0 of unlikely voxel relabeling 294 voxels changed in iteration 1 of unlikely voxel relabeling 9 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 7023 voxels changed in iteration 0 of unlikely voxel relabeling 163 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 5330 voxels changed in iteration 0 of unlikely voxel relabeling 58 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 4206 voxels changed in iteration 0 of unlikely voxel relabeling 21 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 3158.175884 mri_ca_label stimesec 1.663747 mri_ca_label ru_maxrss 2107368 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 757314 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 464 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 158 mri_ca_label ru_nivcsw 320063 auto-labeling took 52 minutes and 45 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /users/zli/test/fs/a003/mri/transforms/cc_up.lta a003 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /users/zli/test/fs/a003/mri/transforms/cc_up.lta reading aseg from /users/zli/test/fs/a003/mri/aseg.auto_noCCseg.mgz reading norm from /users/zli/test/fs/a003/mri/norm.mgz 36058 voxels in left wm, 33864 in right wm, xrange [126, 134] searching rotation angles z=[-6 8], y=[-6 8] searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.6 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.1 searching scale 1 Z rot 7.4 searching scale 1 Z rot 7.6 searching scale 1 Z rot 7.9 global minimum found at slice 130.0, rotations (1.43, 1.14) final transformation (x=130.0, yr=1.426, zr=1.141): 0.99949 -0.01992 0.02488 -2.96766; 0.01991 0.99980 0.00050 22.37071; -0.02488 0.00000 0.99969 7.27333; 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 128 103 124 eigenvectors: 0.00056 0.00341 0.99999; 0.17572 -0.98444 0.00326; 0.98444 0.17571 -0.00115; error in mid anterior detected - correcting... writing aseg with callosum to /users/zli/test/fs/a003/mri/aseg.auto.mgz... corpus callosum segmentation took 0.6 minutes #-------------------------------------- #@# Merge ASeg Tue Feb 5 13:59:24 EST 2019 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue Feb 5 13:59:25 EST 2019 /users/zli/test/fs/a003/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... 841 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 73 (73), valley at 35 (35) csf peak at 36, setting threshold to 60 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 73 (73), valley at 34 (34) csf peak at 37, setting threshold to 61 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 18 seconds. #-------------------------------------------- #@# Mask BFS Tue Feb 5 14:02:45 EST 2019 /users/zli/test/fs/a003/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1583597 voxels in mask (pct= 9.44) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Tue Feb 5 14:02:48 EST 2019 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 103.4 +- 6.9 [79.0 --> 125.0] GM (73.0) : 71.4 +- 9.9 [30.0 --> 95.0] setting bottom of white matter range to 81.3 setting top of gray matter range to 91.3 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 15068 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4555 filled 586 bright non-wm voxels segmented. 4595 diagonally connected voxels added... white matter segmentation took 2.3 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 0.52 minutes reading wm segmentation from wm.seg.mgz... 29 voxels added to wm to prevent paths from MTL structures to cortex 2403 additional wm voxels added 0 additional wm voxels added SEG EDIT: 40200 voxels turned on, 46693 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+): 18 found - 18 modified | TOTAL: 18 pass 2 (xy+): 0 found - 18 modified | TOTAL: 18 pass 1 (xy-): 12 found - 12 modified | TOTAL: 30 pass 2 (xy-): 0 found - 12 modified | TOTAL: 30 pass 1 (yz+): 19 found - 19 modified | TOTAL: 49 pass 2 (yz+): 0 found - 19 modified | TOTAL: 49 pass 1 (yz-): 26 found - 26 modified | TOTAL: 75 pass 2 (yz-): 0 found - 26 modified | TOTAL: 75 pass 1 (xz+): 19 found - 19 modified | TOTAL: 94 pass 2 (xz+): 0 found - 19 modified | TOTAL: 94 pass 1 (xz-): 13 found - 13 modified | TOTAL: 107 pass 2 (xz-): 0 found - 13 modified | TOTAL: 107 Iteration Number : 1 pass 1 (+++): 30 found - 30 modified | TOTAL: 30 pass 2 (+++): 0 found - 30 modified | TOTAL: 30 pass 1 (+++): 34 found - 34 modified | TOTAL: 64 pass 2 (+++): 0 found - 34 modified | TOTAL: 64 pass 1 (+++): 23 found - 23 modified | TOTAL: 87 pass 2 (+++): 0 found - 23 modified | TOTAL: 87 pass 1 (+++): 29 found - 29 modified | TOTAL: 116 pass 2 (+++): 0 found - 29 modified | TOTAL: 116 Iteration Number : 1 pass 1 (++): 116 found - 116 modified | TOTAL: 116 pass 2 (++): 0 found - 116 modified | TOTAL: 116 pass 1 (+-): 179 found - 179 modified | TOTAL: 295 pass 2 (+-): 0 found - 179 modified | TOTAL: 295 pass 1 (--): 144 found - 144 modified | TOTAL: 439 pass 2 (--): 0 found - 144 modified | TOTAL: 439 pass 1 (-+): 184 found - 184 modified | TOTAL: 623 pass 2 (-+): 0 found - 184 modified | TOTAL: 623 Iteration Number : 2 pass 1 (xy+): 9 found - 9 modified | TOTAL: 9 pass 2 (xy+): 0 found - 9 modified | TOTAL: 9 pass 1 (xy-): 15 found - 15 modified | TOTAL: 24 pass 2 (xy-): 0 found - 15 modified | TOTAL: 24 pass 1 (yz+): 11 found - 11 modified | TOTAL: 35 pass 2 (yz+): 0 found - 11 modified | TOTAL: 35 pass 1 (yz-): 10 found - 10 modified | TOTAL: 45 pass 2 (yz-): 0 found - 10 modified | TOTAL: 45 pass 1 (xz+): 8 found - 8 modified | TOTAL: 53 pass 2 (xz+): 0 found - 8 modified | TOTAL: 53 pass 1 (xz-): 9 found - 9 modified | TOTAL: 62 pass 2 (xz-): 0 found - 9 modified | TOTAL: 62 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 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 (--): 4 found - 4 modified | TOTAL: 16 pass 2 (--): 0 found - 4 modified | TOTAL: 16 pass 1 (-+): 5 found - 5 modified | TOTAL: 21 pass 2 (-+): 0 found - 5 modified | TOTAL: 21 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 = 931 (out of 572038: 0.162751) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Tue Feb 5 14:05:43 EST 2019 /users/zli/test/fs/a003/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 1.01777 -0.07100 0.02736 -1.82303; 0.06603 1.09319 0.03558 -25.16615; -0.02713 -0.03469 1.09286 -13.00497; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.01777 -0.07100 0.02736 -1.82303; 0.06603 1.09319 0.03558 -25.16615; -0.02713 -0.03469 1.09286 -13.00497; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1157 (min = 350, max = 1400), aspect = 0.49 (min = 0.10, max = 0.75) no need to search using seed (126, 110, 93), TAL = (2.0, -35.0, 18.0) talairach voxel to voxel transform 0.97777 0.06266 -0.02652 3.01460; -0.05978 0.90998 -0.02813 22.42593; 0.02238 0.03044 0.91348 12.68674; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 110, 93) --> (2.0, -35.0, 18.0) done. writing output to filled.mgz... filling took 0.6 minutes talairach cc position changed to (2.00, -35.00, 18.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -35.00, 18.00) SRC: (113.04, 113.45, 103.41) search lh wm seed point around talairach space (-16.00, -35.00, 18.00), SRC: (148.24, 111.30, 104.21) 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 Tue Feb 5 14:06:21 EST 2019 /users/zli/test/fs/a003/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-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 2 found - 2 modified | TOTAL: 4 pass 2 (xz-): 0 found - 2 modified | TOTAL: 4 Iteration Number : 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 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 = 7 (out of 278006: 0.002518) 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 50: 1511 vertices, 1682 faces slice 60: 8598 vertices, 8859 faces slice 70: 17816 vertices, 18189 faces slice 80: 29322 vertices, 29718 faces slice 90: 40885 vertices, 41313 faces slice 100: 52796 vertices, 53215 faces slice 110: 66247 vertices, 66729 faces slice 120: 79906 vertices, 80428 faces slice 130: 92897 vertices, 93374 faces slice 140: 105448 vertices, 105923 faces slice 150: 117208 vertices, 117742 faces slice 160: 127797 vertices, 128216 faces slice 170: 135857 vertices, 136202 faces slice 180: 142791 vertices, 143109 faces slice 190: 148316 vertices, 148595 faces slice 200: 150586 vertices, 150690 faces slice 210: 150586 vertices, 150690 faces slice 220: 150586 vertices, 150690 faces slice 230: 150586 vertices, 150690 faces slice 240: 150586 vertices, 150690 faces slice 250: 150586 vertices, 150690 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... 150586 voxel in cpt #1: X=-104 [v=150586,e=452070,f=301380] located at (-30.788965, -11.488392, 15.343996) For the whole surface: X=-104 [v=150586,e=452070,f=301380] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Tue Feb 5 14:06:31 EST 2019 /users/zli/test/fs/a003/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 3 found - 3 modified | TOTAL: 3 pass 2 (yz+): 0 found - 3 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 1 found - 1 modified | TOTAL: 5 pass 2 (xz+): 0 found - 1 modified | TOTAL: 5 pass 1 (xz-): 1 found - 1 modified | TOTAL: 6 pass 2 (xz-): 0 found - 1 modified | TOTAL: 6 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 2 found - 2 modified | TOTAL: 2 pass 2 (--): 0 found - 2 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 8 (out of 273707: 0.002923) 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 50: 580 vertices, 667 faces slice 60: 5202 vertices, 5456 faces slice 70: 14076 vertices, 14457 faces slice 80: 25276 vertices, 25687 faces slice 90: 37772 vertices, 38209 faces slice 100: 50189 vertices, 50606 faces slice 110: 64282 vertices, 64801 faces slice 120: 78134 vertices, 78619 faces slice 130: 91276 vertices, 91723 faces slice 140: 103033 vertices, 103499 faces slice 150: 114533 vertices, 114993 faces slice 160: 123978 vertices, 124313 faces slice 170: 131782 vertices, 132105 faces slice 180: 138315 vertices, 138610 faces slice 190: 143721 vertices, 143993 faces slice 200: 146132 vertices, 146212 faces slice 210: 146132 vertices, 146212 faces slice 220: 146132 vertices, 146212 faces slice 230: 146132 vertices, 146212 faces slice 240: 146132 vertices, 146212 faces slice 250: 146132 vertices, 146212 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... 146132 voxel in cpt #1: X=-80 [v=146132,e=438636,f=292424] located at (27.095818, -10.808824, 13.655408) For the whole surface: X=-80 [v=146132,e=438636,f=292424] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Tue Feb 5 14:06:40 EST 2019 /users/zli/test/fs/a003/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 Tue Feb 5 14:06:46 EST 2019 /users/zli/test/fs/a003/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 Tue Feb 5 14:06:52 EST 2019 /users/zli/test/fs/a003/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 46.2 mm, total surface area = 78076 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.6 minutes step 000: RMS=0.161 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.078 (target=0.015) step 020: RMS=0.067 (target=0.015) step 025: RMS=0.061 (target=0.015) step 030: RMS=0.056 (target=0.015) step 035: RMS=0.052 (target=0.015) step 040: RMS=0.049 (target=0.015) step 045: RMS=0.048 (target=0.015) step 050: RMS=0.047 (target=0.015) step 055: RMS=0.047 (target=0.015) step 060: RMS=0.046 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 35.108662 mris_inflate stimesec 0.099984 mris_inflate ru_maxrss 193960 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 25642 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10600 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 342 mris_inflate ru_nivcsw 3577 #-------------------------------------------- #@# Inflation1 rh Tue Feb 5 14:07:27 EST 2019 /users/zli/test/fs/a003/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 45.5 mm, total surface area = 75940 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.6 minutes step 000: RMS=0.158 (target=0.015) step 005: RMS=0.119 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.076 (target=0.015) step 020: RMS=0.065 (target=0.015) step 025: RMS=0.059 (target=0.015) step 030: RMS=0.052 (target=0.015) step 035: RMS=0.049 (target=0.015) step 040: RMS=0.046 (target=0.015) step 045: RMS=0.044 (target=0.015) step 050: RMS=0.043 (target=0.015) step 055: RMS=0.042 (target=0.015) step 060: RMS=0.042 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 35.021675 mris_inflate stimesec 0.104984 mris_inflate ru_maxrss 188312 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 24741 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10288 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 334 mris_inflate ru_nivcsw 3615 #-------------------------------------------- #@# QSphere lh Tue Feb 5 14:08:03 EST 2019 /users/zli/test/fs/a003/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.95 +- 0.55 (0.00-->8.43) (max @ vno 57412 --> 58653) face area 0.03 +- 0.03 (-0.31-->0.97) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.322... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.778, avgs=0 005/300: dt: 0.9000, rms radial error=175.520, avgs=0 010/300: dt: 0.9000, rms radial error=174.968, avgs=0 015/300: dt: 0.9000, rms radial error=174.243, avgs=0 020/300: dt: 0.9000, rms radial error=173.418, avgs=0 025/300: dt: 0.9000, rms radial error=172.535, avgs=0 030/300: dt: 0.9000, rms radial error=171.620, avgs=0 035/300: dt: 0.9000, rms radial error=170.688, avgs=0 040/300: dt: 0.9000, rms radial error=169.748, avgs=0 045/300: dt: 0.9000, rms radial error=168.805, avgs=0 050/300: dt: 0.9000, rms radial error=167.863, avgs=0 055/300: dt: 0.9000, rms radial error=166.923, avgs=0 060/300: dt: 0.9000, rms radial error=165.987, avgs=0 065/300: dt: 0.9000, rms radial error=165.055, avgs=0 070/300: dt: 0.9000, rms radial error=164.127, avgs=0 075/300: dt: 0.9000, rms radial error=163.204, avgs=0 080/300: dt: 0.9000, rms radial error=162.285, avgs=0 085/300: dt: 0.9000, rms radial error=161.372, avgs=0 090/300: dt: 0.9000, rms radial error=160.463, avgs=0 095/300: dt: 0.9000, rms radial error=159.559, avgs=0 100/300: dt: 0.9000, rms radial error=158.660, avgs=0 105/300: dt: 0.9000, rms radial error=157.766, avgs=0 110/300: dt: 0.9000, rms radial error=156.876, avgs=0 115/300: dt: 0.9000, rms radial error=155.992, avgs=0 120/300: dt: 0.9000, rms radial error=155.112, avgs=0 125/300: dt: 0.9000, rms radial error=154.237, avgs=0 130/300: dt: 0.9000, rms radial error=153.366, avgs=0 135/300: dt: 0.9000, rms radial error=152.501, avgs=0 140/300: dt: 0.9000, rms radial error=151.640, avgs=0 145/300: dt: 0.9000, rms radial error=150.784, avgs=0 150/300: dt: 0.9000, rms radial error=149.933, avgs=0 155/300: dt: 0.9000, rms radial error=149.086, avgs=0 160/300: dt: 0.9000, rms radial error=148.244, avgs=0 165/300: dt: 0.9000, rms radial error=147.407, avgs=0 170/300: dt: 0.9000, rms radial error=146.574, avgs=0 175/300: dt: 0.9000, rms radial error=145.746, avgs=0 180/300: dt: 0.9000, rms radial error=144.923, avgs=0 185/300: dt: 0.9000, rms radial error=144.104, avgs=0 190/300: dt: 0.9000, rms radial error=143.290, avgs=0 195/300: dt: 0.9000, rms radial error=142.481, avgs=0 200/300: dt: 0.9000, rms radial error=141.676, avgs=0 205/300: dt: 0.9000, rms radial error=140.875, avgs=0 210/300: dt: 0.9000, rms radial error=140.079, avgs=0 215/300: dt: 0.9000, rms radial error=139.287, avgs=0 220/300: dt: 0.9000, rms radial error=138.500, avgs=0 225/300: dt: 0.9000, rms radial error=137.717, avgs=0 230/300: dt: 0.9000, rms radial error=136.939, avgs=0 235/300: dt: 0.9000, rms radial error=136.165, avgs=0 240/300: dt: 0.9000, rms radial error=135.395, avgs=0 245/300: dt: 0.9000, rms radial error=134.630, avgs=0 250/300: dt: 0.9000, rms radial error=133.869, avgs=0 255/300: dt: 0.9000, rms radial error=133.112, avgs=0 260/300: dt: 0.9000, rms radial error=132.359, avgs=0 265/300: dt: 0.9000, rms radial error=131.611, avgs=0 270/300: dt: 0.9000, rms radial error=130.867, avgs=0 275/300: dt: 0.9000, rms radial error=130.127, avgs=0 280/300: dt: 0.9000, rms radial error=129.391, avgs=0 285/300: dt: 0.9000, rms radial error=128.660, avgs=0 290/300: dt: 0.9000, rms radial error=127.932, avgs=0 295/300: dt: 0.9000, rms radial error=127.209, avgs=0 300/300: dt: 0.9000, rms radial error=126.491, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17454.85 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 2 (K=40.0), pass 1, starting sse = 2848.37 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00004 epoch 3 (K=160.0), pass 1, starting sse = 279.01 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00555 epoch 4 (K=640.0), pass 1, starting sse = 20.37 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/12 = 0.00583 final distance error %25.17 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.06 hours mris_sphere utimesec 207.431465 mris_sphere stimesec 0.102984 mris_sphere ru_maxrss 194156 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 25696 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10600 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 311 mris_sphere ru_nivcsw 21551 FSRUNTIME@ mris_sphere 0.0578 hours 1 threads #-------------------------------------------- #@# QSphere rh Tue Feb 5 14:11:31 EST 2019 /users/zli/test/fs/a003/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.97 +- 0.55 (0.00-->8.26) (max @ vno 56570 --> 58154) face area 0.03 +- 0.03 (-0.26-->0.65) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.329... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.572, avgs=0 005/300: dt: 0.9000, rms radial error=175.315, avgs=0 010/300: dt: 0.9000, rms radial error=174.762, avgs=0 015/300: dt: 0.9000, rms radial error=174.036, avgs=0 020/300: dt: 0.9000, rms radial error=173.210, avgs=0 025/300: dt: 0.9000, rms radial error=172.327, avgs=0 030/300: dt: 0.9000, rms radial error=171.413, avgs=0 035/300: dt: 0.9000, rms radial error=170.482, avgs=0 040/300: dt: 0.9000, rms radial error=169.543, avgs=0 045/300: dt: 0.9000, rms radial error=168.602, avgs=0 050/300: dt: 0.9000, rms radial error=167.662, avgs=0 055/300: dt: 0.9000, rms radial error=166.724, avgs=0 060/300: dt: 0.9000, rms radial error=165.789, avgs=0 065/300: dt: 0.9000, rms radial error=164.859, avgs=0 070/300: dt: 0.9000, rms radial error=163.933, avgs=0 075/300: dt: 0.9000, rms radial error=163.012, avgs=0 080/300: dt: 0.9000, rms radial error=162.096, avgs=0 085/300: dt: 0.9000, rms radial error=161.185, avgs=0 090/300: dt: 0.9000, rms radial error=160.279, avgs=0 095/300: dt: 0.9000, rms radial error=159.377, avgs=0 100/300: dt: 0.9000, rms radial error=158.481, avgs=0 105/300: dt: 0.9000, rms radial error=157.589, avgs=0 110/300: dt: 0.9000, rms radial error=156.702, avgs=0 115/300: dt: 0.9000, rms radial error=155.820, avgs=0 120/300: dt: 0.9000, rms radial error=154.943, avgs=0 125/300: dt: 0.9000, rms radial error=154.070, avgs=0 130/300: dt: 0.9000, rms radial error=153.203, avgs=0 135/300: dt: 0.9000, rms radial error=152.340, avgs=0 140/300: dt: 0.9000, rms radial error=151.481, avgs=0 145/300: dt: 0.9000, rms radial error=150.628, avgs=0 150/300: dt: 0.9000, rms radial error=149.779, avgs=0 155/300: dt: 0.9000, rms radial error=148.935, avgs=0 160/300: dt: 0.9000, rms radial error=148.096, avgs=0 165/300: dt: 0.9000, rms radial error=147.261, avgs=0 170/300: dt: 0.9000, rms radial error=146.431, avgs=0 175/300: dt: 0.9000, rms radial error=145.606, avgs=0 180/300: dt: 0.9000, rms radial error=144.785, avgs=0 185/300: dt: 0.9000, rms radial error=143.969, avgs=0 190/300: dt: 0.9000, rms radial error=143.157, avgs=0 195/300: dt: 0.9000, rms radial error=142.350, avgs=0 200/300: dt: 0.9000, rms radial error=141.548, avgs=0 205/300: dt: 0.9000, rms radial error=140.751, avgs=0 210/300: dt: 0.9000, rms radial error=139.957, avgs=0 215/300: dt: 0.9000, rms radial error=139.169, avgs=0 220/300: dt: 0.9000, rms radial error=138.384, avgs=0 225/300: dt: 0.9000, rms radial error=137.604, avgs=0 230/300: dt: 0.9000, rms radial error=136.828, avgs=0 235/300: dt: 0.9000, rms radial error=136.057, avgs=0 240/300: dt: 0.9000, rms radial error=135.290, avgs=0 245/300: dt: 0.9000, rms radial error=134.527, avgs=0 250/300: dt: 0.9000, rms radial error=133.768, avgs=0 255/300: dt: 0.9000, rms radial error=133.014, avgs=0 260/300: dt: 0.9000, rms radial error=132.264, avgs=0 265/300: dt: 0.9000, rms radial error=131.518, avgs=0 270/300: dt: 0.9000, rms radial error=130.776, avgs=0 275/300: dt: 0.9000, rms radial error=130.039, avgs=0 280/300: dt: 0.9000, rms radial error=129.305, avgs=0 285/300: dt: 0.9000, rms radial error=128.576, avgs=0 290/300: dt: 0.9000, rms radial error=127.851, avgs=0 295/300: dt: 0.9000, rms radial error=127.129, avgs=0 300/300: dt: 0.9000, rms radial error=126.412, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16793.77 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 2 (K=40.0), pass 1, starting sse = 2690.10 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 249.94 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00482 epoch 4 (K=640.0), pass 1, starting sse = 17.04 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/12 = 0.00602 final distance error %24.18 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.06 hours mris_sphere utimesec 223.143077 mris_sphere stimesec 0.120981 mris_sphere ru_maxrss 188512 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 24791 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10288 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 304 mris_sphere ru_nivcsw 41721 FSRUNTIME@ mris_sphere 0.0622 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Tue Feb 5 14:15:15 EST 2019 /users/zli/test/fs/a003/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Tue Feb 5 14:15:16 EST 2019 /users/zli/test/fs/a003/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Tue Feb 5 14:15:16 EST 2019 mris_fix_topology -rusage /users/zli/test/fs/a003/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 a003 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=-104 (nv=150586, nf=301380, ne=452070, g=53) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 7 iterations marking ambiguous vertices... 7306 ambiguous faces found in tessellation segmenting defects... 52 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 44 into 37 -merging segment 39 into 38 50 defects to be corrected 0 vertices coincident reading input surface /users/zli/test/fs/a003/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.3064 (-4.6532) -vertex loglikelihood: -6.1239 (-3.0620) -normal dot loglikelihood: -3.6132 (-3.6132) -quad curv loglikelihood: -6.5254 (-3.2627) Total Loglikelihood : -25.5689 CORRECTING DEFECT 0 (vertices=52, convex hull=75, v0=145) After retessellation of defect 0 (v0=145), euler #=-45 (146311,437533,291177) : difference with theory (-47) = -2 CORRECTING DEFECT 1 (vertices=24, convex hull=50, v0=265) After retessellation of defect 1 (v0=265), euler #=-44 (146319,437577,291214) : difference with theory (-46) = -2 CORRECTING DEFECT 2 (vertices=18, convex hull=43, v0=297) After retessellation of defect 2 (v0=297), euler #=-43 (146327,437617,291247) : difference with theory (-45) = -2 CORRECTING DEFECT 3 (vertices=44, convex hull=77, v0=418) After retessellation of defect 3 (v0=418), euler #=-42 (146341,437694,291311) : difference with theory (-44) = -2 CORRECTING DEFECT 4 (vertices=8, convex hull=17, v0=1120) After retessellation of defect 4 (v0=1120), euler #=-41 (146342,437701,291318) : difference with theory (-43) = -2 CORRECTING DEFECT 5 (vertices=38, convex hull=78, v0=1891) After retessellation of defect 5 (v0=1891), euler #=-40 (146351,437763,291372) : difference with theory (-42) = -2 CORRECTING DEFECT 6 (vertices=28, convex hull=55, v0=2582) After retessellation of defect 6 (v0=2582), euler #=-39 (146356,437798,291403) : difference with theory (-41) = -2 CORRECTING DEFECT 7 (vertices=24, convex hull=60, v0=3550) After retessellation of defect 7 (v0=3550), euler #=-38 (146366,437852,291448) : difference with theory (-40) = -2 CORRECTING DEFECT 8 (vertices=26, convex hull=56, v0=4612) After retessellation of defect 8 (v0=4612), euler #=-37 (146375,437904,291492) : difference with theory (-39) = -2 CORRECTING DEFECT 9 (vertices=14, convex hull=27, v0=4697) After retessellation of defect 9 (v0=4697), euler #=-36 (146377,437918,291505) : difference with theory (-38) = -2 CORRECTING DEFECT 10 (vertices=36, convex hull=25, v0=9415) After retessellation of defect 10 (v0=9415), euler #=-35 (146379,437929,291515) : difference with theory (-37) = -2 CORRECTING DEFECT 11 (vertices=16, convex hull=38, v0=13475) After retessellation of defect 11 (v0=13475), euler #=-34 (146383,437952,291535) : difference with theory (-36) = -2 CORRECTING DEFECT 12 (vertices=28, convex hull=60, v0=13570) After retessellation of defect 12 (v0=13570), euler #=-33 (146392,438003,291578) : difference with theory (-35) = -2 CORRECTING DEFECT 13 (vertices=31, convex hull=28, v0=14221) After retessellation of defect 13 (v0=14221), euler #=-32 (146396,438024,291596) : difference with theory (-34) = -2 CORRECTING DEFECT 14 (vertices=19, convex hull=52, v0=27657) After retessellation of defect 14 (v0=27657), euler #=-31 (146407,438077,291639) : difference with theory (-33) = -2 CORRECTING DEFECT 15 (vertices=8, convex hull=34, v0=28920) After retessellation of defect 15 (v0=28920), euler #=-30 (146411,438100,291659) : difference with theory (-32) = -2 CORRECTING DEFECT 16 (vertices=25, convex hull=28, v0=30619) After retessellation of defect 16 (v0=30619), euler #=-29 (146412,438112,291671) : difference with theory (-31) = -2 CORRECTING DEFECT 17 (vertices=30, convex hull=52, v0=32246) After retessellation of defect 17 (v0=32246), euler #=-28 (146428,438183,291727) : difference with theory (-30) = -2 CORRECTING DEFECT 18 (vertices=164, convex hull=157, v0=52418) normal vector of length zero at vertex 146896 with 3 faces After retessellation of defect 18 (v0=52418), euler #=-27 (146524,438539,291988) : difference with theory (-29) = -2 CORRECTING DEFECT 19 (vertices=5, convex hull=23, v0=53624) After retessellation of defect 19 (v0=53624), euler #=-26 (146525,438548,291997) : difference with theory (-28) = -2 CORRECTING DEFECT 20 (vertices=41, convex hull=66, v0=53687) After retessellation of defect 20 (v0=53687), euler #=-25 (146540,438619,292054) : difference with theory (-27) = -2 CORRECTING DEFECT 21 (vertices=37, convex hull=55, v0=55195) After retessellation of defect 21 (v0=55195), euler #=-24 (146566,438720,292130) : difference with theory (-26) = -2 CORRECTING DEFECT 22 (vertices=27, convex hull=29, v0=58178) After retessellation of defect 22 (v0=58178), euler #=-23 (146570,438744,292151) : difference with theory (-25) = -2 CORRECTING DEFECT 23 (vertices=25, convex hull=59, v0=60542) After retessellation of defect 23 (v0=60542), euler #=-22 (146579,438792,292191) : difference with theory (-24) = -2 CORRECTING DEFECT 24 (vertices=30, convex hull=28, v0=61225) After retessellation of defect 24 (v0=61225), euler #=-21 (146583,438812,292208) : difference with theory (-23) = -2 CORRECTING DEFECT 25 (vertices=9, convex hull=22, v0=62710) After retessellation of defect 25 (v0=62710), euler #=-20 (146587,438830,292223) : difference with theory (-22) = -2 CORRECTING DEFECT 26 (vertices=35, convex hull=71, v0=64745) After retessellation of defect 26 (v0=64745), euler #=-19 (146596,438887,292272) : difference with theory (-21) = -2 CORRECTING DEFECT 27 (vertices=22, convex hull=51, v0=66260) After retessellation of defect 27 (v0=66260), euler #=-18 (146608,438941,292315) : difference with theory (-20) = -2 CORRECTING DEFECT 28 (vertices=31, convex hull=59, v0=66535) After retessellation of defect 28 (v0=66535), euler #=-17 (146622,439007,292368) : difference with theory (-19) = -2 CORRECTING DEFECT 29 (vertices=37, convex hull=63, v0=69683) After retessellation of defect 29 (v0=69683), euler #=-16 (146634,439072,292422) : difference with theory (-18) = -2 CORRECTING DEFECT 30 (vertices=47, convex hull=59, v0=71445) After retessellation of defect 30 (v0=71445), euler #=-15 (146648,439135,292472) : difference with theory (-17) = -2 CORRECTING DEFECT 31 (vertices=635, convex hull=233, v0=75425) After retessellation of defect 31 (v0=75425), euler #=-14 (146736,439513,292763) : difference with theory (-16) = -2 CORRECTING DEFECT 32 (vertices=24, convex hull=63, v0=75712) After retessellation of defect 32 (v0=75712), euler #=-13 (146752,439584,292819) : difference with theory (-15) = -2 CORRECTING DEFECT 33 (vertices=13, convex hull=23, v0=79427) After retessellation of defect 33 (v0=79427), euler #=-12 (146754,439596,292830) : difference with theory (-14) = -2 CORRECTING DEFECT 34 (vertices=502, convex hull=161, v0=84784) After retessellation of defect 34 (v0=84784), euler #=-11 (146791,439786,292984) : difference with theory (-13) = -2 CORRECTING DEFECT 35 (vertices=87, convex hull=107, v0=87331) After retessellation of defect 35 (v0=87331), euler #=-10 (146819,439926,293097) : difference with theory (-12) = -2 CORRECTING DEFECT 36 (vertices=38, convex hull=49, v0=95206) After retessellation of defect 36 (v0=95206), euler #=-9 (146828,439970,293133) : difference with theory (-11) = -2 CORRECTING DEFECT 37 (vertices=1316, convex hull=382, v0=97723) L defect detected... After retessellation of defect 37 (v0=97723), euler #=-11 (147015,440761,293735) : difference with theory (-10) = 1 CORRECTING DEFECT 38 (vertices=103, convex hull=113, v0=100199) After retessellation of defect 38 (v0=100199), euler #=-9 (147052,440924,293863) : difference with theory (-9) = 0 CORRECTING DEFECT 39 (vertices=53, convex hull=85, v0=103716) After retessellation of defect 39 (v0=103716), euler #=-8 (147077,441033,293948) : difference with theory (-8) = 0 CORRECTING DEFECT 40 (vertices=318, convex hull=76, v0=103932) After retessellation of defect 40 (v0=103932), euler #=-7 (147090,441107,294010) : difference with theory (-7) = 0 CORRECTING DEFECT 41 (vertices=13, convex hull=19, v0=105073) After retessellation of defect 41 (v0=105073), euler #=-6 (147090,441111,294015) : difference with theory (-6) = 0 CORRECTING DEFECT 42 (vertices=20, convex hull=22, v0=106071) After retessellation of defect 42 (v0=106071), euler #=-5 (147092,441126,294029) : difference with theory (-5) = 0 CORRECTING DEFECT 43 (vertices=27, convex hull=55, v0=112347) After retessellation of defect 43 (v0=112347), euler #=-4 (147108,441195,294083) : difference with theory (-4) = 0 CORRECTING DEFECT 44 (vertices=21, convex hull=60, v0=113442) After retessellation of defect 44 (v0=113442), euler #=-3 (147120,441253,294130) : difference with theory (-3) = 0 CORRECTING DEFECT 45 (vertices=34, convex hull=45, v0=118186) After retessellation of defect 45 (v0=118186), euler #=-2 (147132,441304,294170) : difference with theory (-2) = 0 CORRECTING DEFECT 46 (vertices=30, convex hull=63, v0=131126) After retessellation of defect 46 (v0=131126), euler #=-1 (147142,441358,294215) : difference with theory (-1) = 0 CORRECTING DEFECT 47 (vertices=33, convex hull=58, v0=134504) After retessellation of defect 47 (v0=134504), euler #=0 (147155,441419,294264) : difference with theory (0) = 0 CORRECTING DEFECT 48 (vertices=19, convex hull=45, v0=140308) After retessellation of defect 48 (v0=140308), euler #=1 (147164,441461,294298) : difference with theory (1) = 0 CORRECTING DEFECT 49 (vertices=20, convex hull=60, v0=145359) After retessellation of defect 49 (v0=145359), euler #=2 (147177,441525,294350) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.03-->7.19) (max @ vno 107182 --> 113501) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.03-->7.19) (max @ vno 107182 --> 113501) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 190 mutations (35.3%), 349 crossovers (64.7%), 294 vertices were eliminated building final representation... 3409 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=147177, nf=294350, ne=441525, g=0) writing corrected surface to /users/zli/test/fs/a003/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 31.9 minutes 0 defective edges removing intersecting faces 000: 433 intersecting 001: 31 intersecting mris_fix_topology utimesec 1908.420875 mris_fix_topology stimesec 0.230964 mris_fix_topology ru_maxrss 469832 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 53216 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 13904 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 456 mris_fix_topology ru_nivcsw 193366 FSRUNTIME@ mris_fix_topology lh 0.5313 hours 1 threads #@# Fix Topology rh Tue Feb 5 14:47:09 EST 2019 mris_fix_topology -rusage /users/zli/test/fs/a003/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 a003 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=-80 (nv=146132, nf=292424, ne=438636, g=41) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 5281 ambiguous faces found in tessellation segmenting defects... 42 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 12 into 11 -merging segment 33 into 30 40 defects to be corrected 0 vertices coincident reading input surface /users/zli/test/fs/a003/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2532 (-4.6266) -vertex loglikelihood: -6.1322 (-3.0661) -normal dot loglikelihood: -3.6111 (-3.6111) -quad curv loglikelihood: -6.3896 (-3.1948) Total Loglikelihood : -25.3861 CORRECTING DEFECT 0 (vertices=26, convex hull=51, v0=835) After retessellation of defect 0 (v0=835), euler #=-37 (143029,428034,284968) : difference with theory (-37) = 0 CORRECTING DEFECT 1 (vertices=26, convex hull=63, v0=1061) After retessellation of defect 1 (v0=1061), euler #=-36 (143043,428097,285018) : difference with theory (-36) = 0 CORRECTING DEFECT 2 (vertices=23, convex hull=48, v0=2604) After retessellation of defect 2 (v0=2604), euler #=-35 (143052,428142,285055) : difference with theory (-35) = 0 CORRECTING DEFECT 3 (vertices=15, convex hull=15, v0=3302) After retessellation of defect 3 (v0=3302), euler #=-34 (143052,428146,285060) : difference with theory (-34) = 0 CORRECTING DEFECT 4 (vertices=39, convex hull=79, v0=5135) After retessellation of defect 4 (v0=5135), euler #=-33 (143068,428227,285126) : difference with theory (-33) = 0 CORRECTING DEFECT 5 (vertices=41, convex hull=56, v0=8966) After retessellation of defect 5 (v0=8966), euler #=-32 (143077,428274,285165) : difference with theory (-32) = 0 CORRECTING DEFECT 6 (vertices=41, convex hull=57, v0=11400) After retessellation of defect 6 (v0=11400), euler #=-31 (143086,428326,285209) : difference with theory (-31) = 0 CORRECTING DEFECT 7 (vertices=81, convex hull=79, v0=12461) After retessellation of defect 7 (v0=12461), euler #=-30 (143113,428443,285300) : difference with theory (-30) = 0 CORRECTING DEFECT 8 (vertices=29, convex hull=59, v0=15663) After retessellation of defect 8 (v0=15663), euler #=-29 (143131,428523,285363) : difference with theory (-29) = 0 CORRECTING DEFECT 9 (vertices=28, convex hull=18, v0=20108) After retessellation of defect 9 (v0=20108), euler #=-28 (143131,428528,285369) : difference with theory (-28) = 0 CORRECTING DEFECT 10 (vertices=57, convex hull=94, v0=22179) After retessellation of defect 10 (v0=22179), euler #=-27 (143165,428668,285476) : difference with theory (-27) = 0 CORRECTING DEFECT 11 (vertices=59, convex hull=79, v0=24908) After retessellation of defect 11 (v0=24908), euler #=-25 (143177,428740,285538) : difference with theory (-26) = -1 CORRECTING DEFECT 12 (vertices=34, convex hull=66, v0=44117) After retessellation of defect 12 (v0=44117), euler #=-24 (143199,428835,285612) : difference with theory (-25) = -1 CORRECTING DEFECT 13 (vertices=26, convex hull=68, v0=48565) After retessellation of defect 13 (v0=48565), euler #=-23 (143209,428888,285656) : difference with theory (-24) = -1 CORRECTING DEFECT 14 (vertices=474, convex hull=243, v0=52313) After retessellation of defect 14 (v0=52313), euler #=-23 (143219,429060,285818) : difference with theory (-23) = 0 CORRECTING DEFECT 15 (vertices=27, convex hull=55, v0=56946) After retessellation of defect 15 (v0=56946), euler #=-22 (143234,429127,285871) : difference with theory (-22) = 0 CORRECTING DEFECT 16 (vertices=21, convex hull=38, v0=58514) After retessellation of defect 16 (v0=58514), euler #=-21 (143236,429144,285887) : difference with theory (-21) = 0 CORRECTING DEFECT 17 (vertices=41, convex hull=53, v0=61735) After retessellation of defect 17 (v0=61735), euler #=-20 (143245,429193,285928) : difference with theory (-20) = 0 CORRECTING DEFECT 18 (vertices=46, convex hull=58, v0=65378) After retessellation of defect 18 (v0=65378), euler #=-19 (143254,429237,285964) : difference with theory (-19) = 0 CORRECTING DEFECT 19 (vertices=29, convex hull=55, v0=69895) After retessellation of defect 19 (v0=69895), euler #=-18 (143266,429287,286003) : difference with theory (-18) = 0 CORRECTING DEFECT 20 (vertices=690, convex hull=169, v0=79193) After retessellation of defect 20 (v0=79193), euler #=-18 (143347,429610,286245) : difference with theory (-17) = 1 CORRECTING DEFECT 21 (vertices=124, convex hull=40, v0=82391) After retessellation of defect 21 (v0=82391), euler #=-17 (143356,429652,286279) : difference with theory (-16) = 1 CORRECTING DEFECT 22 (vertices=50, convex hull=74, v0=93681) After retessellation of defect 22 (v0=93681), euler #=-16 (143375,429738,286347) : difference with theory (-15) = 1 CORRECTING DEFECT 23 (vertices=40, convex hull=71, v0=95542) After retessellation of defect 23 (v0=95542), euler #=-15 (143390,429813,286408) : difference with theory (-14) = 1 CORRECTING DEFECT 24 (vertices=18, convex hull=24, v0=97974) After retessellation of defect 24 (v0=97974), euler #=-14 (143395,429833,286424) : difference with theory (-13) = 1 CORRECTING DEFECT 25 (vertices=275, convex hull=88, v0=99051) After retessellation of defect 25 (v0=99051), euler #=-13 (143403,429898,286482) : difference with theory (-12) = 1 CORRECTING DEFECT 26 (vertices=27, convex hull=16, v0=99536) After retessellation of defect 26 (v0=99536), euler #=-12 (143407,429915,286496) : difference with theory (-11) = 1 CORRECTING DEFECT 27 (vertices=16, convex hull=14, v0=100032) After retessellation of defect 27 (v0=100032), euler #=-11 (143410,429926,286505) : difference with theory (-10) = 1 CORRECTING DEFECT 28 (vertices=5, convex hull=10, v0=100091) After retessellation of defect 28 (v0=100091), euler #=-10 (143410,429928,286508) : difference with theory (-9) = 1 CORRECTING DEFECT 29 (vertices=34, convex hull=51, v0=102559) After retessellation of defect 29 (v0=102559), euler #=-8 (143423,429990,286559) : difference with theory (-8) = 0 CORRECTING DEFECT 30 (vertices=38, convex hull=66, v0=102690) After retessellation of defect 30 (v0=102690), euler #=-7 (143444,430076,286625) : difference with theory (-7) = 0 CORRECTING DEFECT 31 (vertices=286, convex hull=114, v0=104261) After retessellation of defect 31 (v0=104261), euler #=-6 (143495,430290,286789) : difference with theory (-6) = 0 CORRECTING DEFECT 32 (vertices=46, convex hull=58, v0=107337) After retessellation of defect 32 (v0=107337), euler #=-5 (143507,430348,286836) : difference with theory (-5) = 0 CORRECTING DEFECT 33 (vertices=51, convex hull=73, v0=113122) After retessellation of defect 33 (v0=113122), euler #=-4 (143532,430453,286917) : difference with theory (-4) = 0 CORRECTING DEFECT 34 (vertices=89, convex hull=128, v0=115308) After retessellation of defect 34 (v0=115308), euler #=-3 (143559,430595,287033) : difference with theory (-3) = 0 CORRECTING DEFECT 35 (vertices=22, convex hull=18, v0=127267) After retessellation of defect 35 (v0=127267), euler #=-2 (143560,430601,287039) : difference with theory (-2) = 0 CORRECTING DEFECT 36 (vertices=18, convex hull=49, v0=132825) After retessellation of defect 36 (v0=132825), euler #=-1 (143570,430648,287077) : difference with theory (-1) = 0 CORRECTING DEFECT 37 (vertices=19, convex hull=53, v0=133173) After retessellation of defect 37 (v0=133173), euler #=0 (143577,430687,287110) : difference with theory (0) = 0 CORRECTING DEFECT 38 (vertices=25, convex hull=65, v0=140103) After retessellation of defect 38 (v0=140103), euler #=1 (143591,430753,287163) : difference with theory (1) = 0 CORRECTING DEFECT 39 (vertices=81, convex hull=33, v0=142632) After retessellation of defect 39 (v0=142632), euler #=2 (143595,430779,287186) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.10-->7.92) (max @ vno 53038 --> 55779) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.10-->7.92) (max @ vno 53038 --> 55779) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 156 mutations (35.6%), 282 crossovers (64.4%), 283 vertices were eliminated building final representation... 2537 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=143595, nf=287186, ne=430779, g=0) writing corrected surface to /users/zli/test/fs/a003/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 24.1 minutes 0 defective edges removing intersecting faces 000: 184 intersecting 001: 8 intersecting mris_fix_topology utimesec 1442.071771 mris_fix_topology stimesec 0.204968 mris_fix_topology ru_maxrss 450188 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 58120 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 13536 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 500 mris_fix_topology ru_nivcsw 144960 FSRUNTIME@ mris_fix_topology rh 0.4013 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 147177 - 441525 + 294350 = 2 --> 0 holes F =2V-4: 294350 = 294354-4 (0) 2E=3F: 883050 = 883050 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 143595 - 430779 + 287186 = 2 --> 0 holes F =2V-4: 287186 = 287190-4 (0) 2E=3F: 861558 = 861558 (0) total defect index = 0 /users/zli/test/fs/a003/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 70 intersecting 001: 18 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /users/zli/test/fs/a003/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 Tue Feb 5 15:11:24 EST 2019 /users/zli/test/fs/a003/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs a003 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 /users/zli/test/fs/a003/mri/filled.mgz... reading volume /users/zli/test/fs/a003/mri/brain.finalsurfs.mgz... reading volume /users/zli/test/fs/a003/mri/../mri/aseg.presurf.mgz... reading volume /users/zli/test/fs/a003/mri/wm.mgz... 30095 bright wm thresholded. 639 bright non-wm voxels segmented. reading original surface position from /users/zli/test/fs/a003/surf/lh.orig... computing class statistics... border white: 267297 voxels (1.59%) border gray 312271 voxels (1.86%) WM (101.0): 100.1 +- 7.9 [70.0 --> 110.0] GM (75.0) : 74.6 +- 10.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.8 (was 70) setting MAX_BORDER_WHITE to 112.9 (was 105) setting MIN_BORDER_WHITE to 73.0 (was 85) setting MAX_CSF to 52.6 (was 40) setting MAX_GRAY to 97.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 62.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 42.4 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.03-->3.24) (max @ vno 146837 --> 146857) face area 0.28 +- 0.12 (0.00-->2.72) mean absolute distance = 0.67 +- 0.84 4394 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=105+-6.1, GM=73+-6.1 mean inside = 96.0, mean outside = 78.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=82.8, 97 (97) missing vertices, mean dist 0.3 [0.6 (%35.2)->0.7 (%64.8))] %69 local maxima, %27 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.90 +- 0.25 (0.09-->4.73) (max @ vno 147084 --> 147083) face area 0.28 +- 0.13 (0.00-->2.62) mean absolute distance = 0.35 +- 0.48 4383 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3033430.5, rms=9.222 001: dt: 0.5000, sse=1719194.2, rms=6.348 (31.164%) 002: dt: 0.5000, sse=1194546.4, rms=4.686 (26.182%) 003: dt: 0.5000, sse=978403.7, rms=3.797 (18.957%) 004: dt: 0.5000, sse=884557.2, rms=3.334 (12.209%) 005: dt: 0.5000, sse=854959.8, rms=3.164 (5.108%) 006: dt: 0.5000, sse=836006.7, rms=3.062 (3.200%) rms = 3.05, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=835516.5, rms=3.047 (0.497%) 008: dt: 0.2500, sse=694433.5, rms=1.973 (35.262%) 009: dt: 0.2500, sse=667712.2, rms=1.700 (13.824%) 010: dt: 0.2500, sse=662874.6, rms=1.642 (3.389%) rms = 1.60, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=660514.5, rms=1.605 (2.275%) rms = 1.57, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=656363.7, rms=1.570 (2.195%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=86.5, 105 (24) missing vertices, mean dist -0.2 [0.4 (%79.8)->0.2 (%20.2))] %84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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 0.88 +- 0.24 (0.06-->4.81) (max @ vno 147084 --> 147083) face area 0.34 +- 0.16 (0.00-->3.92) mean absolute distance = 0.22 +- 0.30 3641 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1364823.0, rms=4.784 013: dt: 0.5000, sse=960940.8, rms=2.895 (39.494%) rms = 2.87, time step reduction 1 of 3 to 0.250... 014: dt: 0.5000, sse=953212.3, rms=2.868 (0.925%) 015: dt: 0.2500, sse=808065.2, rms=1.737 (39.432%) 016: dt: 0.2500, sse=784069.5, rms=1.488 (14.352%) 017: dt: 0.2500, sse=783076.5, rms=1.418 (4.678%) 018: dt: 0.2500, sse=783127.1, rms=1.356 (4.388%) rms = 1.35, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=780431.2, rms=1.345 (0.774%) rms = 1.31, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=770972.6, rms=1.307 (2.815%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=88.7, 105 (11) missing vertices, mean dist -0.1 [0.2 (%73.1)->0.2 (%26.9))] %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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 0.88 +- 0.24 (0.05-->4.86) (max @ vno 147084 --> 147083) face area 0.33 +- 0.15 (0.00-->3.97) mean absolute distance = 0.18 +- 0.26 3131 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=937384.2, rms=2.920 021: dt: 0.5000, sse=888077.9, rms=2.440 (16.423%) rms = 2.72, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=781408.7, rms=1.661 (31.952%) 023: dt: 0.2500, sse=759000.2, rms=1.306 (21.348%) 024: dt: 0.2500, sse=749404.7, rms=1.217 (6.834%) rms = 1.22, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=745397.4, rms=1.217 (0.025%) rms = 1.18, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=736472.4, rms=1.176 (3.350%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=89.2, 94 (5) missing vertices, mean dist -0.0 [0.2 (%55.4)->0.2 (%44.6))] %93 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /users/zli/test/fs/a003/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=744864.8, rms=1.378 rms = 1.40, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=721143.1, rms=1.038 (24.645%) 028: dt: 0.2500, sse=742487.2, rms=0.879 (15.379%) rms = 0.90, time step reduction 2 of 3 to 0.125... rms = 0.88, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=725270.3, rms=0.878 (0.146%) positioning took 0.4 minutes generating cortex label... 7 non-cortical segments detected only using segment with 7593 vertices erasing segment 1 (vno[0] = 83704) erasing segment 2 (vno[0] = 98841) erasing segment 3 (vno[0] = 101217) erasing segment 4 (vno[0] = 102339) erasing segment 5 (vno[0] = 104628) erasing segment 6 (vno[0] = 107945) writing cortex label to /users/zli/test/fs/a003/label/lh.cortex.label... writing curvature file /users/zli/test/fs/a003/surf/lh.curv writing smoothed area to lh.area writing curvature file /users/zli/test/fs/a003/surf/lh.area vertex spacing 0.88 +- 0.25 (0.04-->4.86) (max @ vno 147083 --> 147084) face area 0.32 +- 0.15 (0.00-->3.95) refinement took 4.8 minutes #-------------------------------------------- #@# Make White Surf rh Tue Feb 5 15:16:11 EST 2019 /users/zli/test/fs/a003/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs a003 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 /users/zli/test/fs/a003/mri/filled.mgz... reading volume /users/zli/test/fs/a003/mri/brain.finalsurfs.mgz... reading volume /users/zli/test/fs/a003/mri/../mri/aseg.presurf.mgz... reading volume /users/zli/test/fs/a003/mri/wm.mgz... 30095 bright wm thresholded. 639 bright non-wm voxels segmented. reading original surface position from /users/zli/test/fs/a003/surf/rh.orig... computing class statistics... border white: 267297 voxels (1.59%) border gray 312271 voxels (1.86%) WM (101.0): 100.1 +- 7.9 [70.0 --> 110.0] GM (75.0) : 74.6 +- 10.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.8 (was 70) setting MAX_BORDER_WHITE to 112.9 (was 105) setting MIN_BORDER_WHITE to 73.0 (was 85) setting MAX_CSF to 52.6 (was 40) setting MAX_GRAY to 97.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 62.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 42.4 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.02-->5.10) (max @ vno 57360 --> 60200) face area 0.28 +- 0.13 (0.00-->5.68) mean absolute distance = 0.66 +- 0.83 4290 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=105+-5.2, GM=73+-7.0 mean inside = 96.2, mean outside = 78.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=83.2, 82 (82) missing vertices, mean dist 0.2 [0.6 (%36.7)->0.7 (%63.3))] %70 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.90 +- 0.25 (0.09-->7.38) (max @ vno 57360 --> 53025) face area 0.28 +- 0.13 (0.00-->5.60) mean absolute distance = 0.33 +- 0.47 3625 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2963408.8, rms=9.239 001: dt: 0.5000, sse=1668563.0, rms=6.325 (31.538%) 002: dt: 0.5000, sse=1164394.4, rms=4.687 (25.900%) 003: dt: 0.5000, sse=963693.8, rms=3.839 (18.083%) 004: dt: 0.5000, sse=874325.5, rms=3.394 (11.602%) 005: dt: 0.5000, sse=845604.8, rms=3.235 (4.670%) 006: dt: 0.5000, sse=829191.2, rms=3.133 (3.151%) rms = 3.12, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=828744.1, rms=3.119 (0.451%) 008: dt: 0.2500, sse=681451.8, rms=1.998 (35.938%) 009: dt: 0.2500, sse=652676.3, rms=1.713 (14.288%) 010: dt: 0.2500, sse=647355.2, rms=1.643 (4.058%) rms = 1.60, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=643544.4, rms=1.603 (2.420%) rms = 1.56, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=640514.2, rms=1.557 (2.908%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=86.7, 81 (26) missing vertices, mean dist -0.2 [0.4 (%77.9)->0.3 (%22.1))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.24 (0.08-->8.64) (max @ vno 57360 --> 53025) face area 0.34 +- 0.16 (0.00-->7.45) mean absolute distance = 0.22 +- 0.31 3898 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1298442.4, rms=4.650 013: dt: 0.5000, sse=929550.4, rms=2.865 (38.395%) rms = 2.90, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=837086.2, rms=2.204 (23.065%) 015: dt: 0.2500, sse=784068.6, rms=1.697 (22.997%) 016: dt: 0.2500, sse=769653.8, rms=1.491 (12.134%) 017: dt: 0.2500, sse=760797.8, rms=1.416 (5.021%) rms = 1.37, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=758078.7, rms=1.374 (2.956%) rms = 1.33, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=753754.7, rms=1.333 (2.989%) 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=88.6, 77 (21) missing vertices, mean dist -0.1 [0.2 (%71.0)->0.2 (%29.0))] %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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 0.88 +- 0.24 (0.04-->9.21) (max @ vno 57360 --> 53025) face area 0.33 +- 0.16 (0.00-->7.55) mean absolute distance = 0.18 +- 0.27 3517 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=895743.9, rms=2.769 020: dt: 0.5000, sse=859905.6, rms=2.452 (11.434%) rms = 2.76, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=766729.4, rms=1.681 (31.473%) 022: dt: 0.2500, sse=736366.7, rms=1.330 (20.870%) 023: dt: 0.2500, sse=730252.6, rms=1.244 (6.433%) rms = 1.24, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=730028.1, rms=1.238 (0.492%) rms = 1.20, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=726109.8, rms=1.195 (3.450%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=89.1, 95 (15) missing vertices, mean dist -0.0 [0.2 (%54.6)->0.2 (%45.4))] %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /users/zli/test/fs/a003/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=734107.8, rms=1.385 rms = 1.42, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=709974.7, rms=1.053 (23.943%) 027: dt: 0.2500, sse=704017.3, rms=0.899 (14.621%) rms = 0.92, time step reduction 2 of 3 to 0.125... rms = 0.90, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=701177.4, rms=0.897 (0.218%) positioning took 0.4 minutes generating cortex label... 10 non-cortical segments detected only using segment with 6967 vertices erasing segment 0 (vno[0] = 40976) erasing segment 2 (vno[0] = 50318) erasing segment 3 (vno[0] = 96889) erasing segment 4 (vno[0] = 96931) erasing segment 5 (vno[0] = 96938) erasing segment 6 (vno[0] = 99365) erasing segment 7 (vno[0] = 100562) erasing segment 8 (vno[0] = 101756) erasing segment 9 (vno[0] = 110381) writing cortex label to /users/zli/test/fs/a003/label/rh.cortex.label... writing curvature file /users/zli/test/fs/a003/surf/rh.curv writing smoothed area to rh.area writing curvature file /users/zli/test/fs/a003/surf/rh.area vertex spacing 0.88 +- 0.25 (0.03-->9.31) (max @ vno 53025 --> 57360) face area 0.33 +- 0.16 (0.00-->7.37) refinement took 4.5 minutes #-------------------------------------------- #@# Smooth2 lh Tue Feb 5 15:20:43 EST 2019 /users/zli/test/fs/a003/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 Tue Feb 5 15:20:50 EST 2019 /users/zli/test/fs/a003/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 Tue Feb 5 15:20:58 EST 2019 /users/zli/test/fs/a003/scripts mris_inflate -rusage /users/zli/test/fs/a003/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 46.3 mm, total surface area = 86850 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.178 (target=0.015) step 005: RMS=0.126 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.076 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.039 (target=0.015) step 040: RMS=0.034 (target=0.015) step 045: RMS=0.030 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. inflation took 0.5 minutes mris_inflate utimesec 32.480062 mris_inflate stimesec 0.102984 mris_inflate ru_maxrss 189652 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 25235 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11512 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 347 mris_inflate ru_nivcsw 4808 #-------------------------------------------- #@# Inflation2 rh Tue Feb 5 15:21:31 EST 2019 /users/zli/test/fs/a003/scripts mris_inflate -rusage /users/zli/test/fs/a003/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 45.6 mm, total surface area = 85145 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.179 (target=0.015) step 005: RMS=0.124 (target=0.015) step 010: RMS=0.094 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.039 (target=0.015) step 040: RMS=0.034 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. inflation took 0.5 minutes mris_inflate utimesec 29.495516 mris_inflate stimesec 0.074988 mris_inflate ru_maxrss 185084 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 24605 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11232 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 365 mris_inflate ru_nivcsw 3007 #-------------------------------------------- #@# Curv .H and .K lh Tue Feb 5 15:22:01 EST 2019 /users/zli/test/fs/a003/surf mris_curvature -w lh.white.preaparc total integrated curvature = -6.478*4pi (-81.409) --> 7 handles ICI = 178.1, FI = 1946.3, variation=30563.156 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 179 vertices thresholded to be in k1 ~ [-0.38 0.73], k2 ~ [-0.09 0.15] total integrated curvature = 0.486*4pi (6.113) --> 1 handles ICI = 1.6, FI = 11.1, variation=185.746 129 vertices thresholded to be in [-0.03 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 124 vertices thresholded to be in [-0.16 0.25] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.025 done. #-------------------------------------------- #@# Curv .H and .K rh Tue Feb 5 15:23:28 EST 2019 /users/zli/test/fs/a003/surf mris_curvature -w rh.white.preaparc total integrated curvature = -6.078*4pi (-76.379) --> 7 handles ICI = 173.3, FI = 1940.2, variation=30280.259 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 160 vertices thresholded to be in k1 ~ [-0.28 0.66], k2 ~ [-0.12 0.10] total integrated curvature = 0.435*4pi (5.461) --> 1 handles ICI = 1.6, FI = 11.4, variation=190.991 138 vertices thresholded to be in [-0.03 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 145 vertices thresholded to be in [-0.16 0.29] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.027 done. #----------------------------------------- #@# Curvature Stats lh Tue Feb 5 15:24:52 EST 2019 /users/zli/test/fs/a003/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm a003 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 [ a003/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 [ 280 ] Gb_filter = 0 WARN: S lookup min: -0.470597 WARN: S explicit min: 0.000000 vertex = 25 #----------------------------------------- #@# Curvature Stats rh Tue Feb 5 15:24:56 EST 2019 /users/zli/test/fs/a003/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm a003 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 [ a003/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 [ 247 ] Gb_filter = 0 #-------------------------------------------- #@# Sphere lh Tue Feb 5 15:25:01 EST 2019 /users/zli/test/fs/a003/scripts mris_sphere -rusage /users/zli/test/fs/a003/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 0.302... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.24 pass 1: epoch 2 of 3 starting distance error %20.12 unfolding complete - removing small folds... starting distance error %20.05 removing remaining folds... final distance error %20.07 MRISunfold() return, current seed 1234 -01: dt=0.0000, 345 negative triangles 229: dt=0.9900, 345 negative triangles 230: dt=0.9900, 191 negative triangles 231: dt=0.9900, 136 negative triangles 232: dt=0.9900, 120 negative triangles 233: dt=0.9900, 103 negative triangles 234: dt=0.9900, 110 negative triangles 235: dt=0.9900, 101 negative triangles 236: dt=0.9900, 88 negative triangles 237: dt=0.9900, 85 negative triangles 238: dt=0.9900, 64 negative triangles 239: dt=0.9900, 79 negative triangles 240: dt=0.9900, 62 negative triangles 241: dt=0.9900, 62 negative triangles 242: dt=0.9900, 60 negative triangles 243: dt=0.9900, 56 negative triangles 244: dt=0.9900, 64 negative triangles 245: dt=0.9900, 65 negative triangles 246: dt=0.9900, 52 negative triangles 247: dt=0.9900, 55 negative triangles 248: dt=0.9900, 56 negative triangles 249: dt=0.9900, 44 negative triangles 250: dt=0.9900, 41 negative triangles 251: dt=0.9900, 42 negative triangles 252: dt=0.9900, 38 negative triangles 253: dt=0.9900, 38 negative triangles 254: dt=0.9900, 35 negative triangles 255: dt=0.9900, 38 negative triangles 256: dt=0.9900, 35 negative triangles 257: dt=0.9900, 30 negative triangles 258: dt=0.9900, 30 negative triangles 259: dt=0.9900, 30 negative triangles 260: dt=0.9900, 30 negative triangles 261: dt=0.9900, 28 negative triangles 262: dt=0.9900, 25 negative triangles 263: dt=0.9900, 27 negative triangles 264: dt=0.9900, 27 negative triangles 265: dt=0.9900, 29 negative triangles 266: dt=0.9900, 28 negative triangles 267: dt=0.9900, 28 negative triangles 268: dt=0.9900, 28 negative triangles 269: dt=0.9900, 28 negative triangles 270: dt=0.9900, 27 negative triangles 271: dt=0.9900, 27 negative triangles 272: dt=0.9405, 28 negative triangles 273: dt=0.9405, 27 negative triangles 274: dt=0.9405, 25 negative triangles 275: dt=0.9405, 31 negative triangles 276: dt=0.9405, 27 negative triangles 277: dt=0.9405, 27 negative triangles 278: dt=0.9405, 25 negative triangles 279: dt=0.9405, 26 negative triangles 280: dt=0.9405, 28 negative triangles 281: dt=0.9405, 26 negative triangles 282: dt=0.8935, 27 negative triangles 283: dt=0.8935, 27 negative triangles 284: dt=0.8935, 27 negative triangles 285: dt=0.8935, 25 negative triangles 286: dt=0.8935, 29 negative triangles 287: dt=0.8935, 27 negative triangles 288: dt=0.8935, 24 negative triangles 289: dt=0.8935, 26 negative triangles 290: dt=0.8935, 24 negative triangles 291: dt=0.8935, 26 negative triangles 292: dt=0.8935, 22 negative triangles 293: dt=0.8935, 26 negative triangles 294: dt=0.8935, 25 negative triangles 295: dt=0.8935, 23 negative triangles 296: dt=0.8935, 22 negative triangles 297: dt=0.8935, 27 negative triangles 298: dt=0.8935, 25 negative triangles 299: dt=0.8935, 27 negative triangles 300: dt=0.8935, 22 negative triangles 301: dt=0.8935, 26 negative triangles 302: dt=0.8488, 24 negative triangles 303: dt=0.8488, 24 negative triangles 304: dt=0.8488, 25 negative triangles 305: dt=0.8488, 22 negative triangles 306: dt=0.8488, 24 negative triangles 307: dt=0.8488, 24 negative triangles 308: dt=0.8488, 22 negative triangles 309: dt=0.8488, 24 negative triangles 310: dt=0.8488, 25 negative triangles 311: dt=0.8488, 24 negative triangles 312: dt=0.8064, 24 negative triangles 313: dt=0.8064, 22 negative triangles 314: dt=0.8064, 26 negative triangles 315: dt=0.8064, 28 negative triangles 316: dt=0.8064, 26 negative triangles 317: dt=0.8064, 23 negative triangles 318: dt=0.8064, 22 negative triangles 319: dt=0.8064, 24 negative triangles 320: dt=0.8064, 23 negative triangles 321: dt=0.8064, 26 negative triangles 322: dt=0.7660, 23 negative triangles 323: dt=0.7660, 22 negative triangles 324: dt=0.7660, 24 negative triangles 325: dt=0.7660, 25 negative triangles 326: dt=0.7660, 25 negative triangles 327: dt=0.7660, 22 negative triangles 328: dt=0.7660, 26 negative triangles 329: dt=0.7660, 23 negative triangles 330: dt=0.7660, 21 negative triangles 331: dt=0.7660, 23 negative triangles 332: dt=0.7660, 22 negative triangles 333: dt=0.7660, 25 negative triangles 334: dt=0.7660, 24 negative triangles 335: dt=0.7660, 22 negative triangles 336: dt=0.7660, 25 negative triangles 337: dt=0.7660, 27 negative triangles 338: dt=0.7660, 22 negative triangles 339: dt=0.7660, 23 negative triangles 340: dt=0.7277, 21 negative triangles 341: dt=0.7277, 18 negative triangles 342: dt=0.7277, 20 negative triangles 343: dt=0.7277, 20 negative triangles 344: dt=0.7277, 24 negative triangles 345: dt=0.7277, 22 negative triangles 346: dt=0.7277, 21 negative triangles 347: dt=0.7277, 22 negative triangles 348: dt=0.7277, 23 negative triangles 349: dt=0.7277, 21 negative triangles 350: dt=0.7277, 22 negative triangles 351: dt=0.6914, 22 negative triangles 352: dt=0.6914, 20 negative triangles 353: dt=0.6914, 23 negative triangles 354: dt=0.6914, 24 negative triangles 355: dt=0.6914, 21 negative triangles 356: dt=0.6914, 21 negative triangles 357: dt=0.6914, 21 negative triangles 358: dt=0.6914, 17 negative triangles 359: dt=0.6914, 22 negative triangles 360: dt=0.6914, 23 negative triangles 361: dt=0.6914, 18 negative triangles 362: dt=0.6914, 20 negative triangles 363: dt=0.6914, 19 negative triangles 364: dt=0.6914, 25 negative triangles 365: dt=0.6914, 21 negative triangles 366: dt=0.6914, 20 negative triangles 367: dt=0.6914, 23 negative triangles 368: dt=0.6568, 22 negative triangles 369: dt=0.6568, 20 negative triangles 370: dt=0.6568, 20 negative triangles 371: dt=0.6568, 23 negative triangles 372: dt=0.6568, 22 negative triangles 373: dt=0.6568, 20 negative triangles 374: dt=0.6568, 19 negative triangles 375: dt=0.6568, 18 negative triangles 376: dt=0.6568, 18 negative triangles 377: dt=0.6568, 17 negative triangles 378: dt=0.6568, 16 negative triangles 379: dt=0.6568, 19 negative triangles 380: dt=0.6568, 18 negative triangles 381: dt=0.6568, 15 negative triangles 382: dt=0.6568, 15 negative triangles 383: dt=0.6568, 15 negative triangles 384: dt=0.6568, 18 negative triangles 385: dt=0.6568, 20 negative triangles 386: dt=0.6568, 16 negative triangles 387: dt=0.6568, 14 negative triangles 388: dt=0.6568, 17 negative triangles 389: dt=0.6568, 16 negative triangles 390: dt=0.6568, 20 negative triangles 391: dt=0.6568, 14 negative triangles 392: dt=0.6568, 13 negative triangles 393: dt=0.6568, 12 negative triangles 394: dt=0.6568, 12 negative triangles 395: dt=0.6568, 7 negative triangles 396: dt=0.6568, 13 negative triangles 397: dt=0.6568, 14 negative triangles 398: dt=0.6568, 12 negative triangles 399: dt=0.6568, 15 negative triangles 400: dt=0.6568, 12 negative triangles 401: dt=0.6568, 8 negative triangles 402: dt=0.6568, 14 negative triangles 403: dt=0.6568, 7 negative triangles 404: dt=0.6568, 13 negative triangles 405: dt=0.6239, 7 negative triangles 406: dt=0.6239, 12 negative triangles 407: dt=0.6239, 10 negative triangles 408: dt=0.6239, 8 negative triangles 409: dt=0.6239, 6 negative triangles 410: dt=0.6239, 6 negative triangles 411: dt=0.6239, 5 negative triangles 412: dt=0.6239, 6 negative triangles 413: dt=0.6239, 7 negative triangles 414: dt=0.6239, 6 negative triangles 415: dt=0.6239, 5 negative triangles 416: dt=0.6239, 5 negative triangles 417: dt=0.6239, 7 negative triangles 418: dt=0.6239, 5 negative triangles 419: dt=0.6239, 7 negative triangles 420: dt=0.6239, 4 negative triangles 421: dt=0.6239, 2 negative triangles 422: dt=0.6239, 4 negative triangles 423: dt=0.6239, 3 negative triangles 424: dt=0.6239, 1 negative triangles 425: dt=0.6239, 2 negative triangles 426: dt=0.6239, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.89 hours mris_sphere utimesec 3185.869674 mris_sphere stimesec 0.398939 mris_sphere ru_maxrss 260712 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 43360 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10360 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 326 mris_sphere ru_nivcsw 334576 FSRUNTIME@ mris_sphere 0.8865 hours 1 threads #-------------------------------------------- #@# Sphere rh Tue Feb 5 16:18:12 EST 2019 /users/zli/test/fs/a003/scripts mris_sphere -rusage /users/zli/test/fs/a003/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 0.309... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.11 pass 1: epoch 2 of 3 starting distance error %20.08 unfolding complete - removing small folds... starting distance error %20.00 removing remaining folds... final distance error %20.01 MRISunfold() return, current seed 1234 -01: dt=0.0000, 268 negative triangles 197: dt=0.9900, 268 negative triangles 198: dt=0.9900, 128 negative triangles 199: dt=0.9900, 130 negative triangles 200: dt=0.9900, 119 negative triangles 201: dt=0.9900, 110 negative triangles 202: dt=0.9900, 102 negative triangles 203: dt=0.9900, 109 negative triangles 204: dt=0.9900, 97 negative triangles 205: dt=0.9900, 100 negative triangles 206: dt=0.9900, 91 negative triangles 207: dt=0.9900, 93 negative triangles 208: dt=0.9900, 89 negative triangles 209: dt=0.9900, 82 negative triangles 210: dt=0.9900, 83 negative triangles 211: dt=0.9900, 79 negative triangles 212: dt=0.9900, 77 negative triangles 213: dt=0.9900, 68 negative triangles 214: dt=0.9900, 72 negative triangles 215: dt=0.9900, 61 negative triangles 216: dt=0.9900, 64 negative triangles 217: dt=0.9900, 62 negative triangles 218: dt=0.9900, 52 negative triangles 219: dt=0.9900, 51 negative triangles 220: dt=0.9900, 44 negative triangles 221: dt=0.9900, 45 negative triangles 222: dt=0.9900, 44 negative triangles 223: dt=0.9900, 45 negative triangles 224: dt=0.9900, 42 negative triangles 225: dt=0.9900, 37 negative triangles 226: dt=0.9900, 34 negative triangles 227: dt=0.9900, 33 negative triangles 228: dt=0.9900, 29 negative triangles 229: dt=0.9900, 32 negative triangles 230: dt=0.9900, 33 negative triangles 231: dt=0.9900, 26 negative triangles 232: dt=0.9900, 26 negative triangles 233: dt=0.9900, 27 negative triangles 234: dt=0.9900, 24 negative triangles 235: dt=0.9900, 19 negative triangles 236: dt=0.9900, 19 negative triangles 237: dt=0.9900, 17 negative triangles 238: dt=0.9900, 18 negative triangles 239: dt=0.9900, 14 negative triangles 240: dt=0.9900, 13 negative triangles 241: dt=0.9900, 15 negative triangles 242: dt=0.9900, 17 negative triangles 243: dt=0.9900, 14 negative triangles 244: dt=0.9900, 15 negative triangles 245: dt=0.9900, 11 negative triangles 246: dt=0.9900, 12 negative triangles 247: dt=0.9900, 13 negative triangles 248: dt=0.9900, 13 negative triangles 249: dt=0.9900, 10 negative triangles 250: dt=0.9900, 12 negative triangles 251: dt=0.9900, 10 negative triangles 252: dt=0.9900, 10 negative triangles 253: dt=0.9900, 8 negative triangles 254: dt=0.9900, 11 negative triangles 255: dt=0.9900, 8 negative triangles 256: dt=0.9900, 7 negative triangles 257: dt=0.9900, 7 negative triangles 258: dt=0.9900, 7 negative triangles 259: dt=0.9900, 6 negative triangles 260: dt=0.9900, 4 negative triangles 261: dt=0.9900, 2 negative triangles 262: dt=0.9900, 3 negative triangles 263: dt=0.9900, 3 negative triangles 264: dt=0.9900, 2 negative triangles 265: dt=0.9900, 1 negative triangles 266: dt=0.9900, 2 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.74 hours mris_sphere utimesec 2642.619260 mris_sphere stimesec 0.229965 mris_sphere ru_maxrss 254400 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 42291 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10104 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 339 mris_sphere ru_nivcsw 267858 FSRUNTIME@ mris_sphere 0.7353 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Tue Feb 5 17:02:19 EST 2019 /users/zli/test/fs/a003/scripts mris_register -curv -rusage /users/zli/test/fs/a003/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /users/zli/Applications/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /users/zli/test/fs/a003/scripts cmdline mris_register -curv -rusage /users/zli/test/fs/a003/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /users/zli/Applications/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 /users/zli/Applications/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=compu, 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=compu, 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 = 5.332 curvature mean = 0.025, std = 0.815 curvature mean = 0.026, std = 0.847 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, 16.00) sse = 342814.6, tmin=0.9118 d=32.00 min @ (8.00, 0.00, -8.00) sse = 292310.1, tmin=1.8364 d=16.00 min @ (-4.00, -4.00, 4.00) sse = 264843.0, tmin=2.7641 d=8.00 min @ (0.00, 2.00, -2.00) sse = 253352.4, tmin=3.7116 d=4.00 min @ (-1.00, -1.00, 0.00) sse = 252318.5, tmin=4.6648 d=2.00 min @ (0.00, 0.50, 0.00) sse = 251814.8, tmin=5.6177 d=1.00 min @ (0.00, 0.00, 0.25) sse = 251698.5, tmin=6.5666 d=0.50 min @ (-0.12, -0.12, 0.00) sse = 251692.0, tmin=7.5132 tol=1.0e+00, sigma=0.5, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 7.51 min curvature mean = -0.002, std = 0.841 curvature mean = 0.008, std = 0.937 curvature mean = -0.007, std = 0.851 curvature mean = 0.003, std = 0.972 curvature mean = -0.009, std = 0.853 curvature mean = 0.000, std = 0.987 2 Reading smoothwm curvature mean = -0.033, std = 0.339 curvature mean = 0.035, std = 0.252 curvature mean = 0.071, std = 0.298 curvature mean = 0.029, std = 0.311 curvature mean = 0.043, std = 0.463 curvature mean = 0.028, std = 0.339 curvature mean = 0.023, std = 0.595 curvature mean = 0.028, std = 0.351 curvature mean = 0.009, std = 0.701 MRISregister() return, current seed 0 -01: dt=0.0000, 75 negative triangles 121: dt=0.9900, 75 negative triangles expanding nbhd size to 1 122: dt=0.9900, 91 negative triangles 123: dt=0.9900, 72 negative triangles 124: dt=0.9900, 76 negative triangles 125: dt=0.9900, 69 negative triangles 126: dt=0.9900, 69 negative triangles 127: dt=0.9900, 65 negative triangles 128: dt=0.9900, 61 negative triangles 129: dt=0.9900, 60 negative triangles 130: dt=0.9900, 59 negative triangles 131: dt=0.9900, 53 negative triangles 132: dt=0.9900, 50 negative triangles 133: dt=0.9900, 48 negative triangles 134: dt=0.9900, 45 negative triangles 135: dt=0.9900, 43 negative triangles 136: dt=0.9900, 41 negative triangles 137: dt=0.9900, 43 negative triangles 138: dt=0.9900, 37 negative triangles 139: dt=0.9900, 37 negative triangles 140: dt=0.9900, 35 negative triangles 141: dt=0.9900, 36 negative triangles 142: dt=0.9900, 31 negative triangles 143: dt=0.9900, 31 negative triangles 144: dt=0.9900, 31 negative triangles 145: dt=0.9900, 28 negative triangles 146: dt=0.9900, 29 negative triangles 147: dt=0.9900, 28 negative triangles 148: dt=0.9900, 26 negative triangles 149: dt=0.9900, 24 negative triangles 150: dt=0.9900, 23 negative triangles 151: dt=0.9900, 23 negative triangles 152: dt=0.9900, 24 negative triangles 153: dt=0.9900, 23 negative triangles 154: dt=0.9900, 22 negative triangles 155: dt=0.9900, 20 negative triangles 156: dt=0.9900, 20 negative triangles 157: dt=0.9900, 20 negative triangles 158: dt=0.9900, 20 negative triangles 159: dt=0.9900, 19 negative triangles 160: dt=0.9900, 19 negative triangles 161: dt=0.9900, 20 negative triangles 162: dt=0.9900, 23 negative triangles 163: dt=0.9900, 20 negative triangles 164: dt=0.9900, 20 negative triangles 165: dt=0.9900, 19 negative triangles 166: dt=0.9900, 19 negative triangles 167: dt=0.9900, 19 negative triangles 168: dt=0.9900, 20 negative triangles 169: dt=0.9900, 18 negative triangles 170: dt=0.9900, 18 negative triangles 171: dt=0.9900, 18 negative triangles 172: dt=0.9900, 19 negative triangles 173: dt=0.9900, 17 negative triangles 174: dt=0.9900, 16 negative triangles 175: dt=0.9900, 16 negative triangles 176: dt=0.9900, 17 negative triangles 177: dt=0.9900, 18 negative triangles 178: dt=0.9900, 14 negative triangles 179: dt=0.9900, 13 negative triangles 180: dt=0.9900, 13 negative triangles 181: dt=0.9900, 14 negative triangles 182: dt=0.9900, 14 negative triangles 183: dt=0.9900, 12 negative triangles 184: dt=0.9900, 11 negative triangles 185: dt=0.9900, 11 negative triangles 186: dt=0.9900, 11 negative triangles 187: dt=0.9900, 13 negative triangles 188: dt=0.9900, 11 negative triangles 189: dt=0.9900, 9 negative triangles 190: dt=0.9900, 9 negative triangles 191: dt=0.9900, 10 negative triangles 192: dt=0.9900, 7 negative triangles 193: dt=0.9900, 7 negative triangles 194: dt=0.9900, 10 negative triangles 195: dt=0.9900, 8 negative triangles 196: dt=0.9900, 6 negative triangles 197: dt=0.9900, 5 negative triangles 198: dt=0.9900, 4 negative triangles 199: dt=0.9900, 4 negative triangles 200: dt=0.9900, 3 negative triangles 201: dt=0.9900, 3 negative triangles 202: dt=0.9900, 2 negative triangles 203: dt=0.9900, 4 negative triangles 204: dt=0.9900, 4 negative triangles 205: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.93 hours mris_register utimesec 3334.505078 mris_register stimesec 0.349946 mris_register ru_maxrss 244568 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 33725 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 5584 mris_register ru_oublock 10360 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 387 mris_register ru_nivcsw 338609 FSRUNTIME@ mris_register 0.9278 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Tue Feb 5 17:58:00 EST 2019 /users/zli/test/fs/a003/scripts mris_register -curv -rusage /users/zli/test/fs/a003/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /users/zli/Applications/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /users/zli/test/fs/a003/scripts cmdline mris_register -curv -rusage /users/zli/test/fs/a003/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /users/zli/Applications/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 /users/zli/Applications/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=compu, 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=compu, 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 = 5.407 curvature mean = 0.024, std = 0.798 curvature mean = 0.023, std = 0.854 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 16.00) sse = 358439.9, tmin=0.9691 d=32.00 min @ (-8.00, 0.00, 0.00) sse = 301436.5, tmin=1.9484 d=16.00 min @ (0.00, -4.00, 4.00) sse = 257404.6, tmin=2.9281 d=8.00 min @ (0.00, 0.00, -2.00) sse = 252915.9, tmin=3.9269 d=4.00 min @ (-1.00, 0.00, 0.00) sse = 250716.2, tmin=4.9243 d=2.00 min @ (0.00, -0.50, 0.50) sse = 250042.4, tmin=5.9204 d=1.00 min @ (-0.25, 0.00, 0.00) sse = 249936.6, tmin=6.9157 d=0.50 min @ (0.12, 0.12, -0.12) sse = 249907.1, tmin=7.9081 tol=1.0e+00, sigma=0.5, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 7.91 min curvature mean = -0.004, std = 0.825 curvature mean = 0.008, std = 0.942 curvature mean = -0.007, std = 0.835 curvature mean = 0.003, std = 0.976 curvature mean = -0.009, std = 0.836 curvature mean = 0.001, std = 0.991 2 Reading smoothwm curvature mean = -0.029, std = 0.321 curvature mean = 0.033, std = 0.241 curvature mean = 0.066, std = 0.310 curvature mean = 0.028, std = 0.300 curvature mean = 0.038, std = 0.483 curvature mean = 0.028, std = 0.327 curvature mean = 0.020, std = 0.622 curvature mean = 0.027, std = 0.338 curvature mean = 0.008, std = 0.732 MRISregister() return, current seed 0 -01: dt=0.0000, 58 negative triangles 112: dt=0.9900, 58 negative triangles expanding nbhd size to 1 113: dt=0.9900, 83 negative triangles 114: dt=0.9900, 59 negative triangles 115: dt=0.9900, 55 negative triangles 116: dt=0.9900, 56 negative triangles 117: dt=0.9900, 51 negative triangles 118: dt=0.9900, 44 negative triangles 119: dt=0.9900, 40 negative triangles 120: dt=0.9900, 32 negative triangles 121: dt=0.9900, 29 negative triangles 122: dt=0.9900, 18 negative triangles 123: dt=0.9900, 21 negative triangles 124: dt=0.9900, 14 negative triangles 125: dt=0.9900, 11 negative triangles 126: dt=0.9900, 11 negative triangles 127: dt=0.9900, 6 negative triangles 128: dt=0.9900, 4 negative triangles 129: dt=0.9900, 5 negative triangles 130: dt=0.9900, 2 negative triangles 131: dt=0.9900, 3 negative triangles 132: dt=0.9900, 1 negative triangles 133: dt=0.9900, 1 negative triangles 134: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.87 hours mris_register utimesec 3120.322638 mris_register stimesec 0.298954 mris_register ru_maxrss 238396 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 32444 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 5584 mris_register ru_oublock 10104 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 314 mris_register ru_nivcsw 316081 FSRUNTIME@ mris_register 0.8683 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Tue Feb 5 18:50:06 EST 2019 /users/zli/test/fs/a003/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 Tue Feb 5 18:50:09 EST 2019 /users/zli/test/fs/a003/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 Tue Feb 5 18:50:11 EST 2019 /users/zli/test/fs/a003/scripts mrisp_paint -a 5 /users/zli/Applications/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 /users/zli/Applications/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh Tue Feb 5 18:50:13 EST 2019 /users/zli/test/fs/a003/scripts mrisp_paint -a 5 /users/zli/Applications/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 /users/zli/Applications/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Tue Feb 5 18:50:15 EST 2019 /users/zli/test/fs/a003/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 a003 lh ../surf/lh.sphere.reg /users/zli/Applications/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 /users/zli/Applications/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... 1132 labels changed using aseg relabeling using gibbs priors... 000: 3342 changed, 147177 examined... 001: 802 changed, 14191 examined... 002: 197 changed, 4374 examined... 003: 80 changed, 1187 examined... 004: 26 changed, 480 examined... 005: 8 changed, 147 examined... 006: 1 changed, 44 examined... 007: 0 changed, 7 examined... 234 labels changed using aseg 000: 116 total segments, 77 labels (331 vertices) changed 001: 42 total segments, 4 labels (7 vertices) changed 002: 38 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... 2291 vertices marked for relabeling... 2291 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 14 seconds. #----------------------------------------- #@# Cortical Parc rh Tue Feb 5 18:50:29 EST 2019 /users/zli/test/fs/a003/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 a003 rh ../surf/rh.sphere.reg /users/zli/Applications/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 /users/zli/Applications/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... 1135 labels changed using aseg relabeling using gibbs priors... 000: 3039 changed, 143595 examined... 001: 713 changed, 12998 examined... 002: 160 changed, 3937 examined... 003: 52 changed, 938 examined... 004: 22 changed, 332 examined... 005: 11 changed, 135 examined... 006: 7 changed, 68 examined... 007: 1 changed, 43 examined... 008: 0 changed, 7 examined... 156 labels changed using aseg 000: 105 total segments, 68 labels (358 vertices) changed 001: 39 total segments, 2 labels (3 vertices) changed 002: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2165 vertices marked for relabeling... 2165 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 14 seconds. #-------------------------------------------- #@# Make Pial Surf lh Tue Feb 5 18:50:43 EST 2019 /users/zli/test/fs/a003/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs a003 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 /users/zli/test/fs/a003/mri/filled.mgz... reading volume /users/zli/test/fs/a003/mri/brain.finalsurfs.mgz... reading volume /users/zli/test/fs/a003/mri/../mri/aseg.presurf.mgz... reading volume /users/zli/test/fs/a003/mri/wm.mgz... 30095 bright wm thresholded. 639 bright non-wm voxels segmented. reading original surface position from /users/zli/test/fs/a003/surf/lh.orig... computing class statistics... border white: 267297 voxels (1.59%) border gray 312271 voxels (1.86%) WM (101.0): 100.1 +- 7.9 [70.0 --> 110.0] GM (75.0) : 74.6 +- 10.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.8 (was 70) setting MAX_BORDER_WHITE to 112.9 (was 105) setting MIN_BORDER_WHITE to 73.0 (was 85) setting MAX_CSF to 52.6 (was 40) setting MAX_GRAY to 97.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 62.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 42.4 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-6.1, GM=73+-6.1 mean inside = 96.0, mean outside = 78.3 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.88 +- 0.25 (0.04-->4.86) (max @ vno 147083 --> 147084) face area 0.32 +- 0.15 (0.00-->3.94) mean absolute distance = 0.63 +- 0.79 3178 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 66 points - only 0.00% unknown removing 1 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 86 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown deleting segment 9 with 6 points - only 0.00% unknown deleting segment 10 with 9 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown deleting segment 12 with 5 points - only 0.00% unknown mean border=82.6, 154 (154) missing vertices, mean dist 0.4 [1.0 (%9.5)->0.6 (%90.5))] %67 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.90 +- 0.25 (0.04-->5.98) (max @ vno 147084 --> 147083) face area 0.32 +- 0.15 (0.00-->2.64) mean absolute distance = 0.34 +- 0.47 3543 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2388842.8, rms=7.731 001: dt: 0.5000, sse=1189810.2, rms=4.201 (45.662%) 002: dt: 0.5000, sse=937691.2, rms=2.998 (28.639%) 003: dt: 0.5000, sse=917206.1, rms=2.891 (3.575%) 004: dt: 0.5000, sse=890142.2, rms=2.743 (5.100%) rms = 2.90, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=797699.9, rms=2.010 (26.740%) 006: dt: 0.2500, sse=765049.0, rms=1.663 (17.262%) 007: dt: 0.2500, sse=758722.9, rms=1.572 (5.431%) rms = 1.55, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=755556.2, rms=1.552 (1.328%) rms = 1.52, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=757426.7, rms=1.519 (2.130%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 52 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 29 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown deleting segment 5 with 10 points - only 0.00% unknown deleting segment 6 with 10 points - only 0.00% unknown mean border=86.5, 65 (29) missing vertices, mean dist -0.2 [0.4 (%80.3)->0.2 (%19.7))] %84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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 0.88 +- 0.25 (0.07-->6.16) (max @ vno 147084 --> 147083) face area 0.34 +- 0.17 (0.00-->3.31) mean absolute distance = 0.22 +- 0.30 3449 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1372791.1, rms=4.764 010: dt: 0.5000, sse=959734.1, rms=2.826 (40.686%) 011: dt: 0.5000, sse=944527.1, rms=2.757 (2.433%) rms = 2.81, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=836162.6, rms=1.938 (29.715%) 013: dt: 0.2500, sse=793376.0, rms=1.422 (26.600%) 014: dt: 0.2500, sse=780942.6, rms=1.305 (8.233%) rms = 1.27, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=778063.9, rms=1.275 (2.327%) rms = 1.24, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=781817.8, rms=1.236 (3.079%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 48 points - only 0.00% unknown deleting segment 2 with 26 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 12 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 14 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 14 points - only 0.00% unknown deleting segment 9 with 5 points - only 0.00% unknown mean border=88.6, 68 (13) missing vertices, mean dist -0.1 [0.2 (%73.4)->0.2 (%26.6))] %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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 0.88 +- 0.25 (0.06-->6.14) (max @ vno 147084 --> 147083) face area 0.33 +- 0.16 (0.00-->3.41) mean absolute distance = 0.18 +- 0.25 3055 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=949337.0, rms=2.920 017: dt: 0.5000, sse=886178.6, rms=2.417 (17.225%) rms = 2.68, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=783796.1, rms=1.630 (32.558%) 019: dt: 0.2500, sse=750939.6, rms=1.267 (22.251%) 020: dt: 0.2500, sse=745124.1, rms=1.173 (7.451%) rms = 1.17, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=745920.7, rms=1.171 (0.128%) rms = 1.13, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=739718.8, rms=1.132 (3.340%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 48 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown deleting segment 2 with 26 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 4 with 12 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 15 points - only 0.00% unknown deleting segment 7 with 8 points - only 0.00% unknown deleting segment 8 with 15 points - only 0.00% unknown deleting segment 9 with 5 points - only 0.00% unknown mean border=89.2, 59 (5) missing vertices, mean dist -0.0 [0.2 (%55.6)->0.2 (%44.4))] %93 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /users/zli/test/fs/a003/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=748210.1, rms=1.351 rms = 1.38, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=724072.8, rms=1.001 (25.894%) 024: dt: 0.2500, sse=717563.9, rms=0.841 (15.930%) rms = 0.86, time step reduction 2 of 3 to 0.125... rms = 0.84, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=714810.7, rms=0.840 (0.147%) positioning took 0.4 minutes generating cortex label... 7 non-cortical segments detected only using segment with 7592 vertices erasing segment 1 (vno[0] = 83704) erasing segment 2 (vno[0] = 100076) erasing segment 3 (vno[0] = 101217) erasing segment 4 (vno[0] = 102339) erasing segment 5 (vno[0] = 104628) erasing segment 6 (vno[0] = 107945) writing cortex label to /users/zli/test/fs/a003/label/lh.cortex.label... writing curvature file /users/zli/test/fs/a003/surf/lh.curv writing smoothed area to lh.area writing curvature file /users/zli/test/fs/a003/surf/lh.area vertex spacing 0.88 +- 0.26 (0.04-->6.08) (max @ vno 147083 --> 147084) face area 0.33 +- 0.16 (0.00-->3.38) 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 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=60.7, 185 (185) missing vertices, mean dist 1.7 [6.9 (%0.0)->2.8 (%100.0))] %14 local maxima, %44 large gradients and %38 min vals, 154 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=compu, 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=24436010.0, rms=29.015 001: dt: 0.0500, sse=21456272.0, rms=27.134 (6.484%) 002: dt: 0.0500, sse=19354730.0, rms=25.724 (5.195%) 003: dt: 0.0500, sse=17771986.0, rms=24.609 (4.335%) 004: dt: 0.0500, sse=16515027.0, rms=23.686 (3.751%) 005: dt: 0.0500, sse=15478683.0, rms=22.897 (3.331%) 006: dt: 0.0500, sse=14597307.0, rms=22.204 (3.027%) 007: dt: 0.0500, sse=13831938.0, rms=21.584 (2.793%) 008: dt: 0.0500, sse=13156568.0, rms=21.021 (2.606%) 009: dt: 0.0500, sse=12554108.0, rms=20.507 (2.449%) 010: dt: 0.0500, sse=12009762.0, rms=20.030 (2.324%) positioning took 0.9 minutes mean border=60.6, 148 (105) missing vertices, mean dist 1.4 [0.1 (%0.0)->2.3 (%100.0))] %15 local maxima, %44 large gradients and %37 min vals, 142 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=12755512.0, rms=20.679 011: dt: 0.0500, sse=12258796.0, rms=20.249 (2.082%) 012: dt: 0.0500, sse=11803720.0, rms=19.846 (1.988%) 013: dt: 0.0500, sse=11385229.0, rms=19.469 (1.903%) 014: dt: 0.0500, sse=10999468.0, rms=19.114 (1.823%) 015: dt: 0.0500, sse=10642526.0, rms=18.779 (1.749%) 016: dt: 0.0500, sse=10311312.0, rms=18.464 (1.681%) 017: dt: 0.0500, sse=10003379.0, rms=18.165 (1.617%) 018: dt: 0.0500, sse=9716183.0, rms=17.882 (1.558%) 019: dt: 0.0500, sse=9447542.0, rms=17.613 (1.504%) 020: dt: 0.0500, sse=9196571.0, rms=17.358 (1.448%) positioning took 0.9 minutes mean border=60.5, 161 (84) missing vertices, mean dist 1.2 [0.1 (%0.4)->2.0 (%99.6))] %15 local maxima, %44 large gradients and %37 min vals, 123 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=9279393.0, rms=17.448 021: dt: 0.0500, sse=9039454.0, rms=17.202 (1.411%) 022: dt: 0.0500, sse=8814207.0, rms=16.967 (1.363%) 023: dt: 0.0500, sse=8600597.0, rms=16.742 (1.329%) 024: dt: 0.0500, sse=8398191.0, rms=16.525 (1.293%) 025: dt: 0.0500, sse=8205925.0, rms=16.317 (1.261%) 026: dt: 0.0500, sse=8022127.0, rms=16.115 (1.237%) 027: dt: 0.0500, sse=7844909.5, rms=15.918 (1.223%) 028: dt: 0.0500, sse=7672862.5, rms=15.724 (1.218%) 029: dt: 0.0500, sse=7505344.0, rms=15.533 (1.215%) 030: dt: 0.0500, sse=7341953.5, rms=15.344 (1.215%) positioning took 0.9 minutes mean border=60.4, 171 (70) missing vertices, mean dist 1.0 [0.1 (%3.8)->1.7 (%96.2))] %15 local maxima, %44 large gradients and %36 min vals, 93 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=7418919.0, rms=15.434 031: dt: 0.5000, sse=6229444.5, rms=13.992 (9.340%) 032: dt: 0.5000, sse=5318211.0, rms=12.773 (8.717%) 033: dt: 0.5000, sse=4623152.0, rms=11.759 (7.934%) 034: dt: 0.5000, sse=4052137.0, rms=10.851 (7.725%) 035: dt: 0.5000, sse=3595030.2, rms=10.065 (7.239%) 036: dt: 0.5000, sse=3119622.2, rms=9.177 (8.827%) 037: dt: 0.5000, sse=2673698.5, rms=8.263 (9.962%) 038: dt: 0.5000, sse=2229564.8, rms=7.238 (12.406%) 039: dt: 0.5000, sse=1919360.0, rms=6.431 (11.152%) 040: dt: 0.5000, sse=1696019.1, rms=5.775 (10.188%) 041: dt: 0.5000, sse=1589082.1, rms=5.438 (5.836%) 042: dt: 0.5000, sse=1509710.4, rms=5.168 (4.965%) 043: dt: 0.5000, sse=1492765.8, rms=5.111 (1.106%) 044: dt: 0.5000, sse=1463465.5, rms=5.006 (2.067%) rms = 5.03, time step reduction 1 of 3 to 0.250... 045: dt: 0.2500, sse=1267038.0, rms=4.207 (15.948%) 046: dt: 0.2500, sse=1225407.5, rms=4.011 (4.662%) rms = 4.01, time step reduction 2 of 3 to 0.125... 047: dt: 0.1250, sse=1200854.5, rms=3.896 (2.868%) 048: dt: 0.1250, sse=1166552.4, rms=3.729 (4.292%) rms = 3.69, time step reduction 3 of 3 to 0.062... 049: dt: 0.1250, sse=1159230.0, rms=3.691 (1.005%) positioning took 2.5 minutes mean border=59.0, 2363 (18) missing vertices, mean dist 0.1 [0.2 (%45.3)->0.4 (%54.7))] %31 local maxima, %31 large gradients and %33 min vals, 70 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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=1530486.4, rms=4.418 rms = 4.80, time step reduction 1 of 3 to 0.250... 050: dt: 0.2500, sse=1378037.0, rms=3.733 (15.512%) 051: dt: 0.2500, sse=1316258.5, rms=3.409 (8.677%) rms = 3.46, time step reduction 2 of 3 to 0.125... 052: dt: 0.1250, sse=1290570.2, rms=3.266 (4.185%) 053: dt: 0.1250, sse=1254338.4, rms=3.058 (6.386%) 054: dt: 0.1250, sse=1241637.2, rms=2.984 (2.427%) rms = 2.95, time step reduction 3 of 3 to 0.062... 055: dt: 0.1250, sse=1235003.9, rms=2.947 (1.240%) positioning took 1.0 minutes mean border=58.1, 2325 (16) missing vertices, mean dist 0.1 [0.1 (%43.5)->0.3 (%56.5))] %45 local maxima, %16 large gradients and %33 min vals, 73 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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=1304387.4, rms=3.371 rms = 4.30, time step reduction 1 of 3 to 0.250... 056: dt: 0.2500, sse=1248943.4, rms=3.057 (9.328%) rms = 3.03, time step reduction 2 of 3 to 0.125... 057: dt: 0.2500, sse=1243061.4, rms=3.030 (0.877%) 058: dt: 0.1250, sse=1223515.4, rms=2.907 (4.034%) rms = 2.86, time step reduction 3 of 3 to 0.062... 059: dt: 0.1250, sse=1215827.5, rms=2.864 (1.495%) positioning took 0.7 minutes mean border=57.5, 4696 (12) missing vertices, mean dist 0.0 [0.1 (%46.9)->0.2 (%53.1))] %48 local maxima, %14 large gradients and %31 min vals, 80 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /users/zli/test/fs/a003/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1238484.1, rms=2.990 rms = 3.78, time step reduction 1 of 3 to 0.250... 060: dt: 0.2500, sse=1218180.5, rms=2.863 (4.248%) rms = 2.85, time step reduction 2 of 3 to 0.125... 061: dt: 0.2500, sse=1212956.8, rms=2.850 (0.439%) 062: dt: 0.1250, sse=1198010.0, rms=2.750 (3.528%) rms = 2.71, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1190179.6, rms=2.705 (1.619%) positioning took 0.7 minutes writing curvature file /users/zli/test/fs/a003/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /users/zli/test/fs/a003/surf/lh.area.pial vertex spacing 1.01 +- 0.44 (0.08-->7.18) (max @ vno 94317 --> 93222) face area 0.40 +- 0.31 (0.00-->6.02) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 147177 vertices processed 25000 of 147177 vertices processed 50000 of 147177 vertices processed 75000 of 147177 vertices processed 100000 of 147177 vertices processed 125000 of 147177 vertices processed 0 of 147177 vertices processed 25000 of 147177 vertices processed 50000 of 147177 vertices processed 75000 of 147177 vertices processed 100000 of 147177 vertices processed 125000 of 147177 vertices processed thickness calculation complete, 106:588 truncations. 33242 vertices at 0 distance 105037 vertices at 1 distance 90993 vertices at 2 distance 37041 vertices at 3 distance 11289 vertices at 4 distance 3264 vertices at 5 distance 939 vertices at 6 distance 300 vertices at 7 distance 106 vertices at 8 distance 44 vertices at 9 distance 27 vertices at 10 distance 21 vertices at 11 distance 19 vertices at 12 distance 25 vertices at 13 distance 23 vertices at 14 distance 13 vertices at 15 distance 7 vertices at 16 distance 15 vertices at 17 distance 8 vertices at 18 distance 7 vertices at 19 distance 14 vertices at 20 distance writing curvature file /users/zli/test/fs/a003/surf/lh.thickness positioning took 14.3 minutes #-------------------------------------------- #@# Make Pial Surf rh Tue Feb 5 19:05:03 EST 2019 /users/zli/test/fs/a003/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs a003 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 /users/zli/test/fs/a003/mri/filled.mgz... reading volume /users/zli/test/fs/a003/mri/brain.finalsurfs.mgz... reading volume /users/zli/test/fs/a003/mri/../mri/aseg.presurf.mgz... reading volume /users/zli/test/fs/a003/mri/wm.mgz... 30095 bright wm thresholded. 639 bright non-wm voxels segmented. reading original surface position from /users/zli/test/fs/a003/surf/rh.orig... computing class statistics... border white: 267297 voxels (1.59%) border gray 312271 voxels (1.86%) WM (101.0): 100.1 +- 7.9 [70.0 --> 110.0] GM (75.0) : 74.6 +- 10.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.8 (was 70) setting MAX_BORDER_WHITE to 112.9 (was 105) setting MIN_BORDER_WHITE to 73.0 (was 85) setting MAX_CSF to 52.6 (was 40) setting MAX_GRAY to 97.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 62.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 42.4 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-5.2, GM=73+-7.0 mean inside = 96.2, mean outside = 78.3 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.88 +- 0.25 (0.03-->9.31) (max @ vno 53025 --> 57360) face area 0.33 +- 0.16 (0.00-->7.35) mean absolute distance = 0.59 +- 0.78 3149 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 39 points - only 0.00% unknown deleting segment 1 with 15 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 21 points - only 0.00% unknown deleting segment 5 with 151 points - only 0.00% unknown deleting segment 6 with 15 points - only 0.00% unknown mean border=83.0, 111 (111) missing vertices, mean dist 0.4 [0.9 (%11.5)->0.6 (%88.5))] %67 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.90 +- 0.25 (0.08-->9.81) (max @ vno 57360 --> 53025) face area 0.33 +- 0.16 (0.00-->7.51) mean absolute distance = 0.33 +- 0.46 3173 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2175486.5, rms=7.365 001: dt: 0.5000, sse=1129606.5, rms=4.054 (44.950%) 002: dt: 0.5000, sse=918950.3, rms=2.999 (26.018%) rms = 2.96, time step reduction 1 of 3 to 0.250... 003: dt: 0.5000, sse=907382.1, rms=2.963 (1.222%) 004: dt: 0.2500, sse=773038.1, rms=1.896 (36.004%) 005: dt: 0.2500, sse=753003.3, rms=1.683 (11.222%) 006: dt: 0.2500, sse=748716.2, rms=1.629 (3.243%) rms = 1.59, time step reduction 2 of 3 to 0.125... 007: dt: 0.2500, sse=745115.3, rms=1.585 (2.684%) rms = 1.55, time step reduction 3 of 3 to 0.062... 008: dt: 0.1250, sse=741832.9, rms=1.546 (2.471%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 39 points - only 0.00% unknown deleting segment 1 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 9 points - only 0.00% unknown deleting segment 5 with 48 points - only 0.00% unknown deleting segment 6 with 7 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 6 points - only 0.00% unknown deleting segment 9 with 7 points - only 0.00% unknown deleting segment 10 with 5 points - only 0.00% unknown mean border=86.6, 65 (28) missing vertices, mean dist -0.2 [0.3 (%78.6)->0.2 (%21.4))] %84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.25 (0.06-->10.08) (max @ vno 57360 --> 53025) face area 0.34 +- 0.17 (0.00-->8.48) mean absolute distance = 0.21 +- 0.31 3609 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1301216.1, rms=4.628 009: dt: 0.5000, sse=927097.6, rms=2.782 (39.893%) rms = 2.80, time step reduction 1 of 3 to 0.250... 010: dt: 0.2500, sse=834119.6, rms=2.104 (24.358%) 011: dt: 0.2500, sse=781278.5, rms=1.552 (26.224%) 012: dt: 0.2500, sse=763220.9, rms=1.344 (13.393%) 013: dt: 0.2500, sse=759962.2, rms=1.291 (3.991%) rms = 1.27, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=759216.9, rms=1.274 (1.314%) rms = 1.24, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=757022.7, rms=1.243 (2.441%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 48 points - only 0.00% unknown deleting segment 1 with 13 points - only 0.00% unknown deleting segment 3 with 21 points - only 0.00% unknown deleting segment 4 with 83 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 32 points - only 0.00% unknown deleting segment 7 with 11 points - only 0.00% unknown mean border=88.5, 67 (17) missing vertices, mean dist -0.1 [0.2 (%71.4)->0.2 (%28.6))] %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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 0.88 +- 0.25 (0.03-->10.26) (max @ vno 57360 --> 53025) face area 0.33 +- 0.16 (0.00-->8.46) mean absolute distance = 0.18 +- 0.27 3369 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=897595.9, rms=2.750 016: dt: 0.5000, sse=876224.9, rms=2.427 (11.742%) rms = 2.72, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=770313.7, rms=1.645 (32.240%) 018: dt: 0.2500, sse=741075.4, rms=1.284 (21.948%) 019: dt: 0.2500, sse=729825.8, rms=1.200 (6.522%) rms = 1.20, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=731835.9, rms=1.197 (0.272%) rms = 1.15, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=726319.9, rms=1.155 (3.510%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 48 points - only 0.00% unknown deleting segment 1 with 13 points - only 0.00% unknown deleting segment 2 with 21 points - only 0.00% unknown deleting segment 3 with 86 points - only 0.00% unknown deleting segment 4 with 7 points - only 0.00% unknown deleting segment 5 with 29 points - only 0.00% unknown deleting segment 6 with 16 points - only 0.00% unknown mean border=89.0, 76 (11) missing vertices, mean dist -0.0 [0.2 (%54.8)->0.2 (%45.2))] %93 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /users/zli/test/fs/a003/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=734148.7, rms=1.352 rms = 1.40, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=712145.9, rms=1.017 (24.768%) 023: dt: 0.2500, sse=715531.7, rms=0.865 (14.958%) rms = 0.89, time step reduction 2 of 3 to 0.125... rms = 0.86, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=704885.6, rms=0.864 (0.130%) positioning took 0.4 minutes generating cortex label... 8 non-cortical segments detected only using segment with 6954 vertices erasing segment 0 (vno[0] = 42258) erasing segment 2 (vno[0] = 96889) erasing segment 3 (vno[0] = 96931) erasing segment 4 (vno[0] = 99365) erasing segment 5 (vno[0] = 100562) erasing segment 6 (vno[0] = 101756) erasing segment 7 (vno[0] = 110381) writing cortex label to /users/zli/test/fs/a003/label/rh.cortex.label... writing curvature file /users/zli/test/fs/a003/surf/rh.curv writing smoothed area to rh.area writing curvature file /users/zli/test/fs/a003/surf/rh.area vertex spacing 0.88 +- 0.26 (0.03-->10.30) (max @ vno 53025 --> 57360) face area 0.33 +- 0.16 (0.00-->8.46) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 13 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=60.9, 121 (121) missing vertices, mean dist 1.7 [0.4 (%0.0)->2.8 (%100.0))] %14 local maxima, %44 large gradients and %38 min vals, 173 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=compu, 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=23403556.0, rms=28.716 001: dt: 0.0500, sse=20525790.0, rms=26.837 (6.545%) 002: dt: 0.0500, sse=18489344.0, rms=25.423 (5.269%) 003: dt: 0.0500, sse=16951728.0, rms=24.301 (4.414%) 004: dt: 0.0500, sse=15731544.0, rms=23.372 (3.823%) 005: dt: 0.0500, sse=14726000.0, rms=22.577 (3.399%) 006: dt: 0.0500, sse=13872479.0, rms=21.880 (3.087%) 007: dt: 0.0500, sse=13131760.0, rms=21.257 (2.849%) 008: dt: 0.0500, sse=12478279.0, rms=20.691 (2.661%) 009: dt: 0.0500, sse=11894698.0, rms=20.173 (2.506%) 010: dt: 0.0500, sse=11368808.0, rms=19.694 (2.375%) positioning took 0.9 minutes mean border=60.7, 108 (69) missing vertices, mean dist 1.4 [0.2 (%0.0)->2.3 (%100.0))] %15 local maxima, %44 large gradients and %38 min vals, 184 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=12098984.0, rms=20.358 011: dt: 0.0500, sse=11618167.0, rms=19.925 (2.129%) 012: dt: 0.0500, sse=11179505.0, rms=19.521 (2.027%) 013: dt: 0.0500, sse=10777091.0, rms=19.143 (1.937%) 014: dt: 0.0500, sse=10406836.0, rms=18.788 (1.853%) 015: dt: 0.0500, sse=10065291.0, rms=18.455 (1.774%) 016: dt: 0.0500, sse=9749626.0, rms=18.141 (1.699%) 017: dt: 0.0500, sse=9457301.0, rms=17.846 (1.628%) 018: dt: 0.0500, sse=9185948.0, rms=17.567 (1.561%) 019: dt: 0.0500, sse=8932962.0, rms=17.303 (1.502%) 020: dt: 0.0500, sse=8696801.0, rms=17.053 (1.446%) positioning took 0.9 minutes mean border=60.6, 121 (60) missing vertices, mean dist 1.2 [0.1 (%0.6)->2.0 (%99.4))] %15 local maxima, %44 large gradients and %37 min vals, 160 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=8796661.0, rms=17.166 021: dt: 0.0500, sse=8570911.0, rms=16.925 (1.404%) 022: dt: 0.0500, sse=8359183.5, rms=16.695 (1.355%) 023: dt: 0.0500, sse=8159075.5, rms=16.476 (1.316%) 024: dt: 0.0500, sse=7969970.0, rms=16.265 (1.278%) 025: dt: 0.0500, sse=7790309.5, rms=16.062 (1.246%) 026: dt: 0.0500, sse=7618883.5, rms=15.867 (1.219%) 027: dt: 0.0500, sse=7453865.5, rms=15.676 (1.203%) 028: dt: 0.0500, sse=7294010.5, rms=15.489 (1.194%) 029: dt: 0.0500, sse=7138808.0, rms=15.304 (1.188%) 030: dt: 0.0500, sse=6987980.0, rms=15.123 (1.183%) positioning took 0.9 minutes mean border=60.5, 153 (51) missing vertices, mean dist 1.0 [0.1 (%4.1)->1.7 (%95.9))] %16 local maxima, %43 large gradients and %37 min vals, 155 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=7073679.5, rms=15.227 031: dt: 0.5000, sse=5975918.0, rms=13.849 (9.055%) 032: dt: 0.5000, sse=5148669.5, rms=12.706 (8.254%) 033: dt: 0.5000, sse=4497535.0, rms=11.729 (7.686%) 034: dt: 0.5000, sse=3955233.5, rms=10.844 (7.549%) 035: dt: 0.5000, sse=3495014.8, rms=10.033 (7.475%) 036: dt: 0.5000, sse=3034315.5, rms=9.149 (8.815%) 037: dt: 0.5000, sse=2599889.8, rms=8.235 (9.991%) 038: dt: 0.5000, sse=2205047.2, rms=7.303 (11.316%) 039: dt: 0.5000, sse=1916203.6, rms=6.543 (10.409%) 040: dt: 0.5000, sse=1710733.2, rms=5.939 (9.223%) 041: dt: 0.5000, sse=1591625.6, rms=5.561 (6.368%) 042: dt: 0.5000, sse=1512393.8, rms=5.292 (4.830%) 043: dt: 0.5000, sse=1475591.0, rms=5.164 (2.423%) 044: dt: 0.5000, sse=1443344.5, rms=5.047 (2.268%) rms = 5.02, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1435848.5, rms=5.022 (0.498%) 046: dt: 0.2500, sse=1250217.9, rms=4.236 (15.649%) 047: dt: 0.2500, sse=1197954.6, rms=4.006 (5.420%) rms = 4.05, time step reduction 2 of 3 to 0.125... 048: dt: 0.1250, sse=1174317.6, rms=3.893 (2.843%) 049: dt: 0.1250, sse=1144078.4, rms=3.740 (3.907%) rms = 3.71, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1138302.6, rms=3.711 (0.798%) positioning took 2.5 minutes mean border=59.0, 2180 (12) missing vertices, mean dist 0.1 [0.2 (%43.8)->0.4 (%56.2))] %31 local maxima, %30 large gradients and %34 min vals, 82 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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=1510999.9, rms=4.482 rms = 4.75, time step reduction 1 of 3 to 0.250... 051: dt: 0.2500, sse=1358633.1, rms=3.791 (15.422%) 052: dt: 0.2500, sse=1287349.6, rms=3.412 (9.985%) rms = 3.43, time step reduction 2 of 3 to 0.125... 053: dt: 0.1250, sse=1262316.8, rms=3.270 (4.170%) 054: dt: 0.1250, sse=1225621.5, rms=3.054 (6.616%) 055: dt: 0.1250, sse=1211398.5, rms=2.969 (2.792%) rms = 2.93, time step reduction 3 of 3 to 0.062... 056: dt: 0.1250, sse=1204563.5, rms=2.929 (1.329%) positioning took 1.0 minutes mean border=58.0, 2395 (11) missing vertices, mean dist 0.1 [0.1 (%42.2)->0.3 (%57.8))] %45 local maxima, %16 large gradients and %33 min vals, 92 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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=1281985.9, rms=3.411 rms = 4.27, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=1220257.2, rms=3.056 (10.415%) 058: dt: 0.2500, sse=1210343.5, rms=3.003 (1.733%) rms = 3.10, time step reduction 2 of 3 to 0.125... 059: dt: 0.1250, sse=1199738.0, rms=2.934 (2.269%) 060: dt: 0.1250, sse=1186249.6, rms=2.851 (2.857%) rms = 2.82, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=1181061.0, rms=2.820 (1.057%) positioning took 0.9 minutes mean border=57.4, 4782 (11) missing vertices, mean dist 0.0 [0.1 (%47.0)->0.2 (%53.0))] %47 local maxima, %14 large gradients and %32 min vals, 93 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /users/zli/test/fs/a003/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1203184.1, rms=2.945 rms = 3.65, time step reduction 1 of 3 to 0.250... 062: dt: 0.2500, sse=1183662.6, rms=2.819 (4.296%) rms = 2.79, time step reduction 2 of 3 to 0.125... 063: dt: 0.2500, sse=1176636.1, rms=2.794 (0.872%) 064: dt: 0.1250, sse=1164291.5, rms=2.706 (3.140%) rms = 2.66, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=1157202.6, rms=2.665 (1.534%) positioning took 0.7 minutes writing curvature file /users/zli/test/fs/a003/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /users/zli/test/fs/a003/surf/rh.area.pial vertex spacing 1.00 +- 0.44 (0.10-->10.71) (max @ vno 57360 --> 53025) face area 0.40 +- 0.32 (0.00-->10.33) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 143595 vertices processed 25000 of 143595 vertices processed 50000 of 143595 vertices processed 75000 of 143595 vertices processed 100000 of 143595 vertices processed 125000 of 143595 vertices processed 0 of 143595 vertices processed 25000 of 143595 vertices processed 50000 of 143595 vertices processed 75000 of 143595 vertices processed 100000 of 143595 vertices processed 125000 of 143595 vertices processed thickness calculation complete, 311:1006 truncations. 32238 vertices at 0 distance 99566 vertices at 1 distance 87986 vertices at 2 distance 38324 vertices at 3 distance 12200 vertices at 4 distance 3527 vertices at 5 distance 1084 vertices at 6 distance 389 vertices at 7 distance 151 vertices at 8 distance 79 vertices at 9 distance 78 vertices at 10 distance 46 vertices at 11 distance 28 vertices at 12 distance 21 vertices at 13 distance 23 vertices at 14 distance 23 vertices at 15 distance 18 vertices at 16 distance 11 vertices at 17 distance 11 vertices at 18 distance 14 vertices at 19 distance 21 vertices at 20 distance writing curvature file /users/zli/test/fs/a003/surf/rh.thickness positioning took 14.1 minutes #-------------------------------------------- #@# Surf Volume lh Tue Feb 5 19:19:10 EST 2019 /users/zli/test/fs/a003/surf /users/zli/test/fs/a003/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 a003 lh /users/zli/test/fs/a003/surf/lh.volume masking with /users/zli/test/fs/a003/label/lh.cortex.label Total face volume 274154 Total vertex volume 270461 (mask=0) #@# a003 lh 270461 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Tue Feb 5 19:19:13 EST 2019 /users/zli/test/fs/a003/surf /users/zli/test/fs/a003/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 a003 rh /users/zli/test/fs/a003/surf/rh.volume masking with /users/zli/test/fs/a003/label/rh.cortex.label Total face volume 271176 Total vertex volume 267790 (mask=0) #@# a003 rh 267790 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Tue Feb 5 19:19:17 EST 2019 /users/zli/test/fs/a003/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 a003 SUBJECTS_DIR is /users/zli/test/fs 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 = 139 writing volume /users/zli/test/fs/a003/mri/ribbon.mgz mris_volmask took 13.49 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Tue Feb 5 19:32:47 EST 2019 /users/zli/test/fs/a003/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 a003 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /users/zli/test/fs/a003/mri/wm.mgz... reading input surface /users/zli/test/fs/a003/surf/lh.white... reading input pial surface /users/zli/test/fs/a003/surf/lh.pial... reading input white surface /users/zli/test/fs/a003/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 274154 Total vertex volume 270461 (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) = 1522624 mm^3 (det: 1.279439 ) lhCtxGM: 269549.613 268799.000 diff= 750.6 pctdiff= 0.278 rhCtxGM: 266718.943 265874.000 diff= 844.9 pctdiff= 0.317 lhCtxWM: 234507.813 233969.000 diff= 538.8 pctdiff= 0.230 rhCtxWM: 234846.227 236525.000 diff=-1678.8 pctdiff=-0.715 SubCortGMVol 55495.000 SupraTentVol 1080061.596 (1076880.000) diff=3181.596 pctdiff=0.295 SupraTentVolNotVent 1063857.596 (1060676.000) diff=3181.596 pctdiff=0.299 BrainSegVol 1208999.000 (1206026.000) diff=2973.000 pctdiff=0.246 BrainSegVolNotVent 1188526.000 (1188819.596) diff=-293.596 pctdiff=-0.025 BrainSegVolNotVent 1188526.000 CerebellumVol 127688.000 VentChorVol 16204.000 3rd4th5thCSF 4269.000 CSFVol 1296.000, OptChiasmVol 162.000 MaskVol 1619410.000 1908 1291 3785 2.635 0.476 0.111 0.021 18 1.8 bankssts 966 623 1929 2.588 0.704 0.119 0.017 11 0.7 caudalanteriorcingulate 3206 2169 6779 2.747 0.547 0.118 0.027 35 3.2 caudalmiddlefrontal 2601 1536 3508 2.090 0.446 0.123 0.032 30 3.2 cuneus 869 564 2543 3.631 0.759 0.101 0.043 8 0.9 entorhinal 4983 3259 11036 2.946 0.590 0.126 0.034 64 6.7 fusiform 7057 4659 13273 2.533 0.489 0.123 0.027 98 7.2 inferiorparietal 4747 3148 10670 2.851 0.659 0.125 0.032 67 6.2 inferiortemporal 1573 995 2492 2.190 0.858 0.125 0.040 27 2.3 isthmuscingulate 8061 4812 12711 2.310 0.522 0.122 0.034 123 10.9 lateraloccipital 4532 2897 8763 2.771 0.662 0.126 0.042 69 8.5 lateralorbitofrontal 4991 3090 7719 2.215 0.618 0.123 0.037 62 7.2 lingual 2758 1800 5260 2.610 0.639 0.129 0.035 45 3.9 medialorbitofrontal 4636 3164 12093 3.001 0.610 0.118 0.028 67 5.3 middletemporal 1262 770 2729 2.980 0.727 0.103 0.031 13 1.4 parahippocampal 2399 1462 4362 2.662 0.568 0.107 0.029 23 3.0 paracentral 2286 1552 4441 2.581 0.398 0.114 0.025 28 2.3 parsopercularis 1045 680 2370 2.629 0.562 0.140 0.033 17 1.4 parsorbitalis 1740 1216 3655 2.580 0.511 0.106 0.019 15 1.3 parstriangularis 2140 1389 2331 1.819 0.472 0.132 0.036 27 2.8 pericalcarine 7154 4309 10781 2.189 0.575 0.107 0.032 84 9.0 postcentral 2012 1373 3874 2.625 0.514 0.144 0.036 34 2.8 posteriorcingulate 8913 5641 17744 2.737 0.567 0.111 0.034 113 12.0 precentral 5774 3889 10330 2.550 0.459 0.132 0.030 81 7.3 precuneus 1322 857 2751 2.973 0.647 0.138 0.030 29 1.5 rostralanteriorcingulate 9183 6233 18842 2.587 0.520 0.132 0.029 139 10.7 rostralmiddlefrontal 10804 7233 24673 2.936 0.559 0.125 0.029 138 12.0 superiorfrontal 9149 5929 15905 2.332 0.490 0.121 0.028 118 10.0 superiorparietal 7310 4835 15130 2.761 0.503 0.106 0.022 78 6.2 superiortemporal 7136 4703 13780 2.600 0.518 0.121 0.026 95 7.3 supramarginal 441 290 1147 2.877 0.637 0.168 0.045 10 0.9 frontalpole 833 521 2598 3.448 0.615 0.108 0.031 10 1.0 temporalpole 1108 567 1717 2.558 0.333 0.084 0.021 11 0.8 transversetemporal 4248 2825 8729 3.116 0.684 0.123 0.039 47 5.9 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab a003 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /users/zli/test/fs/a003/mri/wm.mgz... reading input surface /users/zli/test/fs/a003/surf/lh.pial... reading input pial surface /users/zli/test/fs/a003/surf/lh.pial... reading input white surface /users/zli/test/fs/a003/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 274154 Total vertex volume 270461 (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) = 1522624 mm^3 (det: 1.279439 ) lhCtxGM: 269549.613 268799.000 diff= 750.6 pctdiff= 0.278 rhCtxGM: 266718.943 265874.000 diff= 844.9 pctdiff= 0.317 lhCtxWM: 234507.813 233969.000 diff= 538.8 pctdiff= 0.230 rhCtxWM: 234846.227 236525.000 diff=-1678.8 pctdiff=-0.715 SubCortGMVol 55495.000 SupraTentVol 1080061.596 (1076880.000) diff=3181.596 pctdiff=0.295 SupraTentVolNotVent 1063857.596 (1060676.000) diff=3181.596 pctdiff=0.299 BrainSegVol 1208999.000 (1206026.000) diff=2973.000 pctdiff=0.246 BrainSegVolNotVent 1188526.000 (1188819.596) diff=-293.596 pctdiff=-0.025 BrainSegVolNotVent 1188526.000 CerebellumVol 127688.000 VentChorVol 16204.000 3rd4th5thCSF 4269.000 CSFVol 1296.000, OptChiasmVol 162.000 MaskVol 1619410.000 1908 1544 3785 2.635 0.476 0.138 0.035 26 3.1 bankssts 966 808 1929 2.588 0.704 0.157 0.039 35 1.6 caudalanteriorcingulate 3206 2621 6779 2.747 0.547 0.138 0.029 47 4.2 caudalmiddlefrontal 2601 1883 3508 2.090 0.446 0.122 0.027 30 3.1 cuneus 869 818 2543 3.631 0.759 0.147 0.038 17 1.4 entorhinal 4983 4162 11036 2.946 0.590 0.145 0.037 87 7.8 fusiform 7057 5708 13273 2.533 0.489 0.141 0.031 99 10.3 inferiorparietal 4747 4067 10670 2.851 0.659 0.140 0.030 66 6.6 inferiortemporal 1573 1231 2492 2.190 0.858 0.142 0.058 52 4.1 isthmuscingulate 8061 6050 12711 2.310 0.522 0.125 0.030 133 11.1 lateraloccipital 4532 3280 8763 2.771 0.662 0.129 0.034 73 6.4 lateralorbitofrontal 4991 3947 7719 2.215 0.618 0.136 0.033 69 7.5 lingual 2758 2213 5260 2.610 0.639 0.146 0.034 41 4.4 medialorbitofrontal 4636 4560 12093 3.001 0.610 0.144 0.028 60 6.0 middletemporal 1262 1083 2729 2.980 0.727 0.138 0.034 12 1.9 parahippocampal 2399 1788 4362 2.662 0.568 0.118 0.025 25 2.6 paracentral 2286 1899 4441 2.581 0.398 0.138 0.030 29 2.9 parsopercularis 1045 1056 2370 2.629 0.562 0.178 0.036 14 1.9 parsorbitalis 1740 1519 3655 2.580 0.511 0.140 0.028 23 2.3 parstriangularis 2140 1230 2331 1.819 0.472 0.119 0.063 59 3.0 pericalcarine 7154 5425 10781 2.189 0.575 0.119 0.024 63 7.5 postcentral 2012 1639 3874 2.625 0.514 0.171 0.044 70 3.7 posteriorcingulate 8913 6844 17744 2.737 0.567 0.115 0.027 114 10.4 precentral 5774 4203 10330 2.550 0.459 0.137 0.034 84 8.6 precuneus 1322 1033 2751 2.973 0.647 0.148 0.035 37 2.0 rostralanteriorcingulate 9183 8028 18842 2.587 0.520 0.156 0.032 133 13.8 rostralmiddlefrontal 10804 9205 24673 2.936 0.559 0.143 0.034 165 15.7 superiorfrontal 9149 7431 15905 2.332 0.490 0.139 0.030 119 12.2 superiorparietal 7310 5910 15130 2.761 0.503 0.129 0.026 85 8.5 superiortemporal 7136 5743 13780 2.600 0.518 0.139 0.031 94 9.7 supramarginal 441 493 1147 2.877 0.637 0.207 0.043 7 0.9 frontalpole 833 940 2598 3.448 0.615 0.149 0.026 6 1.0 temporalpole 1108 825 1717 2.558 0.333 0.101 0.021 5 1.0 transversetemporal 4248 2640 8729 3.116 0.684 0.132 0.040 78 7.2 insula #----------------------------------------- #@# Parcellation Stats rh Tue Feb 5 19:33:52 EST 2019 /users/zli/test/fs/a003/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 a003 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /users/zli/test/fs/a003/mri/wm.mgz... reading input surface /users/zli/test/fs/a003/surf/rh.white... reading input pial surface /users/zli/test/fs/a003/surf/rh.pial... reading input white surface /users/zli/test/fs/a003/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 271176 Total vertex volume 267790 (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) = 1522624 mm^3 (det: 1.279439 ) lhCtxGM: 269549.613 268799.000 diff= 750.6 pctdiff= 0.278 rhCtxGM: 266718.943 265874.000 diff= 844.9 pctdiff= 0.317 lhCtxWM: 234507.813 233969.000 diff= 538.8 pctdiff= 0.230 rhCtxWM: 234846.227 236525.000 diff=-1678.8 pctdiff=-0.715 SubCortGMVol 55495.000 SupraTentVol 1080061.596 (1076880.000) diff=3181.596 pctdiff=0.295 SupraTentVolNotVent 1063857.596 (1060676.000) diff=3181.596 pctdiff=0.299 BrainSegVol 1208999.000 (1206026.000) diff=2973.000 pctdiff=0.246 BrainSegVolNotVent 1188526.000 (1188819.596) diff=-293.596 pctdiff=-0.025 BrainSegVolNotVent 1188526.000 CerebellumVol 127688.000 VentChorVol 16204.000 3rd4th5thCSF 4269.000 CSFVol 1296.000, OptChiasmVol 162.000 MaskVol 1619410.000 1465 994 2587 2.686 0.367 0.121 0.022 15 1.4 bankssts 1459 924 2830 2.531 0.892 0.126 0.029 23 1.7 caudalanteriorcingulate 2789 1835 5586 2.726 0.528 0.107 0.024 29 2.6 caudalmiddlefrontal 3376 1946 4424 2.054 0.458 0.126 0.037 47 4.8 cuneus 905 582 3477 3.924 0.880 0.117 0.042 11 1.4 entorhinal 4864 3163 10504 2.940 0.607 0.130 0.032 64 5.8 fusiform 8158 5401 15844 2.547 0.501 0.122 0.030 119 10.2 inferiorparietal 4968 3297 11459 2.904 0.710 0.127 0.037 90 7.6 inferiortemporal 1386 872 2169 2.181 0.833 0.122 0.029 20 1.3 isthmuscingulate 8207 4992 13392 2.397 0.582 0.130 0.037 126 12.2 lateraloccipital 4293 2827 8875 2.949 0.693 0.128 0.034 60 5.2 lateralorbitofrontal 5353 3345 8441 2.267 0.657 0.136 0.045 80 9.0 lingual 2976 1956 6003 2.772 0.637 0.136 0.043 57 5.3 medialorbitofrontal 5386 3706 13305 2.918 0.626 0.129 0.028 79 6.3 middletemporal 924 578 2177 3.199 0.862 0.095 0.021 7 0.6 parahippocampal 2224 1416 4111 2.647 0.511 0.109 0.027 20 2.1 paracentral 1894 1317 4018 2.718 0.362 0.114 0.022 23 1.5 parsopercularis 1347 906 3595 3.112 0.571 0.142 0.035 20 1.9 parsorbitalis 2424 1667 4753 2.541 0.478 0.115 0.023 26 2.1 parstriangularis 2651 1665 2531 1.662 0.456 0.138 0.040 39 4.1 pericalcarine 6016 3680 8990 2.190 0.559 0.096 0.023 56 5.2 postcentral 1953 1325 4069 2.740 0.613 0.139 0.033 32 2.7 posteriorcingulate 8333 5291 15964 2.746 0.526 0.101 0.023 78 8.0 precentral 6497 4400 11523 2.566 0.466 0.126 0.030 76 7.3 precuneus 1014 687 2506 2.976 0.747 0.135 0.036 21 1.6 rostralanteriorcingulate 8774 5871 17867 2.542 0.563 0.137 0.034 144 11.7 rostralmiddlefrontal 10102 6783 23965 2.957 0.597 0.122 0.028 115 11.1 superiorfrontal 8562 5558 15526 2.395 0.461 0.116 0.023 97 7.8 superiorparietal 6379 4288 13501 2.752 0.489 0.111 0.021 69 5.4 superiortemporal 5940 3899 11177 2.605 0.489 0.118 0.026 74 5.9 supramarginal 476 284 1245 2.935 0.623 0.145 0.042 12 0.7 frontalpole 764 504 2540 3.546 0.662 0.130 0.032 10 1.0 temporalpole 537 322 948 2.829 0.412 0.127 0.030 6 0.6 transversetemporal 4011 2615 7883 2.952 1.021 0.125 0.035 55 5.0 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab a003 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /users/zli/test/fs/a003/mri/wm.mgz... reading input surface /users/zli/test/fs/a003/surf/rh.pial... reading input pial surface /users/zli/test/fs/a003/surf/rh.pial... reading input white surface /users/zli/test/fs/a003/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 271176 Total vertex volume 267790 (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) = 1522624 mm^3 (det: 1.279439 ) lhCtxGM: 269549.613 268799.000 diff= 750.6 pctdiff= 0.278 rhCtxGM: 266718.943 265874.000 diff= 844.9 pctdiff= 0.317 lhCtxWM: 234507.813 233969.000 diff= 538.8 pctdiff= 0.230 rhCtxWM: 234846.227 236525.000 diff=-1678.8 pctdiff=-0.715 SubCortGMVol 55495.000 SupraTentVol 1080061.596 (1076880.000) diff=3181.596 pctdiff=0.295 SupraTentVolNotVent 1063857.596 (1060676.000) diff=3181.596 pctdiff=0.299 BrainSegVol 1208999.000 (1206026.000) diff=2973.000 pctdiff=0.246 BrainSegVolNotVent 1188526.000 (1188819.596) diff=-293.596 pctdiff=-0.025 BrainSegVolNotVent 1188526.000 CerebellumVol 127688.000 VentChorVol 16204.000 3rd4th5thCSF 4269.000 CSFVol 1296.000, OptChiasmVol 162.000 MaskVol 1619410.000 1465 920 2587 2.686 0.367 0.130 0.037 36 2.3 bankssts 1459 1178 2830 2.531 0.892 0.159 0.047 21 2.8 caudalanteriorcingulate 2789 2188 5586 2.726 0.528 0.128 0.028 37 3.5 caudalmiddlefrontal 3376 2457 4424 2.054 0.458 0.130 0.031 46 4.7 cuneus 905 1157 3477 3.924 0.880 0.172 0.035 11 1.6 entorhinal 4864 3855 10504 2.940 0.607 0.139 0.034 80 7.4 fusiform 8158 6834 15844 2.547 0.501 0.138 0.032 125 12.0 inferiorparietal 4968 4340 11459 2.904 0.710 0.143 0.032 68 7.5 inferiortemporal 1386 1061 2169 2.181 0.833 0.135 0.036 36 1.9 isthmuscingulate 8207 5928 13392 2.397 0.582 0.125 0.030 162 11.1 lateraloccipital 4293 3191 8875 2.949 0.693 0.133 0.032 78 6.4 lateralorbitofrontal 5353 4142 8441 2.267 0.657 0.138 0.035 73 8.5 lingual 2976 2348 6003 2.772 0.637 0.153 0.042 49 5.9 medialorbitofrontal 5386 5188 13305 2.918 0.626 0.156 0.034 82 8.3 middletemporal 924 762 2177 3.199 0.862 0.122 0.029 9 1.2 parahippocampal 2224 1586 4111 2.647 0.511 0.124 0.032 38 3.0 paracentral 1894 1622 4018 2.718 0.362 0.135 0.030 23 2.2 parsopercularis 1347 1411 3595 3.112 0.571 0.183 0.034 18 2.2 parsorbitalis 2424 2038 4753 2.541 0.478 0.145 0.029 29 3.1 parstriangularis 2651 1483 2531 1.662 0.456 0.110 0.031 56 3.1 pericalcarine 6016 4543 8990 2.190 0.559 0.109 0.021 44 5.5 postcentral 1953 1624 4069 2.740 0.613 0.158 0.039 36 3.2 posteriorcingulate 8333 6036 15964 2.746 0.526 0.105 0.021 85 7.4 precentral 6497 4588 11523 2.566 0.466 0.129 0.032 101 8.8 precuneus 1014 991 2506 2.976 0.747 0.159 0.038 17 1.6 rostralanteriorcingulate 8774 7885 17867 2.542 0.563 0.163 0.033 129 13.2 rostralmiddlefrontal 10102 8799 23965 2.957 0.597 0.146 0.033 139 14.8 superiorfrontal 8562 7155 15526 2.395 0.461 0.131 0.027 100 10.0 superiorparietal 6379 5373 13501 2.752 0.489 0.131 0.026 71 7.1 superiortemporal 5940 4572 11177 2.605 0.489 0.130 0.031 76 7.5 supramarginal 476 543 1245 2.935 0.623 0.179 0.034 6 0.7 frontalpole 764 915 2540 3.546 0.662 0.173 0.028 8 1.1 temporalpole 537 357 948 2.829 0.412 0.111 0.031 5 0.7 transversetemporal 4011 2399 7883 2.952 1.021 0.130 0.038 79 6.4 insula #----------------------------------------- #@# Cortical Parc 2 lh Tue Feb 5 19:34:56 EST 2019 /users/zli/test/fs/a003/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 a003 lh ../surf/lh.sphere.reg /users/zli/Applications/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 /users/zli/Applications/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... 20 labels changed using aseg relabeling using gibbs priors... 000: 9841 changed, 147177 examined... 001: 2198 changed, 38116 examined... 002: 701 changed, 11579 examined... 003: 301 changed, 3850 examined... 004: 120 changed, 1653 examined... 005: 64 changed, 689 examined... 006: 35 changed, 362 examined... 007: 16 changed, 190 examined... 008: 6 changed, 86 examined... 009: 5 changed, 45 examined... 010: 2 changed, 32 examined... 011: 2 changed, 11 examined... 012: 0 changed, 10 examined... 6 labels changed using aseg 000: 278 total segments, 197 labels (2670 vertices) changed 001: 89 total segments, 8 labels (42 vertices) changed 002: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 29 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1412 vertices marked for relabeling... 1412 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 18 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Tue Feb 5 19:35:14 EST 2019 /users/zli/test/fs/a003/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 a003 rh ../surf/rh.sphere.reg /users/zli/Applications/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 /users/zli/Applications/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: 9374 changed, 143595 examined... 001: 2172 changed, 36555 examined... 002: 609 changed, 11374 examined... 003: 238 changed, 3520 examined... 004: 95 changed, 1422 examined... 005: 37 changed, 551 examined... 006: 17 changed, 207 examined... 007: 11 changed, 104 examined... 008: 9 changed, 63 examined... 009: 5 changed, 45 examined... 010: 2 changed, 23 examined... 011: 2 changed, 18 examined... 012: 1 changed, 9 examined... 013: 0 changed, 8 examined... 0 labels changed using aseg 000: 282 total segments, 191 labels (2574 vertices) changed 001: 98 total segments, 11 labels (313 vertices) changed 002: 87 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 38 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1576 vertices marked for relabeling... 1576 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 17 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Tue Feb 5 19:35:32 EST 2019 /users/zli/test/fs/a003/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 a003 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /users/zli/test/fs/a003/mri/wm.mgz... reading input surface /users/zli/test/fs/a003/surf/lh.white... reading input pial surface /users/zli/test/fs/a003/surf/lh.pial... reading input white surface /users/zli/test/fs/a003/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 274154 Total vertex volume 270461 (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) = 1522624 mm^3 (det: 1.279439 ) lhCtxGM: 269549.613 268799.000 diff= 750.6 pctdiff= 0.278 rhCtxGM: 266718.943 265874.000 diff= 844.9 pctdiff= 0.317 lhCtxWM: 234507.813 233969.000 diff= 538.8 pctdiff= 0.230 rhCtxWM: 234846.227 236525.000 diff=-1678.8 pctdiff=-0.715 SubCortGMVol 55495.000 SupraTentVol 1080061.596 (1076880.000) diff=3181.596 pctdiff=0.295 SupraTentVolNotVent 1063857.596 (1060676.000) diff=3181.596 pctdiff=0.299 BrainSegVol 1208999.000 (1206026.000) diff=2973.000 pctdiff=0.246 BrainSegVolNotVent 1188526.000 (1188819.596) diff=-293.596 pctdiff=-0.025 BrainSegVolNotVent 1188526.000 CerebellumVol 127688.000 VentChorVol 16204.000 3rd4th5thCSF 4269.000 CSFVol 1296.000, OptChiasmVol 162.000 MaskVol 1619410.000 1731 1195 3437 2.485 0.571 0.142 0.031 28 2.2 G&S_frontomargin 1513 982 2976 2.512 0.500 0.126 0.025 19 1.6 G&S_occipital_inf 2104 1073 3416 2.517 0.589 0.109 0.050 39 4.3 G&S_paracentral 2065 1342 4314 2.684 0.486 0.128 0.029 30 2.2 G&S_subcentral 847 551 2201 2.883 0.591 0.163 0.045 21 1.6 G&S_transv_frontopol 2344 1644 5135 2.964 0.471 0.130 0.026 38 2.5 G&S_cingul-Ant 1256 871 2516 2.796 0.424 0.103 0.018 8 0.9 G&S_cingul-Mid-Ant 1410 969 2708 2.678 0.377 0.137 0.039 20 2.0 G&S_cingul-Mid-Post 649 433 1732 2.954 0.462 0.146 0.036 14 0.9 G_cingul-Post-dorsal 354 213 675 2.336 0.751 0.147 0.064 9 0.9 G_cingul-Post-ventral 2409 1392 3320 2.029 0.506 0.130 0.038 37 3.4 G_cuneus 1365 936 3360 2.716 0.393 0.123 0.031 24 1.7 G_front_inf-Opercular 489 295 1343 2.941 0.443 0.154 0.032 10 0.7 G_front_inf-Orbital 883 602 2408 2.906 0.407 0.128 0.029 13 1.0 G_front_inf-Triangul 4475 2951 10534 2.738 0.554 0.131 0.031 80 5.3 G_front_middle 7358 4818 18912 3.066 0.568 0.133 0.032 111 9.4 G_front_sup 743 482 1652 3.415 0.599 0.136 0.052 11 1.3 G_Ins_lg&S_cent_ins 740 472 2469 3.588 0.626 0.134 0.053 13 1.4 G_insular_short 2171 1295 4937 2.751 0.448 0.129 0.035 45 2.6 G_occipital_middle 1479 857 2462 2.279 0.476 0.115 0.045 34 2.8 G_occipital_sup 1916 1206 4891 3.138 0.464 0.134 0.034 32 2.4 G_oc-temp_lat-fusifor 3545 2102 5767 2.227 0.659 0.136 0.046 56 6.5 G_oc-temp_med-Lingual 1796 1117 4883 3.398 0.748 0.104 0.040 18 2.0 G_oc-temp_med-Parahip 2843 1751 6475 2.743 0.738 0.132 0.053 56 7.0 G_orbital 2953 1886 6638 2.707 0.544 0.132 0.033 54 3.7 G_pariet_inf-Angular 3749 2407 8476 2.822 0.478 0.132 0.031 63 4.4 G_pariet_inf-Supramar 3345 2117 6860 2.478 0.563 0.128 0.029 51 3.7 G_parietal_sup 2738 1411 4234 2.265 0.587 0.111 0.046 45 5.0 G_postcentral 3348 2122 8102 2.964 0.535 0.118 0.038 49 4.7 G_precentral 2785 1793 5899 2.597 0.485 0.143 0.036 53 4.1 G_precuneus 1019 602 2136 2.515 0.752 0.143 0.050 25 2.0 G_rectus 911 600 1635 2.744 0.829 0.126 0.046 13 1.3 G_subcallosal 904 438 1497 2.588 0.323 0.082 0.022 11 0.7 G_temp_sup-G_T_transv 2634 1679 6711 2.936 0.518 0.127 0.029 47 3.1 G_temp_sup-Lateral 847 554 1976 3.264 0.565 0.090 0.016 5 0.6 G_temp_sup-Plan_polar 1257 839 2569 2.655 0.470 0.102 0.024 11 1.1 G_temp_sup-Plan_tempo 2177 1387 5733 2.957 0.739 0.130 0.043 41 3.7 G_temporal_inf 2568 1708 8175 3.210 0.602 0.132 0.036 53 3.8 G_temporal_middle 327 226 455 2.212 0.359 0.096 0.015 2 0.1 Lat_Fis-ant-Horizont 354 280 556 2.280 0.215 0.097 0.012 1 0.2 Lat_Fis-ant-Vertical 1355 906 1829 2.468 0.411 0.110 0.021 8 1.2 Lat_Fis-post 2528 1350 2966 1.993 0.488 0.122 0.045 40 4.7 Pole_occipital 2093 1344 6133 3.217 0.744 0.136 0.047 35 4.1 Pole_temporal 2637 1773 3074 1.936 0.571 0.123 0.030 30 2.9 S_calcarine 3805 2481 4988 2.197 0.626 0.098 0.026 27 4.2 S_central 1258 832 1810 2.464 0.389 0.110 0.022 11 1.0 S_cingul-Marginalis 508 358 840 2.950 0.361 0.099 0.020 2 0.4 S_circular_insula_ant 1604 1079 2495 2.749 0.531 0.091 0.017 7 1.3 S_circular_insula_inf 1680 1159 2560 2.751 0.411 0.111 0.022 8 1.6 S_circular_insula_sup 1136 767 2042 2.874 0.514 0.096 0.019 7 0.8 S_collat_transv_ant 561 375 681 2.228 0.393 0.133 0.029 5 0.7 S_collat_transv_post 2006 1375 3120 2.401 0.359 0.100 0.019 12 1.5 S_front_inf 1770 1240 3198 2.403 0.442 0.130 0.026 22 1.9 S_front_middle 3201 2173 6025 2.682 0.473 0.115 0.025 28 3.1 S_front_sup 334 237 534 2.451 0.577 0.113 0.015 2 0.2 S_interm_prim-Jensen 3466 2314 5076 2.233 0.375 0.104 0.017 27 2.4 S_intrapariet&P_trans 1256 838 1644 2.247 0.275 0.108 0.023 7 1.2 S_oc_middle&Lunatus 1255 851 1824 2.348 0.311 0.096 0.016 6 0.8 S_oc_sup&transversal 570 398 1053 2.504 0.612 0.123 0.022 6 0.5 S_occipital_ant 717 494 1341 2.589 0.489 0.119 0.022 6 0.6 S_oc-temp_lat 2420 1647 3857 2.592 0.491 0.109 0.020 17 2.0 S_oc-temp_med&Lingual 358 249 508 2.408 0.571 0.122 0.022 2 0.4 S_orbital_lateral 808 561 1101 2.421 0.547 0.114 0.018 6 0.6 S_orbital_med-olfact 1667 1128 3205 2.881 0.603 0.125 0.028 16 1.9 S_orbital-H_Shaped 2813 1878 4144 2.465 0.461 0.125 0.025 28 2.9 S_parieto_occipital 1450 873 1181 1.777 0.636 0.125 0.028 27 1.4 S_pericallosal 3107 2157 4332 2.160 0.318 0.107 0.020 23 2.5 S_postcentral 2116 1431 3887 2.630 0.553 0.106 0.021 17 1.7 S_precentral-inf-part 972 675 1586 2.437 0.508 0.101 0.019 6 0.7 S_precentral-sup-part 990 660 1611 2.686 0.471 0.121 0.025 11 1.0 S_suborbital 840 580 1379 2.540 0.369 0.128 0.030 8 1.1 S_subparietal 1596 1154 2570 2.604 0.486 0.111 0.015 12 1.0 S_temporal_inf 7281 4945 12900 2.554 0.460 0.111 0.022 72 6.3 S_temporal_sup 594 399 791 2.314 0.283 0.087 0.015 3 0.3 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Tue Feb 5 19:36:06 EST 2019 /users/zli/test/fs/a003/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 a003 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /users/zli/test/fs/a003/mri/wm.mgz... reading input surface /users/zli/test/fs/a003/surf/rh.white... reading input pial surface /users/zli/test/fs/a003/surf/rh.pial... reading input white surface /users/zli/test/fs/a003/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 271176 Total vertex volume 267790 (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) = 1522624 mm^3 (det: 1.279439 ) lhCtxGM: 269549.613 268799.000 diff= 750.6 pctdiff= 0.278 rhCtxGM: 266718.943 265874.000 diff= 844.9 pctdiff= 0.317 lhCtxWM: 234507.813 233969.000 diff= 538.8 pctdiff= 0.230 rhCtxWM: 234846.227 236525.000 diff=-1678.8 pctdiff=-0.715 SubCortGMVol 55495.000 SupraTentVol 1080061.596 (1076880.000) diff=3181.596 pctdiff=0.295 SupraTentVolNotVent 1063857.596 (1060676.000) diff=3181.596 pctdiff=0.299 BrainSegVol 1208999.000 (1206026.000) diff=2973.000 pctdiff=0.246 BrainSegVolNotVent 1188526.000 (1188819.596) diff=-293.596 pctdiff=-0.025 BrainSegVolNotVent 1188526.000 CerebellumVol 127688.000 VentChorVol 16204.000 3rd4th5thCSF 4269.000 CSFVol 1296.000, OptChiasmVol 162.000 MaskVol 1619410.000 1219 803 2259 2.379 0.595 0.131 0.030 19 1.6 G&S_frontomargin 1176 755 2452 2.755 0.542 0.129 0.030 16 1.4 G&S_occipital_inf 1643 899 2604 2.361 0.492 0.110 0.042 23 2.5 G&S_paracentral 1573 1047 3294 2.814 0.414 0.131 0.029 20 1.8 G&S_subcentral 1320 871 3265 2.767 0.623 0.148 0.040 24 2.0 G&S_transv_frontopol 3065 2116 6690 2.948 0.541 0.134 0.034 50 4.2 G&S_cingul-Ant 1458 982 3045 2.946 0.499 0.121 0.029 19 1.6 G&S_cingul-Mid-Ant 1556 1035 3126 2.867 0.446 0.131 0.033 19 2.1 G&S_cingul-Mid-Post 544 366 1464 2.781 0.462 0.162 0.053 13 1.1 G_cingul-Post-dorsal 400 238 774 2.488 0.817 0.129 0.031 6 0.5 G_cingul-Post-ventral 3017 1767 4317 2.072 0.506 0.132 0.038 44 4.6 G_cuneus 1358 913 3422 2.842 0.359 0.122 0.027 24 1.3 G_front_inf-Opercular 338 211 940 3.155 0.417 0.147 0.036 6 0.5 G_front_inf-Orbital 925 660 2228 2.628 0.512 0.130 0.028 14 1.1 G_front_inf-Triangul 3815 2436 9776 2.882 0.553 0.145 0.042 86 6.0 G_front_middle 6549 4324 18261 3.132 0.610 0.129 0.032 93 7.9 G_front_sup 1003 660 2031 3.227 0.845 0.138 0.050 18 1.7 G_Ins_lg&S_cent_ins 611 403 2160 3.595 0.852 0.142 0.038 12 0.9 G_insular_short 2716 1740 6430 2.821 0.565 0.146 0.041 59 4.2 G_occipital_middle 1588 1012 3099 2.465 0.431 0.130 0.031 21 1.8 G_occipital_sup 2075 1275 4885 3.020 0.496 0.148 0.042 40 3.4 G_oc-temp_lat-fusifor 3469 2091 5829 2.328 0.705 0.145 0.051 58 6.5 G_oc-temp_med-Lingual 1630 1041 5536 3.779 0.862 0.111 0.033 16 2.0 G_oc-temp_med-Parahip 3183 2026 8280 3.029 0.722 0.138 0.042 62 4.9 G_orbital 3330 2100 7922 2.694 0.567 0.136 0.040 70 5.8 G_pariet_inf-Angular 2764 1767 6514 2.831 0.460 0.135 0.032 52 3.4 G_pariet_inf-Supramar 3437 2202 7286 2.506 0.523 0.131 0.028 56 3.8 G_parietal_sup 2033 1088 3268 2.257 0.483 0.096 0.028 28 2.0 G_postcentral 3454 2029 8085 2.996 0.510 0.104 0.027 45 3.8 G_precentral 2604 1729 5610 2.615 0.450 0.140 0.036 45 3.1 G_precuneus 906 563 2148 2.597 0.627 0.162 0.072 29 2.9 G_rectus 753 433 946 2.017 1.421 0.093 0.032 9 0.7 G_subcallosal 442 240 899 2.908 0.396 0.122 0.035 6 0.5 G_temp_sup-G_T_transv 2310 1505 5988 2.947 0.511 0.127 0.028 37 2.6 G_temp_sup-Lateral 876 602 2038 3.167 0.628 0.077 0.015 3 0.6 G_temp_sup-Plan_polar 1159 808 2222 2.493 0.390 0.096 0.016 9 0.7 G_temp_sup-Plan_tempo 2720 1764 7034 2.904 0.809 0.142 0.048 70 5.3 G_temporal_inf 3168 2117 9084 3.065 0.664 0.142 0.035 63 4.5 G_temporal_middle 522 355 943 2.526 0.355 0.086 0.011 3 0.3 Lat_Fis-ant-Horizont 305 229 432 2.244 0.402 0.098 0.010 1 0.1 Lat_Fis-ant-Vertical 1578 1063 2260 2.618 0.405 0.114 0.024 11 1.5 Lat_Fis-post 4039 2213 5115 2.037 0.478 0.129 0.049 75 7.7 Pole_occipital 2239 1493 6960 3.343 0.685 0.133 0.036 37 3.2 Pole_temporal 2804 1824 2797 1.770 0.572 0.130 0.032 35 3.6 S_calcarine 3374 2260 4313 2.154 0.611 0.093 0.017 16 2.4 S_central 1163 813 1888 2.502 0.352 0.101 0.016 6 0.8 S_cingul-Marginalis 635 431 990 2.884 0.489 0.104 0.018 3 0.5 S_circular_insula_ant 1220 818 1748 2.649 0.523 0.091 0.016 8 0.7 S_circular_insula_inf 1442 979 2349 2.743 0.362 0.112 0.022 10 1.3 S_circular_insula_sup 1360 941 2377 2.778 0.520 0.099 0.017 8 0.9 S_collat_transv_ant 583 375 847 2.592 0.398 0.152 0.035 7 0.9 S_collat_transv_post 2071 1375 3007 2.279 0.385 0.116 0.021 23 1.6 S_front_inf 2179 1512 3566 2.348 0.430 0.123 0.026 20 2.4 S_front_middle 2422 1688 4222 2.550 0.464 0.103 0.020 14 2.0 S_front_sup 738 486 919 2.318 0.286 0.112 0.021 5 0.6 S_interm_prim-Jensen 3334 2237 4646 2.266 0.320 0.094 0.016 17 2.1 S_intrapariet&P_trans 1348 915 1805 2.343 0.356 0.117 0.024 9 1.3 S_oc_middle&Lunatus 914 612 1213 2.278 0.329 0.097 0.016 5 0.5 S_oc_sup&transversal 513 344 869 2.553 0.411 0.101 0.022 3 0.4 S_occipital_ant 836 566 1558 2.743 0.572 0.113 0.027 8 0.7 S_oc-temp_lat 2022 1398 3212 2.554 0.505 0.105 0.020 14 1.6 S_oc-temp_med&Lingual 554 377 1014 2.577 0.600 0.123 0.029 5 0.8 S_orbital_lateral 721 512 1034 2.568 0.496 0.114 0.018 5 0.6 S_orbital_med-olfact 1608 1091 3106 3.050 0.616 0.128 0.026 16 1.8 S_orbital-H_Shaped 3265 2129 4555 2.390 0.545 0.117 0.026 29 3.3 S_parieto_occipital 1713 1058 1502 1.775 0.679 0.118 0.018 25 1.0 S_pericallosal 2296 1545 2862 2.084 0.310 0.087 0.014 12 1.2 S_postcentral 1445 1005 2435 2.647 0.342 0.093 0.015 7 0.9 S_precentral-inf-part 1535 1064 2459 2.601 0.387 0.084 0.011 5 0.8 S_precentral-sup-part 306 229 615 3.136 0.493 0.150 0.029 3 0.4 S_suborbital 1205 846 2030 2.585 0.457 0.115 0.029 10 1.2 S_subparietal 1155 818 1756 2.615 0.389 0.130 0.023 8 1.3 S_temporal_inf 6543 4508 10794 2.553 0.416 0.110 0.020 50 5.3 S_temporal_sup 234 169 379 2.683 0.410 0.120 0.014 1 0.2 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Tue Feb 5 19:36:39 EST 2019 /users/zli/test/fs/a003/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 a003 lh ../surf/lh.sphere.reg /users/zli/Applications/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 /users/zli/Applications/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... 1267 labels changed using aseg relabeling using gibbs priors... 000: 2082 changed, 147177 examined... 001: 495 changed, 9642 examined... 002: 140 changed, 2785 examined... 003: 66 changed, 851 examined... 004: 33 changed, 362 examined... 005: 21 changed, 179 examined... 006: 10 changed, 108 examined... 007: 4 changed, 58 examined... 008: 2 changed, 25 examined... 009: 2 changed, 15 examined... 010: 2 changed, 15 examined... 011: 0 changed, 13 examined... 218 labels changed using aseg 000: 56 total segments, 23 labels (153 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 891 vertices marked for relabeling... 891 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 14 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Tue Feb 5 19:36:53 EST 2019 /users/zli/test/fs/a003/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 a003 rh ../surf/rh.sphere.reg /users/zli/Applications/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 /users/zli/Applications/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... 1198 labels changed using aseg relabeling using gibbs priors... 000: 2073 changed, 143595 examined... 001: 466 changed, 9783 examined... 002: 151 changed, 2612 examined... 003: 38 changed, 869 examined... 004: 23 changed, 230 examined... 005: 8 changed, 121 examined... 006: 0 changed, 50 examined... 126 labels changed using aseg 000: 48 total segments, 15 labels (147 vertices) changed 001: 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... 1494 vertices marked for relabeling... 1494 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 14 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Tue Feb 5 19:37:07 EST 2019 /users/zli/test/fs/a003/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 a003 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /users/zli/test/fs/a003/mri/wm.mgz... reading input surface /users/zli/test/fs/a003/surf/lh.white... reading input pial surface /users/zli/test/fs/a003/surf/lh.pial... reading input white surface /users/zli/test/fs/a003/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 274154 Total vertex volume 270461 (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) = 1522624 mm^3 (det: 1.279439 ) lhCtxGM: 269549.613 268799.000 diff= 750.6 pctdiff= 0.278 rhCtxGM: 266718.943 265874.000 diff= 844.9 pctdiff= 0.317 lhCtxWM: 234507.813 233969.000 diff= 538.8 pctdiff= 0.230 rhCtxWM: 234846.227 236525.000 diff=-1678.8 pctdiff=-0.715 SubCortGMVol 55495.000 SupraTentVol 1080061.596 (1076880.000) diff=3181.596 pctdiff=0.295 SupraTentVolNotVent 1063857.596 (1060676.000) diff=3181.596 pctdiff=0.299 BrainSegVol 1208999.000 (1206026.000) diff=2973.000 pctdiff=0.246 BrainSegVolNotVent 1188526.000 (1188819.596) diff=-293.596 pctdiff=-0.025 BrainSegVolNotVent 1188526.000 CerebellumVol 127688.000 VentChorVol 16204.000 3rd4th5thCSF 4269.000 CSFVol 1296.000, OptChiasmVol 162.000 MaskVol 1619410.000 1445 956 2697 2.646 0.632 0.114 0.018 14 1.0 caudalanteriorcingulate 3367 2283 7098 2.745 0.536 0.118 0.027 38 3.4 caudalmiddlefrontal 3553 2179 4902 2.119 0.459 0.124 0.033 44 4.6 cuneus 818 533 2399 3.636 0.755 0.098 0.043 7 0.8 entorhinal 4588 2975 9756 2.901 0.567 0.124 0.032 58 6.0 fusiform 7208 4750 13515 2.541 0.488 0.121 0.027 98 7.2 inferiorparietal 4847 3214 11074 2.887 0.680 0.128 0.035 69 6.7 inferiortemporal 1567 989 2544 2.221 0.846 0.126 0.041 28 2.4 isthmuscingulate 8017 4801 12674 2.306 0.519 0.122 0.034 120 10.6 lateraloccipital 5365 3453 10599 2.774 0.680 0.129 0.042 85 9.9 lateralorbitofrontal 5089 3138 7771 2.203 0.613 0.124 0.037 66 7.5 lingual 2610 1695 5030 2.598 0.721 0.129 0.039 47 3.8 medialorbitofrontal 5936 4076 14705 2.934 0.605 0.119 0.027 81 6.6 middletemporal 1290 793 2859 3.025 0.710 0.099 0.029 12 1.3 parahippocampal 2727 1684 5078 2.688 0.570 0.109 0.028 26 3.3 paracentral 2241 1514 4280 2.578 0.390 0.117 0.027 29 2.3 parsopercularis 1023 665 2220 2.725 0.519 0.135 0.029 14 1.2 parsorbitalis 1989 1403 4139 2.553 0.526 0.106 0.019 18 1.6 parstriangularis 2105 1370 2276 1.812 0.469 0.132 0.035 27 2.7 pericalcarine 8023 4875 11979 2.196 0.572 0.108 0.032 93 9.8 postcentral 2209 1501 4120 2.619 0.534 0.142 0.035 36 3.0 posteriorcingulate 8928 5635 17741 2.742 0.565 0.111 0.034 114 12.0 precentral 5645 3774 10218 2.547 0.457 0.134 0.031 83 7.2 precuneus 1844 1234 3755 2.919 0.611 0.137 0.028 37 1.9 rostralanteriorcingulate 6445 4358 13377 2.605 0.517 0.132 0.030 98 7.5 rostralmiddlefrontal 12290 8231 27949 2.863 0.586 0.128 0.030 163 14.5 superiorfrontal 7444 4815 13373 2.375 0.495 0.118 0.026 91 8.0 superiorparietal 9907 6515 21359 2.808 0.570 0.108 0.023 110 9.0 superiortemporal 6514 4297 12662 2.619 0.518 0.123 0.026 88 6.9 supramarginal 1105 563 1715 2.562 0.331 0.082 0.021 11 0.8 transversetemporal 3014 2013 6598 3.185 0.588 0.121 0.035 32 4.1 insula #----------------------------------------- #@# Parcellation Stats 3 rh Tue Feb 5 19:37:41 EST 2019 /users/zli/test/fs/a003/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 a003 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /users/zli/test/fs/a003/mri/wm.mgz... reading input surface /users/zli/test/fs/a003/surf/rh.white... reading input pial surface /users/zli/test/fs/a003/surf/rh.pial... reading input white surface /users/zli/test/fs/a003/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 271176 Total vertex volume 267790 (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) = 1522624 mm^3 (det: 1.279439 ) lhCtxGM: 269549.613 268799.000 diff= 750.6 pctdiff= 0.278 rhCtxGM: 266718.943 265874.000 diff= 844.9 pctdiff= 0.317 lhCtxWM: 234507.813 233969.000 diff= 538.8 pctdiff= 0.230 rhCtxWM: 234846.227 236525.000 diff=-1678.8 pctdiff=-0.715 SubCortGMVol 55495.000 SupraTentVol 1080061.596 (1076880.000) diff=3181.596 pctdiff=0.295 SupraTentVolNotVent 1063857.596 (1060676.000) diff=3181.596 pctdiff=0.299 BrainSegVol 1208999.000 (1206026.000) diff=2973.000 pctdiff=0.246 BrainSegVolNotVent 1188526.000 (1188819.596) diff=-293.596 pctdiff=-0.025 BrainSegVolNotVent 1188526.000 CerebellumVol 127688.000 VentChorVol 16204.000 3rd4th5thCSF 4269.000 CSFVol 1296.000, OptChiasmVol 162.000 MaskVol 1619410.000 1530 973 2966 2.547 0.874 0.128 0.029 25 1.8 caudalanteriorcingulate 3018 1985 5826 2.697 0.528 0.108 0.024 30 2.8 caudalmiddlefrontal 3951 2338 5443 2.094 0.485 0.128 0.036 54 5.6 cuneus 837 541 3139 3.887 0.898 0.113 0.039 9 1.2 entorhinal 4304 2825 9042 2.888 0.561 0.131 0.031 55 5.1 fusiform 8174 5393 15907 2.547 0.509 0.123 0.030 119 10.3 inferiorparietal 5533 3626 13083 2.955 0.739 0.127 0.037 98 8.2 inferiortemporal 1349 850 2125 2.193 0.831 0.121 0.029 19 1.3 isthmuscingulate 8208 5010 13380 2.392 0.577 0.130 0.037 124 12.0 lateraloccipital 4984 3272 10222 2.864 0.721 0.131 0.035 74 6.5 lateralorbitofrontal 5216 3271 8250 2.268 0.661 0.137 0.043 77 8.6 lingual 2445 1552 4768 2.516 0.989 0.134 0.047 51 4.7 medialorbitofrontal 6535 4481 15216 2.885 0.594 0.130 0.028 93 7.5 middletemporal 985 619 2312 3.177 0.867 0.095 0.022 8 0.7 parahippocampal 2353 1489 4433 2.665 0.537 0.110 0.030 24 2.6 paracentral 2139 1485 4458 2.678 0.394 0.118 0.023 27 1.8 parsopercularis 1099 725 2610 2.973 0.585 0.115 0.024 10 1.0 parsorbitalis 2586 1751 5295 2.614 0.534 0.118 0.025 31 2.7 parstriangularis 2716 1672 2631 1.692 0.462 0.136 0.044 41 4.6 pericalcarine 6565 4062 9835 2.188 0.555 0.099 0.023 63 5.6 postcentral 1999 1354 4089 2.719 0.622 0.138 0.033 32 2.7 posteriorcingulate 7921 5026 15347 2.758 0.518 0.101 0.022 74 7.3 precentral 6558 4450 11871 2.554 0.476 0.124 0.029 75 7.1 precuneus 1376 909 2974 2.907 0.751 0.123 0.032 23 1.8 rostralanteriorcingulate 5917 3946 11811 2.523 0.543 0.137 0.034 100 8.1 rostralmiddlefrontal 13424 9030 31224 2.899 0.606 0.126 0.030 171 15.6 superiorfrontal 7131 4606 12801 2.400 0.456 0.114 0.023 82 6.4 superiorparietal 8189 5482 18236 2.853 0.583 0.113 0.023 90 7.6 superiortemporal 5729 3764 10802 2.604 0.475 0.116 0.026 70 5.8 supramarginal 546 326 969 2.810 0.410 0.127 0.029 6 0.6 transversetemporal 3091 2080 6728 3.198 0.706 0.128 0.032 41 3.5 insula #----------------------------------------- #@# WM/GM Contrast lh Tue Feb 5 19:38:13 EST 2019 /users/zli/test/fs/a003/scripts pctsurfcon --s a003 --lh-only Log file is /users/zli/test/fs/a003/scripts/pctsurfcon.log Tue Feb 5 19:38:13 EST 2019 setenv SUBJECTS_DIR /users/zli/test/fs cd /users/zli/test/fs/a003/scripts /users/zli/Applications/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux compute-104 2.6.32-696.18.7.el6.x86_64 #1 SMP Thu Dec 28 20:15:47 EST 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /users/zli/Applications/freesurfer mri_vol2surf --mov /users/zli/test/fs/a003/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /users/zli/test/fs/a003/surf/tmp.pctsurfcon.31528/lh.wm.mgh --regheader a003 --cortex srcvol = /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/label/lh.cortex.label Reading surface /users/zli/test/fs/a003/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 = 78047 Masking with /users/zli/test/fs/a003/label/lh.cortex.label Writing to /users/zli/test/fs/a003/surf/tmp.pctsurfcon.31528/lh.wm.mgh Dim: 147177 1 1 mri_vol2surf --mov /users/zli/test/fs/a003/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /users/zli/test/fs/a003/surf/tmp.pctsurfcon.31528/lh.gm.mgh --projfrac 0.3 --regheader a003 --cortex srcvol = /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/label/lh.cortex.label Reading surface /users/zli/test/fs/a003/surf/lh.white Done reading source surface Reading thickness /users/zli/test/fs/a003/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 = 97073 Masking with /users/zli/test/fs/a003/label/lh.cortex.label Writing to /users/zli/test/fs/a003/surf/tmp.pctsurfcon.31528/lh.gm.mgh Dim: 147177 1 1 mri_concat /users/zli/test/fs/a003/surf/tmp.pctsurfcon.31528/lh.wm.mgh /users/zli/test/fs/a003/surf/tmp.pctsurfcon.31528/lh.gm.mgh --paired-diff-norm --mul 100 --o /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/surf/lh.w-g.pct.mgh mri_segstats --in /users/zli/test/fs/a003/surf/lh.w-g.pct.mgh --annot a003 lh aparc --sum /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/surf/lh.w-g.pct.mgh --annot a003 lh aparc --sum /users/zli/test/fs/a003/stats/lh.w-g.pct.stats --snr sysname Linux hostname compute-104 machine x86_64 user zli UseRobust 0 Constructing seg from annotation Reading annotation /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/surf/lh.w-g.pct.mgh Vertex Area is 0.649092 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 Tue Feb 5 19:38:20 EST 2019 /users/zli/test/fs/a003/scripts pctsurfcon --s a003 --rh-only Log file is /users/zli/test/fs/a003/scripts/pctsurfcon.log Tue Feb 5 19:38:20 EST 2019 setenv SUBJECTS_DIR /users/zli/test/fs cd /users/zli/test/fs/a003/scripts /users/zli/Applications/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux compute-104 2.6.32-696.18.7.el6.x86_64 #1 SMP Thu Dec 28 20:15:47 EST 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /users/zli/Applications/freesurfer mri_vol2surf --mov /users/zli/test/fs/a003/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /users/zli/test/fs/a003/surf/tmp.pctsurfcon.31581/rh.wm.mgh --regheader a003 --cortex srcvol = /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/label/rh.cortex.label Reading surface /users/zli/test/fs/a003/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 = 77059 Masking with /users/zli/test/fs/a003/label/rh.cortex.label Writing to /users/zli/test/fs/a003/surf/tmp.pctsurfcon.31581/rh.wm.mgh Dim: 143595 1 1 mri_vol2surf --mov /users/zli/test/fs/a003/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /users/zli/test/fs/a003/surf/tmp.pctsurfcon.31581/rh.gm.mgh --projfrac 0.3 --regheader a003 --cortex srcvol = /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/label/rh.cortex.label Reading surface /users/zli/test/fs/a003/surf/rh.white Done reading source surface Reading thickness /users/zli/test/fs/a003/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 = 94791 Masking with /users/zli/test/fs/a003/label/rh.cortex.label Writing to /users/zli/test/fs/a003/surf/tmp.pctsurfcon.31581/rh.gm.mgh Dim: 143595 1 1 mri_concat /users/zli/test/fs/a003/surf/tmp.pctsurfcon.31581/rh.wm.mgh /users/zli/test/fs/a003/surf/tmp.pctsurfcon.31581/rh.gm.mgh --paired-diff-norm --mul 100 --o /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/surf/rh.w-g.pct.mgh mri_segstats --in /users/zli/test/fs/a003/surf/rh.w-g.pct.mgh --annot a003 rh aparc --sum /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/surf/rh.w-g.pct.mgh --annot a003 rh aparc --sum /users/zli/test/fs/a003/stats/rh.w-g.pct.stats --snr sysname Linux hostname compute-104 machine x86_64 user zli UseRobust 0 Constructing seg from annotation Reading annotation /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/surf/rh.w-g.pct.mgh Vertex Area is 0.653376 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 Tue Feb 5 19:38:27 EST 2019 /users/zli/test/fs/a003/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 1528 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 1830 voxels changed to hypointensity... 3313 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Tue Feb 5 19:38:47 EST 2019 /users/zli/test/fs/a003 mri_aparc2aseg --s a003 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /users/zli/Applications/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: /users/zli/Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /users/zli/test/fs subject a003 outvol /users/zli/test/fs/a003/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /users/zli/test/fs/a003/surf/lh.white Reading lh pial surface /users/zli/test/fs/a003/surf/lh.pial Loading lh annotations from /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/surf/rh.white Reading rh pial surface /users/zli/test/fs/a003/surf/rh.pial Loading rh annotations from /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.54 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 68 rescaling Left_Lateral_Ventricle from 13 --> 24 rescaling Left_Inf_Lat_Vent from 34 --> 39 rescaling Left_Cerebellum_White_Matter from 86 --> 89 rescaling Left_Cerebellum_Cortex from 60 --> 66 rescaling Left_Thalamus from 94 --> 104 rescaling Left_Thalamus_Proper from 84 --> 93 rescaling Left_Caudate from 75 --> 73 rescaling Left_Putamen from 80 --> 83 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 31 rescaling Fourth_Ventricle from 22 --> 23 rescaling Brain_Stem from 81 --> 85 rescaling Left_Hippocampus from 57 --> 68 rescaling Left_Amygdala from 56 --> 69 rescaling CSF from 32 --> 53 rescaling Left_Accumbens_area from 62 --> 66 rescaling Left_VentralDC from 87 --> 91 rescaling Right_Cerebral_White_Matter from 105 --> 105 rescaling Right_Cerebral_Cortex from 58 --> 66 rescaling Right_Lateral_Ventricle from 13 --> 23 rescaling Right_Inf_Lat_Vent from 25 --> 28 rescaling Right_Cerebellum_White_Matter from 87 --> 89 rescaling Right_Cerebellum_Cortex from 59 --> 66 rescaling Right_Thalamus_Proper from 85 --> 88 rescaling Right_Caudate from 62 --> 77 rescaling Right_Putamen from 80 --> 85 rescaling Right_Pallidum from 97 --> 101 rescaling Right_Hippocampus from 53 --> 68 rescaling Right_Amygdala from 55 --> 69 rescaling Right_Accumbens_area from 65 --> 75 rescaling Right_VentralDC from 86 --> 92 rescaling Fifth_Ventricle from 40 --> 45 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 = 534718 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 164 changed. pass 2: 10 changed. pass 3: 1 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /users/zli/test/fs/a003/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Tue Feb 5 19:43:02 EST 2019 /users/zli/test/fs/a003 mri_aparc2aseg --s a003 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /users/zli/Applications/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: /users/zli/Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /users/zli/test/fs subject a003 outvol /users/zli/test/fs/a003/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /users/zli/test/fs/a003/surf/lh.white Reading lh pial surface /users/zli/test/fs/a003/surf/lh.pial Loading lh annotations from /users/zli/test/fs/a003/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /users/zli/test/fs/a003/surf/rh.white Reading rh pial surface /users/zli/test/fs/a003/surf/rh.pial Loading rh annotations from /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.54 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 68 rescaling Left_Lateral_Ventricle from 13 --> 24 rescaling Left_Inf_Lat_Vent from 34 --> 39 rescaling Left_Cerebellum_White_Matter from 86 --> 89 rescaling Left_Cerebellum_Cortex from 60 --> 66 rescaling Left_Thalamus from 94 --> 104 rescaling Left_Thalamus_Proper from 84 --> 93 rescaling Left_Caudate from 75 --> 73 rescaling Left_Putamen from 80 --> 83 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 31 rescaling Fourth_Ventricle from 22 --> 23 rescaling Brain_Stem from 81 --> 85 rescaling Left_Hippocampus from 57 --> 68 rescaling Left_Amygdala from 56 --> 69 rescaling CSF from 32 --> 53 rescaling Left_Accumbens_area from 62 --> 66 rescaling Left_VentralDC from 87 --> 91 rescaling Right_Cerebral_White_Matter from 105 --> 105 rescaling Right_Cerebral_Cortex from 58 --> 66 rescaling Right_Lateral_Ventricle from 13 --> 23 rescaling Right_Inf_Lat_Vent from 25 --> 28 rescaling Right_Cerebellum_White_Matter from 87 --> 89 rescaling Right_Cerebellum_Cortex from 59 --> 66 rescaling Right_Thalamus_Proper from 85 --> 88 rescaling Right_Caudate from 62 --> 77 rescaling Right_Putamen from 80 --> 85 rescaling Right_Pallidum from 97 --> 101 rescaling Right_Hippocampus from 53 --> 68 rescaling Right_Amygdala from 55 --> 69 rescaling Right_Accumbens_area from 65 --> 75 rescaling Right_VentralDC from 86 --> 92 rescaling Fifth_Ventricle from 40 --> 45 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 = 534671 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 164 changed. pass 2: 10 changed. pass 3: 1 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /users/zli/test/fs/a003/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Tue Feb 5 19:47:18 EST 2019 /users/zli/test/fs/a003 mri_aparc2aseg --s a003 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /users/zli/Applications/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: /users/zli/Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /users/zli/test/fs subject a003 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /users/zli/test/fs/a003/surf/lh.white Reading lh pial surface /users/zli/test/fs/a003/surf/lh.pial Loading lh annotations from /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/surf/rh.white Reading rh pial surface /users/zli/test/fs/a003/surf/rh.pial Loading rh annotations from /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.54 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 68 rescaling Left_Lateral_Ventricle from 13 --> 24 rescaling Left_Inf_Lat_Vent from 34 --> 39 rescaling Left_Cerebellum_White_Matter from 86 --> 89 rescaling Left_Cerebellum_Cortex from 60 --> 66 rescaling Left_Thalamus from 94 --> 104 rescaling Left_Thalamus_Proper from 84 --> 93 rescaling Left_Caudate from 75 --> 73 rescaling Left_Putamen from 80 --> 83 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 31 rescaling Fourth_Ventricle from 22 --> 23 rescaling Brain_Stem from 81 --> 85 rescaling Left_Hippocampus from 57 --> 68 rescaling Left_Amygdala from 56 --> 69 rescaling CSF from 32 --> 53 rescaling Left_Accumbens_area from 62 --> 66 rescaling Left_VentralDC from 87 --> 91 rescaling Right_Cerebral_White_Matter from 105 --> 105 rescaling Right_Cerebral_Cortex from 58 --> 66 rescaling Right_Lateral_Ventricle from 13 --> 23 rescaling Right_Inf_Lat_Vent from 25 --> 28 rescaling Right_Cerebellum_White_Matter from 87 --> 89 rescaling Right_Cerebellum_Cortex from 59 --> 66 rescaling Right_Thalamus_Proper from 85 --> 88 rescaling Right_Caudate from 62 --> 77 rescaling Right_Putamen from 80 --> 85 rescaling Right_Pallidum from 97 --> 101 rescaling Right_Hippocampus from 53 --> 68 rescaling Right_Amygdala from 55 --> 69 rescaling Right_Accumbens_area from 65 --> 75 rescaling Right_VentralDC from 86 --> 92 rescaling Fifth_Ventricle from 40 --> 45 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 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21:43:14 zkaufman Exp $ Linux compute-104 2.6.32-696.18.7.el6.x86_64 #1 SMP Thu Dec 28 20:15:47 EST 2017 x86_64 x86_64 x86_64 GNU/Linux mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /users/zli/test/fs/a003/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 compute-104 machine x86_64 user zli 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 Tue Feb 5 19:51:35 EST 2019 Ended at Tue Feb 5 19:51:42 EST 2019 Apas2aseg-Run-Time-Sec 7 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Tue Feb 5 19:51:42 EST 2019 /users/zli/test/fs/a003 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 /users/zli/Applications/freesurfer/ASegStatsLUT.txt --subject a003 $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 /users/zli/Applications/freesurfer/ASegStatsLUT.txt --subject a003 sysname Linux hostname compute-104 machine x86_64 user zli UseRobust 0 atlas_icv (eTIV) = 1522624 mm^3 (det: 1.279439 ) Computing euler number orig.nofix lheno = -104, rheno = -80 orig.nofix lhholes = 53, rhholes = 41 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 269549.613 268799.000 diff= 750.6 pctdiff= 0.278 rhCtxGM: 266718.943 265874.000 diff= 844.9 pctdiff= 0.317 lhCtxWM: 234507.813 233969.000 diff= 538.8 pctdiff= 0.230 rhCtxWM: 234846.227 236525.000 diff=-1678.8 pctdiff=-0.715 SubCortGMVol 55495.000 SupraTentVol 1080061.596 (1076880.000) diff=3181.596 pctdiff=0.295 SupraTentVolNotVent 1063857.596 (1060676.000) diff=3181.596 pctdiff=0.299 BrainSegVol 1208999.000 (1206026.000) diff=2973.000 pctdiff=0.246 BrainSegVolNotVent 1188526.000 (1188819.596) diff=-293.596 pctdiff=-0.025 BrainSegVolNotVent 1188526.000 CerebellumVol 127688.000 VentChorVol 16204.000 3rd4th5thCSF 4269.000 CSFVol 1296.000, OptChiasmVol 162.000 MaskVol 1619410.000 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 Tue Feb 5 19:54:17 EST 2019 /users/zli/test/fs/a003 mri_aparc2aseg --s a003 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /users/zli/test/fs subject a003 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /users/zli/test/fs/a003/mri/aparc+aseg.mgz Reading lh white surface /users/zli/test/fs/a003/surf/lh.white Reading lh pial surface /users/zli/test/fs/a003/surf/lh.pial Loading lh annotations from /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/surf/rh.white Reading rh pial surface /users/zli/test/fs/a003/surf/rh.pial Loading rh annotations from /users/zli/test/fs/a003/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 /users/zli/test/fs/a003/mri/ribbon.mgz Loading filled from /users/zli/test/fs/a003/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 8030 vertices from left hemi Ripped 7188 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 /users/zli/test/fs/a003/mri/aseg.mgz Loading Ctx Seg File /users/zli/test/fs/a003/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 = 1002727 Used brute-force search on 236 voxels Fixing Parahip LH WM Found 9 clusters 0 k 1609.000000 1 k 2.000000 2 k 1.000000 3 k 1.000000 4 k 2.000000 5 k 1.000000 6 k 1.000000 7 k 1.000000 8 k 41.000000 Fixing Parahip RH WM Found 8 clusters 0 k 1.000000 1 k 1.000000 2 k 2.000000 3 k 1349.000000 4 k 1.000000 5 k 2.000000 6 k 22.000000 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 a003 --surf-wm-vol --ctab /users/zli/Applications/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 a003 --surf-wm-vol --ctab /users/zli/Applications/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname compute-104 machine x86_64 user zli UseRobust 0 atlas_icv (eTIV) = 1522624 mm^3 (det: 1.279439 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 269549.613 268799.000 diff= 750.6 pctdiff= 0.278 rhCtxGM: 266718.943 265874.000 diff= 844.9 pctdiff= 0.317 lhCtxWM: 234507.813 233969.000 diff= 538.8 pctdiff= 0.230 rhCtxWM: 234846.227 236525.000 diff=-1678.8 pctdiff=-0.715 SubCortGMVol 55495.000 SupraTentVol 1080061.596 (1076880.000) diff=3181.596 pctdiff=0.295 SupraTentVolNotVent 1063857.596 (1060676.000) diff=3181.596 pctdiff=0.299 BrainSegVol 1208999.000 (1206026.000) diff=2973.000 pctdiff=0.246 BrainSegVolNotVent 1188526.000 (1188819.596) diff=-293.596 pctdiff=-0.025 BrainSegVolNotVent 1188526.000 CerebellumVol 127688.000 VentChorVol 16204.000 3rd4th5thCSF 4269.000 CSFVol 1296.000, OptChiasmVol 162.000 MaskVol 1619410.000 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 /users/zli/test/fs/a003/label INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /users/zli/test/fs; ln -s /users/zli/Applications/freesurfer/subjects/fsaverage; cd - #-------------------------------------------- #@# BA_exvivo Labels lh Tue Feb 5 20:03:18 EST 2019 mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.BA1_exvivo.label --trgsubject a003 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 513 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4642 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.BA2_exvivo.label --trgsubject a003 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 734 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8643 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.BA3a_exvivo.label --trgsubject a003 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 324 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4401 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.BA3b_exvivo.label --trgsubject a003 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 531 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6514 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.BA4a_exvivo.label --trgsubject a003 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 789 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6573 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.BA4p_exvivo.label --trgsubject a003 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 554 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4624 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.BA6_exvivo.label --trgsubject a003 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 1395 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14984 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.BA44_exvivo.label --trgsubject a003 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 633 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4814 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.BA45_exvivo.label --trgsubject a003 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 471 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3893 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.V1_exvivo.label --trgsubject a003 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 1831 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6472 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.V2_exvivo.label --trgsubject a003 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 3824 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 11938 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.MT_exvivo.label --trgsubject a003 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 256 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2274 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject a003 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 309 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1599 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject a003 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 334 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1533 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject a003 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 204 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1218 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject a003 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 165 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2257 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject a003 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1574 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject a003 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 192 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2188 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject a003 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 360 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2679 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject a003 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 222 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1771 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject a003 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 550 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7585 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject a003 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 197 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2109 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject a003 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 175 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1326 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject a003 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 1214 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4619 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject a003 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 1758 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 5092 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject a003 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 42 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 555 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject a003 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 113 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 583 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject a003 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/lh.white Reading target registration /users/zli/test/fs/a003/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 147177 Number of reverse mapping hits = 122 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 572 mri_label2label: Done mris_label2annot --s a003 --hemi lh --ctab /users/zli/Applications/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 /users/zli/Applications/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 /users/zli/test/fs/a003/label cmdline mris_label2annot --s a003 --hemi lh --ctab /users/zli/Applications/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 compute-104 machine x86_64 user zli subject a003 hemi lh SUBJECTS_DIR /users/zli/test/fs ColorTable /users/zli/Applications/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /users/zli/test/fs/a003/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 102693 unhit vertices Writing annot to /users/zli/test/fs/a003/label/lh.BA_exvivo.annot mris_label2annot --s a003 --hemi lh --ctab /users/zli/Applications/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 /users/zli/Applications/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 /users/zli/test/fs/a003/label cmdline mris_label2annot --s a003 --hemi lh --ctab /users/zli/Applications/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 compute-104 machine x86_64 user zli subject a003 hemi lh SUBJECTS_DIR /users/zli/test/fs ColorTable /users/zli/Applications/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /users/zli/test/fs/a003/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 120823 unhit vertices Writing annot to /users/zli/test/fs/a003/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 a003 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /users/zli/test/fs/a003/mri/wm.mgz... reading input surface /users/zli/test/fs/a003/surf/lh.white... reading input pial surface /users/zli/test/fs/a003/surf/lh.pial... reading input white surface /users/zli/test/fs/a003/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 274154 Total vertex volume 270461 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /users/zli/Applications/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) = 1522624 mm^3 (det: 1.279439 ) lhCtxGM: 269549.613 268799.000 diff= 750.6 pctdiff= 0.278 rhCtxGM: 266718.943 265874.000 diff= 844.9 pctdiff= 0.317 lhCtxWM: 234507.813 233969.000 diff= 538.8 pctdiff= 0.230 rhCtxWM: 234846.227 236525.000 diff=-1678.8 pctdiff=-0.715 SubCortGMVol 55495.000 SupraTentVol 1080061.596 (1076880.000) diff=3181.596 pctdiff=0.295 SupraTentVolNotVent 1063857.596 (1060676.000) diff=3181.596 pctdiff=0.299 BrainSegVol 1208999.000 (1206026.000) diff=2973.000 pctdiff=0.246 BrainSegVolNotVent 1188526.000 (1188819.596) diff=-293.596 pctdiff=-0.025 BrainSegVolNotVent 1188526.000 CerebellumVol 127688.000 VentChorVol 16204.000 3rd4th5thCSF 4269.000 CSFVol 1296.000, OptChiasmVol 162.000 MaskVol 1619410.000 1424 679 2136 2.264 0.606 0.127 0.065 30 3.9 BA1_exvivo 4165 2693 6775 2.321 0.490 0.107 0.024 42 3.8 BA2_exvivo 1219 814 1305 1.993 0.421 0.125 0.029 9 1.3 BA3a_exvivo 2758 1706 4138 2.131 0.658 0.098 0.024 26 2.7 BA3b_exvivo 2024 1130 3895 2.874 0.433 0.100 0.039 32 3.0 BA4a_exvivo 1611 1016 2839 2.698 0.543 0.090 0.035 14 2.4 BA4p_exvivo 9335 6183 21816 2.882 0.609 0.120 0.030 113 11.4 BA6_exvivo 2482 1695 5388 2.662 0.435 0.117 0.026 32 2.7 BA44_exvivo 2705 1857 5982 2.635 0.512 0.116 0.023 34 2.5 BA45_exvivo 3853 2357 4448 1.845 0.467 0.126 0.041 54 5.9 V1_exvivo 9432 5562 13090 2.151 0.524 0.129 0.038 138 14.4 V2_exvivo 1705 1086 3412 2.629 0.550 0.119 0.031 26 1.9 MT_exvivo 783 470 2208 3.452 0.783 0.079 0.027 5 0.7 perirhinal_exvivo 988 653 2535 3.341 0.720 0.124 0.033 12 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 a003 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /users/zli/test/fs/a003/mri/wm.mgz... reading input surface /users/zli/test/fs/a003/surf/lh.white... reading input pial surface /users/zli/test/fs/a003/surf/lh.pial... reading input white surface /users/zli/test/fs/a003/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 274154 Total vertex volume 270461 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /users/zli/Applications/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) = 1522624 mm^3 (det: 1.279439 ) lhCtxGM: 269549.613 268799.000 diff= 750.6 pctdiff= 0.278 rhCtxGM: 266718.943 265874.000 diff= 844.9 pctdiff= 0.317 lhCtxWM: 234507.813 233969.000 diff= 538.8 pctdiff= 0.230 rhCtxWM: 234846.227 236525.000 diff=-1678.8 pctdiff=-0.715 SubCortGMVol 55495.000 SupraTentVol 1080061.596 (1076880.000) diff=3181.596 pctdiff=0.295 SupraTentVolNotVent 1063857.596 (1060676.000) diff=3181.596 pctdiff=0.299 BrainSegVol 1208999.000 (1206026.000) diff=2973.000 pctdiff=0.246 BrainSegVolNotVent 1188526.000 (1188819.596) diff=-293.596 pctdiff=-0.025 BrainSegVolNotVent 1188526.000 CerebellumVol 127688.000 VentChorVol 16204.000 3rd4th5thCSF 4269.000 CSFVol 1296.000, OptChiasmVol 162.000 MaskVol 1619410.000 969 404 1179 2.164 0.550 0.116 0.065 19 2.8 BA1_exvivo 1581 987 2408 2.234 0.439 0.100 0.029 18 1.6 BA2_exvivo 990 655 1013 1.978 0.431 0.124 0.030 7 1.1 BA3a_exvivo 1643 1067 2106 1.874 0.484 0.089 0.018 10 1.2 BA3b_exvivo 1942 1107 3819 2.922 0.415 0.093 0.036 29 2.7 BA4a_exvivo 1320 803 2143 2.631 0.559 0.095 0.044 14 2.3 BA4p_exvivo 5055 3299 11743 2.878 0.621 0.121 0.035 64 7.2 BA6_exvivo 1554 1080 3214 2.577 0.396 0.119 0.026 22 1.8 BA44_exvivo 1078 740 2556 2.700 0.489 0.121 0.025 14 1.1 BA45_exvivo 4099 2486 4836 1.870 0.473 0.121 0.040 55 6.2 V1_exvivo 4770 2717 6176 2.039 0.548 0.130 0.044 81 8.3 V2_exvivo 422 264 861 2.694 0.602 0.122 0.027 8 0.3 MT_exvivo 423 256 1242 3.495 0.694 0.074 0.027 3 0.4 perirhinal_exvivo 508 350 1358 3.588 0.571 0.104 0.023 3 0.4 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Tue Feb 5 20:08:10 EST 2019 mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.BA1_exvivo.label --trgsubject a003 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 341 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4303 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.BA2_exvivo.label --trgsubject a003 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 354 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7041 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.BA3a_exvivo.label --trgsubject a003 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 247 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4227 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.BA3b_exvivo.label --trgsubject a003 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 320 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4842 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.BA4a_exvivo.label --trgsubject a003 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 750 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6497 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.BA4p_exvivo.label --trgsubject a003 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 554 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 5027 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.BA6_exvivo.label --trgsubject a003 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 1258 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13514 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.BA44_exvivo.label --trgsubject a003 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 536 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7448 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.BA45_exvivo.label --trgsubject a003 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 947 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6302 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.V1_exvivo.label --trgsubject a003 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 2539 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 7266 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.V2_exvivo.label --trgsubject a003 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 4069 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 12085 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.MT_exvivo.label --trgsubject a003 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 462 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2394 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject a003 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 297 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1335 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject a003 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 216 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 968 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject a003 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 150 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 1026 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject a003 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 76 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2764 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject a003 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 59 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1757 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject a003 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 130 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2313 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject a003 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 190 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1578 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject a003 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 221 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1710 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject a003 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 683 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7642 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject a003 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 125 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1137 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject a003 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 132 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1310 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject a003 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 1721 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4953 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject a003 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 2005 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 5442 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject a003 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 37 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 305 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject a003 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 189 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 883 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /users/zli/test/fs/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject a003 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /users/zli/test/fs/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = a003 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 /users/zli/test/fs FREESURFER_HOME /users/zli/Applications/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /users/zli/test/fs/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /users/zli/test/fs/a003/surf/rh.white Reading target registration /users/zli/test/fs/a003/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 143595 Number of reverse mapping hits = 78 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 369 mri_label2label: Done mris_label2annot --s a003 --hemi rh --ctab /users/zli/Applications/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 /users/zli/Applications/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 /users/zli/test/fs/a003/label cmdline mris_label2annot --s a003 --hemi rh --ctab /users/zli/Applications/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 compute-104 machine x86_64 user zli subject a003 hemi rh SUBJECTS_DIR /users/zli/test/fs ColorTable /users/zli/Applications/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /users/zli/test/fs/a003/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 99371 unhit vertices Writing annot to /users/zli/test/fs/a003/label/rh.BA_exvivo.annot mris_label2annot --s a003 --hemi rh --ctab /users/zli/Applications/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 /users/zli/Applications/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 /users/zli/test/fs/a003/label cmdline mris_label2annot --s a003 --hemi rh --ctab /users/zli/Applications/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 compute-104 machine x86_64 user zli subject a003 hemi rh SUBJECTS_DIR /users/zli/test/fs ColorTable /users/zli/Applications/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /users/zli/test/fs/a003/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 118168 unhit vertices Writing annot to /users/zli/test/fs/a003/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 a003 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /users/zli/test/fs/a003/mri/wm.mgz... reading input surface /users/zli/test/fs/a003/surf/rh.white... reading input pial surface /users/zli/test/fs/a003/surf/rh.pial... reading input white surface /users/zli/test/fs/a003/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 271176 Total vertex volume 267790 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /users/zli/Applications/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) = 1522624 mm^3 (det: 1.279439 ) lhCtxGM: 269549.613 268799.000 diff= 750.6 pctdiff= 0.278 rhCtxGM: 266718.943 265874.000 diff= 844.9 pctdiff= 0.317 lhCtxWM: 234507.813 233969.000 diff= 538.8 pctdiff= 0.230 rhCtxWM: 234846.227 236525.000 diff=-1678.8 pctdiff=-0.715 SubCortGMVol 55495.000 SupraTentVol 1080061.596 (1076880.000) diff=3181.596 pctdiff=0.295 SupraTentVolNotVent 1063857.596 (1060676.000) diff=3181.596 pctdiff=0.299 BrainSegVol 1208999.000 (1206026.000) diff=2973.000 pctdiff=0.246 BrainSegVolNotVent 1188526.000 (1188819.596) diff=-293.596 pctdiff=-0.025 BrainSegVolNotVent 1188526.000 CerebellumVol 127688.000 VentChorVol 16204.000 3rd4th5thCSF 4269.000 CSFVol 1296.000, OptChiasmVol 162.000 MaskVol 1619410.000 1045 461 1549 2.345 0.451 0.107 0.035 19 1.3 BA1_exvivo 2753 1835 4142 2.181 0.418 0.091 0.017 19 1.8 BA2_exvivo 1134 786 1146 1.914 0.453 0.115 0.022 8 1.0 BA3a_exvivo 1980 1243 2638 1.907 0.520 0.092 0.022 15 1.7 BA3b_exvivo 1785 1019 3448 2.721 0.543 0.099 0.042 25 3.0 BA4a_exvivo 1537 922 2545 2.800 0.437 0.084 0.017 7 1.0 BA4p_exvivo 8451 5598 19927 2.941 0.574 0.109 0.023 86 7.7 BA6_exvivo 3336 2318 6743 2.678 0.394 0.108 0.018 35 2.5 BA44_exvivo 4401 2962 9592 2.664 0.586 0.128 0.028 65 4.7 BA45_exvivo 4833 2807 5309 1.809 0.512 0.139 0.052 85 10.0 V1_exvivo 9596 5846 13783 2.179 0.569 0.132 0.037 139 13.7 V2_exvivo 2075 1387 3818 2.582 0.497 0.121 0.027 24 2.1 MT_exvivo 812 511 2613 3.746 0.897 0.111 0.038 9 1.2 perirhinal_exvivo 486 294 1770 3.979 0.664 0.140 0.046 7 0.9 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 a003 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /users/zli/test/fs/a003/mri/wm.mgz... reading input surface /users/zli/test/fs/a003/surf/rh.white... reading input pial surface /users/zli/test/fs/a003/surf/rh.pial... reading input white surface /users/zli/test/fs/a003/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 271176 Total vertex volume 267790 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /users/zli/Applications/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) = 1522624 mm^3 (det: 1.279439 ) lhCtxGM: 269549.613 268799.000 diff= 750.6 pctdiff= 0.278 rhCtxGM: 266718.943 265874.000 diff= 844.9 pctdiff= 0.317 lhCtxWM: 234507.813 233969.000 diff= 538.8 pctdiff= 0.230 rhCtxWM: 234846.227 236525.000 diff=-1678.8 pctdiff=-0.715 SubCortGMVol 55495.000 SupraTentVol 1080061.596 (1076880.000) diff=3181.596 pctdiff=0.295 SupraTentVolNotVent 1063857.596 (1060676.000) diff=3181.596 pctdiff=0.299 BrainSegVol 1208999.000 (1206026.000) diff=2973.000 pctdiff=0.246 BrainSegVolNotVent 1188526.000 (1188819.596) diff=-293.596 pctdiff=-0.025 BrainSegVolNotVent 1188526.000 CerebellumVol 127688.000 VentChorVol 16204.000 3rd4th5thCSF 4269.000 CSFVol 1296.000, OptChiasmVol 162.000 MaskVol 1619410.000 684 297 895 2.229 0.445 0.087 0.035 12 0.8 BA1_exvivo 1527 961 2417 2.206 0.385 0.080 0.016 11 0.9 BA2_exvivo 1016 700 949 1.884 0.454 0.121 0.025 7 1.0 BA3a_exvivo 1543 1030 1829 1.750 0.405 0.080 0.014 6 0.9 BA3b_exvivo 1045 604 2093 2.572 0.595 0.125 0.060 24 2.7 BA4a_exvivo 1282 771 2146 2.875 0.438 0.080 0.015 5 0.8 BA4p_exvivo 5564 3663 12952 2.890 0.568 0.110 0.024 60 5.2 BA6_exvivo 914 638 2106 2.766 0.331 0.102 0.021 11 0.7 BA44_exvivo 1043 749 2332 2.521 0.494 0.125 0.026 14 1.1 BA45_exvivo 4590 2678 4977 1.795 0.521 0.139 0.052 81 9.7 V1_exvivo 5144 2999 6914 2.074 0.547 0.138 0.044 86 8.4 V2_exvivo 249 166 700 3.007 0.423 0.143 0.039 4 0.3 MT_exvivo 487 311 1473 3.536 0.958 0.104 0.036 5 0.7 perirhinal_exvivo 339 212 1448 4.351 0.434 0.136 0.042 5 0.6 entorhinal_exvivo Started at Tue Feb 5 10:05:20 EST 2019 Ended at Tue Feb 5 20:13:00 EST 2019 #@#%# recon-all-run-time-hours 10.128 recon-all -s a003 finished without error at Tue Feb 5 20:13:00 EST 2019