Wed Sep 4 19:26:56 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220 /usr/local/freesurfer/bin/recon-all -all -i 19590000/79537359 -s 220 subjid 220 setenv SUBJECTS_DIR /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux dell 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 256786 maxlocks unlimited maxsignal 256786 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 32890164 29232860 3657304 26028 18710416 8622544 -/+ buffers/cache: 1899900 30990264 Swap: 33495036 0 33495036 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-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: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-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: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-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: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/04-11:26:56-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: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-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: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-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: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/04-11:26:56-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: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/04-11:26:56-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: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/04-11:26:56-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: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/04-11:26:56-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: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/04-11:26:56-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: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/04-11:26:56-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: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-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: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-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: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/04-11:26:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: dell Machine: dell Platform: Linux PlatformVersion: 3.13.0-24-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220 mri_convert /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/19590000/79537359 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/orig/001.mgz mri_convert.bin /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/19590000/79537359 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/19590000/79537359... Getting Series No INFO: Found 819 files in /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/19590000 INFO: Scanning for Series Number 3 Scanning Directory INFO: found 176 files in series INFO: loading series header info. RunNo = 2 INFO: sorting. sdfiSameSlicePos() eps = 0.000001 INFO: (256 256 176), nframes = 1, ismosaic=0 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; FileName /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/19590000/79541084 Identification NumarisVer syngo MR D13 ScannerModel Skyra PatientName LIU JIAYUE Date and time StudyDate 20181217 StudyTime 192156.019000 SeriesTime 194535.400000 AcqTime 193727.462500 Acquisition parameters PulseSeq *tfl3d1_16ns Protocol MPRAGE PhEncDir ROW EchoNo 1 FlipAngle 9 EchoTime 2.01 InversionTime 900 RepetitionTime 1900 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 2 SeriesNo 3 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 84.0282 119.3719 131.3000 VolRes 1.0000 1.0000 1.0000 VolDim 256 256 176 Vc -0.0075 -1.0000 0.0000 Vr 0.0347 -0.0003 -0.9994 Vs -0.9994 0.0075 -0.0347 VolCenter -0.4345 -7.9954 0.3205 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 0 INFO: no Siemens slice order reversal detected (good!). TR=1900.00, TE=2.01, TI=900.00, flip angle=9.00 i_ras = (-0.00753482, -0.999972, 1.83308e-07) j_ras = (0.0347355, -0.000261916, -0.999397) k_ras = (-0.999368, 0.00753026, -0.0347365) writing to /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Wed Sep 4 19:27:11 CST 2019 Found 1 runs /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/orig/001.mgz /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/rawavg.mgz /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220 mri_convert /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/rawavg.mgz /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/orig.mgz --conform mri_convert.bin /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/rawavg.mgz /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/rawavg.mgz... TR=1900.00, TE=2.01, TI=900.00, flip angle=9.00 i_ras = (-0.00753482, -0.999972, 1.83308e-07) j_ras = (0.0347355, -0.000261916, -0.999397) k_ras = (-0.999368, 0.00753026, -0.0347365) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/orig.mgz... mri_add_xform_to_header -c /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/transforms/talairach.xfm /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/orig.mgz /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Wed Sep 4 19:27:19 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux dell 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Wed Sep 4 19:27:19 CST 2019 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.19874 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.19874/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.19874/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=1900.00, TE=2.01, TI=900.00, flip angle=9.00 i_ras = (-1, -4.65661e-10, 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.19874/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Sep 4 19:27:22 CST 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.19874/nu0.mnc ./tmp.mri_nu_correct.mni.19874/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.19874/0/ -iterations 1000 -distance 50 defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [dell@dell:/media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/] [2019-09-04 19:27:22] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.19874/0/ ./tmp.mri_nu_correct.mni.19874/nu0.mnc ./tmp.mri_nu_correct.mni.19874/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 27 CV of field change: 0.00096481 [dell@dell:/media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/] [2019-09-04 19:27:47] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.19874/nu0.mnc ./tmp.mri_nu_correct.mni.19874/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_convert ./tmp.mri_nu_correct.mni.19874/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.19874/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.19874/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -4.65661e-10, 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... Wed Sep 4 19:27:56 CST 2019 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Wed Sep 4 19:27:56 CST 2019 Ended at Wed Sep 4 19:28:21 CST 2019 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Wed Sep 4 19:28:23 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.8337, pval=0.9628 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/transforms/talairach_avi.log tal_QC_AZS /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/transforms/talairach_avi.log TalAviQA: 0.97840 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Wed Sep 4 19:28:23 CST 2019 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux dell 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Wed Sep 4 19:28:23 CST 2019 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.20476 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20476/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.20476/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=1900.00, TE=2.01, TI=900.00, flip angle=9.00 i_ras = (-1, -4.65661e-10, 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.20476/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Sep 4 19:28:25 CST 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.20476/nu0.mnc ./tmp.mri_nu_correct.mni.20476/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.20476/0/ defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [dell@dell:/media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/] [2019-09-04 19:28:25] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.20476/0/ ./tmp.mri_nu_correct.mni.20476/nu0.mnc ./tmp.mri_nu_correct.mni.20476/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 21 CV of field change: 0.000965364 [dell@dell:/media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/] [2019-09-04 19:28:38] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.20476/nu0.mnc ./tmp.mri_nu_correct.mni.20476/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Wed Sep 4 19:28:42 CST 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.20476/nu1.mnc ./tmp.mri_nu_correct.mni.20476/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.20476/1/ defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [dell@dell:/media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/] [2019-09-04 19:28:42] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.20476/1/ ./tmp.mri_nu_correct.mni.20476/nu1.mnc ./tmp.mri_nu_correct.mni.20476/nu2.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 12 CV of field change: 0.000977893 [dell@dell:/media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/] [2019-09-04 19:28:50] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.20476/nu1.mnc ./tmp.mri_nu_correct.mni.20476/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.20476/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.20476/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.20476/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.20476/ones.mgz sysname Linux hostname dell machine x86_64 user dell input ./tmp.mri_nu_correct.mni.20476/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.20476/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.20476/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.20476/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20476/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.20476/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.20476/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20476/input.mean.dat sysname Linux hostname dell machine x86_64 user dell UseRobust 0 Loading ./tmp.mri_nu_correct.mni.20476/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.20476/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.20476/ones.mgz --i ./tmp.mri_nu_correct.mni.20476/nu2.mnc --sum ./tmp.mri_nu_correct.mni.20476/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20476/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.20476/ones.mgz --i ./tmp.mri_nu_correct.mni.20476/nu2.mnc --sum ./tmp.mri_nu_correct.mni.20476/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20476/output.mean.dat sysname Linux hostname dell machine x86_64 user dell UseRobust 0 Loading ./tmp.mri_nu_correct.mni.20476/ones.mgz Loading ./tmp.mri_nu_correct.mni.20476/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.20476/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.20476/nu2.mnc ./tmp.mri_nu_correct.mni.20476/nu2.mnc mul 1.00510941458936033233 Saving result to './tmp.mri_nu_correct.mni.20476/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.20476/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.20476/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.20476/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -4.65661e-10, 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 6 seconds. mapping ( 2, 125) to ( 3, 110) Wed Sep 4 19:29:19 CST 2019 mri_nu_correct.mni done mri_add_xform_to_header -c /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Wed Sep 4 19:29:20 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 1.07782 -0.00082 0.00739 1.57275; 0.01073 1.08517 0.23061 2.04996; -0.05799 -0.18306 1.17329 -10.24190; 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 75 (75), valley at 43 (43) csf peak at 38, setting threshold to 62 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 75 (75), valley at 38 (38) 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 33 seconds. #-------------------------------------------- #@# Skull Stripping Wed Sep 4 19:30:54 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri mri_em_register -rusage /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (48, 37, 24) --> (206, 255, 215) using (101, 110, 120) as brain centroid... mean wm in atlas = 108, using box (82,83,96) --> (120, 136,143) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 106 +- 4.1 after smoothing, mri peak at 106, scaling input intensities by 1.019 scaling channel 0 by 1.01887 initial log_p = -4.298 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.312488 @ (0.000, 0.000, 0.000) max log p = -4.243332 @ (-4.545, 4.545, -4.545) max log p = -4.243332 @ (0.000, 0.000, 0.000) max log p = -4.235084 @ (3.409, -7.955, -3.409) max log p = -4.228975 @ (0.568, 5.114, -6.250) max log p = -4.228975 @ (0.000, 0.000, 0.000) Found translation: (-0.6, 1.7, -14.2): log p = -4.229 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.890, old_max_log_p =-4.229 (thresh=-4.2) 1.07500 0.00000 0.00000 -9.97645; 0.00000 1.22567 0.16136 -42.68675; 0.00000 -0.13885 1.05465 5.96111; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.890, old_max_log_p =-3.890 (thresh=-3.9) 1.07500 0.00000 0.00000 -9.97645; 0.00000 1.22567 0.16136 -42.68675; 0.00000 -0.13885 1.05465 5.96111; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.805, old_max_log_p =-3.890 (thresh=-3.9) 1.05428 0.04083 0.00537 -15.21708; -0.03517 1.27096 0.16732 -41.23344; 0.00000 -0.14405 1.09420 0.15003; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.799, old_max_log_p =-3.805 (thresh=-3.8) 1.03457 0.00237 -0.03422 -4.80409; -0.00067 1.29967 0.13281 -45.32176; 0.03272 -0.09911 1.07807 -8.03961; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.796, old_max_log_p =-3.799 (thresh=-3.8) 1.03451 0.04165 0.00542 -12.81523; -0.03518 1.32336 0.13519 -42.41005; -0.00117 -0.10099 1.09884 -4.00772; 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=-3.780, old_max_log_p =-3.796 (thresh=-3.8) 1.03690 0.04286 -0.00385 -12.20270; -0.03550 1.32181 0.13480 -42.57524; 0.00758 -0.10080 1.10143 -6.38611; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.776, old_max_log_p =-3.780 (thresh=-3.8) 1.04055 0.04301 -0.00386 -12.68498; -0.03559 1.32491 0.13512 -43.00825; 0.00758 -0.10080 1.10143 -6.38611; 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 1.04055 0.04301 -0.00386 -12.68498; -0.03559 1.32491 0.13512 -43.00825; 0.00758 -0.10080 1.10143 -6.38611; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.04055 0.04301 -0.00386 -12.68498; -0.03559 1.32491 0.13512 -43.00825; 0.00758 -0.10080 1.10143 -6.38611; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.04055 0.04301 -0.00386 -12.68498; -0.03559 1.32491 0.13512 -43.00825; 0.00758 -0.10080 1.10143 -6.38611; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.776 (old=-4.298) transform before final EM align: 1.04055 0.04301 -0.00386 -12.68498; -0.03559 1.32491 0.13512 -43.00825; 0.00758 -0.10080 1.10143 -6.38611; 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 1.04055 0.04301 -0.00386 -12.68498; -0.03559 1.32491 0.13512 -43.00825; 0.00758 -0.10080 1.10143 -6.38611; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.04055 0.04301 -0.00386 -12.68498; -0.03559 1.32491 0.13512 -43.00825; 0.00758 -0.10080 1.10143 -6.38611; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.2 tol 0.000000 final transform: 1.04055 0.04301 -0.00386 -12.68498; -0.03559 1.32491 0.13512 -43.00825; 0.00758 -0.10080 1.10143 -6.38611; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 802.266917 mri_em_register stimesec 1.045533 mri_em_register ru_maxrss 609816 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157305 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 0 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 145 mri_em_register ru_nivcsw 80269 registration took 13 minutes and 23 seconds. mri_watershed -rusage /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/touch/rusage.mri_watershed.dat -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=129 y=114 z=117 r=83 first estimation of the main basin volume: 2413355 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=159, y=104, z=79, 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=668731438 voxels, voxel volume =1.000 = 668731438 mmm3 = 668731.456 cm3 done. PostAnalyze...Basin Prior 5 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=128,y=117, z=111, r=9356 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=12, CSF_MAX=67 , nb = 43820 RIGHT_CER CSF_MIN=0, CSF_intensity=11, CSF_MAX=55 , nb = -1034728818 LEFT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=59 , nb = -1044818287 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=13, CSF_MAX=69 , nb = -1076650771 LEFT_BRAIN CSF_MIN=0, CSF_intensity=14, CSF_MAX=66 , nb = 1079242114 OTHER CSF_MIN=0, CSF_intensity=25, CSF_MAX=35 , nb = 1049583238 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 67, 54, 50, 69 after analyzing : 43, 54, 54, 57 RIGHT_CER before analyzing : 55, 52, 51, 68 after analyzing : 39, 52, 52, 56 LEFT_CER before analyzing : 59, 52, 50, 71 after analyzing : 40, 52, 52, 56 RIGHT_BRAIN before analyzing : 69, 54, 50, 69 after analyzing : 43, 54, 54, 57 LEFT_BRAIN before analyzing : 66, 53, 49, 69 after analyzing : 43, 53, 53, 57 OTHER before analyzing : 35, 46, 70, 90 after analyzing : 35, 62, 70, 69 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...72 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.013 curvature mean = 66.506, std = 7.289 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.19, sigma = 4.41 after rotation: sse = 3.19, sigma = 4.41 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.33, its var is 3.93 before Erosion-Dilatation 0.44% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...46 iterations mri_strip_skull: done peeling brain Brain Size = 1493045 voxels, voxel volume = 1.000 mm3 = 1493045 mmm3 = 1493.045 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 17.481318 mri_watershed stimesec 0.168942 mri_watershed ru_maxrss 860148 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 216190 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 0 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 647 mri_watershed ru_nivcsw 1923 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Wed Sep 4 19:44:36 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri mri_em_register -rusage /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=26.0 skull bounding box = (59, 57, 37) --> (195, 183, 190) using (104, 99, 114) as brain centroid... mean wm in atlas = 107, using box (87,84,95) --> (120, 114,132) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 106 +- 3.6 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 initial log_p = -3.878 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.884258 @ (0.000, 0.000, 0.000) max log p = -3.811829 @ (-4.545, 4.545, -4.545) max log p = -3.738934 @ (2.273, -6.818, -2.273) max log p = -3.723287 @ (-1.136, -1.136, -3.409) max log p = -3.708754 @ (0.568, -1.705, 0.568) max log p = -3.708754 @ (0.000, 0.000, 0.000) Found translation: (-2.8, -5.1, -9.7): log p = -3.709 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.484, old_max_log_p =-3.709 (thresh=-3.7) 1.07500 0.00000 0.00000 -12.55927; 0.00000 1.15000 0.00000 -16.27418; 0.00000 0.00000 1.00000 -9.65909; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.484, old_max_log_p =-3.484 (thresh=-3.5) 1.07500 0.00000 0.00000 -12.55927; 0.00000 1.15000 0.00000 -16.27418; 0.00000 0.00000 1.00000 -9.65909; 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=-3.360, old_max_log_p =-3.484 (thresh=-3.5) 1.01257 0.07093 0.04164 -17.26345; -0.06890 1.20286 0.13542 -25.36023; -0.03385 -0.15565 1.02807 13.59271; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.360, old_max_log_p =-3.360 (thresh=-3.4) 1.01257 0.07093 0.04164 -17.26345; -0.06890 1.20286 0.13542 -25.36023; -0.03385 -0.15565 1.02807 13.59271; 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=-3.339, old_max_log_p =-3.360 (thresh=-3.4) 1.01160 0.05365 0.02255 -13.02717; -0.05220 1.20108 0.13549 -27.32761; -0.01730 -0.15465 1.02982 10.19992; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.339, old_max_log_p =-3.339 (thresh=-3.3) 1.01329 0.04504 0.01309 -11.19722; -0.04372 1.20130 0.12702 -27.03459; -0.00946 -0.14454 1.03225 8.21780; 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 1.01329 0.04504 0.01309 -11.19722; -0.04372 1.20130 0.12702 -27.03459; -0.00946 -0.14454 1.03225 8.21780; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.01329 0.04504 0.01309 -11.19722; -0.04372 1.20130 0.12702 -27.03459; -0.00946 -0.14454 1.03225 8.21780; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.01329 0.04504 0.01309 -11.19722; -0.04372 1.20130 0.12702 -27.03459; -0.00946 -0.14454 1.03225 8.21780; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.339 (old=-3.878) transform before final EM align: 1.01329 0.04504 0.01309 -11.19722; -0.04372 1.20130 0.12702 -27.03459; -0.00946 -0.14454 1.03225 8.21780; 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 1.01329 0.04504 0.01309 -11.19722; -0.04372 1.20130 0.12702 -27.03459; -0.00946 -0.14454 1.03225 8.21780; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.01329 0.04504 0.01309 -11.19722; -0.04372 1.20130 0.12702 -27.03459; -0.00946 -0.14454 1.03225 8.21780; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 3.8 tol 0.000000 final transform: 1.01329 0.04504 0.01309 -11.19722; -0.04372 1.20130 0.12702 -27.03459; -0.00946 -0.14454 1.03225 8.21780; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 557.094130 mri_em_register stimesec 0.843265 mri_em_register ru_maxrss 598944 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 159072 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 0 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 229 mri_em_register ru_nivcsw 55846 registration took 9 minutes and 18 seconds. #-------------------------------------- #@# CA Normalize Wed Sep 4 19:53:54 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=26.0 skull bounding box = (59, 57, 37) --> (195, 183, 190) using (104, 99, 114) as brain centroid... mean wm in atlas = 107, using box (87,84,95) --> (120, 114,132) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 106 +- 3.6 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 using 246344 sample points... INFO: compute sample coordinates transform 1.01329 0.04504 0.01309 -11.19722; -0.04372 1.20130 0.12702 -27.03459; -0.00946 -0.14454 1.03225 8.21780; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 59, 37) --> (195, 157, 197) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 5506 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 60, 35) --> (131, 155, 197) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 132.0 7 of 6101 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 133, 62) --> (177, 170, 114) Left_Cerebellum_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 272 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (84, 133, 59) --> (128, 167, 114) Right_Cerebellum_White_Matter: limiting intensities to 91.0 --> 132.0 0 of 354 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (111, 124, 96) --> (146, 182, 125) Brain_Stem: limiting intensities to 88.0 --> 132.0 0 of 154 (0.0%) samples deleted using 12387 total control points for intensity normalization... bias field = 0.977 +- 0.051 68 of 12380 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 59, 37) --> (195, 157, 197) Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 3 of 5804 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 60, 35) --> (131, 155, 197) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 5 of 6360 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 133, 62) --> (177, 170, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 38 of 422 (9.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (84, 133, 59) --> (128, 167, 114) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 49 of 437 (11.2%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (111, 124, 96) --> (146, 182, 125) Brain_Stem: limiting intensities to 88.0 --> 132.0 46 of 211 (21.8%) samples deleted using 13234 total control points for intensity normalization... bias field = 1.004 +- 0.038 44 of 12957 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 59, 37) --> (195, 157, 197) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 6 of 5786 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 60, 35) --> (131, 155, 197) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 13 of 6437 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 133, 62) --> (177, 170, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 242 of 462 (52.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (84, 133, 59) --> (128, 167, 114) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 324 of 467 (69.4%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (111, 124, 96) --> (146, 182, 125) Brain_Stem: limiting intensities to 88.0 --> 132.0 106 of 249 (42.6%) samples deleted using 13401 total control points for intensity normalization... bias field = 1.002 +- 0.032 25 of 12492 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 8 seconds. #-------------------------------------- #@# CA Reg Wed Sep 4 19:55:02 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri mri_ca_register -rusage /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.28 (predicted orig area = 6.3) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.790, neg=0, invalid=762 0001: dt=220.917431, rms=0.715 (9.462%), neg=0, invalid=762 0002: dt=144.461942, rms=0.700 (2.057%), neg=0, invalid=762 0003: dt=443.904000, rms=0.690 (1.406%), neg=0, invalid=762 0004: dt=134.453782, rms=0.685 (0.723%), neg=0, invalid=762 0005: dt=517.888000, rms=0.681 (0.611%), neg=0, invalid=762 0006: dt=129.472000, rms=0.679 (0.355%), neg=0, invalid=762 0007: dt=517.888000, rms=0.675 (0.491%), neg=0, invalid=762 0008: dt=129.472000, rms=0.674 (0.166%), neg=0, invalid=762 0009: dt=129.472000, rms=0.674 (0.097%), neg=0, invalid=762 0010: dt=129.472000, rms=0.672 (0.178%), neg=0, invalid=762 0011: dt=129.472000, rms=0.671 (0.237%), neg=0, invalid=762 0012: dt=129.472000, rms=0.669 (0.249%), neg=0, invalid=762 0013: dt=129.472000, rms=0.667 (0.267%), neg=0, invalid=762 0014: dt=129.472000, rms=0.666 (0.267%), neg=0, invalid=762 0015: dt=129.472000, rms=0.664 (0.229%), neg=0, invalid=762 0016: dt=129.472000, rms=0.663 (0.170%), neg=0, invalid=762 0017: dt=129.472000, rms=0.662 (0.136%), neg=0, invalid=762 0018: dt=129.472000, rms=0.661 (0.127%), neg=0, invalid=762 0019: dt=129.472000, rms=0.660 (0.153%), neg=0, invalid=762 0020: dt=129.472000, rms=0.659 (0.140%), neg=0, invalid=762 0021: dt=129.472000, rms=0.658 (0.115%), neg=0, invalid=762 0022: dt=129.472000, rms=0.658 (0.097%), neg=0, invalid=762 0023: dt=1479.680000, rms=0.657 (0.170%), neg=0, invalid=762 0024: dt=92.480000, rms=0.656 (0.061%), neg=0, invalid=762 0025: dt=92.480000, rms=0.656 (0.023%), neg=0, invalid=762 0026: dt=92.480000, rms=0.656 (0.034%), neg=0, invalid=762 0027: dt=92.480000, rms=0.656 (0.040%), neg=0, invalid=762 0028: dt=92.480000, rms=0.655 (0.037%), neg=0, invalid=762 0029: dt=92.480000, rms=0.655 (0.033%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.656, neg=0, invalid=762 0030: dt=369.920000, rms=0.653 (0.437%), neg=0, invalid=762 0031: dt=129.472000, rms=0.652 (0.091%), neg=0, invalid=762 0032: dt=129.472000, rms=0.652 (0.050%), neg=0, invalid=762 0033: dt=129.472000, rms=0.652 (0.080%), neg=0, invalid=762 0034: dt=129.472000, rms=0.651 (0.098%), neg=0, invalid=762 0035: dt=129.472000, rms=0.650 (0.111%), neg=0, invalid=762 0036: dt=129.472000, rms=0.650 (0.110%), neg=0, invalid=762 0037: dt=129.472000, rms=0.649 (0.104%), neg=0, invalid=762 0038: dt=517.888000, rms=0.649 (0.017%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.654, neg=0, invalid=762 0039: dt=119.322034, rms=0.649 (0.720%), neg=0, invalid=762 0040: dt=275.800458, rms=0.636 (2.077%), neg=0, invalid=762 0041: dt=45.781022, rms=0.632 (0.629%), neg=0, invalid=762 0042: dt=103.680000, rms=0.631 (0.163%), neg=0, invalid=762 0043: dt=103.680000, rms=0.627 (0.581%), neg=0, invalid=762 0044: dt=103.680000, rms=0.623 (0.703%), neg=0, invalid=762 0045: dt=103.680000, rms=0.619 (0.631%), neg=0, invalid=762 0046: dt=103.680000, rms=0.614 (0.719%), neg=0, invalid=762 0047: dt=103.680000, rms=0.609 (0.780%), neg=0, invalid=762 0048: dt=103.680000, rms=0.606 (0.587%), neg=0, invalid=762 0049: dt=103.680000, rms=0.603 (0.415%), neg=0, invalid=762 0050: dt=103.680000, rms=0.601 (0.344%), neg=0, invalid=762 0051: dt=103.680000, rms=0.599 (0.402%), neg=0, invalid=762 0052: dt=103.680000, rms=0.597 (0.354%), neg=0, invalid=762 0053: dt=103.680000, rms=0.595 (0.283%), neg=0, invalid=762 0054: dt=103.680000, rms=0.594 (0.232%), neg=0, invalid=762 0055: dt=103.680000, rms=0.593 (0.197%), neg=0, invalid=762 0056: dt=103.680000, rms=0.591 (0.207%), neg=0, invalid=762 0057: dt=103.680000, rms=0.590 (0.151%), neg=0, invalid=762 0058: dt=103.680000, rms=0.590 (0.112%), neg=0, invalid=762 0059: dt=103.680000, rms=0.589 (0.122%), neg=0, invalid=762 0060: dt=103.680000, rms=0.588 (0.211%), neg=0, invalid=762 0061: dt=103.680000, rms=0.587 (0.160%), neg=0, invalid=762 0062: dt=103.680000, rms=0.586 (0.078%), neg=0, invalid=762 0063: dt=103.680000, rms=0.586 (0.120%), neg=0, invalid=762 0064: dt=103.680000, rms=0.585 (0.091%), neg=0, invalid=762 0065: dt=103.680000, rms=0.585 (0.021%), neg=0, invalid=762 0066: dt=103.680000, rms=0.585 (0.046%), neg=0, invalid=762 0067: dt=103.680000, rms=0.585 (0.002%), neg=0, invalid=762 0068: dt=103.680000, rms=0.585 (0.018%), neg=0, invalid=762 0069: dt=103.680000, rms=0.584 (0.046%), neg=0, invalid=762 0070: dt=103.680000, rms=0.584 (-0.019%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.585, neg=0, invalid=762 0071: dt=124.416000, rms=0.582 (0.565%), neg=0, invalid=762 0072: dt=66.406015, rms=0.581 (0.104%), neg=0, invalid=762 0073: dt=66.406015, rms=0.581 (0.053%), neg=0, invalid=762 0074: dt=66.406015, rms=0.580 (0.082%), neg=0, invalid=762 0075: dt=66.406015, rms=0.580 (0.083%), neg=0, invalid=762 0076: dt=66.406015, rms=0.580 (0.045%), neg=0, invalid=762 0077: dt=66.406015, rms=0.580 (0.024%), neg=0, invalid=762 0078: dt=145.152000, rms=0.579 (0.038%), neg=0, invalid=762 0079: dt=36.288000, rms=0.579 (0.009%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.606, neg=0, invalid=762 0080: dt=2.400000, rms=0.605 (0.118%), neg=0, invalid=762 0081: dt=0.600000, rms=0.605 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.606, neg=0, invalid=762 0082: dt=2.400000, rms=0.605 (0.116%), neg=0, invalid=762 0083: dt=0.600000, rms=0.605 (0.002%), neg=0, invalid=762 0084: dt=0.600000, rms=0.605 (-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=0.677, neg=0, invalid=762 0085: dt=5.650000, rms=0.652 (3.698%), neg=0, invalid=762 0086: dt=3.760000, rms=0.650 (0.201%), neg=0, invalid=762 0087: dt=3.760000, rms=0.650 (-0.058%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.651, neg=0, invalid=762 0088: dt=0.252000, rms=0.650 (0.085%), neg=0, invalid=762 0089: dt=0.180000, rms=0.650 (0.001%), neg=0, invalid=762 0090: dt=0.180000, rms=0.650 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.705, neg=0, invalid=762 0091: dt=1.024000, rms=0.703 (0.361%), neg=0, invalid=762 0092: dt=1.806452, rms=0.699 (0.554%), neg=0, invalid=762 0093: dt=1.280000, rms=0.698 (0.091%), neg=0, invalid=762 0094: dt=1.280000, rms=0.696 (0.230%), neg=0, invalid=762 0095: dt=1.280000, rms=0.696 (0.035%), neg=0, invalid=762 0096: dt=1.280000, rms=0.696 (-0.318%), neg=0, invalid=762 0097: dt=0.000000, rms=0.696 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.697, neg=0, invalid=762 0098: dt=1.024000, rms=0.696 (0.143%), neg=0, invalid=762 0099: dt=1.024000, rms=0.696 (0.020%), neg=0, invalid=762 0100: dt=1.024000, rms=0.696 (-0.004%), 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=0.663, neg=0, invalid=762 0101: dt=0.748670, rms=0.648 (2.217%), neg=0, invalid=762 0102: dt=0.064000, rms=0.648 (0.106%), neg=0, invalid=762 0103: dt=0.064000, rms=0.648 (-0.046%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.648, neg=0, invalid=762 0104: dt=0.028000, rms=0.648 (0.099%), neg=0, invalid=762 0105: dt=0.007000, rms=0.648 (0.000%), neg=0, invalid=762 0106: dt=0.007000, rms=0.648 (0.000%), neg=0, invalid=762 0107: dt=0.007000, rms=0.648 (-0.003%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.07263 (31) Left_Lateral_Ventricle (4): linear fit = 1.78 x + 0.0 (793 voxels, overlap=0.303) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (793 voxels, peak = 36), gca=30.0 gca peak = 0.15565 (16) mri peak = 0.06806 (27) Right_Lateral_Ventricle (43): linear fit = 3.23 x + 0.0 (1114 voxels, overlap=0.092) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1114 voxels, peak = 52), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.06993 (98) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (924 voxels, overlap=0.928) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (924 voxels, peak = 98), gca=98.4 gca peak = 0.20183 (93) mri peak = 0.11280 (103) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (785 voxels, overlap=0.599) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (785 voxels, peak = 100), gca=100.0 gca peak = 0.21683 (55) mri peak = 0.12069 (69) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (988 voxels, overlap=0.012) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (988 voxels, peak = 67), gca=67.4 gca peak = 0.30730 (58) mri peak = 0.07493 (67) Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (884 voxels, overlap=0.019) Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (884 voxels, peak = 68), gca=67.6 gca peak = 0.11430 (101) mri peak = 0.11222 (106) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (60737 voxels, overlap=0.473) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (60737 voxels, peak = 107), gca=106.6 gca peak = 0.12076 (102) mri peak = 0.11267 (109) Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (60364 voxels, overlap=0.353) Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (60364 voxels, peak = 109), gca=108.6 gca peak = 0.14995 (59) mri peak = 0.04723 (66) Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (27969 voxels, overlap=0.684) Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (27969 voxels, peak = 66), gca=66.4 gca peak = 0.15082 (58) mri peak = 0.04655 (68) Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (30286 voxels, overlap=0.385) Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (30286 voxels, peak = 68), gca=67.6 gca peak = 0.14161 (67) mri peak = 0.13465 (82) Right_Caudate (50): linear fit = 1.20 x + 0.0 (900 voxels, overlap=0.010) Right_Caudate (50): linear fit = 1.20 x + 0.0 (900 voxels, peak = 80), gca=80.1 gca peak = 0.15243 (71) mri peak = 0.13763 (85) Left_Caudate (11): linear fit = 1.12 x + 0.0 (935 voxels, overlap=0.145) Left_Caudate (11): linear fit = 1.12 x + 0.0 (935 voxels, peak = 80), gca=79.9 gca peak = 0.13336 (57) mri peak = 0.05266 (63) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (31939 voxels, overlap=0.647) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (31939 voxels, peak = 65), gca=64.7 gca peak = 0.13252 (56) mri peak = 0.05243 (63) Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (33204 voxels, overlap=0.555) Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (33204 voxels, peak = 64), gca=63.6 gca peak = 0.18181 (84) mri peak = 0.09922 (86) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (9756 voxels, overlap=0.780) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (9756 voxels, peak = 87), gca=86.9 gca peak = 0.20573 (83) mri peak = 0.12394 (86) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (8492 voxels, overlap=0.679) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (8492 voxels, peak = 87), gca=86.7 gca peak = 0.21969 (57) mri peak = 0.14450 (70) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (431 voxels, overlap=0.043) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (431 voxels, peak = 68), gca=67.5 gca peak = 0.39313 (56) mri peak = 0.14914 (67) Right_Amygdala (54): linear fit = 1.17 x + 0.0 (522 voxels, overlap=0.052) Right_Amygdala (54): linear fit = 1.17 x + 0.0 (522 voxels, peak = 66), gca=65.8 gca peak = 0.14181 (85) mri peak = 0.06832 (95) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (5399 voxels, overlap=0.416) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (5399 voxels, peak = 96), gca=96.5 gca peak = 0.11978 (83) mri peak = 0.07473 (94) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4456 voxels, overlap=0.249) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4456 voxels, peak = 93), gca=93.4 gca peak = 0.13399 (79) mri peak = 0.08337 (92) Left_Putamen (12): linear fit = 1.15 x + 0.0 (2328 voxels, overlap=0.161) Left_Putamen (12): linear fit = 1.15 x + 0.0 (2328 voxels, peak = 91), gca=91.2 gca peak = 0.14159 (79) mri peak = 0.07544 (90) Right_Putamen (51): linear fit = 1.13 x + 0.0 (2387 voxels, overlap=0.340) Right_Putamen (51): linear fit = 1.13 x + 0.0 (2387 voxels, peak = 90), gca=89.7 gca peak = 0.10025 (80) mri peak = 0.08563 (88) Brain_Stem (16): linear fit = 1.11 x + 0.0 (12684 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.11 x + 0.0 (12684 voxels, peak = 88), gca=88.4 gca peak = 0.13281 (86) mri peak = 0.08646 (99) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1212 voxels, overlap=0.116) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1212 voxels, peak = 97), gca=96.8 gca peak = 0.12801 (89) mri peak = 0.09266 (100) Left_VentralDC (28): linear fit = 1.14 x + 0.0 (1402 voxels, overlap=0.292) Left_VentralDC (28): linear fit = 1.14 x + 0.0 (1402 voxels, peak = 102), gca=101.9 gca peak = 0.20494 (23) mri peak = 0.28571 (30) gca peak = 0.15061 (21) mri peak = 0.20406 (27) Fourth_Ventricle (15): linear fit = 1.22 x + 0.0 (332 voxels, overlap=0.459) Fourth_Ventricle (15): linear fit = 1.22 x + 0.0 (332 voxels, peak = 26), gca=25.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak 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 1.17 x + 0.0 estimating mean wm scale to be 1.06 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=0.653, neg=0, invalid=762 0108: dt=105.658182, rms=0.640 (1.984%), neg=0, invalid=762 0109: dt=295.936000, rms=0.636 (0.657%), neg=0, invalid=762 0110: dt=295.936000, rms=0.631 (0.704%), neg=0, invalid=762 0111: dt=92.480000, rms=0.629 (0.321%), neg=0, invalid=762 0112: dt=517.888000, rms=0.627 (0.382%), neg=0, invalid=762 0113: dt=129.472000, rms=0.625 (0.245%), neg=0, invalid=762 0114: dt=443.904000, rms=0.624 (0.208%), neg=0, invalid=762 0115: dt=92.480000, rms=0.623 (0.157%), neg=0, invalid=762 0116: dt=887.808000, rms=0.621 (0.311%), neg=0, invalid=762 0117: dt=92.480000, rms=0.620 (0.141%), neg=0, invalid=762 0118: dt=517.888000, rms=0.619 (0.151%), neg=0, invalid=762 0119: dt=110.976000, rms=0.619 (0.071%), neg=0, invalid=762 0120: dt=295.936000, rms=0.618 (0.075%), neg=0, invalid=762 0121: dt=92.480000, rms=0.618 (0.038%), neg=0, invalid=762 0122: dt=92.480000, rms=0.618 (0.030%), neg=0, invalid=762 0123: dt=92.480000, rms=0.618 (0.049%), neg=0, invalid=762 0124: dt=92.480000, rms=0.617 (0.065%), neg=0, invalid=762 0125: dt=92.480000, rms=0.617 (0.078%), neg=0, invalid=762 0126: dt=92.480000, rms=0.616 (0.087%), neg=0, invalid=762 0127: dt=92.480000, rms=0.615 (0.095%), neg=0, invalid=762 0128: dt=92.480000, rms=0.615 (0.099%), neg=0, invalid=762 0129: dt=92.480000, rms=0.614 (0.097%), neg=0, invalid=762 0130: dt=92.480000, rms=0.614 (0.095%), neg=0, invalid=762 0131: dt=92.480000, rms=0.613 (0.092%), neg=0, invalid=762 0132: dt=92.480000, rms=0.613 (0.090%), neg=0, invalid=762 0133: dt=92.480000, rms=0.612 (0.088%), neg=0, invalid=762 0134: dt=92.480000, rms=0.612 (0.082%), neg=0, invalid=762 0135: dt=92.480000, rms=0.611 (0.074%), neg=0, invalid=762 0136: dt=92.480000, rms=0.611 (0.067%), neg=0, invalid=762 0137: dt=92.480000, rms=0.610 (0.061%), neg=0, invalid=762 0138: dt=92.480000, rms=0.610 (0.062%), neg=0, invalid=762 0139: dt=92.480000, rms=0.610 (0.062%), neg=0, invalid=762 0140: dt=92.480000, rms=0.609 (0.056%), neg=0, invalid=762 0141: dt=92.480000, rms=0.609 (0.052%), neg=0, invalid=762 0142: dt=92.480000, rms=0.609 (0.050%), neg=0, invalid=762 0143: dt=92.480000, rms=0.608 (0.049%), neg=0, invalid=762 0144: dt=92.480000, rms=0.608 (0.050%), neg=0, invalid=762 0145: dt=92.480000, rms=0.608 (0.048%), neg=0, invalid=762 0146: dt=92.480000, rms=0.607 (0.044%), neg=0, invalid=762 0147: dt=92.480000, rms=0.607 (0.040%), neg=0, invalid=762 0148: dt=92.480000, rms=0.607 (0.040%), neg=0, invalid=762 0149: dt=92.480000, rms=0.607 (0.040%), neg=0, invalid=762 0150: dt=92.480000, rms=0.606 (0.040%), neg=0, invalid=762 0151: dt=92.480000, rms=0.606 (0.039%), neg=0, invalid=762 0152: dt=92.480000, rms=0.606 (0.038%), neg=0, invalid=762 0153: dt=92.480000, rms=0.606 (0.036%), neg=0, invalid=762 0154: dt=92.480000, rms=0.606 (0.037%), neg=0, invalid=762 0155: dt=92.480000, rms=0.605 (0.034%), neg=0, invalid=762 0156: dt=92.480000, rms=0.605 (0.035%), neg=0, invalid=762 0157: dt=92.480000, rms=0.605 (0.036%), neg=0, invalid=762 0158: dt=92.480000, rms=0.605 (0.035%), neg=0, invalid=762 0159: dt=92.480000, rms=0.604 (0.034%), neg=0, invalid=762 0160: dt=92.480000, rms=0.604 (0.034%), neg=0, invalid=762 0161: dt=92.480000, rms=0.604 (0.034%), neg=0, invalid=762 0162: dt=92.480000, rms=0.604 (0.034%), neg=0, invalid=762 0163: dt=92.480000, rms=0.604 (0.033%), neg=0, invalid=762 0164: dt=92.480000, rms=0.603 (0.031%), neg=0, invalid=762 0165: dt=92.480000, rms=0.603 (0.030%), neg=0, invalid=762 0166: dt=92.480000, rms=0.603 (0.029%), neg=0, invalid=762 0167: dt=92.480000, rms=0.603 (0.029%), neg=0, invalid=762 0168: dt=92.480000, rms=0.603 (0.029%), neg=0, invalid=762 0169: dt=92.480000, rms=0.603 (0.029%), neg=0, invalid=762 0170: dt=92.480000, rms=0.602 (0.028%), neg=0, invalid=762 0171: dt=92.480000, rms=0.602 (0.028%), neg=0, invalid=762 0172: dt=92.480000, rms=0.602 (0.029%), neg=0, invalid=762 0173: dt=92.480000, rms=0.602 (0.029%), neg=0, invalid=762 0174: dt=92.480000, rms=0.602 (0.025%), neg=0, invalid=762 0175: dt=92.480000, rms=0.602 (0.024%), neg=0, invalid=762 0176: dt=92.480000, rms=0.601 (0.023%), neg=0, invalid=762 0177: dt=517.888000, rms=0.601 (0.012%), neg=0, invalid=762 0178: dt=517.888000, rms=0.601 (-0.129%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.602, neg=0, invalid=762 0179: dt=295.936000, rms=0.601 (0.200%), neg=0, invalid=762 0180: dt=129.472000, rms=0.600 (0.064%), neg=0, invalid=762 0181: dt=295.936000, rms=0.600 (0.032%), neg=0, invalid=762 0182: dt=295.936000, rms=0.600 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.601, neg=0, invalid=762 0183: dt=168.727273, rms=0.596 (0.857%), neg=0, invalid=762 0184: dt=103.680000, rms=0.591 (0.913%), neg=0, invalid=762 0185: dt=62.208000, rms=0.588 (0.475%), neg=0, invalid=762 0186: dt=145.152000, rms=0.585 (0.528%), neg=0, invalid=762 0187: dt=73.777778, rms=0.583 (0.390%), neg=0, invalid=762 0188: dt=62.208000, rms=0.581 (0.352%), neg=0, invalid=762 0189: dt=103.680000, rms=0.579 (0.275%), neg=0, invalid=762 0190: dt=62.208000, rms=0.577 (0.305%), neg=0, invalid=762 0191: dt=103.680000, rms=0.576 (0.226%), neg=0, invalid=762 0192: dt=62.208000, rms=0.574 (0.275%), neg=0, invalid=762 0193: dt=82.944000, rms=0.573 (0.181%), neg=0, invalid=762 0194: dt=82.944000, rms=0.572 (0.234%), neg=0, invalid=762 0195: dt=36.288000, rms=0.571 (0.126%), neg=0, invalid=762 0196: dt=580.608000, rms=0.565 (1.101%), neg=0, invalid=762 0197: dt=36.288000, rms=0.564 (0.175%), neg=0, invalid=762 0198: dt=580.608000, rms=0.560 (0.675%), neg=0, invalid=762 0199: dt=36.288000, rms=0.560 (0.118%), neg=0, invalid=762 0200: dt=124.416000, rms=0.559 (0.108%), neg=0, invalid=762 0201: dt=82.944000, rms=0.558 (0.123%), neg=0, invalid=762 0202: dt=36.288000, rms=0.558 (0.042%), neg=0, invalid=762 0203: dt=36.288000, rms=0.558 (0.036%), neg=0, invalid=762 0204: dt=36.288000, rms=0.557 (0.063%), neg=0, invalid=762 0205: dt=36.288000, rms=0.557 (0.088%), neg=0, invalid=762 0206: dt=36.288000, rms=0.556 (0.110%), neg=0, invalid=762 0207: dt=36.288000, rms=0.556 (0.127%), neg=0, invalid=762 0208: dt=36.288000, rms=0.555 (0.139%), neg=0, invalid=762 0209: dt=36.288000, rms=0.554 (0.148%), neg=0, invalid=762 0210: dt=36.288000, rms=0.553 (0.154%), neg=0, invalid=762 0211: dt=36.288000, rms=0.552 (0.161%), neg=0, invalid=762 0212: dt=36.288000, rms=0.551 (0.161%), neg=0, invalid=762 0213: dt=36.288000, rms=0.551 (0.160%), neg=0, invalid=762 0214: dt=36.288000, rms=0.550 (0.154%), neg=0, invalid=762 0215: dt=36.288000, rms=0.549 (0.145%), neg=0, invalid=762 0216: dt=36.288000, rms=0.548 (0.139%), neg=0, invalid=762 0217: dt=36.288000, rms=0.547 (0.136%), neg=0, invalid=762 0218: dt=36.288000, rms=0.547 (0.131%), neg=0, invalid=762 0219: dt=36.288000, rms=0.546 (0.123%), neg=0, invalid=762 0220: dt=36.288000, rms=0.545 (0.117%), neg=0, invalid=762 0221: dt=36.288000, rms=0.545 (0.114%), neg=0, invalid=762 0222: dt=36.288000, rms=0.544 (0.112%), neg=0, invalid=762 0223: dt=36.288000, rms=0.544 (0.110%), neg=0, invalid=762 0224: dt=36.288000, rms=0.543 (0.105%), neg=0, invalid=762 0225: dt=36.288000, rms=0.542 (0.100%), neg=0, invalid=762 0226: dt=36.288000, rms=0.542 (0.096%), neg=0, invalid=762 0227: dt=36.288000, rms=0.541 (0.094%), neg=0, invalid=762 0228: dt=36.288000, rms=0.541 (0.089%), neg=0, invalid=762 0229: dt=36.288000, rms=0.540 (0.087%), neg=0, invalid=762 0230: dt=36.288000, rms=0.540 (0.083%), neg=0, invalid=762 0231: dt=36.288000, rms=0.540 (0.078%), neg=0, invalid=762 0232: dt=36.288000, rms=0.539 (0.075%), neg=0, invalid=762 0233: dt=36.288000, rms=0.539 (0.074%), neg=0, invalid=762 0234: dt=36.288000, rms=0.538 (0.073%), neg=0, invalid=762 0235: dt=36.288000, rms=0.538 (0.070%), neg=0, invalid=762 0236: dt=36.288000, rms=0.538 (0.070%), neg=0, invalid=762 0237: dt=36.288000, rms=0.537 (0.068%), neg=0, invalid=762 0238: dt=36.288000, rms=0.537 (0.066%), neg=0, invalid=762 0239: dt=36.288000, rms=0.537 (0.065%), neg=0, invalid=762 0240: dt=36.288000, rms=0.536 (0.055%), neg=0, invalid=762 0241: dt=36.288000, rms=0.536 (0.057%), neg=0, invalid=762 0242: dt=36.288000, rms=0.536 (0.056%), neg=0, invalid=762 0243: dt=36.288000, rms=0.535 (0.056%), neg=0, invalid=762 0244: dt=36.288000, rms=0.535 (0.055%), neg=0, invalid=762 0245: dt=36.288000, rms=0.535 (0.055%), neg=0, invalid=762 0246: dt=36.288000, rms=0.534 (0.051%), neg=0, invalid=762 0247: dt=36.288000, rms=0.534 (0.052%), neg=0, invalid=762 0248: dt=36.288000, rms=0.534 (0.050%), neg=0, invalid=762 0249: dt=36.288000, rms=0.534 (0.049%), neg=0, invalid=762 0250: dt=36.288000, rms=0.533 (0.048%), neg=0, invalid=762 0251: dt=36.288000, rms=0.533 (0.048%), neg=0, invalid=762 0252: dt=36.288000, rms=0.533 (0.046%), neg=0, invalid=762 0253: dt=36.288000, rms=0.533 (0.043%), neg=0, invalid=762 0254: dt=36.288000, rms=0.532 (0.041%), neg=0, invalid=762 0255: dt=36.288000, rms=0.532 (0.039%), neg=0, invalid=762 0256: dt=36.288000, rms=0.532 (0.038%), neg=0, invalid=762 0257: dt=36.288000, rms=0.532 (0.038%), neg=0, invalid=762 0258: dt=36.288000, rms=0.532 (0.037%), neg=0, invalid=762 0259: dt=36.288000, rms=0.531 (0.039%), neg=0, invalid=762 0260: dt=36.288000, rms=0.531 (0.035%), neg=0, invalid=762 0261: dt=36.288000, rms=0.531 (0.032%), neg=0, invalid=762 0262: dt=36.288000, rms=0.531 (0.034%), neg=0, invalid=762 0263: dt=36.288000, rms=0.531 (0.034%), neg=0, invalid=762 0264: dt=36.288000, rms=0.531 (0.031%), neg=0, invalid=762 0265: dt=36.288000, rms=0.530 (0.030%), neg=0, invalid=762 0266: dt=36.288000, rms=0.530 (0.029%), neg=0, invalid=762 0267: dt=36.288000, rms=0.530 (0.028%), neg=0, invalid=762 0268: dt=36.288000, rms=0.530 (0.028%), neg=0, invalid=762 0269: dt=36.288000, rms=0.530 (0.028%), neg=0, invalid=762 0270: dt=36.288000, rms=0.530 (0.027%), neg=0, invalid=762 0271: dt=36.288000, rms=0.530 (0.029%), neg=0, invalid=762 0272: dt=36.288000, rms=0.529 (0.027%), neg=0, invalid=762 0273: dt=36.288000, rms=0.529 (0.025%), neg=0, invalid=762 0274: dt=36.288000, rms=0.529 (0.025%), neg=0, invalid=762 0275: dt=36.288000, rms=0.529 (0.022%), neg=0, invalid=762 0276: dt=145.152000, rms=0.529 (0.008%), neg=0, invalid=762 0277: dt=145.152000, rms=0.529 (0.002%), neg=0, invalid=762 0278: dt=145.152000, rms=0.529 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.529, neg=0, invalid=762 0279: dt=116.729560, rms=0.527 (0.476%), neg=0, invalid=762 0280: dt=36.288000, rms=0.527 (0.084%), neg=0, invalid=762 0281: dt=145.152000, rms=0.526 (0.082%), neg=0, invalid=762 0282: dt=145.152000, rms=0.525 (0.111%), neg=0, invalid=762 0283: dt=36.288000, rms=0.525 (0.037%), neg=0, invalid=762 0284: dt=36.288000, rms=0.525 (0.015%), neg=0, invalid=762 0285: dt=36.288000, rms=0.525 (0.022%), neg=0, invalid=762 0286: dt=36.288000, rms=0.525 (0.035%), neg=0, invalid=762 0287: dt=36.288000, rms=0.525 (0.053%), neg=0, invalid=762 0288: dt=36.288000, rms=0.524 (0.065%), neg=0, invalid=762 0289: dt=36.288000, rms=0.524 (0.058%), neg=0, invalid=762 0290: dt=36.288000, rms=0.524 (0.057%), neg=0, invalid=762 0291: dt=36.288000, rms=0.523 (0.049%), neg=0, invalid=762 0292: dt=36.288000, rms=0.523 (0.042%), neg=0, invalid=762 0293: dt=36.288000, rms=0.523 (0.044%), neg=0, invalid=762 0294: dt=36.288000, rms=0.523 (0.043%), neg=0, invalid=762 0295: dt=36.288000, rms=0.523 (0.042%), neg=0, invalid=762 0296: dt=36.288000, rms=0.522 (0.041%), neg=0, invalid=762 0297: dt=36.288000, rms=0.522 (0.040%), neg=0, invalid=762 0298: dt=36.288000, rms=0.522 (0.039%), neg=0, invalid=762 0299: dt=36.288000, rms=0.522 (0.038%), neg=0, invalid=762 0300: dt=36.288000, rms=0.522 (0.036%), neg=0, invalid=762 0301: dt=36.288000, rms=0.521 (0.040%), neg=0, invalid=762 0302: dt=36.288000, rms=0.521 (0.039%), neg=0, invalid=762 0303: dt=36.288000, rms=0.521 (0.036%), neg=0, invalid=762 0304: dt=36.288000, rms=0.521 (0.032%), neg=0, invalid=762 0305: dt=36.288000, rms=0.521 (0.028%), neg=0, invalid=762 0306: dt=36.288000, rms=0.520 (0.029%), neg=0, invalid=762 0307: dt=36.288000, rms=0.520 (0.026%), neg=0, invalid=762 0308: dt=36.288000, rms=0.520 (0.029%), neg=0, invalid=762 0309: dt=36.288000, rms=0.520 (0.023%), neg=0, invalid=762 0310: dt=36.288000, rms=0.520 (0.026%), neg=0, invalid=762 0311: dt=36.288000, rms=0.520 (0.023%), neg=0, invalid=762 0312: dt=36.288000, rms=0.520 (0.021%), neg=0, invalid=762 0313: dt=414.720000, rms=0.520 (0.022%), neg=0, invalid=762 0314: dt=31.104000, rms=0.520 (0.006%), neg=0, invalid=762 0315: dt=31.104000, rms=0.520 (0.005%), neg=0, invalid=762 0316: dt=31.104000, rms=0.520 (0.001%), neg=0, invalid=762 0317: dt=31.104000, rms=0.519 (0.005%), neg=0, invalid=762 0318: dt=31.104000, rms=0.519 (0.006%), neg=0, invalid=762 0319: dt=31.104000, rms=0.519 (0.010%), neg=0, invalid=762 0320: dt=31.104000, rms=0.519 (0.010%), neg=0, invalid=762 0321: dt=31.104000, rms=0.519 (0.011%), neg=0, invalid=762 0322: dt=31.104000, rms=0.519 (0.011%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.530, neg=0, invalid=762 0323: dt=11.200000, rms=0.528 (0.236%), neg=0, invalid=762 0324: dt=25.600000, rms=0.528 (0.147%), neg=0, invalid=762 0325: dt=109.679849, rms=0.524 (0.618%), neg=0, invalid=762 0326: dt=116.646957, rms=0.519 (0.921%), neg=0, invalid=762 0327: dt=32.000000, rms=0.515 (0.823%), neg=0, invalid=762 0328: dt=11.200000, rms=0.514 (0.144%), neg=0, invalid=762 0329: dt=38.400000, rms=0.514 (0.125%), neg=0, invalid=762 0330: dt=67.333333, rms=0.513 (0.233%), neg=0, invalid=762 0331: dt=29.480315, rms=0.512 (0.218%), neg=0, invalid=762 0332: dt=44.800000, rms=0.510 (0.278%), neg=0, invalid=762 0333: dt=22.320988, rms=0.510 (0.109%), neg=0, invalid=762 0334: dt=153.600000, rms=0.508 (0.387%), neg=0, invalid=762 0335: dt=24.255319, rms=0.506 (0.245%), neg=0, invalid=762 0336: dt=44.800000, rms=0.505 (0.231%), neg=0, invalid=762 0337: dt=19.200000, rms=0.505 (0.051%), neg=0, invalid=762 0338: dt=76.800000, rms=0.504 (0.146%), neg=0, invalid=762 0339: dt=21.101449, rms=0.504 (0.091%), neg=0, invalid=762 0340: dt=76.800000, rms=0.503 (0.177%), neg=0, invalid=762 0341: dt=11.200000, rms=0.503 (0.051%), neg=0, invalid=762 0342: dt=25.600000, rms=0.502 (0.049%), neg=0, invalid=762 0343: dt=25.600000, rms=0.502 (0.082%), neg=0, invalid=762 0344: dt=25.600000, rms=0.501 (0.100%), neg=0, invalid=762 0345: dt=25.600000, rms=0.501 (0.116%), neg=0, invalid=762 0346: dt=25.600000, rms=0.500 (0.184%), neg=0, invalid=762 0347: dt=25.600000, rms=0.499 (0.205%), neg=0, invalid=762 0348: dt=25.600000, rms=0.498 (0.202%), neg=0, invalid=762 0349: dt=25.600000, rms=0.497 (0.180%), neg=0, invalid=762 0350: dt=25.600000, rms=0.496 (0.228%), neg=0, invalid=762 0351: dt=25.600000, rms=0.496 (0.033%), neg=0, invalid=762 0352: dt=25.600000, rms=0.495 (0.034%), neg=0, invalid=762 0353: dt=25.600000, rms=0.495 (0.046%), neg=0, invalid=762 0354: dt=3.200000, rms=0.495 (0.006%), neg=0, invalid=762 0355: dt=1.600000, rms=0.495 (0.003%), neg=0, invalid=762 0356: dt=0.043750, rms=0.495 (0.001%), neg=0, invalid=762 0357: dt=0.021875, rms=0.495 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.496, neg=0, invalid=762 0358: dt=0.010937, rms=0.495 (0.106%), neg=0, invalid=762 0359: dt=0.010937, rms=0.495 (0.000%), neg=0, invalid=762 0360: dt=0.005469, rms=0.495 (0.000%), neg=0, invalid=762 0361: dt=0.001367, rms=0.495 (0.000%), neg=0, invalid=762 0362: dt=0.000684, rms=0.495 (0.000%), neg=0, invalid=762 0363: dt=0.000586, rms=0.495 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.522, neg=0, invalid=762 0364: dt=0.600000, rms=0.522 (0.099%), neg=0, invalid=762 0365: dt=0.180000, rms=0.522 (0.000%), neg=0, invalid=762 0366: dt=0.180000, rms=0.522 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.522, neg=0, invalid=762 0367: dt=3.456000, rms=0.521 (0.227%), neg=0, invalid=762 0368: dt=1.008000, rms=0.521 (0.014%), neg=0, invalid=762 0369: dt=1.008000, rms=0.521 (0.003%), neg=0, invalid=762 0370: dt=1.008000, rms=0.521 (-0.019%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.564, neg=0, invalid=762 0371: dt=1.792000, rms=0.560 (0.729%), neg=0, invalid=762 0372: dt=0.768000, rms=0.560 (0.064%), neg=0, invalid=762 0373: dt=0.384000, rms=0.560 (0.010%), neg=0, invalid=762 0374: dt=0.384000, rms=0.560 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.560, neg=0, invalid=762 0375: dt=1.792000, rms=0.558 (0.361%), neg=0, invalid=762 0376: dt=1.280000, rms=0.558 (0.068%), neg=0, invalid=762 0377: dt=0.768000, rms=0.558 (0.012%), neg=0, invalid=762 0378: dt=0.768000, rms=0.558 (0.003%), neg=0, invalid=762 0379: dt=0.768000, rms=0.558 (-0.042%), 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=0.527, neg=0, invalid=762 0380: dt=0.448000, rms=0.514 (2.453%), neg=0, invalid=762 0381: dt=1.280000, rms=0.504 (1.941%), neg=0, invalid=762 0382: dt=0.007000, rms=0.504 (-0.001%), neg=0, invalid=762 0383: dt=0.007000, rms=0.504 (0.000%), neg=0, invalid=762 0384: dt=0.007000, rms=0.504 (0.000%), neg=0, invalid=762 0385: dt=0.007000, rms=0.504 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.504, neg=0, invalid=762 0386: dt=0.448000, rms=0.501 (0.783%), neg=0, invalid=762 0387: dt=0.448000, rms=0.500 (0.141%), neg=0, invalid=762 0388: dt=0.448000, rms=0.499 (0.114%), neg=0, invalid=762 0389: dt=0.448000, rms=0.499 (0.085%), neg=0, invalid=762 0390: dt=0.448000, rms=0.498 (0.080%), neg=0, invalid=762 0391: dt=0.448000, rms=0.498 (0.065%), neg=0, invalid=762 0392: dt=0.448000, rms=0.498 (0.062%), neg=0, invalid=762 0393: dt=0.448000, rms=0.498 (0.051%), neg=0, invalid=762 0394: dt=0.448000, rms=0.497 (0.050%), neg=0, invalid=762 0395: dt=0.448000, rms=0.497 (0.041%), neg=0, invalid=762 0396: dt=0.448000, rms=0.497 (0.044%), neg=0, invalid=762 0397: dt=0.448000, rms=0.497 (0.069%), neg=0, invalid=762 0398: dt=0.448000, rms=0.496 (0.091%), neg=0, invalid=762 0399: dt=0.448000, rms=0.496 (0.103%), neg=0, invalid=762 0400: dt=0.448000, rms=0.495 (0.107%), neg=0, invalid=762 0401: dt=0.448000, rms=0.495 (0.092%), neg=0, invalid=762 0402: dt=0.448000, rms=0.494 (0.079%), neg=0, invalid=762 0403: dt=0.448000, rms=0.494 (0.068%), neg=0, invalid=762 0404: dt=0.448000, rms=0.494 (0.049%), neg=0, invalid=762 0405: dt=0.448000, rms=0.493 (0.027%), neg=0, invalid=762 0406: dt=0.448000, rms=0.493 (0.015%), neg=0, invalid=762 0407: dt=0.448000, rms=0.493 (0.009%), neg=0, invalid=762 0408: dt=0.112000, rms=0.493 (-0.001%), 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=0.491, neg=0, invalid=762 0409: dt=0.000000, rms=0.491 (0.111%), neg=0, invalid=762 0410: dt=0.000000, rms=0.491 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.491, neg=0, invalid=762 0411: dt=221.952000, rms=0.490 (0.183%), neg=0, invalid=762 0412: dt=129.472000, rms=0.490 (0.062%), neg=0, invalid=762 0413: dt=129.472000, rms=0.490 (0.012%), neg=0, invalid=762 0414: dt=129.472000, rms=0.490 (0.043%), neg=0, invalid=762 0415: dt=129.472000, rms=0.489 (0.053%), neg=0, invalid=762 0416: dt=129.472000, rms=0.489 (0.049%), neg=0, invalid=762 0417: dt=129.472000, rms=0.489 (0.040%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.490, neg=0, invalid=762 0418: dt=31.104000, rms=0.489 (0.172%), neg=0, invalid=762 0419: dt=36.288000, rms=0.489 (0.045%), neg=0, invalid=762 0420: dt=36.288000, rms=0.488 (0.058%), neg=0, invalid=762 0421: dt=36.288000, rms=0.488 (0.071%), neg=0, invalid=762 0422: dt=36.288000, rms=0.488 (0.060%), neg=0, invalid=762 0423: dt=36.288000, rms=0.487 (0.054%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.488, neg=0, invalid=762 0424: dt=103.680000, rms=0.484 (0.812%), neg=0, invalid=762 0425: dt=36.288000, rms=0.483 (0.148%), neg=0, invalid=762 0426: dt=36.288000, rms=0.483 (0.065%), neg=0, invalid=762 0427: dt=36.288000, rms=0.482 (0.098%), neg=0, invalid=762 0428: dt=36.288000, rms=0.482 (0.128%), neg=0, invalid=762 0429: dt=36.288000, rms=0.481 (0.146%), neg=0, invalid=762 0430: dt=36.288000, rms=0.480 (0.149%), neg=0, invalid=762 0431: dt=36.288000, rms=0.480 (0.139%), neg=0, invalid=762 0432: dt=36.288000, rms=0.479 (0.129%), neg=0, invalid=762 0433: dt=36.288000, rms=0.479 (0.121%), neg=0, invalid=762 0434: dt=36.288000, rms=0.478 (0.110%), neg=0, invalid=762 0435: dt=248.832000, rms=0.478 (0.075%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0436: dt=248.832000, rms=0.478 (-0.644%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.479, neg=0, invalid=762 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0437: dt=30.000000, rms=0.476 (0.599%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 9 iterations, nbhd size=1, neg = 0 0438: dt=87.470113, rms=0.471 (1.093%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0439: dt=25.600000, rms=0.469 (0.389%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 8 iterations, nbhd size=1, neg = 0 0440: dt=83.525424, rms=0.466 (0.598%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0441: dt=30.353698, rms=0.465 (0.329%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0442: dt=44.800000, rms=0.463 (0.370%), neg=0, invalid=762 0443: dt=25.600000, rms=0.462 (0.109%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0444: dt=25.600000, rms=0.462 (0.095%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0445: dt=25.600000, rms=0.461 (0.231%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0446: dt=25.600000, rms=0.460 (0.240%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 2 iterations, nbhd size=0, neg = 0 0447: dt=25.600000, rms=0.459 (0.240%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 12 iterations, nbhd size=1, neg = 0 0448: dt=25.600000, rms=0.458 (0.193%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 9 iterations, nbhd size=1, neg = 0 0449: dt=25.600000, rms=0.457 (0.278%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 6 iterations, nbhd size=0, neg = 0 0450: dt=25.600000, rms=0.455 (0.251%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 0 iterations, nbhd size=0, neg = 0 0451: dt=25.600000, rms=0.454 (0.207%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 0452: dt=25.600000, rms=0.454 (0.119%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0453: dt=25.600000, rms=0.453 (0.155%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0454: dt=25.600000, rms=0.452 (0.171%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0455: dt=25.600000, rms=0.452 (0.138%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 5 iterations, nbhd size=0, neg = 0 0456: dt=25.600000, rms=0.452 (0.050%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0457: dt=25.600000, rms=0.451 (0.123%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 9 iterations, nbhd size=1, neg = 0 0458: dt=25.600000, rms=0.451 (0.068%), neg=0, invalid=762 0459: dt=11.200000, rms=0.451 (0.036%), neg=0, invalid=762 0460: dt=11.200000, rms=0.450 (0.022%), neg=0, invalid=762 0461: dt=11.200000, rms=0.450 (0.013%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0462: dt=11.200000, rms=0.450 (0.023%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0463: dt=11.200000, rms=0.450 (0.024%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0464: dt=11.200000, rms=0.450 (0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.451, neg=0, invalid=762 iter 0, gcam->neg = 4 after 8 iterations, nbhd size=1, neg = 0 0465: dt=44.800000, rms=0.447 (0.764%), neg=0, invalid=762 0466: dt=25.600000, rms=0.446 (0.224%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0467: dt=25.600000, rms=0.446 (0.087%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0468: dt=25.600000, rms=0.445 (0.170%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 0469: dt=25.600000, rms=0.445 (0.122%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0470: dt=25.600000, rms=0.444 (0.076%), neg=0, invalid=762 0471: dt=11.200000, rms=0.444 (0.052%), neg=0, invalid=762 0472: dt=11.200000, rms=0.444 (0.022%), neg=0, invalid=762 0473: dt=11.200000, rms=0.444 (0.015%), neg=0, invalid=762 0474: dt=11.200000, rms=0.444 (0.027%), neg=0, invalid=762 0475: dt=11.200000, rms=0.444 (0.027%), neg=0, invalid=762 0476: dt=11.200000, rms=0.443 (0.025%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.454, neg=0, invalid=762 0477: dt=0.000000, rms=0.453 (0.129%), neg=0, invalid=762 0478: dt=0.000000, rms=0.453 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.454, neg=0, invalid=762 0479: dt=1.733333, rms=0.453 (0.149%), neg=0, invalid=762 0480: dt=0.720000, rms=0.453 (0.002%), neg=0, invalid=762 0481: dt=0.720000, rms=0.453 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.472, neg=0, invalid=762 0482: dt=1.536000, rms=0.470 (0.580%), neg=0, invalid=762 0483: dt=0.256000, rms=0.470 (0.008%), neg=0, invalid=762 0484: dt=0.256000, rms=0.470 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.470, neg=0, invalid=762 0485: dt=1.536000, rms=0.469 (0.320%), neg=0, invalid=762 0486: dt=0.384000, rms=0.469 (0.008%), neg=0, invalid=762 0487: dt=0.384000, rms=0.469 (-0.004%), 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=0.455, neg=0, invalid=762 iter 0, gcam->neg = 770 after 16 iterations, nbhd size=1, neg = 0 0488: dt=2.075690, rms=0.430 (5.356%), neg=0, invalid=762 0489: dt=0.064000, rms=0.430 (0.031%), neg=0, invalid=762 0490: dt=0.064000, rms=0.430 (-0.028%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.431, neg=0, invalid=762 0491: dt=0.080000, rms=0.430 (0.188%), neg=0, invalid=762 0492: dt=0.000000, rms=0.430 (0.001%), neg=0, invalid=762 0493: dt=0.050000, rms=0.430 (-0.014%), 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=0.418, neg=0, invalid=762 0494: dt=0.000000, rms=0.418 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.418, neg=0, invalid=762 0495: dt=92.480000, rms=0.418 (0.018%), neg=0, invalid=762 0496: dt=129.472000, rms=0.418 (0.006%), neg=0, invalid=762 0497: dt=129.472000, rms=0.418 (0.006%), neg=0, invalid=762 0498: dt=129.472000, rms=0.418 (0.008%), neg=0, invalid=762 0499: dt=129.472000, rms=0.418 (0.005%), neg=0, invalid=762 0500: dt=129.472000, rms=0.418 (0.006%), neg=0, invalid=762 0501: dt=129.472000, rms=0.418 (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=0.418, neg=0, invalid=762 0502: dt=5.200000, rms=0.418 (0.002%), neg=0, invalid=762 0503: dt=0.405000, rms=0.418 (0.000%), neg=0, invalid=762 0504: dt=0.405000, rms=0.418 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.418, neg=0, invalid=762 0505: dt=145.152000, rms=0.418 (0.158%), neg=0, invalid=762 0506: dt=103.680000, rms=0.417 (0.060%), neg=0, invalid=762 0507: dt=103.680000, rms=0.417 (0.013%), neg=0, invalid=762 0508: dt=103.680000, rms=0.417 (0.116%), neg=0, invalid=762 0509: dt=103.680000, rms=0.416 (0.087%), neg=0, invalid=762 0510: dt=103.680000, rms=0.416 (0.061%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.417, neg=0, invalid=762 0511: dt=11.200000, rms=0.416 (0.126%), neg=0, invalid=762 0512: dt=11.200000, rms=0.416 (0.045%), neg=0, invalid=762 0513: dt=11.200000, rms=0.416 (0.034%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 9 iterations, nbhd size=1, neg = 0 0514: dt=11.200000, rms=0.416 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.416, neg=0, invalid=762 0515: dt=44.436019, rms=0.413 (0.671%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0516: dt=32.000000, rms=0.412 (0.350%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0517: dt=32.000000, rms=0.411 (0.227%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0518: dt=32.000000, rms=0.410 (0.153%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0519: dt=32.000000, rms=0.409 (0.276%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 9 iterations, nbhd size=1, neg = 0 0520: dt=32.000000, rms=0.408 (0.305%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0521: dt=32.000000, rms=0.407 (0.299%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 9 iterations, nbhd size=1, neg = 0 0522: dt=32.000000, rms=0.406 (0.245%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 5 iterations, nbhd size=0, neg = 0 0523: dt=32.000000, rms=0.405 (0.200%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 14 iterations, nbhd size=1, neg = 0 0524: dt=32.000000, rms=0.404 (0.196%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 9 iterations, nbhd size=1, neg = 0 0525: dt=32.000000, rms=0.403 (0.137%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 8 iterations, nbhd size=1, neg = 0 0526: dt=32.000000, rms=0.403 (0.115%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 1 iterations, nbhd size=0, neg = 0 0527: dt=32.000000, rms=0.403 (0.097%), neg=0, invalid=762 0528: dt=25.600000, rms=0.402 (0.043%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0529: dt=25.600000, rms=0.402 (0.010%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0530: dt=25.600000, rms=0.402 (0.012%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0531: dt=25.600000, rms=0.402 (0.014%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0532: dt=25.600000, rms=0.402 (0.004%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0533: dt=25.600000, rms=0.402 (-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=0.407, neg=0, invalid=762 0534: dt=0.000246, rms=0.407 (0.000%), neg=0, invalid=762 0535: dt=0.000000, rms=0.407 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.407, neg=0, invalid=762 0536: dt=2.304000, rms=0.407 (0.015%), neg=0, invalid=762 0537: dt=1.500000, rms=0.407 (0.003%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0538: dt=1.500000, rms=0.407 (0.000%), neg=0, invalid=762 0539: dt=1.500000, rms=0.407 (-0.014%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.416, neg=0, invalid=762 0540: dt=0.000040, rms=0.416 (0.000%), neg=0, invalid=762 0541: dt=0.000000, rms=0.416 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.416, neg=0, invalid=762 0542: dt=0.096000, rms=0.416 (0.001%), neg=0, invalid=762 0543: dt=0.024000, rms=0.416 (0.000%), neg=0, invalid=762 0544: dt=0.024000, rms=0.416 (-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=0.401, neg=0, invalid=762 iter 0, gcam->neg = 480 after 14 iterations, nbhd size=1, neg = 0 0545: dt=1.080614, rms=0.394 (1.782%), neg=0, invalid=762 0546: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=762 0547: dt=0.000027, rms=0.394 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.394, neg=0, invalid=762 0548: dt=0.112000, rms=0.394 (0.077%), neg=0, invalid=762 0549: dt=0.112000, rms=0.394 (0.046%), neg=0, invalid=762 0550: dt=0.112000, rms=0.394 (0.039%), neg=0, invalid=762 0551: dt=0.112000, rms=0.393 (0.023%), neg=0, invalid=762 0552: dt=0.112000, rms=0.393 (-0.035%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 51 minutes and 0 seconds. mri_ca_register utimesec 6649.494015 mri_ca_register stimesec 10.770871 mri_ca_register ru_maxrss 1332112 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4619035 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 0 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 12069 mri_ca_register ru_nivcsw 684344 FSRUNTIME@ mri_ca_register 1.8501 hours 1 threads #-------------------------------------- #@# SubCort Seg Wed Sep 4 21:46:02 CST 2019 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname dell machine x86_64 setenv SUBJECTS_DIR /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217 cd /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 6.26 Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.11864 (31) Left_Lateral_Ventricle (4): linear fit = 1.51 x + 0.0 (379 voxels, overlap=0.106) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (379 voxels, peak = 30), gca=30.0 gca peak = 0.17677 (13) mri peak = 0.09787 (28) Right_Lateral_Ventricle (43): linear fit = 2.08 x + 0.0 (291 voxels, overlap=0.105) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (291 voxels, peak = 27), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.14559 (101) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (673 voxels, overlap=0.739) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (673 voxels, peak = 102), gca=102.1 gca peak = 0.16930 (96) mri peak = 0.15337 (103) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (652 voxels, overlap=0.195) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (652 voxels, peak = 103), gca=103.2 gca peak = 0.24553 (55) mri peak = 0.11582 (69) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (740 voxels, overlap=0.017) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (740 voxels, peak = 66), gca=66.3 gca peak = 0.30264 (59) mri peak = 0.10617 (69) Left_Hippocampus (17): linear fit = 1.14 x + 0.0 (634 voxels, overlap=0.018) Left_Hippocampus (17): linear fit = 1.14 x + 0.0 (634 voxels, peak = 68), gca=67.6 gca peak = 0.07580 (103) mri peak = 0.12774 (106) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (34094 voxels, overlap=0.495) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (34094 voxels, peak = 107), gca=106.6 gca peak = 0.07714 (104) mri peak = 0.13340 (109) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (37314 voxels, overlap=0.413) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (37314 voxels, peak = 109), gca=108.7 gca peak = 0.09712 (58) mri peak = 0.05078 (67) Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (39409 voxels, overlap=0.641) Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (39409 voxels, peak = 65), gca=64.7 gca peak = 0.11620 (58) mri peak = 0.05345 (68) Right_Cerebral_Cortex (42): linear fit = 1.15 x + 0.0 (37967 voxels, overlap=0.548) Right_Cerebral_Cortex (42): linear fit = 1.15 x + 0.0 (37967 voxels, peak = 67), gca=67.0 gca peak = 0.30970 (66) mri peak = 0.15758 (84) Right_Caudate (50): linear fit = 1.24 x + 0.0 (658 voxels, overlap=0.018) Right_Caudate (50): linear fit = 1.24 x + 0.0 (658 voxels, peak = 82), gca=81.5 gca peak = 0.15280 (69) mri peak = 0.15317 (85) Left_Caudate (11): linear fit = 1.12 x + 0.0 (677 voxels, overlap=0.081) Left_Caudate (11): linear fit = 1.12 x + 0.0 (677 voxels, peak = 78), gca=77.6 gca peak = 0.13902 (56) mri peak = 0.06081 (65) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (29246 voxels, overlap=0.721) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (29246 voxels, peak = 64), gca=63.6 gca peak = 0.14777 (55) mri peak = 0.06101 (63) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (29387 voxels, overlap=0.587) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (29387 voxels, peak = 64), gca=63.5 gca peak = 0.16765 (84) mri peak = 0.13461 (86) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (6949 voxels, overlap=0.728) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (6949 voxels, peak = 86), gca=86.1 gca peak = 0.18739 (84) mri peak = 0.14260 (86) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6774 voxels, overlap=0.671) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6774 voxels, peak = 87), gca=86.9 gca peak = 0.29869 (57) mri peak = 0.13028 (70) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (536 voxels, overlap=0.053) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (536 voxels, peak = 68), gca=67.5 gca peak = 0.33601 (57) mri peak = 0.12526 (67) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (484 voxels, overlap=0.049) Right_Amygdala (54): linear fit = 1.18 x + 0.0 (484 voxels, peak = 68), gca=67.5 gca peak = 0.11131 (90) mri peak = 0.08247 (95) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (4814 voxels, overlap=0.529) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (4814 voxels, peak = 96), gca=95.9 gca peak = 0.11793 (83) mri peak = 0.07722 (94) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4716 voxels, overlap=0.498) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4716 voxels, peak = 93), gca=92.5 gca peak = 0.08324 (81) mri peak = 0.08308 (90) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1945 voxels, overlap=0.212) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1945 voxels, peak = 94), gca=93.6 gca peak = 0.10360 (77) mri peak = 0.09514 (90) Right_Putamen (51): linear fit = 1.12 x + 0.0 (1879 voxels, overlap=0.379) Right_Putamen (51): linear fit = 1.12 x + 0.0 (1879 voxels, peak = 87), gca=86.6 gca peak = 0.08424 (78) mri peak = 0.08623 (88) Brain_Stem (16): linear fit = 1.11 x + 0.0 (12331 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.11 x + 0.0 (12331 voxels, peak = 86), gca=86.2 gca peak = 0.12631 (89) mri peak = 0.08575 (95) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1560 voxels, overlap=0.209) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1560 voxels, peak = 97), gca=97.5 gca peak = 0.14500 (87) mri peak = 0.08246 (99) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1647 voxels, overlap=0.247) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1647 voxels, peak = 97), gca=97.0 gca peak = 0.14975 (24) mri peak = 0.11906 (31) gca peak = 0.19357 (14) mri peak = 0.20974 (27) Fourth_Ventricle (15): linear fit = 1.76 x + 0.0 (187 voxels, overlap=0.195) Fourth_Ventricle (15): linear fit = 1.76 x + 0.0 (187 voxels, peak = 25), gca=24.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.16 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 1.50 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.12544 (31) mri peak = 0.11864 (31) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (379 voxels, overlap=0.671) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (379 voxels, peak = 30), gca=30.2 gca peak = 0.13981 (19) mri peak = 0.09787 (28) Right_Lateral_Ventricle (43): linear fit = 1.39 x + 0.0 (291 voxels, overlap=0.189) Right_Lateral_Ventricle (43): linear fit = 1.39 x + 0.0 (291 voxels, peak = 27), gca=26.5 gca peak = 0.21628 (102) mri peak = 0.14559 (101) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (673 voxels, overlap=0.934) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (673 voxels, peak = 102), gca=102.0 gca peak = 0.15796 (103) mri peak = 0.15337 (103) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (652 voxels, overlap=0.879) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (652 voxels, peak = 103), gca=103.0 gca peak = 0.28157 (67) mri peak = 0.11582 (69) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (740 voxels, overlap=0.978) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (740 voxels, peak = 68), gca=68.0 gca peak = 0.22430 (64) mri peak = 0.10617 (69) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (634 voxels, overlap=1.006) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (634 voxels, peak = 65), gca=65.0 gca peak = 0.07501 (106) mri peak = 0.12774 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (34094 voxels, overlap=0.638) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (34094 voxels, peak = 106), gca=106.0 gca peak = 0.07788 (109) mri peak = 0.13340 (109) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37314 voxels, overlap=0.629) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37314 voxels, peak = 109), gca=109.0 gca peak = 0.08833 (64) mri peak = 0.05078 (67) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (39409 voxels, overlap=0.959) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (39409 voxels, peak = 64), gca=64.0 gca peak = 0.10164 (67) mri peak = 0.05345 (68) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (37967 voxels, overlap=0.961) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (37967 voxels, peak = 66), gca=66.0 gca peak = 0.22995 (81) mri peak = 0.15758 (84) Right_Caudate (50): linear fit = 1.00 x + 0.0 (658 voxels, overlap=1.001) Right_Caudate (50): linear fit = 1.00 x + 0.0 (658 voxels, peak = 81), gca=81.0 gca peak = 0.16640 (87) mri peak = 0.15317 (85) Left_Caudate (11): linear fit = 1.00 x + 0.0 (677 voxels, overlap=0.835) Left_Caudate (11): linear fit = 1.00 x + 0.0 (677 voxels, peak = 87), gca=87.0 gca peak = 0.12579 (63) mri peak = 0.06081 (65) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (29246 voxels, overlap=0.993) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (29246 voxels, peak = 63), gca=63.0 gca peak = 0.13021 (63) mri peak = 0.06101 (63) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (29387 voxels, overlap=0.989) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (29387 voxels, peak = 63), gca=63.0 gca peak = 0.15750 (86) mri peak = 0.13461 (86) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6949 voxels, overlap=0.862) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6949 voxels, peak = 86), gca=86.0 gca peak = 0.18134 (87) mri peak = 0.14260 (86) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6774 voxels, overlap=0.854) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6774 voxels, peak = 87), gca=87.0 gca peak = 0.27951 (69) mri peak = 0.13028 (70) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (536 voxels, overlap=1.008) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (536 voxels, peak = 68), gca=68.0 gca peak = 0.30102 (68) mri peak = 0.12526 (67) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (484 voxels, overlap=1.007) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (484 voxels, peak = 67), gca=67.0 gca peak = 0.11331 (94) mri peak = 0.08247 (95) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4814 voxels, overlap=0.837) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4814 voxels, peak = 96), gca=96.3 gca peak = 0.10424 (90) mri peak = 0.07722 (94) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4716 voxels, overlap=0.969) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (4716 voxels, peak = 91), gca=91.3 gca peak = 0.07900 (87) mri peak = 0.08308 (90) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1945 voxels, overlap=0.820) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1945 voxels, peak = 87), gca=86.6 gca peak = 0.08717 (88) mri peak = 0.09514 (90) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1879 voxels, overlap=0.918) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1879 voxels, peak = 89), gca=89.3 gca peak = 0.07059 (86) mri peak = 0.08623 (88) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12331 voxels, overlap=0.804) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12331 voxels, peak = 86), gca=85.6 gca peak = 0.12268 (92) mri peak = 0.08575 (95) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1560 voxels, overlap=0.789) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1560 voxels, peak = 93), gca=93.4 gca peak = 0.14105 (95) mri peak = 0.08246 (99) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1647 voxels, overlap=0.891) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1647 voxels, peak = 95), gca=95.5 gca peak = 0.12656 (38) mri peak = 0.11906 (31) gca peak = 0.16542 (24) mri peak = 0.20974 (27) Fourth_Ventricle (15): linear fit = 1.08 x + 0.0 (187 voxels, overlap=0.714) Fourth_Ventricle (15): linear fit = 1.08 x + 0.0 (187 voxels, peak = 26), gca=25.8 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16611 (31) gca peak Left_Thalamus = 0.64095 (106) gca peak Third_Ventricle = 0.12656 (38) gca peak CSF = 0.15446 (55) gca peak Left_Accumbens_area = 0.65018 (70) gca peak Left_undetermined = 0.95280 (34) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.12303 (35) gca peak Right_Inf_Lat_Vent = 0.24202 (28) gca peak Right_Accumbens_area = 0.29890 (80) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14504 (37) gca peak Fifth_Ventricle = 0.51780 (46) gca peak WM_hypointensities = 0.07681 (79) gca peak non_WM_hypointensities = 0.09744 (45) gca peak Optic_Chiasm = 0.57333 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.15 x + 0.0 Left_Pallidum too bright - rescaling by 1.012 (from 1.000) to 104.3 (was 103.0) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 50596 voxels changed in iteration 0 of unlikely voxel relabeling 141 voxels changed in iteration 1 of unlikely voxel relabeling 6 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 35509 gm and wm labels changed (%28 to gray, %72 to white out of all changed labels) 312 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 56008 changed. image ll: -2.075, PF=0.500 pass 2: 15234 changed. image ll: -2.074, PF=0.500 pass 3: 4634 changed. 33553 voxels changed in iteration 0 of unlikely voxel relabeling 325 voxels changed in iteration 1 of unlikely voxel relabeling 5 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5167 voxels changed in iteration 0 of unlikely voxel relabeling 55 voxels changed in iteration 1 of unlikely voxel relabeling 6 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5302 voxels changed in iteration 0 of unlikely voxel relabeling 61 voxels changed in iteration 1 of unlikely voxel relabeling 10 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 3852 voxels changed in iteration 0 of unlikely voxel relabeling 19 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 2174.502151 mri_ca_label stimesec 1.464689 mri_ca_label ru_maxrss 2097560 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 641170 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 0 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 250 mri_ca_label ru_nivcsw 221325 auto-labeling took 36 minutes and 16 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/transforms/cc_up.lta 220 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/transforms/cc_up.lta reading aseg from /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/aseg.auto_noCCseg.mgz reading norm from /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/norm.mgz 17226 voxels in left wm, 43940 in right wm, xrange [124, 131] searching rotation angles z=[-9 5], y=[-7 7] searching scale 1 Z rot -9.2 searching scale 1 Z rot -9.0 searching scale 1 Z rot -8.7 searching scale 1 Z rot -8.5 searching scale 1 Z rot -8.2 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 global minimum found at slice 128.5, rotations (-0.45, -2.21) final transformation (x=128.5, yr=-0.453, zr=-2.215): 0.99922 0.03865 -0.00789 -3.38244; -0.03865 0.99925 0.00031 33.00676; 0.00790 0.00000 0.99997 17.98868; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 131] in xformed coordinates best xformed slice 129 cc center is found at 129 100 109 eigenvectors: 0.00230 -0.00582 0.99998; 0.06951 -0.99756 -0.00597; 0.99758 0.06952 -0.00189; writing aseg with callosum to /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/aseg.auto.mgz... corpus callosum segmentation took 0.4 minutes #-------------------------------------- #@# Merge ASeg Wed Sep 4 22:22:43 CST 2019 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Wed Sep 4 22:22:43 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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... 491 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 37, setting threshold to 61 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 73 (73), valley at 36 (36) 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 2 minutes and 15 seconds. #-------------------------------------------- #@# Mask BFS Wed Sep 4 22:24:59 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1477271 voxels in mask (pct= 8.81) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Wed Sep 4 22:25:00 CST 2019 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (102.0): 101.6 +- 7.0 [79.0 --> 125.0] GM (74.0) : 73.5 +- 9.2 [30.0 --> 95.0] setting bottom of white matter range to 82.7 setting top of gray matter range to 91.9 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... 3585 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4626 filled 1645 bright non-wm voxels segmented. 2342 diagonally connected voxels added... white matter segmentation took 1.1 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 0.32 minutes reading wm segmentation from wm.seg.mgz... 47 voxels added to wm to prevent paths from MTL structures to cortex 2431 additional wm voxels added 0 additional wm voxels added SEG EDIT: 25997 voxels turned on, 55741 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+): 10 found - 10 modified | TOTAL: 10 pass 2 (xy+): 0 found - 10 modified | TOTAL: 10 pass 1 (xy-): 13 found - 13 modified | TOTAL: 23 pass 2 (xy-): 0 found - 13 modified | TOTAL: 23 pass 1 (yz+): 30 found - 30 modified | TOTAL: 53 pass 2 (yz+): 0 found - 30 modified | TOTAL: 53 pass 1 (yz-): 26 found - 26 modified | TOTAL: 79 pass 2 (yz-): 0 found - 26 modified | TOTAL: 79 pass 1 (xz+): 11 found - 11 modified | TOTAL: 90 pass 2 (xz+): 0 found - 11 modified | TOTAL: 90 pass 1 (xz-): 19 found - 19 modified | TOTAL: 109 pass 2 (xz-): 0 found - 19 modified | TOTAL: 109 Iteration Number : 1 pass 1 (+++): 8 found - 8 modified | TOTAL: 8 pass 2 (+++): 0 found - 8 modified | TOTAL: 8 pass 1 (+++): 4 found - 4 modified | TOTAL: 12 pass 2 (+++): 0 found - 4 modified | TOTAL: 12 pass 1 (+++): 13 found - 13 modified | TOTAL: 25 pass 2 (+++): 0 found - 13 modified | TOTAL: 25 pass 1 (+++): 12 found - 12 modified | TOTAL: 37 pass 2 (+++): 0 found - 12 modified | TOTAL: 37 Iteration Number : 1 pass 1 (++): 80 found - 80 modified | TOTAL: 80 pass 2 (++): 0 found - 80 modified | TOTAL: 80 pass 1 (+-): 78 found - 78 modified | TOTAL: 158 pass 2 (+-): 0 found - 78 modified | TOTAL: 158 pass 1 (--): 69 found - 69 modified | TOTAL: 227 pass 2 (--): 0 found - 69 modified | TOTAL: 227 pass 1 (-+): 69 found - 69 modified | TOTAL: 296 pass 2 (-+): 0 found - 69 modified | TOTAL: 296 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 6 found - 6 modified | TOTAL: 9 pass 2 (xy-): 0 found - 6 modified | TOTAL: 9 pass 1 (yz+): 5 found - 5 modified | TOTAL: 14 pass 2 (yz+): 0 found - 5 modified | TOTAL: 14 pass 1 (yz-): 1 found - 1 modified | TOTAL: 15 pass 2 (yz-): 0 found - 1 modified | TOTAL: 15 pass 1 (xz+): 2 found - 2 modified | TOTAL: 17 pass 2 (xz+): 0 found - 2 modified | TOTAL: 17 pass 1 (xz-): 3 found - 3 modified | TOTAL: 20 pass 2 (xz-): 0 found - 3 modified | TOTAL: 20 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 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 3 found - 3 modified | TOTAL: 7 pass 2 (+-): 0 found - 3 modified | TOTAL: 7 pass 1 (--): 1 found - 1 modified | TOTAL: 8 pass 2 (--): 0 found - 1 modified | TOTAL: 8 pass 1 (-+): 0 found - 0 modified | TOTAL: 8 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 = 470 (out of 519802: 0.090419) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Wed Sep 4 22:26:31 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 1.01329 0.04504 0.01309 -11.19720; -0.04372 1.20130 0.12702 -27.03459; -0.00946 -0.14454 1.03225 8.21779; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.01329 0.04504 0.01309 -11.19720; -0.04372 1.20130 0.12702 -27.03459; -0.00946 -0.14454 1.03225 8.21779; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 732 (min = 350, max = 1400), aspect = 0.40 (min = 0.10, max = 0.75) no need to search using seed (127, 119, 144), TAL = (1.0, 16.0, 9.0) talairach voxel to voxel transform 0.98517 -0.03788 -0.00783 10.07140; 0.03439 0.81896 -0.10121 23.35720; 0.01385 0.11433 0.95451 -4.59802; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (127, 119, 144) --> (1.0, 16.0, 9.0) done. writing output to filled.mgz... filling took 0.5 minutes talairach cc position changed to (1.00, 16.00, 9.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, 16.00, 9.00) SRC: (111.82, 109.99, 147.97) search lh wm seed point around talairach space (-17.00, 16.00, 9.00), SRC: (147.29, 111.23, 148.46) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Wed Sep 4 22:26:59 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 5 found - 5 modified | TOTAL: 7 pass 2 (xy-): 0 found - 5 modified | TOTAL: 7 pass 1 (yz+): 1 found - 1 modified | TOTAL: 8 pass 2 (yz+): 0 found - 1 modified | TOTAL: 8 pass 1 (yz-): 0 found - 0 modified | TOTAL: 8 pass 1 (xz+): 1 found - 1 modified | TOTAL: 9 pass 2 (xz+): 0 found - 1 modified | TOTAL: 9 pass 1 (xz-): 2 found - 2 modified | TOTAL: 11 pass 2 (xz-): 0 found - 2 modified | TOTAL: 11 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 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 = 13 (out of 248415: 0.005233) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 343 vertices, 389 faces slice 50: 4504 vertices, 4736 faces slice 60: 12490 vertices, 12764 faces slice 70: 22583 vertices, 22973 faces slice 80: 33427 vertices, 33781 faces slice 90: 44523 vertices, 44880 faces slice 100: 56481 vertices, 56874 faces slice 110: 67746 vertices, 68136 faces slice 120: 78917 vertices, 79301 faces slice 130: 89307 vertices, 89673 faces slice 140: 99381 vertices, 99755 faces slice 150: 108418 vertices, 108749 faces slice 160: 116074 vertices, 116341 faces slice 170: 122348 vertices, 122583 faces slice 180: 127778 vertices, 127982 faces slice 190: 131862 vertices, 131967 faces slice 200: 132476 vertices, 132508 faces slice 210: 132476 vertices, 132508 faces slice 220: 132476 vertices, 132508 faces slice 230: 132476 vertices, 132508 faces slice 240: 132476 vertices, 132508 faces slice 250: 132476 vertices, 132508 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... 132476 voxel in cpt #1: X=-32 [v=132476,e=397524,f=265016] located at (-27.950581, -18.258144, 16.991787) For the whole surface: X=-32 [v=132476,e=397524,f=265016] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Wed Sep 4 22:27:02 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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+): 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 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 1 found - 1 modified | TOTAL: 4 pass 2 (xz-): 0 found - 1 modified | TOTAL: 4 Iteration Number : 1 pass 1 (+++): 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 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 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 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 = 7 (out of 250669: 0.002793) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 641 vertices, 710 faces slice 50: 5330 vertices, 5528 faces slice 60: 13361 vertices, 13684 faces slice 70: 23171 vertices, 23515 faces slice 80: 33618 vertices, 33982 faces slice 90: 44999 vertices, 45383 faces slice 100: 57030 vertices, 57426 faces slice 110: 69129 vertices, 69515 faces slice 120: 80266 vertices, 80639 faces slice 130: 90926 vertices, 91309 faces slice 140: 102142 vertices, 102532 faces slice 150: 111169 vertices, 111493 faces slice 160: 118926 vertices, 119191 faces slice 170: 125348 vertices, 125586 faces slice 180: 130921 vertices, 131127 faces slice 190: 134780 vertices, 134887 faces slice 200: 135530 vertices, 135556 faces slice 210: 135530 vertices, 135556 faces slice 220: 135530 vertices, 135556 faces slice 230: 135530 vertices, 135556 faces slice 240: 135530 vertices, 135556 faces slice 250: 135530 vertices, 135556 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... 135530 voxel in cpt #1: X=-26 [v=135530,e=406668,f=271112] located at (27.095345, -18.233150, 20.332369) For the whole surface: X=-26 [v=135530,e=406668,f=271112] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Wed Sep 4 22:27:06 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh Wed Sep 4 22:27:10 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Wed Sep 4 22:27:13 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 45.5 mm, total surface area = 69925 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.4 minutes step 000: RMS=0.155 (target=0.015) step 005: RMS=0.116 (target=0.015) step 010: RMS=0.085 (target=0.015) step 015: RMS=0.070 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.044 (target=0.015) step 040: RMS=0.041 (target=0.015) step 045: RMS=0.039 (target=0.015) step 050: RMS=0.038 (target=0.015) step 055: RMS=0.038 (target=0.015) step 060: RMS=0.037 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 21.633406 mris_inflate stimesec 0.061643 mris_inflate ru_maxrss 169772 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 22145 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2408 mris_inflate ru_nivcsw 2213 #-------------------------------------------- #@# Inflation1 rh Wed Sep 4 22:27:35 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 45.0 mm, total surface area = 71560 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.4 minutes step 000: RMS=0.152 (target=0.015) step 005: RMS=0.114 (target=0.015) step 010: RMS=0.083 (target=0.015) step 015: RMS=0.069 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.040 (target=0.015) step 040: RMS=0.037 (target=0.015) step 045: RMS=0.035 (target=0.015) step 050: RMS=0.034 (target=0.015) step 055: RMS=0.033 (target=0.015) step 060: RMS=0.033 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 22.419189 mris_inflate stimesec 0.059280 mris_inflate ru_maxrss 173728 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 22625 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2462 mris_inflate ru_nivcsw 2311 #-------------------------------------------- #@# QSphere lh Wed Sep 4 22:27:58 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.01 +- 0.57 (0.00-->7.89) (max @ vno 52307 --> 53532) face area 0.03 +- 0.03 (-0.10-->0.79) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.322... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.387, avgs=0 005/300: dt: 0.9000, rms radial error=176.128, avgs=0 010/300: dt: 0.9000, rms radial error=175.572, avgs=0 015/300: dt: 0.9000, rms radial error=174.844, avgs=0 020/300: dt: 0.9000, rms radial error=174.015, avgs=0 025/300: dt: 0.9000, rms radial error=173.130, avgs=0 030/300: dt: 0.9000, rms radial error=172.212, avgs=0 035/300: dt: 0.9000, rms radial error=171.278, avgs=0 040/300: dt: 0.9000, rms radial error=170.335, avgs=0 045/300: dt: 0.9000, rms radial error=169.389, avgs=0 050/300: dt: 0.9000, rms radial error=168.444, avgs=0 055/300: dt: 0.9000, rms radial error=167.502, avgs=0 060/300: dt: 0.9000, rms radial error=166.562, avgs=0 065/300: dt: 0.9000, rms radial error=165.628, avgs=0 070/300: dt: 0.9000, rms radial error=164.699, avgs=0 075/300: dt: 0.9000, rms radial error=163.775, avgs=0 080/300: dt: 0.9000, rms radial error=162.855, avgs=0 085/300: dt: 0.9000, rms radial error=161.941, avgs=0 090/300: dt: 0.9000, rms radial error=161.031, avgs=0 095/300: dt: 0.9000, rms radial error=160.126, avgs=0 100/300: dt: 0.9000, rms radial error=159.226, avgs=0 105/300: dt: 0.9000, rms radial error=158.331, avgs=0 110/300: dt: 0.9000, rms radial error=157.441, avgs=0 115/300: dt: 0.9000, rms radial error=156.555, avgs=0 120/300: dt: 0.9000, rms radial error=155.675, avgs=0 125/300: dt: 0.9000, rms radial error=154.799, avgs=0 130/300: dt: 0.9000, rms radial error=153.928, avgs=0 135/300: dt: 0.9000, rms radial error=153.062, avgs=0 140/300: dt: 0.9000, rms radial error=152.200, avgs=0 145/300: dt: 0.9000, rms radial error=151.343, avgs=0 150/300: dt: 0.9000, rms radial error=150.491, avgs=0 155/300: dt: 0.9000, rms radial error=149.643, avgs=0 160/300: dt: 0.9000, rms radial error=148.800, avgs=0 165/300: dt: 0.9000, rms radial error=147.962, avgs=0 170/300: dt: 0.9000, rms radial error=147.128, avgs=0 175/300: dt: 0.9000, rms radial error=146.299, avgs=0 180/300: dt: 0.9000, rms radial error=145.474, avgs=0 185/300: dt: 0.9000, rms radial error=144.654, avgs=0 190/300: dt: 0.9000, rms radial error=143.838, avgs=0 195/300: dt: 0.9000, rms radial error=143.027, avgs=0 200/300: dt: 0.9000, rms radial error=142.221, avgs=0 205/300: dt: 0.9000, rms radial error=141.419, avgs=0 210/300: dt: 0.9000, rms radial error=140.621, avgs=0 215/300: dt: 0.9000, rms radial error=139.828, avgs=0 220/300: dt: 0.9000, rms radial error=139.039, avgs=0 225/300: dt: 0.9000, rms radial error=138.255, avgs=0 230/300: dt: 0.9000, rms radial error=137.475, avgs=0 235/300: dt: 0.9000, rms radial error=136.700, avgs=0 240/300: dt: 0.9000, rms radial error=135.928, avgs=0 245/300: dt: 0.9000, rms radial error=135.162, avgs=0 250/300: dt: 0.9000, rms radial error=134.399, avgs=0 255/300: dt: 0.9000, rms radial error=133.641, avgs=0 260/300: dt: 0.9000, rms radial error=132.887, avgs=0 265/300: dt: 0.9000, rms radial error=132.137, avgs=0 270/300: dt: 0.9000, rms radial error=131.391, avgs=0 275/300: dt: 0.9000, rms radial error=130.650, avgs=0 280/300: dt: 0.9000, rms radial error=129.912, avgs=0 285/300: dt: 0.9000, rms radial error=129.179, avgs=0 290/300: dt: 0.9000, rms radial error=128.450, avgs=0 295/300: dt: 0.9000, rms radial error=127.725, avgs=0 300/300: dt: 0.9000, rms radial error=127.004, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15296.63 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 2481.67 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 = 240.62 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00401 epoch 4 (K=640.0), pass 1, starting sse = 16.49 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/13 = 0.00611 final distance error %26.69 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.04 hours mris_sphere utimesec 140.905484 mris_sphere stimesec 0.195436 mris_sphere ru_maxrss 169988 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 21691 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 2408 mris_sphere ru_nivcsw 14424 FSRUNTIME@ mris_sphere 0.0392 hours 1 threads #-------------------------------------------- #@# QSphere rh Wed Sep 4 22:30:19 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.00 +- 0.56 (0.00-->6.35) (max @ vno 101785 --> 101786) face area 0.03 +- 0.03 (-0.30-->0.62) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.312... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.989, avgs=0 005/300: dt: 0.9000, rms radial error=176.729, avgs=0 010/300: dt: 0.9000, rms radial error=176.172, avgs=0 015/300: dt: 0.9000, rms radial error=175.439, avgs=0 020/300: dt: 0.9000, rms radial error=174.605, avgs=0 025/300: dt: 0.9000, rms radial error=173.713, avgs=0 030/300: dt: 0.9000, rms radial error=172.790, avgs=0 035/300: dt: 0.9000, rms radial error=171.853, avgs=0 040/300: dt: 0.9000, rms radial error=170.907, avgs=0 045/300: dt: 0.9000, rms radial error=169.959, avgs=0 050/300: dt: 0.9000, rms radial error=169.011, avgs=0 055/300: dt: 0.9000, rms radial error=168.065, avgs=0 060/300: dt: 0.9000, rms radial error=167.123, avgs=0 065/300: dt: 0.9000, rms radial error=166.185, avgs=0 070/300: dt: 0.9000, rms radial error=165.252, avgs=0 075/300: dt: 0.9000, rms radial error=164.323, avgs=0 080/300: dt: 0.9000, rms radial error=163.399, avgs=0 085/300: dt: 0.9000, rms radial error=162.480, avgs=0 090/300: dt: 0.9000, rms radial error=161.567, avgs=0 095/300: dt: 0.9000, rms radial error=160.658, avgs=0 100/300: dt: 0.9000, rms radial error=159.754, avgs=0 105/300: dt: 0.9000, rms radial error=158.855, avgs=0 110/300: dt: 0.9000, rms radial error=157.961, avgs=0 115/300: dt: 0.9000, rms radial error=157.072, avgs=0 120/300: dt: 0.9000, rms radial error=156.188, avgs=0 125/300: dt: 0.9000, rms radial error=155.308, avgs=0 130/300: dt: 0.9000, rms radial error=154.433, avgs=0 135/300: dt: 0.9000, rms radial error=153.563, avgs=0 140/300: dt: 0.9000, rms radial error=152.698, avgs=0 145/300: dt: 0.9000, rms radial error=151.837, avgs=0 150/300: dt: 0.9000, rms radial error=150.982, avgs=0 155/300: dt: 0.9000, rms radial error=150.131, avgs=0 160/300: dt: 0.9000, rms radial error=149.285, avgs=0 165/300: dt: 0.9000, rms radial error=148.443, avgs=0 170/300: dt: 0.9000, rms radial error=147.606, avgs=0 175/300: dt: 0.9000, rms radial error=146.774, avgs=0 180/300: dt: 0.9000, rms radial error=145.946, avgs=0 185/300: dt: 0.9000, rms radial error=145.123, avgs=0 190/300: dt: 0.9000, rms radial error=144.305, avgs=0 195/300: dt: 0.9000, rms radial error=143.491, avgs=0 200/300: dt: 0.9000, rms radial error=142.682, avgs=0 205/300: dt: 0.9000, rms radial error=141.877, avgs=0 210/300: dt: 0.9000, rms radial error=141.078, avgs=0 215/300: dt: 0.9000, rms radial error=140.284, avgs=0 220/300: dt: 0.9000, rms radial error=139.494, avgs=0 225/300: dt: 0.9000, rms radial error=138.708, avgs=0 230/300: dt: 0.9000, rms radial error=137.927, avgs=0 235/300: dt: 0.9000, rms radial error=137.150, avgs=0 240/300: dt: 0.9000, rms radial error=136.378, avgs=0 245/300: dt: 0.9000, rms radial error=135.610, avgs=0 250/300: dt: 0.9000, rms radial error=134.846, avgs=0 255/300: dt: 0.9000, rms radial error=134.086, avgs=0 260/300: dt: 0.9000, rms radial error=133.331, avgs=0 265/300: dt: 0.9000, rms radial error=132.579, avgs=0 270/300: dt: 0.9000, rms radial error=131.832, avgs=0 275/300: dt: 0.9000, rms radial error=131.090, avgs=0 280/300: dt: 0.9000, rms radial error=130.351, avgs=0 285/300: dt: 0.9000, rms radial error=129.617, avgs=0 290/300: dt: 0.9000, rms radial error=128.886, avgs=0 295/300: dt: 0.9000, rms radial error=128.160, avgs=0 300/300: dt: 0.9000, rms radial error=127.438, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15798.22 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00008 epoch 2 (K=40.0), pass 1, starting sse = 2603.25 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00001 epoch 3 (K=160.0), pass 1, starting sse = 254.73 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00515 epoch 4 (K=640.0), pass 1, starting sse = 16.58 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/14 = 0.00734 final distance error %26.22 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.04 hours mris_sphere utimesec 146.336774 mris_sphere stimesec 0.192609 mris_sphere ru_maxrss 173948 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 22169 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 2462 mris_sphere ru_nivcsw 14941 FSRUNTIME@ mris_sphere 0.0407 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Wed Sep 4 22:32:45 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Wed Sep 4 22:32:45 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Wed Sep 4 22:32:46 CST 2019 mris_fix_topology -rusage /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 220 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=-32 (nv=132476, nf=265016, ne=397524, g=17) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 4372 ambiguous faces found in tessellation segmenting defects... 25 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 25 defects to be corrected 0 vertices coincident reading input surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1517 (-4.5758) -vertex loglikelihood: -5.8192 (-2.9096) -normal dot loglikelihood: -3.6237 (-3.6237) -quad curv loglikelihood: -6.0288 (-3.0144) Total Loglikelihood : -24.6233 CORRECTING DEFECT 0 (vertices=17, convex hull=25, v0=34243) After retessellation of defect 0 (v0=34243), euler #=-22 (129963,389205,259220) : difference with theory (-22) = 0 CORRECTING DEFECT 1 (vertices=8, convex hull=19, v0=39647) After retessellation of defect 1 (v0=39647), euler #=-21 (129964,389213,259228) : difference with theory (-21) = 0 CORRECTING DEFECT 2 (vertices=43, convex hull=75, v0=46360) After retessellation of defect 2 (v0=46360), euler #=-20 (129973,389270,259277) : difference with theory (-20) = 0 CORRECTING DEFECT 3 (vertices=25, convex hull=52, v0=47989) After retessellation of defect 3 (v0=47989), euler #=-19 (129987,389332,259326) : difference with theory (-19) = 0 CORRECTING DEFECT 4 (vertices=823, convex hull=302, v0=48681) normal vector of length zero at vertex 130418 with 4 faces normal vector of length zero at vertex 130341 with 3 faces normal vector of length zero at vertex 130341 with 3 faces normal vector of length zero at vertex 130341 with 3 faces normal vector of length zero at vertex 130341 with 3 faces normal vector of length zero at vertex 130341 with 3 faces normal vector of length zero at vertex 130341 with 3 faces normal vector of length zero at vertex 130341 with 3 faces normal vector of length zero at vertex 130341 with 3 faces normal vector of length zero at vertex 130341 with 3 faces normal vector of length zero at vertex 130341 with 3 faces normal vector of length zero at vertex 130341 with 3 faces normal vector of length zero at vertex 130341 with 3 faces normal vector of length zero at vertex 130341 with 3 faces normal vector of length zero at vertex 130341 with 3 faces normal vector of length zero at vertex 130341 with 3 faces normal vector of length zero at vertex 130341 with 3 faces normal vector of length zero at vertex 130341 with 3 faces normal vector of length zero at vertex 130341 with 3 faces normal vector of length zero at vertex 130341 with 3 faces normal vector of length zero at vertex 130341 with 3 faces normal vector of length zero at vertex 130341 with 3 faces After retessellation of defect 4 (v0=48681), euler #=-18 (130167,390020,259835) : difference with theory (-18) = 0 CORRECTING DEFECT 5 (vertices=25, convex hull=29, v0=60709) After retessellation of defect 5 (v0=60709), euler #=-17 (130173,390046,259856) : difference with theory (-17) = 0 CORRECTING DEFECT 6 (vertices=184, convex hull=78, v0=69793) After retessellation of defect 6 (v0=69793), euler #=-16 (130212,390196,259968) : difference with theory (-16) = 0 CORRECTING DEFECT 7 (vertices=5, convex hull=27, v0=87006) After retessellation of defect 7 (v0=87006), euler #=-15 (130213,390205,259977) : difference with theory (-15) = 0 CORRECTING DEFECT 8 (vertices=59, convex hull=27, v0=90016) After retessellation of defect 8 (v0=90016), euler #=-14 (130219,390231,259998) : difference with theory (-14) = 0 CORRECTING DEFECT 9 (vertices=34, convex hull=46, v0=90858) After retessellation of defect 9 (v0=90858), euler #=-13 (130228,390276,260035) : difference with theory (-13) = 0 CORRECTING DEFECT 10 (vertices=25, convex hull=42, v0=91063) After retessellation of defect 10 (v0=91063), euler #=-12 (130238,390322,260072) : difference with theory (-12) = 0 CORRECTING DEFECT 11 (vertices=108, convex hull=28, v0=94983) After retessellation of defect 11 (v0=94983), euler #=-11 (130246,390353,260096) : difference with theory (-11) = 0 CORRECTING DEFECT 12 (vertices=16, convex hull=41, v0=96947) After retessellation of defect 12 (v0=96947), euler #=-10 (130256,390396,260130) : difference with theory (-10) = 0 CORRECTING DEFECT 13 (vertices=29, convex hull=35, v0=98086) After retessellation of defect 13 (v0=98086), euler #=-9 (130262,390428,260157) : difference with theory (-9) = 0 CORRECTING DEFECT 14 (vertices=120, convex hull=41, v0=98106) After retessellation of defect 14 (v0=98106), euler #=-8 (130270,390469,260191) : difference with theory (-8) = 0 CORRECTING DEFECT 15 (vertices=10, convex hull=20, v0=99553) After retessellation of defect 15 (v0=99553), euler #=-7 (130271,390479,260201) : difference with theory (-7) = 0 CORRECTING DEFECT 16 (vertices=323, convex hull=178, v0=99956) After retessellation of defect 16 (v0=99956), euler #=-6 (130315,390691,260370) : difference with theory (-6) = 0 CORRECTING DEFECT 17 (vertices=11, convex hull=24, v0=101887) After retessellation of defect 17 (v0=101887), euler #=-5 (130318,390709,260386) : difference with theory (-5) = 0 CORRECTING DEFECT 18 (vertices=349, convex hull=177, v0=105668) After retessellation of defect 18 (v0=105668), euler #=-4 (130399,391035,260632) : difference with theory (-4) = 0 CORRECTING DEFECT 19 (vertices=148, convex hull=78, v0=107496) After retessellation of defect 19 (v0=107496), euler #=-3 (130421,391131,260707) : difference with theory (-3) = 0 CORRECTING DEFECT 20 (vertices=37, convex hull=74, v0=109472) After retessellation of defect 20 (v0=109472), euler #=-2 (130431,391191,260758) : difference with theory (-2) = 0 CORRECTING DEFECT 21 (vertices=5, convex hull=23, v0=110107) After retessellation of defect 21 (v0=110107), euler #=-1 (130433,391203,260769) : difference with theory (-1) = 0 CORRECTING DEFECT 22 (vertices=27, convex hull=65, v0=118577) After retessellation of defect 22 (v0=118577), euler #=0 (130447,391270,260823) : difference with theory (0) = 0 CORRECTING DEFECT 23 (vertices=51, convex hull=82, v0=119323) After retessellation of defect 23 (v0=119323), euler #=1 (130475,391389,260915) : difference with theory (1) = 0 CORRECTING DEFECT 24 (vertices=33, convex hull=71, v0=129318) After retessellation of defect 24 (v0=129318), euler #=2 (130488,391458,260972) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.24 (0.04-->18.61) (max @ vno 54264 --> 57473) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.24 (0.04-->18.61) (max @ vno 54264 --> 57473) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 92 mutations (33.5%), 183 crossovers (66.5%), 150 vertices were eliminated building final representation... 1988 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=130488, nf=260972, ne=391458, g=0) writing corrected surface to /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 10.0 minutes 0 defective edges removing intersecting faces 000: 235 intersecting 001: 6 intersecting mris_fix_topology utimesec 598.464748 mris_fix_topology stimesec 0.681550 mris_fix_topology ru_maxrss 413116 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 51573 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 0 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 3531 mris_fix_topology ru_nivcsw 61203 FSRUNTIME@ mris_fix_topology lh 0.1664 hours 1 threads #@# Fix Topology rh Wed Sep 4 22:42:45 CST 2019 mris_fix_topology -rusage /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 220 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-26 (nv=135530, nf=271112, ne=406668, g=14) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 3898 ambiguous faces found in tessellation segmenting defects... 13 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 13 defects to be corrected 0 vertices coincident reading input surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.0806 (-4.5403) -vertex loglikelihood: -5.7856 (-2.8928) -normal dot loglikelihood: -3.6093 (-3.6093) -quad curv loglikelihood: -6.2983 (-3.1491) Total Loglikelihood : -24.7738 CORRECTING DEFECT 0 (vertices=533, convex hull=207, v0=48990) After retessellation of defect 0 (v0=48990), euler #=-10 (133466,399929,266453) : difference with theory (-10) = 0 CORRECTING DEFECT 1 (vertices=206, convex hull=219, v0=56773) After retessellation of defect 1 (v0=56773), euler #=-9 (133595,400424,266820) : difference with theory (-9) = 0 CORRECTING DEFECT 2 (vertices=38, convex hull=22, v0=57796) After retessellation of defect 2 (v0=57796), euler #=-8 (133603,400457,266846) : difference with theory (-8) = 0 CORRECTING DEFECT 3 (vertices=46, convex hull=48, v0=60868) After retessellation of defect 3 (v0=60868), euler #=-7 (133612,400502,266883) : difference with theory (-7) = 0 CORRECTING DEFECT 4 (vertices=36, convex hull=71, v0=74838) After retessellation of defect 4 (v0=74838), euler #=-6 (133639,400612,266967) : difference with theory (-6) = 0 CORRECTING DEFECT 5 (vertices=20, convex hull=25, v0=82026) After retessellation of defect 5 (v0=82026), euler #=-5 (133641,400627,266981) : difference with theory (-5) = 0 CORRECTING DEFECT 6 (vertices=31, convex hull=31, v0=87389) After retessellation of defect 6 (v0=87389), euler #=-4 (133643,400642,266995) : difference with theory (-4) = 0 CORRECTING DEFECT 7 (vertices=43, convex hull=37, v0=90922) After retessellation of defect 7 (v0=90922), euler #=-3 (133649,400673,267021) : difference with theory (-3) = 0 CORRECTING DEFECT 8 (vertices=1078, convex hull=267, v0=93861) After retessellation of defect 8 (v0=93861), euler #=-2 (133745,401102,267355) : difference with theory (-2) = 0 CORRECTING DEFECT 9 (vertices=64, convex hull=85, v0=111903) After retessellation of defect 9 (v0=111903), euler #=-1 (133770,401214,267443) : difference with theory (-1) = 0 CORRECTING DEFECT 10 (vertices=37, convex hull=79, v0=122249) After retessellation of defect 10 (v0=122249), euler #=0 (133784,401288,267504) : difference with theory (0) = 0 CORRECTING DEFECT 11 (vertices=57, convex hull=90, v0=126076) After retessellation of defect 11 (v0=126076), euler #=1 (133805,401391,267587) : difference with theory (1) = 0 CORRECTING DEFECT 12 (vertices=25, convex hull=49, v0=129930) After retessellation of defect 12 (v0=129930), euler #=2 (133815,401439,267626) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.05-->10.21) (max @ vno 53760 --> 58681) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.05-->10.21) (max @ vno 53760 --> 58681) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 42 mutations (31.6%), 91 crossovers (68.4%), 186 vertices were eliminated building final representation... 1715 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=133815, nf=267626, ne=401439, g=0) writing corrected surface to /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 7.3 minutes 0 defective edges removing intersecting faces 000: 148 intersecting 001: 12 intersecting mris_fix_topology utimesec 434.939649 mris_fix_topology stimesec 0.477168 mris_fix_topology ru_maxrss 420848 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 52869 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 0 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 3599 mris_fix_topology ru_nivcsw 44519 FSRUNTIME@ mris_fix_topology rh 0.1210 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 130488 - 391458 + 260972 = 2 --> 0 holes F =2V-4: 260972 = 260976-4 (0) 2E=3F: 782916 = 782916 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 133815 - 401439 + 267626 = 2 --> 0 holes F =2V-4: 267626 = 267630-4 (0) 2E=3F: 802878 = 802878 (0) total defect index = 0 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 63 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 37 intersecting 001: 9 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Wed Sep 4 22:50:06 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 220 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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/filled.mgz... reading volume /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/brain.finalsurfs.mgz... reading volume /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/../mri/aseg.presurf.mgz... reading volume /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/wm.mgz... 17541 bright wm thresholded. 1896 bright non-wm voxels segmented. reading original surface position from /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.orig... computing class statistics... border white: 244391 voxels (1.46%) border gray 279041 voxels (1.66%) WM (99.0): 99.5 +- 7.5 [70.0 --> 110.0] GM (77.0) : 76.4 +- 9.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 63.9 (was 70) setting MAX_BORDER_WHITE to 111.5 (was 105) setting MIN_BORDER_WHITE to 73.0 (was 85) setting MAX_CSF to 54.8 (was 40) setting MAX_GRAY to 96.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 63.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 45.7 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->5.94) (max @ vno 130014 --> 130015) face area 0.28 +- 0.12 (0.00-->6.24) mean absolute distance = 0.70 +- 0.89 3610 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104+-5.2, GM=73+-6.1 mean inside = 95.5, mean outside = 79.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=83.3, 24 (24) missing vertices, mean dist 0.3 [0.6 (%36.7)->0.8 (%63.3))] %71 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= dell, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.09-->8.56) (max @ vno 58634 --> 57473) face area 0.28 +- 0.13 (0.00-->8.96) mean absolute distance = 0.32 +- 0.52 2363 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2504273.2, rms=8.857 001: dt: 0.5000, sse=1511648.9, rms=6.291 (28.973%) 002: dt: 0.5000, sse=1070271.2, rms=4.705 (25.207%) 003: dt: 0.5000, sse=864486.9, rms=3.738 (20.564%) 004: dt: 0.5000, sse=763210.2, rms=3.153 (15.641%) 005: dt: 0.5000, sse=717748.6, rms=2.843 (9.817%) 006: dt: 0.5000, sse=696302.3, rms=2.668 (6.181%) 007: dt: 0.5000, sse=687633.8, rms=2.614 (2.022%) 008: dt: 0.5000, sse=681035.2, rms=2.559 (2.091%) rms = 2.54, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=679481.9, rms=2.543 (0.615%) 010: dt: 0.2500, sse=590507.4, rms=1.546 (39.230%) 011: dt: 0.2500, sse=576917.2, rms=1.383 (10.535%) rms = 1.35, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=575252.3, rms=1.350 (2.342%) rms = 1.31, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=573497.9, rms=1.313 (2.771%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=85.9, 38 (8) missing vertices, mean dist -0.2 [0.4 (%73.9)->0.3 (%26.1))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= dell, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.24 (0.12-->9.08) (max @ vno 58634 --> 57473) face area 0.35 +- 0.16 (0.00-->12.70) mean absolute distance = 0.24 +- 0.35 2992 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1071836.6, rms=4.016 014: dt: 0.5000, sse=826054.8, rms=2.414 (39.901%) 015: dt: 0.5000, sse=777824.7, rms=2.135 (11.558%) 016: dt: 0.5000, sse=761641.4, rms=2.002 (6.225%) rms = 2.18, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=720156.9, rms=1.460 (27.086%) 018: dt: 0.2500, sse=702116.1, rms=1.196 (18.090%) 019: dt: 0.2500, sse=698911.6, rms=1.136 (4.965%) rms = 1.15, time step reduction 2 of 3 to 0.125... rms = 1.13, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=698492.1, rms=1.130 (0.521%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=88.2, 47 (6) missing vertices, mean dist -0.1 [0.3 (%75.4)->0.2 (%24.6))] %89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= dell, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.24 (0.06-->9.27) (max @ vno 58634 --> 57473) face area 0.34 +- 0.16 (0.00-->12.81) mean absolute distance = 0.20 +- 0.29 2702 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=864019.1, rms=2.947 021: dt: 0.5000, sse=740816.9, rms=1.905 (35.371%) rms = 1.98, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=696180.8, rms=1.370 (28.061%) 023: dt: 0.2500, sse=679945.8, rms=1.077 (21.386%) 024: dt: 0.2500, sse=674404.9, rms=1.013 (5.983%) rms = 1.02, time step reduction 2 of 3 to 0.125... rms = 1.01, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=673941.8, rms=1.005 (0.747%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=89.0, 42 (3) missing vertices, mean dist -0.0 [0.2 (%58.3)->0.2 (%41.7))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= dell, 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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=684843.0, rms=1.364 026: dt: 0.5000, sse=673653.5, rms=1.187 (12.968%) rms = 1.57, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=658173.9, rms=0.893 (24.719%) 028: dt: 0.2500, sse=655517.7, rms=0.834 (6.643%) rms = 0.81, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=656521.7, rms=0.808 (3.115%) rms = 0.80, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=652497.5, rms=0.805 (0.436%) positioning took 0.4 minutes generating cortex label... 17 non-cortical segments detected only using segment with 6452 vertices erasing segment 0 (vno[0] = 37411) erasing segment 1 (vno[0] = 38501) erasing segment 3 (vno[0] = 53090) erasing segment 4 (vno[0] = 54214) erasing segment 5 (vno[0] = 56306) erasing segment 6 (vno[0] = 58410) erasing segment 7 (vno[0] = 67250) erasing segment 8 (vno[0] = 71774) erasing segment 9 (vno[0] = 75078) erasing segment 10 (vno[0] = 79162) erasing segment 11 (vno[0] = 89393) erasing segment 12 (vno[0] = 93602) erasing segment 13 (vno[0] = 100349) erasing segment 14 (vno[0] = 101058) erasing segment 15 (vno[0] = 101061) erasing segment 16 (vno[0] = 102981) writing cortex label to /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/label/lh.cortex.label... writing curvature file /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.curv writing smoothed area to lh.area writing curvature file /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.area vertex spacing 0.90 +- 0.25 (0.03-->9.42) (max @ vno 57473 --> 58634) face area 0.34 +- 0.16 (0.00-->12.92) refinement took 3.2 minutes #-------------------------------------------- #@# Make White Surf rh Wed Sep 4 22:53:21 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 220 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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/filled.mgz... reading volume /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/brain.finalsurfs.mgz... reading volume /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/../mri/aseg.presurf.mgz... reading volume /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/wm.mgz... 17541 bright wm thresholded. 1896 bright non-wm voxels segmented. reading original surface position from /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.orig... computing class statistics... border white: 244391 voxels (1.46%) border gray 279041 voxels (1.66%) WM (99.0): 99.5 +- 7.5 [70.0 --> 110.0] GM (77.0) : 76.4 +- 9.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 64.9 (was 70) setting MAX_BORDER_WHITE to 111.5 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 55.8 (was 40) setting MAX_GRAY to 96.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.7 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.01-->6.13) (max @ vno 133334 --> 133357) face area 0.28 +- 0.12 (0.00-->4.90) mean absolute distance = 0.69 +- 0.85 4111 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104+-4.3, GM=74+-6.1 mean inside = 95.6, mean outside = 80.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=84.0, 60 (60) missing vertices, mean dist 0.3 [0.6 (%37.3)->0.8 (%62.7))] %69 local maxima, %27 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= dell, 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 0.92 +- 0.24 (0.10-->5.56) (max @ vno 133355 --> 133334) face area 0.28 +- 0.13 (0.00-->6.22) mean absolute distance = 0.33 +- 0.51 3003 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2482663.5, rms=8.644 001: dt: 0.5000, sse=1459312.1, rms=5.986 (30.750%) 002: dt: 0.5000, sse=1010777.1, rms=4.314 (27.929%) 003: dt: 0.5000, sse=815671.5, rms=3.332 (22.758%) 004: dt: 0.5000, sse=727569.6, rms=2.773 (16.789%) 005: dt: 0.5000, sse=695460.9, rms=2.534 (8.632%) 006: dt: 0.5000, sse=682585.2, rms=2.417 (4.613%) rms = 2.39, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=678348.6, rms=2.389 (1.149%) 008: dt: 0.2500, sse=594839.4, rms=1.428 (40.245%) 009: dt: 0.2500, sse=583809.9, rms=1.257 (11.913%) rms = 1.22, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=581856.3, rms=1.220 (3.002%) rms = 1.19, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=579974.8, rms=1.192 (2.276%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=86.8, 29 (8) missing vertices, mean dist -0.2 [0.4 (%75.0)->0.2 (%25.0))] %80 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= dell, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.23 (0.09-->5.76) (max @ vno 133355 --> 133334) face area 0.35 +- 0.16 (0.00-->8.76) mean absolute distance = 0.24 +- 0.35 3020 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1131441.9, rms=4.202 012: dt: 0.5000, sse=838789.9, rms=2.524 (39.927%) 013: dt: 0.5000, sse=786060.6, rms=2.096 (16.955%) 014: dt: 0.5000, sse=766708.8, rms=1.933 (7.802%) rms = 2.06, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=726092.8, rms=1.417 (26.659%) 016: dt: 0.2500, sse=709540.7, rms=1.146 (19.128%) 017: dt: 0.2500, sse=705144.2, rms=1.071 (6.551%) rms = 1.05, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=704027.9, rms=1.047 (2.230%) rms = 1.03, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=703042.9, rms=1.029 (1.796%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=89.1, 19 (2) missing vertices, mean dist -0.1 [0.3 (%75.9)->0.2 (%24.1))] %89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= dell, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.08-->5.79) (max @ vno 133355 --> 133334) face area 0.34 +- 0.16 (0.00-->8.79) mean absolute distance = 0.19 +- 0.28 2642 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=882585.0, rms=2.995 020: dt: 0.5000, sse=739699.6, rms=1.817 (39.334%) rms = 1.83, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=698881.3, rms=1.314 (27.688%) 022: dt: 0.2500, sse=680983.9, rms=1.008 (23.265%) 023: dt: 0.2500, sse=677037.2, rms=0.945 (6.289%) rms = 0.95, time step reduction 2 of 3 to 0.125... rms = 0.94, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=676403.6, rms=0.936 (0.888%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=89.8, 18 (2) missing vertices, mean dist -0.0 [0.2 (%58.4)->0.2 (%41.6))] %92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= dell, 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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=686709.8, rms=1.295 025: dt: 0.5000, sse=676507.3, rms=1.101 (15.013%) rms = 1.45, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=661603.2, rms=0.829 (24.692%) 027: dt: 0.2500, sse=658667.9, rms=0.773 (6.736%) rms = 0.75, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=658695.2, rms=0.749 (3.061%) rms = 0.74, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=656700.6, rms=0.743 (0.803%) positioning took 0.4 minutes generating cortex label... 13 non-cortical segments detected only using segment with 6448 vertices erasing segment 0 (vno[0] = 38955) erasing segment 2 (vno[0] = 53662) erasing segment 3 (vno[0] = 56256) erasing segment 4 (vno[0] = 57155) erasing segment 5 (vno[0] = 68725) erasing segment 6 (vno[0] = 84064) erasing segment 7 (vno[0] = 91813) erasing segment 8 (vno[0] = 98141) erasing segment 9 (vno[0] = 98227) erasing segment 10 (vno[0] = 116627) erasing segment 11 (vno[0] = 133599) erasing segment 12 (vno[0] = 133602) writing cortex label to /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/label/rh.cortex.label... writing curvature file /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.curv writing smoothed area to rh.area writing curvature file /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.area vertex spacing 0.89 +- 0.24 (0.01-->6.13) (max @ vno 133334 --> 133357) face area 0.33 +- 0.15 (0.00-->9.06) refinement took 3.2 minutes #-------------------------------------------- #@# Smooth2 lh Wed Sep 4 22:56:34 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth2 rh Wed Sep 4 22:56:37 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Wed Sep 4 22:56:41 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_inflate -rusage /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 45.8 mm, total surface area = 80053 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.177 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 0.4 minutes mris_inflate utimesec 21.300972 mris_inflate stimesec 0.060488 mris_inflate ru_maxrss 167432 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 22077 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2700 mris_inflate ru_nivcsw 2204 #-------------------------------------------- #@# Inflation2 rh Wed Sep 4 22:57:02 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_inflate -rusage /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 45.3 mm, total surface area = 80760 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.174 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.041 (target=0.015) step 035: RMS=0.035 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 0.4 minutes mris_inflate utimesec 21.829171 mris_inflate stimesec 0.060101 mris_inflate ru_maxrss 171704 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 22123 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 0 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2763 mris_inflate ru_nivcsw 2277 #-------------------------------------------- #@# Curv .H and .K lh Wed Sep 4 22:57:24 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf mris_curvature -w lh.white.preaparc total integrated curvature = -0.131*4pi (-1.641) --> 1 handles ICI = 137.7, FI = 1704.3, variation=25955.025 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 136 vertices thresholded to be in k1 ~ [-0.22 0.52], k2 ~ [-0.11 0.13] total integrated curvature = 0.647*4pi (8.135) --> 0 handles ICI = 1.5, FI = 8.4, variation=146.200 134 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 = 0.001 136 vertices thresholded to be in [-0.12 0.21] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.022 done. #-------------------------------------------- #@# Curv .H and .K rh Wed Sep 4 22:58:16 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf mris_curvature -w rh.white.preaparc total integrated curvature = -1.232*4pi (-15.477) --> 2 handles ICI = 135.4, FI = 1681.9, variation=25617.552 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 152 vertices thresholded to be in k1 ~ [-0.37 0.71], k2 ~ [-0.09 0.10] total integrated curvature = 0.621*4pi (7.805) --> 0 handles ICI = 1.5, FI = 9.3, variation=158.769 121 vertices thresholded to be in [-0.03 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 130 vertices thresholded to be in [-0.12 0.33] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.024 done. #----------------------------------------- #@# Curvature Stats lh Wed Sep 4 22:59:09 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 220 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 [ 220/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 [ 246 ] Gb_filter = 0 WARN: S lookup min: -0.303260 WARN: S explicit min: 0.000000 vertex = 220 #----------------------------------------- #@# Curvature Stats rh Wed Sep 4 22:59:11 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 220 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 [ 220/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 [ 227 ] Gb_filter = 0 WARN: S lookup min: -0.091277 WARN: S explicit min: 0.000000 vertex = 20 #-------------------------------------------- #@# Sphere lh Wed Sep 4 22:59:13 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_sphere -rusage /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 0.299... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= dell, 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 %19.57 pass 1: epoch 2 of 3 starting distance error %19.57 unfolding complete - removing small folds... starting distance error %19.49 removing remaining folds... final distance error %19.50 MRISunfold() return, current seed 1234 -01: dt=0.0000, 153 negative triangles 166: dt=0.9900, 153 negative triangles 167: dt=0.9900, 109 negative triangles 168: dt=0.9900, 93 negative triangles 169: dt=0.9900, 103 negative triangles 170: dt=0.9900, 98 negative triangles 171: dt=0.9900, 96 negative triangles 172: dt=0.9900, 94 negative triangles 173: dt=0.9900, 103 negative triangles 174: dt=0.9900, 93 negative triangles 175: dt=0.9900, 91 negative triangles 176: dt=0.9900, 94 negative triangles 177: dt=0.9900, 87 negative triangles 178: dt=0.9900, 88 negative triangles 179: dt=0.9900, 83 negative triangles 180: dt=0.9900, 80 negative triangles 181: dt=0.9900, 82 negative triangles 182: dt=0.9900, 82 negative triangles 183: dt=0.9900, 81 negative triangles 184: dt=0.9900, 74 negative triangles 185: dt=0.9900, 76 negative triangles 186: dt=0.9900, 71 negative triangles 187: dt=0.9900, 69 negative triangles 188: dt=0.9900, 72 negative triangles 189: dt=0.9900, 72 negative triangles 190: dt=0.9900, 72 negative triangles 191: dt=0.9900, 66 negative triangles 192: dt=0.9900, 67 negative triangles 193: dt=0.9900, 66 negative triangles 194: dt=0.9900, 68 negative triangles 195: dt=0.9900, 65 negative triangles 196: dt=0.9900, 60 negative triangles 197: dt=0.9900, 65 negative triangles 198: dt=0.9900, 60 negative triangles 199: dt=0.9900, 60 negative triangles 200: dt=0.9900, 57 negative triangles 201: dt=0.9900, 61 negative triangles 202: dt=0.9900, 59 negative triangles 203: dt=0.9900, 62 negative triangles 204: dt=0.9900, 60 negative triangles 205: dt=0.9900, 59 negative triangles 206: dt=0.9900, 62 negative triangles 207: dt=0.9900, 59 negative triangles 208: dt=0.9900, 55 negative triangles 209: dt=0.9900, 60 negative triangles 210: dt=0.9900, 55 negative triangles 211: dt=0.9900, 56 negative triangles 212: dt=0.9900, 56 negative triangles 213: dt=0.9900, 58 negative triangles 214: dt=0.9900, 56 negative triangles 215: dt=0.9900, 55 negative triangles 216: dt=0.9900, 63 negative triangles 217: dt=0.9900, 57 negative triangles 218: dt=0.9405, 56 negative triangles 219: dt=0.9405, 55 negative triangles 220: dt=0.9405, 55 negative triangles 221: dt=0.9405, 55 negative triangles 222: dt=0.9405, 55 negative triangles 223: dt=0.9405, 59 negative triangles 224: dt=0.9405, 58 negative triangles 225: dt=0.9405, 54 negative triangles 226: dt=0.9405, 55 negative triangles 227: dt=0.9405, 53 negative triangles 228: dt=0.9405, 55 negative triangles 229: dt=0.9405, 55 negative triangles 230: dt=0.9405, 60 negative triangles 231: dt=0.9405, 54 negative triangles 232: dt=0.9405, 47 negative triangles 233: dt=0.9405, 49 negative triangles 234: dt=0.9405, 49 negative triangles 235: dt=0.9405, 49 negative triangles 236: dt=0.9405, 47 negative triangles 237: dt=0.9405, 48 negative triangles 238: dt=0.9405, 46 negative triangles 239: dt=0.9405, 49 negative triangles 240: dt=0.9405, 50 negative triangles 241: dt=0.9405, 51 negative triangles 242: dt=0.9405, 50 negative triangles 243: dt=0.9405, 50 negative triangles 244: dt=0.9405, 52 negative triangles 245: dt=0.9405, 52 negative triangles 246: dt=0.9405, 50 negative triangles 247: dt=0.9405, 42 negative triangles 248: dt=0.9405, 46 negative triangles 249: dt=0.9405, 43 negative triangles 250: dt=0.9405, 45 negative triangles 251: dt=0.9405, 43 negative triangles 252: dt=0.9405, 44 negative triangles 253: dt=0.9405, 45 negative triangles 254: dt=0.9405, 46 negative triangles 255: dt=0.9405, 45 negative triangles 256: dt=0.9405, 46 negative triangles 257: dt=0.8935, 45 negative triangles 258: dt=0.8935, 44 negative triangles 259: dt=0.8935, 46 negative triangles 260: dt=0.8935, 45 negative triangles 261: dt=0.8935, 38 negative triangles 262: dt=0.8935, 42 negative triangles 263: dt=0.8935, 40 negative triangles 264: dt=0.8935, 38 negative triangles 265: dt=0.8935, 37 negative triangles 266: dt=0.8935, 41 negative triangles 267: dt=0.8935, 39 negative triangles 268: dt=0.8935, 40 negative triangles 269: dt=0.8935, 40 negative triangles 270: dt=0.8935, 38 negative triangles 271: dt=0.8935, 36 negative triangles 272: dt=0.8935, 35 negative triangles 273: dt=0.8935, 34 negative triangles 274: dt=0.8935, 24 negative triangles 275: dt=0.8935, 25 negative triangles 276: dt=0.8935, 26 negative triangles 277: dt=0.8935, 24 negative triangles 278: dt=0.8935, 24 negative triangles 279: dt=0.8935, 28 negative triangles 280: dt=0.8935, 25 negative triangles 281: dt=0.8935, 23 negative triangles 282: dt=0.8935, 20 negative triangles 283: dt=0.8935, 22 negative triangles 284: dt=0.8935, 24 negative triangles 285: dt=0.8935, 23 negative triangles 286: dt=0.8935, 24 negative triangles 287: dt=0.8935, 27 negative triangles 288: dt=0.8935, 26 negative triangles 289: dt=0.8935, 24 negative triangles 290: dt=0.8935, 20 negative triangles 291: dt=0.8935, 16 negative triangles 292: dt=0.8935, 16 negative triangles 293: dt=0.8935, 13 negative triangles 294: dt=0.8935, 9 negative triangles 295: dt=0.8935, 14 negative triangles 296: dt=0.8935, 10 negative triangles 297: dt=0.8935, 9 negative triangles 298: dt=0.8935, 9 negative triangles 299: dt=0.8935, 12 negative triangles 300: dt=0.8935, 10 negative triangles 301: dt=0.8935, 9 negative triangles 302: dt=0.8935, 8 negative triangles 303: dt=0.8935, 10 negative triangles 304: dt=0.8935, 6 negative triangles 305: dt=0.8935, 7 negative triangles 306: dt=0.8935, 7 negative triangles 307: dt=0.8935, 7 negative triangles 308: dt=0.8935, 6 negative triangles 309: dt=0.8935, 6 negative triangles 310: dt=0.8935, 4 negative triangles 311: dt=0.8935, 6 negative triangles 312: dt=0.8935, 6 negative triangles 313: dt=0.8935, 6 negative triangles 314: dt=0.8935, 3 negative triangles 315: dt=0.8935, 4 negative triangles 316: dt=0.8935, 5 negative triangles 317: dt=0.8935, 4 negative triangles 318: dt=0.8935, 1 negative triangles 319: dt=0.8935, 3 negative triangles 320: dt=0.8935, 2 negative triangles 321: dt=0.8935, 2 negative triangles 322: dt=0.8935, 2 negative triangles 323: dt=0.8935, 2 negative triangles 324: dt=0.8935, 4 negative triangles 325: dt=0.8935, 2 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.48 hours mris_sphere utimesec 1743.820299 mris_sphere stimesec 1.530933 mris_sphere ru_maxrss 230488 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 37330 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 2395 mris_sphere ru_nivcsw 178704 FSRUNTIME@ mris_sphere 0.4848 hours 1 threads #-------------------------------------------- #@# Sphere rh Wed Sep 4 23:28:19 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_sphere -rusage /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 0.292... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= dell, 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 %19.35 pass 1: epoch 2 of 3 starting distance error %19.28 unfolding complete - removing small folds... starting distance error %19.24 removing remaining folds... final distance error %19.26 MRISunfold() return, current seed 1234 -01: dt=0.0000, 74 negative triangles 183: dt=0.9900, 74 negative triangles 184: dt=0.9900, 31 negative triangles 185: dt=0.9900, 23 negative triangles 186: dt=0.9900, 20 negative triangles 187: dt=0.9900, 14 negative triangles 188: dt=0.9900, 15 negative triangles 189: dt=0.9900, 12 negative triangles 190: dt=0.9900, 9 negative triangles 191: dt=0.9900, 11 negative triangles 192: dt=0.9900, 9 negative triangles 193: dt=0.9900, 8 negative triangles 194: dt=0.9900, 4 negative triangles 195: dt=0.9900, 3 negative triangles 196: dt=0.9900, 3 negative triangles 197: dt=0.9900, 1 negative triangles 198: dt=0.9900, 4 negative triangles 199: dt=0.9900, 1 negative triangles 200: dt=0.9900, 4 negative triangles 201: dt=0.9900, 2 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.47 hours mris_sphere utimesec 1681.214742 mris_sphere stimesec 1.698523 mris_sphere ru_maxrss 236256 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 38262 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 0 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 2446 mris_sphere ru_nivcsw 173108 FSRUNTIME@ mris_sphere 0.4675 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Wed Sep 4 23:56:21 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_register -curv -rusage /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts cmdline mris_register -curv -rusage /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host= dell, 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= dell, 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 = 5.475 curvature mean = 0.024, std = 0.817 curvature mean = 0.021, std = 0.863 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 318830.2, tmin=0.6808 d=32.00 min @ (8.00, 8.00, 8.00) sse = 233450.6, tmin=1.3731 d=16.00 min @ (-4.00, 0.00, -4.00) sse = 190218.1, tmin=2.0757 d=8.00 min @ (2.00, 0.00, 0.00) sse = 185348.5, tmin=2.7908 d=4.00 min @ (-1.00, -1.00, 0.00) sse = 182377.2, tmin=3.5099 d=2.00 min @ (0.50, 0.00, 0.50) sse = 181734.1, tmin=4.2324 d=1.00 min @ (-0.25, 0.00, 0.00) sse = 181587.7, tmin=4.9497 d=0.50 min @ (0.00, 0.00, -0.12) sse = 181587.2, tmin=5.6665 tol=1.0e+00, sigma=0.5, host= dell, 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 5.67 min curvature mean = -0.007, std = 0.832 curvature mean = 0.008, std = 0.948 curvature mean = -0.011, std = 0.842 curvature mean = 0.003, std = 0.979 curvature mean = -0.012, std = 0.844 curvature mean = 0.000, std = 0.992 2 Reading smoothwm curvature mean = -0.029, std = 0.300 curvature mean = 0.036, std = 0.247 curvature mean = 0.066, std = 0.343 curvature mean = 0.033, std = 0.306 curvature mean = 0.031, std = 0.540 curvature mean = 0.032, std = 0.332 curvature mean = 0.016, std = 0.678 curvature mean = 0.032, std = 0.342 curvature mean = 0.006, std = 0.778 MRISregister() return, current seed 0 -01: dt=0.0000, 33 negative triangles 114: dt=0.9900, 33 negative triangles expanding nbhd size to 1 115: dt=0.9900, 48 negative triangles 116: dt=0.9900, 35 negative triangles 117: dt=0.9900, 36 negative triangles 118: dt=0.9900, 37 negative triangles 119: dt=0.9900, 33 negative triangles 120: dt=0.9900, 32 negative triangles 121: dt=0.9900, 33 negative triangles 122: dt=0.9900, 25 negative triangles 123: dt=0.9900, 24 negative triangles 124: dt=0.9900, 23 negative triangles 125: dt=0.9900, 23 negative triangles 126: dt=0.9900, 19 negative triangles 127: dt=0.9900, 22 negative triangles 128: dt=0.9900, 18 negative triangles 129: dt=0.9900, 20 negative triangles 130: dt=0.9900, 19 negative triangles 131: dt=0.9900, 17 negative triangles 132: dt=0.9900, 14 negative triangles 133: dt=0.9900, 14 negative triangles 134: dt=0.9900, 12 negative triangles 135: dt=0.9900, 14 negative triangles 136: dt=0.9900, 13 negative triangles 137: dt=0.9900, 13 negative triangles 138: dt=0.9900, 11 negative triangles 139: dt=0.9900, 12 negative triangles 140: dt=0.9900, 11 negative triangles 141: dt=0.9900, 11 negative triangles 142: dt=0.9900, 10 negative triangles 143: dt=0.9900, 11 negative triangles 144: dt=0.9900, 11 negative triangles 145: dt=0.9900, 12 negative triangles 146: dt=0.9900, 10 negative triangles 147: dt=0.9900, 11 negative triangles 148: dt=0.9900, 10 negative triangles 149: dt=0.9900, 11 negative triangles 150: dt=0.9900, 11 negative triangles 151: dt=0.9900, 10 negative triangles 152: dt=0.9900, 9 negative triangles 153: dt=0.9900, 10 negative triangles 154: dt=0.9900, 9 negative triangles 155: dt=0.9900, 9 negative triangles 156: dt=0.9900, 9 negative triangles 157: dt=0.9900, 9 negative triangles 158: dt=0.9900, 8 negative triangles 159: dt=0.9900, 9 negative triangles 160: dt=0.9900, 10 negative triangles 161: dt=0.9900, 8 negative triangles 162: dt=0.9900, 10 negative triangles 163: dt=0.9900, 8 negative triangles 164: dt=0.9900, 10 negative triangles 165: dt=0.9900, 8 negative triangles 166: dt=0.9900, 9 negative triangles 167: dt=0.9900, 9 negative triangles 168: dt=0.9405, 9 negative triangles 169: dt=0.9405, 8 negative triangles 170: dt=0.9405, 9 negative triangles 171: dt=0.9405, 8 negative triangles 172: dt=0.9405, 7 negative triangles 173: dt=0.9405, 8 negative triangles 174: dt=0.9405, 6 negative triangles 175: dt=0.9405, 7 negative triangles 176: dt=0.9405, 6 negative triangles 177: dt=0.9405, 7 negative triangles 178: dt=0.9405, 5 negative triangles 179: dt=0.9405, 5 negative triangles 180: dt=0.9405, 6 negative triangles 181: dt=0.9405, 4 negative triangles 182: dt=0.9405, 4 negative triangles 183: dt=0.9405, 4 negative triangles 184: dt=0.9405, 4 negative triangles 185: dt=0.9405, 5 negative triangles 186: dt=0.9405, 4 negative triangles 187: dt=0.9405, 5 negative triangles 188: dt=0.9405, 4 negative triangles 189: dt=0.9405, 5 negative triangles 190: dt=0.9405, 4 negative triangles 191: dt=0.8935, 4 negative triangles 192: dt=0.8935, 4 negative triangles 193: dt=0.8935, 5 negative triangles 194: dt=0.8935, 5 negative triangles 195: dt=0.8935, 4 negative triangles 196: dt=0.8935, 4 negative triangles 197: dt=0.8935, 4 negative triangles 198: dt=0.8935, 5 negative triangles 199: dt=0.8935, 5 negative triangles 200: dt=0.8935, 4 negative triangles 201: dt=0.8488, 6 negative triangles 202: dt=0.8488, 5 negative triangles 203: dt=0.8488, 5 negative triangles 204: dt=0.8488, 6 negative triangles 205: dt=0.8488, 4 negative triangles 206: dt=0.8488, 4 negative triangles 207: dt=0.8488, 6 negative triangles 208: dt=0.8488, 4 negative triangles 209: dt=0.8488, 6 negative triangles 210: dt=0.8488, 4 negative triangles 211: dt=0.8064, 4 negative triangles 212: dt=0.8064, 5 negative triangles 213: dt=0.8064, 5 negative triangles 214: dt=0.8064, 5 negative triangles 215: dt=0.8064, 5 negative triangles 216: dt=0.8064, 4 negative triangles 217: dt=0.8064, 4 negative triangles 218: dt=0.8064, 5 negative triangles 219: dt=0.8064, 4 negative triangles 220: dt=0.8064, 4 negative triangles 221: dt=0.7660, 4 negative triangles 222: dt=0.7660, 5 negative triangles 223: dt=0.7660, 4 negative triangles 224: dt=0.7660, 5 negative triangles 225: dt=0.7660, 4 negative triangles 226: dt=0.7660, 5 negative triangles 227: dt=0.7660, 4 negative triangles 228: dt=0.7660, 4 negative triangles 229: dt=0.7660, 4 negative triangles 230: dt=0.7660, 4 negative triangles 231: dt=0.7277, 4 negative triangles 232: dt=0.7277, 5 negative triangles 233: dt=0.7277, 4 negative triangles 234: dt=0.7277, 3 negative triangles 235: dt=0.7277, 2 negative triangles 236: dt=0.7277, 2 negative triangles 237: dt=0.7277, 1 negative triangles 238: dt=0.7277, 1 negative triangles 239: dt=0.7277, 1 negative triangles 240: dt=0.7277, 4 negative triangles 241: dt=0.7277, 2 negative triangles 242: dt=0.7277, 1 negative triangles 243: dt=0.7277, 1 negative triangles 244: dt=0.7277, 3 negative triangles 245: dt=0.7277, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.55 hours mris_register utimesec 1977.172054 mris_register stimesec 2.347224 mris_register ru_maxrss 222232 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 28130 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 0 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 2475 mris_register ru_nivcsw 202722 FSRUNTIME@ mris_register 0.5499 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Thu Sep 5 00:29:21 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_register -curv -rusage /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts cmdline mris_register -curv -rusage /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host= dell, 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= dell, 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 = 5.510 curvature mean = 0.042, std = 0.814 curvature mean = 0.023, std = 0.865 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 16.00) sse = 347863.7, tmin=0.7007 d=32.00 min @ (8.00, 8.00, -8.00) sse = 286019.0, tmin=1.4176 d=16.00 min @ (-4.00, -4.00, 0.00) sse = 268161.7, tmin=2.1481 d=8.00 min @ (0.00, 2.00, 2.00) sse = 264554.8, tmin=2.8793 d=4.00 min @ (0.00, -1.00, -1.00) sse = 264123.8, tmin=3.6161 d=2.00 min @ (0.00, 0.50, 0.50) sse = 263880.2, tmin=4.3584 d=1.00 min @ (0.00, -0.25, 0.00) sse = 263842.3, tmin=5.0967 tol=1.0e+00, sigma=0.5, host= dell, 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 5.83 min curvature mean = 0.012, std = 0.822 curvature mean = 0.007, std = 0.948 curvature mean = 0.007, std = 0.830 curvature mean = 0.003, std = 0.979 curvature mean = 0.004, std = 0.830 curvature mean = 0.001, std = 0.992 2 Reading smoothwm curvature mean = -0.030, std = 0.287 curvature mean = 0.034, std = 0.242 curvature mean = 0.062, std = 0.369 curvature mean = 0.028, std = 0.302 curvature mean = 0.030, std = 0.569 curvature mean = 0.027, std = 0.329 curvature mean = 0.015, std = 0.710 curvature mean = 0.027, std = 0.340 curvature mean = 0.006, std = 0.812 MRISregister() return, current seed 0 -01: dt=0.0000, 52 negative triangles 113: dt=0.9900, 52 negative triangles expanding nbhd size to 1 114: dt=0.9900, 72 negative triangles 115: dt=0.9900, 52 negative triangles 116: dt=0.9900, 50 negative triangles 117: dt=0.9900, 57 negative triangles 118: dt=0.9900, 57 negative triangles 119: dt=0.9900, 60 negative triangles 120: dt=0.9900, 54 negative triangles 121: dt=0.9900, 55 negative triangles 122: dt=0.9900, 51 negative triangles 123: dt=0.9900, 54 negative triangles 124: dt=0.9900, 44 negative triangles 125: dt=0.9900, 48 negative triangles 126: dt=0.9900, 45 negative triangles 127: dt=0.9900, 49 negative triangles 128: dt=0.9900, 42 negative triangles 129: dt=0.9900, 43 negative triangles 130: dt=0.9900, 34 negative triangles 131: dt=0.9900, 32 negative triangles 132: dt=0.9900, 32 negative triangles 133: dt=0.9900, 32 negative triangles 134: dt=0.9900, 26 negative triangles 135: dt=0.9900, 23 negative triangles 136: dt=0.9900, 19 negative triangles 137: dt=0.9900, 15 negative triangles 138: dt=0.9900, 16 negative triangles 139: dt=0.9900, 15 negative triangles 140: dt=0.9900, 19 negative triangles 141: dt=0.9900, 16 negative triangles 142: dt=0.9900, 14 negative triangles 143: dt=0.9900, 9 negative triangles 144: dt=0.9900, 9 negative triangles 145: dt=0.9900, 7 negative triangles 146: dt=0.9900, 11 negative triangles 147: dt=0.9900, 8 negative triangles 148: dt=0.9900, 6 negative triangles 149: dt=0.9900, 4 negative triangles 150: dt=0.9900, 7 negative triangles 151: dt=0.9900, 5 negative triangles 152: dt=0.9900, 3 negative triangles 153: dt=0.9900, 3 negative triangles 154: dt=0.9900, 4 negative triangles 155: dt=0.9900, 1 negative triangles 156: dt=0.9900, 1 negative triangles 157: dt=0.9900, 1 negative triangles 158: dt=0.9900, 1 negative triangles 159: dt=0.9900, 1 negative triangles 160: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.56 hours mris_register utimesec 2003.840978 mris_register stimesec 2.547372 mris_register ru_maxrss 225468 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 28935 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 0 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 2530 mris_register ru_nivcsw 206451 FSRUNTIME@ mris_register 0.5574 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Thu Sep 5 01:02:47 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Thu Sep 5 01:02:49 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Thu Sep 5 01:02:50 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh Thu Sep 5 01:02:51 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Thu Sep 5 01:02:52 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 220 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1221 labels changed using aseg relabeling using gibbs priors... 000: 2964 changed, 130488 examined... 001: 715 changed, 12561 examined... 002: 153 changed, 3876 examined... 003: 48 changed, 897 examined... 004: 17 changed, 273 examined... 005: 7 changed, 107 examined... 006: 5 changed, 46 examined... 007: 2 changed, 34 examined... 008: 2 changed, 14 examined... 009: 2 changed, 13 examined... 010: 0 changed, 6 examined... 164 labels changed using aseg 000: 119 total segments, 74 labels (195 vertices) changed 001: 46 total segments, 1 labels (1 vertices) changed 002: 44 total segments, 1 labels (2 vertices) changed 003: 43 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... 1598 vertices marked for relabeling... 1598 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 9 seconds. #----------------------------------------- #@# Cortical Parc rh Thu Sep 5 01:03:00 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 220 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1593 labels changed using aseg relabeling using gibbs priors... 000: 2768 changed, 133815 examined... 001: 655 changed, 11886 examined... 002: 157 changed, 3630 examined... 003: 50 changed, 972 examined... 004: 18 changed, 326 examined... 005: 4 changed, 124 examined... 006: 1 changed, 26 examined... 007: 2 changed, 6 examined... 008: 3 changed, 10 examined... 009: 1 changed, 13 examined... 010: 0 changed, 7 examined... 132 labels changed using aseg 000: 98 total segments, 61 labels (208 vertices) changed 001: 39 total segments, 2 labels (8 vertices) changed 002: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 11 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1653 vertices marked for relabeling... 1653 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 9 seconds. #-------------------------------------------- #@# Make Pial Surf lh Thu Sep 5 01:03:09 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 220 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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/filled.mgz... reading volume /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/brain.finalsurfs.mgz... reading volume /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/../mri/aseg.presurf.mgz... reading volume /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/wm.mgz... 17541 bright wm thresholded. 1896 bright non-wm voxels segmented. reading original surface position from /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.orig... computing class statistics... border white: 244391 voxels (1.46%) border gray 279041 voxels (1.66%) WM (99.0): 99.5 +- 7.5 [70.0 --> 110.0] GM (77.0) : 76.4 +- 9.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 63.9 (was 70) setting MAX_BORDER_WHITE to 111.5 (was 105) setting MIN_BORDER_WHITE to 73.0 (was 85) setting MAX_CSF to 54.8 (was 40) setting MAX_GRAY to 96.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 63.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 45.7 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104+-5.2, GM=73+-6.1 mean inside = 95.5, mean outside = 79.7 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.25 (0.03-->9.42) (max @ vno 57473 --> 58634) face area 0.34 +- 0.16 (0.00-->12.78) mean absolute distance = 0.62 +- 0.83 2029 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 126 points - only 0.00% unknown deleting segment 2 with 10 points - only 0.00% unknown deleting segment 3 with 48 points - only 0.00% unknown deleting segment 4 with 13 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown mean border=83.0, 46 (43) missing vertices, mean dist 0.4 [1.0 (%10.9)->0.6 (%89.1))] %68 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= dell, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.25 (0.09-->9.64) (max @ vno 58634 --> 57473) face area 0.34 +- 0.16 (0.00-->12.08) mean absolute distance = 0.33 +- 0.53 2059 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1962222.5, rms=7.299 001: dt: 0.5000, sse=1065817.8, rms=4.183 (42.681%) 002: dt: 0.5000, sse=814832.9, rms=2.755 (34.148%) 003: dt: 0.5000, sse=755675.1, rms=2.298 (16.593%) 004: dt: 0.5000, sse=734087.2, rms=2.107 (8.298%) rms = 2.17, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=693315.9, rms=1.616 (23.316%) 006: dt: 0.2500, sse=677252.6, rms=1.372 (15.119%) 007: dt: 0.2500, sse=673799.2, rms=1.312 (4.343%) rms = 1.29, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=672837.4, rms=1.289 (1.741%) rms = 1.27, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=671720.9, rms=1.269 (1.537%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 129 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown deleting segment 4 with 17 points - only 0.00% unknown deleting segment 5 with 6 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown mean border=85.8, 33 (7) missing vertices, mean dist -0.2 [0.4 (%75.2)->0.2 (%24.8))] %80 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= dell, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.07-->9.56) (max @ vno 58634 --> 57473) face area 0.36 +- 0.17 (0.00-->13.36) mean absolute distance = 0.24 +- 0.36 2447 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1084443.4, rms=4.036 010: dt: 0.5000, sse=817164.5, rms=2.368 (41.312%) 011: dt: 0.5000, sse=778487.9, rms=2.034 (14.131%) 012: dt: 0.5000, sse=763683.3, rms=1.906 (6.264%) rms = 2.09, time step reduction 1 of 3 to 0.250... 013: dt: 0.2500, sse=722991.4, rms=1.359 (28.719%) 014: dt: 0.2500, sse=709252.4, rms=1.111 (18.247%) rms = 1.07, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=707276.1, rms=1.074 (3.347%) rms = 1.06, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=706063.5, rms=1.057 (1.542%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 132 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 7 points - only 0.00% unknown deleting segment 3 with 14 points - only 0.00% unknown deleting segment 4 with 45 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown mean border=88.1, 32 (4) missing vertices, mean dist -0.1 [0.3 (%75.8)->0.2 (%24.2))] %89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= dell, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.07-->9.77) (max @ vno 58634 --> 57473) face area 0.35 +- 0.17 (0.00-->13.13) mean absolute distance = 0.20 +- 0.29 2846 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=868887.0, rms=2.940 017: dt: 0.5000, sse=745538.4, rms=1.874 (36.269%) rms = 1.95, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=703494.1, rms=1.339 (28.546%) 019: dt: 0.2500, sse=685008.0, rms=1.049 (21.641%) 020: dt: 0.2500, sse=679862.2, rms=0.989 (5.695%) rms = 0.99, time step reduction 2 of 3 to 0.125... rms = 0.98, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=678971.4, rms=0.981 (0.888%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 132 points - only 0.00% unknown deleting segment 1 with 9 points - only 0.00% unknown deleting segment 2 with 52 points - only 0.00% unknown deleting segment 3 with 14 points - only 0.00% unknown deleting segment 4 with 12 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown mean border=88.9, 48 (1) missing vertices, mean dist -0.0 [0.2 (%58.4)->0.2 (%41.6))] %92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= dell, 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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=690212.1, rms=1.357 022: dt: 0.5000, sse=680396.6, rms=1.178 (13.161%) rms = 1.55, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=664041.0, rms=0.883 (25.003%) 024: dt: 0.2500, sse=661198.9, rms=0.821 (7.025%) rms = 0.80, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=659023.9, rms=0.797 (2.942%) rms = 0.79, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=657924.1, rms=0.788 (1.163%) positioning took 0.4 minutes generating cortex label... 17 non-cortical segments detected only using segment with 6449 vertices erasing segment 0 (vno[0] = 36258) erasing segment 2 (vno[0] = 54214) erasing segment 3 (vno[0] = 56306) erasing segment 4 (vno[0] = 58410) erasing segment 5 (vno[0] = 67250) erasing segment 6 (vno[0] = 71774) erasing segment 7 (vno[0] = 75078) erasing segment 8 (vno[0] = 78148) erasing segment 9 (vno[0] = 89393) erasing segment 10 (vno[0] = 93602) erasing segment 11 (vno[0] = 100349) erasing segment 12 (vno[0] = 101058) erasing segment 13 (vno[0] = 101061) erasing segment 14 (vno[0] = 102981) erasing segment 15 (vno[0] = 130013) erasing segment 16 (vno[0] = 130033) writing cortex label to /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/label/lh.cortex.label... writing curvature file /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.curv writing smoothed area to lh.area writing curvature file /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.area vertex spacing 0.90 +- 0.26 (0.03-->9.62) (max @ vno 57473 --> 58634) face area 0.34 +- 0.16 (0.00-->12.60) 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 57 points - only 0.00% unknown deleting segment 2 with 13 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=62.4, 58 (58) missing vertices, mean dist 1.6 [0.1 (%0.0)->2.7 (%100.0))] %14 local maxima, %41 large gradients and %41 min vals, 221 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host= dell, 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=19098776.0, rms=27.186 001: dt: 0.0500, sse=16992166.0, rms=25.589 (5.875%) 002: dt: 0.0500, sse=15479505.0, rms=24.377 (4.735%) 003: dt: 0.0500, sse=14320115.0, rms=23.406 (3.984%) 004: dt: 0.0500, sse=13381112.0, rms=22.589 (3.491%) 005: dt: 0.0500, sse=12590696.0, rms=21.877 (3.150%) 006: dt: 0.0500, sse=11906522.0, rms=21.242 (2.904%) 007: dt: 0.0500, sse=11301285.0, rms=20.664 (2.723%) 008: dt: 0.0500, sse=10756836.0, rms=20.129 (2.587%) 009: dt: 0.0500, sse=10261146.0, rms=19.630 (2.481%) 010: dt: 0.0500, sse=9806057.0, rms=19.160 (2.394%) positioning took 0.6 minutes mean border=62.2, 26 (16) missing vertices, mean dist 1.3 [0.1 (%0.0)->2.3 (%100.0))] %15 local maxima, %41 large gradients and %40 min vals, 203 gradients ignored tol=1.0e-04, sigma=2.0, host= dell, 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=10475018.0, rms=19.846 011: dt: 0.0500, sse=10050974.0, rms=19.413 (2.180%) 012: dt: 0.0500, sse=9656358.0, rms=19.002 (2.120%) 013: dt: 0.0500, sse=9287863.0, rms=18.609 (2.066%) 014: dt: 0.0500, sse=8942969.0, rms=18.234 (2.016%) 015: dt: 0.0500, sse=8619214.0, rms=17.875 (1.971%) 016: dt: 0.0500, sse=8314671.5, rms=17.530 (1.929%) 017: dt: 0.0500, sse=8028191.5, rms=17.199 (1.887%) 018: dt: 0.0500, sse=7758530.0, rms=16.881 (1.845%) 019: dt: 0.0500, sse=7504333.0, rms=16.577 (1.806%) 020: dt: 0.0500, sse=7264784.0, rms=16.284 (1.765%) positioning took 0.6 minutes mean border=62.1, 40 (12) missing vertices, mean dist 1.1 [0.1 (%0.3)->1.9 (%99.7))] %15 local maxima, %41 large gradients and %40 min vals, 180 gradients ignored tol=1.0e-04, sigma=2.0, host= dell, 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=7361659.5, rms=16.409 021: dt: 0.0500, sse=7132020.0, rms=16.126 (1.727%) 022: dt: 0.0500, sse=6915589.5, rms=15.854 (1.686%) 023: dt: 0.0500, sse=6711019.5, rms=15.593 (1.649%) 024: dt: 0.0500, sse=6518116.5, rms=15.342 (1.607%) 025: dt: 0.0500, sse=6335987.5, rms=15.102 (1.568%) 026: dt: 0.0500, sse=6163865.0, rms=14.870 (1.530%) 027: dt: 0.0500, sse=6000799.5, rms=14.648 (1.495%) 028: dt: 0.0500, sse=5845123.5, rms=14.433 (1.472%) 029: dt: 0.0500, sse=5696225.0, rms=14.223 (1.450%) 030: dt: 0.0500, sse=5553736.5, rms=14.020 (1.430%) positioning took 0.6 minutes mean border=61.9, 58 (9) missing vertices, mean dist 1.0 [0.1 (%5.3)->1.7 (%94.7))] %15 local maxima, %41 large gradients and %40 min vals, 174 gradients ignored tol=1.0e-04, sigma=2.0, host= dell, 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=5641227.5, rms=14.146 031: dt: 0.5000, sse=4609799.5, rms=12.591 (10.993%) 032: dt: 0.5000, sse=3848627.2, rms=11.300 (10.249%) 033: dt: 0.5000, sse=3243176.2, rms=10.158 (10.110%) 034: dt: 0.5000, sse=2748411.0, rms=9.113 (10.285%) 035: dt: 0.5000, sse=2350373.5, rms=8.176 (10.280%) 036: dt: 0.5000, sse=2011961.9, rms=7.284 (10.916%) 037: dt: 0.5000, sse=1738665.4, rms=6.477 (11.072%) 038: dt: 0.5000, sse=1520504.4, rms=5.752 (11.203%) 039: dt: 0.5000, sse=1371509.8, rms=5.202 (9.554%) 040: dt: 0.5000, sse=1266814.6, rms=4.774 (8.238%) 041: dt: 0.5000, sse=1202835.8, rms=4.496 (5.812%) 042: dt: 0.5000, sse=1158325.6, rms=4.287 (4.653%) 043: dt: 0.5000, sse=1133810.6, rms=4.172 (2.675%) 044: dt: 0.5000, sse=1116353.0, rms=4.083 (2.153%) rms = 4.04, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1107578.0, rms=4.041 (1.010%) 046: dt: 0.2500, sse=1032508.2, rms=3.590 (11.162%) 047: dt: 0.2500, sse=1011810.4, rms=3.471 (3.317%) rms = 3.46, time step reduction 2 of 3 to 0.125... 048: dt: 0.2500, sse=1011084.3, rms=3.464 (0.211%) 049: dt: 0.1250, sse=1000213.6, rms=3.395 (1.988%) rms = 3.38, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=998094.1, rms=3.382 (0.377%) positioning took 1.6 minutes mean border=61.2, 2420 (4) missing vertices, mean dist 0.1 [0.2 (%48.3)->0.4 (%51.7))] %27 local maxima, %31 large gradients and %36 min vals, 109 gradients ignored tol=1.0e-04, sigma=1.0, host= dell, 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=1258442.9, rms=3.792 051: dt: 0.5000, sse=1192733.5, rms=3.444 (9.189%) 052: dt: 0.5000, sse=1172115.6, rms=3.356 (2.547%) rms = 3.47, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1102263.8, rms=2.852 (15.028%) 054: dt: 0.2500, sse=1081886.0, rms=2.685 (5.851%) rms = 2.68, time step reduction 2 of 3 to 0.125... 055: dt: 0.2500, sse=1081387.1, rms=2.679 (0.199%) 056: dt: 0.1250, sse=1069428.0, rms=2.580 (3.728%) rms = 2.57, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1067479.8, rms=2.566 (0.525%) positioning took 0.7 minutes mean border=60.4, 2401 (2) missing vertices, mean dist 0.1 [0.2 (%42.2)->0.3 (%57.8))] %40 local maxima, %19 large gradients and %35 min vals, 129 gradients ignored tol=1.0e-04, sigma=0.5, host= dell, 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=1112408.4, rms=2.874 rms = 3.13, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1085956.9, rms=2.674 (6.976%) 059: dt: 0.2500, sse=1077646.1, rms=2.612 (2.299%) rms = 2.64, time step reduction 2 of 3 to 0.125... rms = 2.59, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1075152.9, rms=2.591 (0.826%) positioning took 0.4 minutes mean border=59.9, 4572 (2) missing vertices, mean dist 0.0 [0.2 (%44.0)->0.3 (%56.0))] %45 local maxima, %14 large gradients and %34 min vals, 136 gradients ignored tol=1.0e-04, sigma=0.2, host= dell, 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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1091599.6, rms=2.717 rms = 2.95, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1076837.6, rms=2.599 (4.351%) 062: dt: 0.2500, sse=1068022.0, rms=2.544 (2.094%) rms = 2.54, time step reduction 2 of 3 to 0.125... 063: dt: 0.2500, sse=1066709.4, rms=2.542 (0.090%) 064: dt: 0.1250, sse=1055225.8, rms=2.446 (3.772%) rms = 2.43, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=1052164.9, rms=2.427 (0.796%) positioning took 0.6 minutes writing curvature file /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.area.pial vertex spacing 1.03 +- 0.43 (0.06-->7.97) (max @ vno 94738 --> 93705) face area 0.42 +- 0.32 (0.00-->12.79) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 130488 vertices processed 25000 of 130488 vertices processed 50000 of 130488 vertices processed 75000 of 130488 vertices processed 100000 of 130488 vertices processed 125000 of 130488 vertices processed 0 of 130488 vertices processed 25000 of 130488 vertices processed 50000 of 130488 vertices processed 75000 of 130488 vertices processed 100000 of 130488 vertices processed 125000 of 130488 vertices processed thickness calculation complete, 351:998 truncations. 30771 vertices at 0 distance 94713 vertices at 1 distance 79168 vertices at 2 distance 31341 vertices at 3 distance 9525 vertices at 4 distance 2814 vertices at 5 distance 919 vertices at 6 distance 324 vertices at 7 distance 110 vertices at 8 distance 71 vertices at 9 distance 37 vertices at 10 distance 37 vertices at 11 distance 39 vertices at 12 distance 20 vertices at 13 distance 31 vertices at 14 distance 21 vertices at 15 distance 7 vertices at 16 distance 12 vertices at 17 distance 13 vertices at 18 distance 7 vertices at 19 distance 12 vertices at 20 distance writing curvature file /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.thickness positioning took 9.4 minutes #-------------------------------------------- #@# Make Pial Surf rh Thu Sep 5 01:12:32 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 220 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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/filled.mgz... reading volume /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/brain.finalsurfs.mgz... reading volume /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/../mri/aseg.presurf.mgz... reading volume /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/wm.mgz... 17541 bright wm thresholded. 1896 bright non-wm voxels segmented. reading original surface position from /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.orig... computing class statistics... border white: 244391 voxels (1.46%) border gray 279041 voxels (1.66%) WM (99.0): 99.5 +- 7.5 [70.0 --> 110.0] GM (77.0) : 76.4 +- 9.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 64.9 (was 70) setting MAX_BORDER_WHITE to 111.5 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 55.8 (was 40) setting MAX_GRAY to 96.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.7 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104+-4.3, GM=74+-6.1 mean inside = 95.6, mean outside = 80.1 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.24 (0.01-->6.13) (max @ vno 133334 --> 133357) face area 0.33 +- 0.15 (0.00-->8.97) mean absolute distance = 0.63 +- 0.81 2440 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown deleting segment 3 with 6 points - only 0.00% unknown deleting segment 4 with 10 points - only 0.00% unknown deleting segment 5 with 6 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 17 points - only 0.00% unknown deleting segment 9 with 96 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown deleting segment 12 with 6 points - only 0.00% unknown mean border=83.7, 70 (70) missing vertices, mean dist 0.4 [0.9 (%11.2)->0.6 (%88.8))] %67 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= dell, 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 0.92 +- 0.25 (0.11-->5.99) (max @ vno 51390 --> 133387) face area 0.33 +- 0.15 (0.00-->8.71) mean absolute distance = 0.34 +- 0.52 2122 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2069236.8, rms=7.463 001: dt: 0.5000, sse=1117026.8, rms=4.331 (41.970%) 002: dt: 0.5000, sse=823903.1, rms=2.740 (36.726%) 003: dt: 0.5000, sse=755090.0, rms=2.214 (19.188%) 004: dt: 0.5000, sse=731251.8, rms=1.997 (9.831%) rms = 2.05, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=692826.5, rms=1.522 (23.780%) 006: dt: 0.2500, sse=677833.8, rms=1.285 (15.534%) 007: dt: 0.2500, sse=674800.0, rms=1.223 (4.873%) rms = 1.20, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=673267.6, rms=1.196 (2.173%) rms = 1.18, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=672563.2, rms=1.177 (1.644%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 27 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown deleting segment 5 with 61 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown mean border=86.7, 42 (14) missing vertices, mean dist -0.2 [0.4 (%75.7)->0.2 (%24.3))] %80 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= dell, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.10-->6.10) (max @ vno 51390 --> 133387) face area 0.35 +- 0.17 (0.00-->9.74) mean absolute distance = 0.24 +- 0.35 3069 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1133150.1, rms=4.174 010: dt: 0.5000, sse=840399.8, rms=2.471 (40.785%) 011: dt: 0.5000, sse=785152.9, rms=2.000 (19.088%) 012: dt: 0.5000, sse=766328.2, rms=1.835 (8.254%) rms = 1.97, time step reduction 1 of 3 to 0.250... 013: dt: 0.2500, sse=727602.8, rms=1.311 (28.513%) 014: dt: 0.2500, sse=713072.9, rms=1.048 (20.096%) rms = 1.00, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=710386.5, rms=0.999 (4.686%) rms = 0.98, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=709430.7, rms=0.978 (2.057%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown deleting segment 2 with 32 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 16 points - only 0.00% unknown deleting segment 5 with 66 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown mean border=89.0, 32 (5) missing vertices, mean dist -0.2 [0.3 (%76.3)->0.2 (%23.7))] %89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= dell, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.09-->6.17) (max @ vno 51390 --> 133387) face area 0.34 +- 0.16 (0.00-->9.44) mean absolute distance = 0.19 +- 0.28 2747 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=885139.0, rms=2.985 017: dt: 0.5000, sse=742344.2, rms=1.792 (39.976%) rms = 1.80, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=702401.9, rms=1.291 (27.929%) 019: dt: 0.2500, sse=684779.1, rms=0.981 (24.037%) 020: dt: 0.2500, sse=681502.3, rms=0.917 (6.540%) rms = 0.92, time step reduction 2 of 3 to 0.125... rms = 0.91, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=679951.9, rms=0.909 (0.884%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 1 with 7 points - only 0.00% unknown deleting segment 2 with 32 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 19 points - only 0.00% unknown deleting segment 5 with 72 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown mean border=89.8, 30 (4) missing vertices, mean dist -0.0 [0.2 (%58.4)->0.2 (%41.6))] %92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= dell, 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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=690146.0, rms=1.280 022: dt: 0.5000, sse=680768.2, rms=1.086 (15.132%) rms = 1.43, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=666030.9, rms=0.813 (25.173%) 024: dt: 0.2500, sse=663100.4, rms=0.755 (7.120%) rms = 0.73, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=662936.2, rms=0.731 (3.247%) rms = 0.73, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=660711.6, rms=0.726 (0.676%) positioning took 0.4 minutes generating cortex label... 15 non-cortical segments detected only using segment with 6439 vertices erasing segment 0 (vno[0] = 38974) erasing segment 1 (vno[0] = 39987) erasing segment 3 (vno[0] = 53662) erasing segment 4 (vno[0] = 56256) erasing segment 5 (vno[0] = 57175) erasing segment 6 (vno[0] = 68725) erasing segment 7 (vno[0] = 84080) erasing segment 8 (vno[0] = 91813) erasing segment 9 (vno[0] = 98141) erasing segment 10 (vno[0] = 98227) erasing segment 11 (vno[0] = 116627) erasing segment 12 (vno[0] = 117290) erasing segment 13 (vno[0] = 133599) erasing segment 14 (vno[0] = 133602) writing cortex label to /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/label/rh.cortex.label... writing curvature file /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.curv writing smoothed area to rh.area writing curvature file /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.area vertex spacing 0.89 +- 0.25 (0.01-->6.22) (max @ vno 51390 --> 133387) face area 0.33 +- 0.16 (0.00-->9.50) 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 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown deleting segment 2 with 32 points - only 0.00% unknown removing 1 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown deleting segment 6 with 9 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=63.4, 75 (75) missing vertices, mean dist 1.6 [2.3 (%0.0)->2.8 (%100.0))] %14 local maxima, %40 large gradients and %41 min vals, 218 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host= dell, 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=19370182.0, rms=27.030 001: dt: 0.0500, sse=17224988.0, rms=25.436 (5.898%) 002: dt: 0.0500, sse=15702471.0, rms=24.241 (4.698%) 003: dt: 0.0500, sse=14540020.0, rms=23.287 (3.935%) 004: dt: 0.0500, sse=13600939.0, rms=22.487 (3.436%) 005: dt: 0.0500, sse=12810304.0, rms=21.791 (3.097%) 006: dt: 0.0500, sse=12124999.0, rms=21.168 (2.856%) 007: dt: 0.0500, sse=11518600.0, rms=20.602 (2.676%) 008: dt: 0.0500, sse=10973212.0, rms=20.079 (2.539%) 009: dt: 0.0500, sse=10476279.0, rms=19.590 (2.435%) 010: dt: 0.0500, sse=10019355.0, rms=19.129 (2.351%) positioning took 0.6 minutes mean border=63.3, 56 (40) missing vertices, mean dist 1.3 [0.1 (%0.0)->2.3 (%100.0))] %15 local maxima, %40 large gradients and %41 min vals, 157 gradients ignored tol=1.0e-04, sigma=2.0, host= dell, 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=10669462.0, rms=19.780 011: dt: 0.0500, sse=10243930.0, rms=19.356 (2.145%) 012: dt: 0.0500, sse=9847856.0, rms=18.952 (2.085%) 013: dt: 0.0500, sse=9477397.0, rms=18.567 (2.034%) 014: dt: 0.0500, sse=9129863.0, rms=18.198 (1.988%) 015: dt: 0.0500, sse=8803503.0, rms=17.844 (1.943%) 016: dt: 0.0500, sse=8496226.0, rms=17.505 (1.903%) 017: dt: 0.0500, sse=8206542.0, rms=17.178 (1.864%) 018: dt: 0.0500, sse=7933342.0, rms=16.865 (1.826%) 019: dt: 0.0500, sse=7675396.5, rms=16.563 (1.789%) 020: dt: 0.0500, sse=7431719.5, rms=16.273 (1.752%) positioning took 0.6 minutes mean border=63.2, 65 (34) missing vertices, mean dist 1.1 [0.1 (%0.3)->2.0 (%99.7))] %16 local maxima, %40 large gradients and %40 min vals, 145 gradients ignored tol=1.0e-04, sigma=2.0, host= dell, 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=7513590.0, rms=16.376 021: dt: 0.0500, sse=7280022.0, rms=16.095 (1.718%) 022: dt: 0.0500, sse=7059119.5, rms=15.824 (1.683%) 023: dt: 0.0500, sse=6849518.0, rms=15.562 (1.652%) 024: dt: 0.0500, sse=6651276.5, rms=15.311 (1.616%) 025: dt: 0.0500, sse=6463710.5, rms=15.069 (1.580%) 026: dt: 0.0500, sse=6285592.0, rms=14.836 (1.549%) 027: dt: 0.0500, sse=6115756.0, rms=14.609 (1.524%) 028: dt: 0.0500, sse=5952974.0, rms=14.389 (1.507%) 029: dt: 0.0500, sse=5796896.0, rms=14.175 (1.490%) 030: dt: 0.0500, sse=5647034.0, rms=13.966 (1.475%) positioning took 0.6 minutes mean border=63.1, 104 (33) missing vertices, mean dist 0.9 [0.1 (%4.6)->1.7 (%95.4))] %16 local maxima, %40 large gradients and %40 min vals, 144 gradients ignored tol=1.0e-04, sigma=2.0, host= dell, 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=5720169.0, rms=14.068 031: dt: 0.5000, sse=4650050.5, rms=12.485 (11.253%) 032: dt: 0.5000, sse=3871441.0, rms=11.187 (10.396%) 033: dt: 0.5000, sse=3258772.8, rms=10.049 (10.174%) 034: dt: 0.5000, sse=2755229.5, rms=9.001 (10.426%) 035: dt: 0.5000, sse=2334965.5, rms=8.023 (10.871%) 036: dt: 0.5000, sse=1974420.1, rms=7.075 (11.812%) 037: dt: 0.5000, sse=1686625.9, rms=6.218 (12.121%) 038: dt: 0.5000, sse=1458346.9, rms=5.442 (12.478%) 039: dt: 0.5000, sse=1314249.9, rms=4.891 (10.117%) 040: dt: 0.5000, sse=1212705.0, rms=4.459 (8.843%) 041: dt: 0.5000, sse=1162400.2, rms=4.231 (5.110%) 042: dt: 0.5000, sse=1122459.4, rms=4.037 (4.580%) 043: dt: 0.5000, sse=1110166.6, rms=3.979 (1.447%) 044: dt: 0.5000, sse=1090771.8, rms=3.880 (2.483%) rms = 3.88, time step reduction 1 of 3 to 0.250... 045: dt: 0.2500, sse=1012631.3, rms=3.419 (11.871%) 046: dt: 0.2500, sse=988910.2, rms=3.262 (4.588%) rms = 3.25, time step reduction 2 of 3 to 0.125... 047: dt: 0.2500, sse=986697.0, rms=3.245 (0.522%) 048: dt: 0.1250, sse=972975.1, rms=3.155 (2.771%) rms = 3.14, time step reduction 3 of 3 to 0.062... 049: dt: 0.1250, sse=970116.2, rms=3.137 (0.577%) positioning took 1.6 minutes mean border=62.1, 2004 (5) missing vertices, mean dist 0.1 [0.2 (%45.7)->0.5 (%54.3))] %30 local maxima, %28 large gradients and %36 min vals, 97 gradients ignored tol=1.0e-04, sigma=1.0, host= dell, 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=1260809.6, rms=3.770 050: dt: 0.5000, sse=1197750.2, rms=3.437 (8.831%) 051: dt: 0.5000, sse=1172312.0, rms=3.322 (3.353%) rms = 3.48, time step reduction 1 of 3 to 0.250... 052: dt: 0.2500, sse=1092428.8, rms=2.754 (17.091%) 053: dt: 0.2500, sse=1072544.0, rms=2.588 (6.025%) rms = 2.59, time step reduction 2 of 3 to 0.125... 054: dt: 0.1250, sse=1065311.9, rms=2.528 (2.327%) 055: dt: 0.1250, sse=1055551.2, rms=2.444 (3.312%) rms = 2.43, time step reduction 3 of 3 to 0.062... 056: dt: 0.1250, sse=1053173.1, rms=2.426 (0.769%) positioning took 0.8 minutes mean border=61.3, 2083 (4) missing vertices, mean dist 0.1 [0.2 (%40.5)->0.3 (%59.5))] %41 local maxima, %18 large gradients and %36 min vals, 94 gradients ignored tol=1.0e-04, sigma=0.5, host= dell, 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=1102608.5, rms=2.786 rms = 3.13, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=1073057.1, rms=2.559 (8.155%) 058: dt: 0.2500, sse=1066307.0, rms=2.507 (2.043%) rms = 2.54, time step reduction 2 of 3 to 0.125... rms = 2.48, time step reduction 3 of 3 to 0.062... 059: dt: 0.1250, sse=1062674.0, rms=2.476 (1.238%) positioning took 0.4 minutes mean border=60.8, 4471 (3) missing vertices, mean dist 0.0 [0.2 (%43.9)->0.2 (%56.1))] %45 local maxima, %13 large gradients and %34 min vals, 124 gradients ignored tol=1.0e-04, sigma=0.2, host= dell, 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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1078022.0, rms=2.597 rms = 2.90, time step reduction 1 of 3 to 0.250... 060: dt: 0.2500, sse=1062206.1, rms=2.469 (4.929%) rms = 2.43, time step reduction 2 of 3 to 0.125... 061: dt: 0.2500, sse=1055797.4, rms=2.432 (1.501%) 062: dt: 0.1250, sse=1047446.9, rms=2.360 (2.974%) rms = 2.32, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1042348.4, rms=2.323 (1.546%) positioning took 0.5 minutes writing curvature file /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.area.pial vertex spacing 1.01 +- 0.43 (0.06-->7.53) (max @ vno 87571 --> 86522) face area 0.41 +- 0.31 (0.00-->10.76) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 133815 vertices processed 25000 of 133815 vertices processed 50000 of 133815 vertices processed 75000 of 133815 vertices processed 100000 of 133815 vertices processed 125000 of 133815 vertices processed 0 of 133815 vertices processed 25000 of 133815 vertices processed 50000 of 133815 vertices processed 75000 of 133815 vertices processed 100000 of 133815 vertices processed 125000 of 133815 vertices processed thickness calculation complete, 295:1026 truncations. 34299 vertices at 0 distance 98552 vertices at 1 distance 79051 vertices at 2 distance 30785 vertices at 3 distance 9579 vertices at 4 distance 2732 vertices at 5 distance 876 vertices at 6 distance 262 vertices at 7 distance 122 vertices at 8 distance 60 vertices at 9 distance 44 vertices at 10 distance 30 vertices at 11 distance 22 vertices at 12 distance 25 vertices at 13 distance 13 vertices at 14 distance 21 vertices at 15 distance 20 vertices at 16 distance 16 vertices at 17 distance 15 vertices at 18 distance 10 vertices at 19 distance 22 vertices at 20 distance writing curvature file /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.thickness positioning took 9.5 minutes #-------------------------------------------- #@# Surf Volume lh Thu Sep 5 01:22:03 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 220 lh /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.volume masking with /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/label/lh.cortex.label Total face volume 248162 Total vertex volume 245116 (mask=0) #@# 220 lh 245116 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Thu Sep 5 01:22:05 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 220 rh /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.volume masking with /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/label/rh.cortex.label Total face volume 249201 Total vertex volume 246094 (mask=0) #@# 220 rh 246094 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Thu Sep 5 01:22:07 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 220 SUBJECTS_DIR is /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217 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 = 294 writing volume /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/ribbon.mgz mris_volmask took 7.35 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Thu Sep 5 01:29:28 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 220 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/wm.mgz... reading input surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.white... reading input pial surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.pial... reading input white surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 248162 Total vertex volume 245116 (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) = 1373565 mm^3 (det: 1.418284 ) lhCtxGM: 244499.922 244288.000 diff= 211.9 pctdiff= 0.087 rhCtxGM: 244873.397 244419.000 diff= 454.4 pctdiff= 0.186 lhCtxWM: 214523.229 214464.000 diff= 59.2 pctdiff= 0.028 rhCtxWM: 212586.530 214152.000 diff=-1565.5 pctdiff=-0.736 SubCortGMVol 57045.000 SupraTentVol 984245.078 (981411.000) diff=2834.078 pctdiff=0.288 SupraTentVolNotVent 977208.078 (974374.000) diff=2834.078 pctdiff=0.290 BrainSegVol 1125586.000 (1123295.000) diff=2291.000 pctdiff=0.204 BrainSegVolNotVent 1115193.000 (1114279.078) diff=913.922 pctdiff=0.082 BrainSegVolNotVent 1115193.000 CerebellumVol 140745.000 VentChorVol 7037.000 3rd4th5thCSF 3356.000 CSFVol 1065.000, OptChiasmVol 74.000 MaskVol 1493038.000 1343 936 2347 2.533 0.435 0.115 0.027 12 1.2 bankssts 662 442 1315 2.716 0.577 0.136 0.018 10 0.5 caudalanteriorcingulate 4382 2981 8880 2.580 0.534 0.116 0.020 45 3.6 caudalmiddlefrontal 2522 1602 3167 1.858 0.419 0.137 0.030 33 3.0 cuneus 558 391 1903 3.478 0.782 0.099 0.021 4 0.4 entorhinal 4592 3127 10041 2.836 0.564 0.130 0.028 65 5.0 fusiform 7233 4869 14219 2.622 0.517 0.133 0.026 103 7.6 inferiorparietal 4819 3341 12238 3.086 0.683 0.139 0.034 77 6.5 inferiortemporal 1711 1143 3078 2.381 0.808 0.132 0.034 27 2.0 isthmuscingulate 7636 4897 12762 2.348 0.538 0.133 0.027 101 8.4 lateraloccipital 3418 2345 7668 2.969 0.691 0.140 0.036 50 5.0 lateralorbitofrontal 4690 3161 6997 2.093 0.593 0.144 0.036 67 6.7 lingual 2357 1636 5099 2.558 0.747 0.127 0.034 38 3.2 medialorbitofrontal 4689 3178 11700 2.980 0.640 0.131 0.027 71 5.2 middletemporal 890 558 1663 2.580 0.593 0.080 0.017 5 0.5 parahippocampal 1950 1287 3686 2.534 0.587 0.106 0.017 15 1.3 paracentral 1995 1319 4649 2.853 0.612 0.119 0.020 22 1.6 parsopercularis 905 619 2393 2.888 0.624 0.146 0.031 13 1.1 parsorbitalis 1597 1113 3396 2.522 0.555 0.139 0.028 25 1.8 parstriangularis 2470 1604 2364 1.660 0.471 0.132 0.027 28 2.7 pericalcarine 6389 4247 10431 2.225 0.641 0.118 0.021 68 5.5 postcentral 1695 1164 3201 2.527 0.604 0.146 0.028 28 2.0 posteriorcingulate 7515 4870 14541 2.701 0.527 0.114 0.021 73 5.9 precentral 5499 3772 9804 2.418 0.541 0.127 0.024 72 5.2 precuneus 957 608 2272 3.272 0.760 0.124 0.032 13 1.3 rostralanteriorcingulate 7526 5196 15304 2.488 0.570 0.142 0.033 127 10.4 rostralmiddlefrontal 10526 7220 23025 2.755 0.540 0.121 0.023 122 9.6 superiorfrontal 7572 5129 12627 2.211 0.437 0.121 0.021 96 6.0 superiorparietal 5715 3856 13283 2.936 0.642 0.114 0.020 66 4.8 superiortemporal 4810 3272 9456 2.599 0.501 0.129 0.025 67 4.7 supramarginal 332 250 953 2.824 0.722 0.187 0.055 10 0.7 frontalpole 614 433 2718 3.964 0.683 0.142 0.036 12 0.7 temporalpole 706 457 1079 2.286 0.405 0.146 0.026 10 0.6 transversetemporal 3331 2155 6837 3.064 0.932 0.124 0.035 77 4.7 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 220 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/wm.mgz... reading input surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.pial... reading input pial surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.pial... reading input white surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 248162 Total vertex volume 245116 (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) = 1373565 mm^3 (det: 1.418284 ) lhCtxGM: 244499.922 244288.000 diff= 211.9 pctdiff= 0.087 rhCtxGM: 244873.397 244419.000 diff= 454.4 pctdiff= 0.186 lhCtxWM: 214523.229 214464.000 diff= 59.2 pctdiff= 0.028 rhCtxWM: 212586.530 214152.000 diff=-1565.5 pctdiff=-0.736 SubCortGMVol 57045.000 SupraTentVol 984245.078 (981411.000) diff=2834.078 pctdiff=0.288 SupraTentVolNotVent 977208.078 (974374.000) diff=2834.078 pctdiff=0.290 BrainSegVol 1125586.000 (1123295.000) diff=2291.000 pctdiff=0.204 BrainSegVolNotVent 1115193.000 (1114279.078) diff=913.922 pctdiff=0.082 BrainSegVolNotVent 1115193.000 CerebellumVol 140745.000 VentChorVol 7037.000 3rd4th5thCSF 3356.000 CSFVol 1065.000, OptChiasmVol 74.000 MaskVol 1493038.000 1343 901 2347 2.533 0.435 0.123 0.031 18 1.9 bankssts 662 547 1315 2.716 0.577 0.151 0.031 18 0.9 caudalanteriorcingulate 4382 3825 8880 2.580 0.534 0.137 0.025 48 4.9 caudalmiddlefrontal 2522 1963 3167 1.858 0.419 0.140 0.032 30 3.7 cuneus 558 710 1903 3.478 0.782 0.167 0.033 5 0.8 entorhinal 4592 4003 10041 2.836 0.564 0.140 0.030 63 6.5 fusiform 7233 5946 14219 2.622 0.517 0.144 0.031 88 10.0 inferiorparietal 4819 4417 12238 3.086 0.683 0.150 0.033 65 7.5 inferiortemporal 1711 1456 3078 2.381 0.808 0.155 0.044 29 3.4 isthmuscingulate 7636 6044 12762 2.348 0.538 0.132 0.028 97 9.4 lateraloccipital 3418 2732 7668 2.969 0.691 0.144 0.034 48 5.1 lateralorbitofrontal 4690 3760 6997 2.093 0.593 0.148 0.038 69 8.9 lingual 2357 2249 5099 2.558 0.747 0.163 0.034 32 4.1 medialorbitofrontal 4689 4445 11700 2.980 0.640 0.154 0.030 63 7.0 middletemporal 890 784 1663 2.580 0.593 0.128 0.028 6 1.3 parahippocampal 1950 1623 3686 2.534 0.587 0.128 0.026 18 2.3 paracentral 1995 1876 4649 2.853 0.612 0.161 0.033 26 3.1 parsopercularis 905 968 2393 2.888 0.624 0.197 0.038 17 1.7 parsorbitalis 1597 1518 3396 2.522 0.555 0.180 0.034 24 2.5 parstriangularis 2470 1414 2364 1.660 0.471 0.117 0.030 35 3.3 pericalcarine 6389 5286 10431 2.225 0.641 0.134 0.026 54 7.5 postcentral 1695 1378 3201 2.527 0.604 0.152 0.034 26 2.7 posteriorcingulate 7515 5663 14541 2.701 0.527 0.117 0.024 80 7.8 precentral 5499 4267 9804 2.418 0.541 0.139 0.032 73 7.7 precuneus 957 822 2272 3.272 0.760 0.171 0.055 24 2.8 rostralanteriorcingulate 7526 6889 15304 2.488 0.570 0.167 0.033 103 11.8 rostralmiddlefrontal 10526 9118 23025 2.755 0.540 0.139 0.029 127 12.5 superiorfrontal 7572 6229 12627 2.211 0.437 0.136 0.024 97 7.9 superiorparietal 5715 4927 13283 2.936 0.642 0.143 0.030 69 8.0 superiortemporal 4810 3989 9456 2.599 0.501 0.143 0.030 55 6.0 supramarginal 332 415 953 2.824 0.722 0.236 0.044 5 0.7 frontalpole 614 916 2718 3.964 0.683 0.202 0.033 7 1.1 temporalpole 706 548 1079 2.286 0.405 0.133 0.034 6 1.0 transversetemporal 3331 2143 6837 3.064 0.932 0.130 0.039 66 5.1 insula #----------------------------------------- #@# Parcellation Stats rh Thu Sep 5 01:30:12 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 220 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/wm.mgz... reading input surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.white... reading input pial surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.pial... reading input white surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 249201 Total vertex volume 246094 (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) = 1373565 mm^3 (det: 1.418284 ) lhCtxGM: 244499.922 244288.000 diff= 211.9 pctdiff= 0.087 rhCtxGM: 244873.397 244419.000 diff= 454.4 pctdiff= 0.186 lhCtxWM: 214523.229 214464.000 diff= 59.2 pctdiff= 0.028 rhCtxWM: 212586.530 214152.000 diff=-1565.5 pctdiff=-0.736 SubCortGMVol 57045.000 SupraTentVol 984245.078 (981411.000) diff=2834.078 pctdiff=0.288 SupraTentVolNotVent 977208.078 (974374.000) diff=2834.078 pctdiff=0.290 BrainSegVol 1125586.000 (1123295.000) diff=2291.000 pctdiff=0.204 BrainSegVolNotVent 1115193.000 (1114279.078) diff=913.922 pctdiff=0.082 BrainSegVolNotVent 1115193.000 CerebellumVol 140745.000 VentChorVol 7037.000 3rd4th5thCSF 3356.000 CSFVol 1065.000, OptChiasmVol 74.000 MaskVol 1493038.000 1095 735 1978 2.899 0.471 0.123 0.020 11 0.9 bankssts 1081 722 2108 2.449 0.904 0.132 0.018 16 0.8 caudalanteriorcingulate 3185 2113 5965 2.638 0.424 0.113 0.020 32 2.6 caudalmiddlefrontal 2468 1564 3489 2.010 0.414 0.147 0.030 39 2.9 cuneus 599 398 1918 3.784 0.783 0.118 0.055 11 1.9 entorhinal 4712 3087 10569 2.857 0.679 0.131 0.027 64 5.2 fusiform 8625 5839 17403 2.624 0.485 0.131 0.024 111 8.4 inferiorparietal 4883 3222 11981 3.070 0.730 0.130 0.029 74 5.5 inferiortemporal 1722 1126 3285 2.551 0.928 0.133 0.035 27 2.2 isthmuscingulate 8110 5141 13405 2.329 0.583 0.132 0.027 106 8.5 lateraloccipital 3885 2535 7438 2.735 0.709 0.132 0.041 57 6.6 lateralorbitofrontal 4990 3248 7310 2.112 0.633 0.140 0.033 65 7.0 lingual 2638 1823 5595 2.659 0.680 0.129 0.028 44 3.0 medialorbitofrontal 4965 3305 11143 2.943 0.592 0.114 0.021 62 4.0 middletemporal 1052 673 2145 2.700 0.717 0.085 0.013 7 0.5 parahippocampal 1684 1108 3208 2.579 0.508 0.095 0.015 9 1.0 paracentral 1989 1333 3790 2.616 0.448 0.105 0.018 20 1.3 parsopercularis 1001 612 2388 2.945 0.531 0.131 0.031 15 1.2 parsorbitalis 1903 1296 4090 2.751 0.591 0.128 0.022 25 1.7 parstriangularis 2625 1723 2876 1.790 0.451 0.134 0.031 31 3.3 pericalcarine 5798 3664 8891 2.149 0.634 0.101 0.018 51 4.4 postcentral 2164 1417 3561 2.187 1.092 0.134 0.029 33 2.5 posteriorcingulate 6852 4392 13020 2.647 0.582 0.103 0.017 54 4.4 precentral 6019 4053 10596 2.425 0.494 0.131 0.024 79 5.8 precuneus 861 561 2017 2.993 0.733 0.132 0.031 14 1.0 rostralanteriorcingulate 9578 6483 19019 2.475 0.529 0.131 0.027 137 10.7 rostralmiddlefrontal 9292 6314 20374 2.769 0.531 0.130 0.027 115 9.8 superiorfrontal 8037 5217 13279 2.313 0.414 0.123 0.023 102 6.9 superiorparietal 5218 3420 11356 2.856 0.604 0.100 0.015 49 2.9 superiortemporal 5021 3331 9502 2.632 0.476 0.123 0.024 64 4.6 supramarginal 477 324 1339 2.880 0.685 0.172 0.049 11 1.1 frontalpole 600 415 2605 4.073 0.528 0.151 0.039 11 1.0 temporalpole 599 353 967 2.431 0.363 0.134 0.021 7 0.4 transversetemporal 3307 2265 7449 3.258 0.777 0.120 0.031 44 3.9 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 220 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/wm.mgz... reading input surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.pial... reading input pial surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.pial... reading input white surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 249201 Total vertex volume 246094 (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) = 1373565 mm^3 (det: 1.418284 ) lhCtxGM: 244499.922 244288.000 diff= 211.9 pctdiff= 0.087 rhCtxGM: 244873.397 244419.000 diff= 454.4 pctdiff= 0.186 lhCtxWM: 214523.229 214464.000 diff= 59.2 pctdiff= 0.028 rhCtxWM: 212586.530 214152.000 diff=-1565.5 pctdiff=-0.736 SubCortGMVol 57045.000 SupraTentVol 984245.078 (981411.000) diff=2834.078 pctdiff=0.288 SupraTentVolNotVent 977208.078 (974374.000) diff=2834.078 pctdiff=0.290 BrainSegVol 1125586.000 (1123295.000) diff=2291.000 pctdiff=0.204 BrainSegVolNotVent 1115193.000 (1114279.078) diff=913.922 pctdiff=0.082 BrainSegVolNotVent 1115193.000 CerebellumVol 140745.000 VentChorVol 7037.000 3rd4th5thCSF 3356.000 CSFVol 1065.000, OptChiasmVol 74.000 MaskVol 1493038.000 1095 606 1978 2.899 0.471 0.106 0.026 15 1.2 bankssts 1081 894 2108 2.449 0.904 0.144 0.034 17 1.7 caudalanteriorcingulate 3185 2337 5965 2.638 0.424 0.116 0.023 33 3.2 caudalmiddlefrontal 2468 1984 3489 2.010 0.414 0.139 0.030 28 3.4 cuneus 599 571 1918 3.784 0.783 0.159 0.054 12 1.6 entorhinal 4712 4065 10569 2.857 0.679 0.145 0.033 67 7.5 fusiform 8625 7286 17403 2.624 0.485 0.144 0.029 119 11.5 inferiorparietal 4883 4403 11981 3.070 0.730 0.134 0.027 71 6.1 inferiortemporal 1722 1436 3285 2.551 0.928 0.156 0.044 69 3.3 isthmuscingulate 8110 6242 13405 2.329 0.583 0.127 0.028 108 9.6 lateraloccipital 3885 2936 7438 2.735 0.709 0.143 0.037 61 6.8 lateralorbitofrontal 4990 3810 7310 2.112 0.633 0.135 0.031 59 7.1 lingual 2638 2388 5595 2.659 0.680 0.159 0.033 39 4.0 medialorbitofrontal 4965 4209 11143 2.943 0.592 0.126 0.025 50 5.4 middletemporal 1052 882 2145 2.700 0.717 0.123 0.025 7 1.3 parahippocampal 1684 1320 3208 2.579 0.508 0.110 0.023 14 1.8 paracentral 1989 1564 3790 2.616 0.448 0.130 0.024 23 2.2 parsopercularis 1001 964 2388 2.945 0.531 0.160 0.032 16 1.4 parsorbitalis 1903 1702 4090 2.751 0.591 0.145 0.026 18 2.4 parstriangularis 2625 1574 2876 1.790 0.451 0.119 0.029 44 3.2 pericalcarine 5798 4581 8891 2.149 0.634 0.120 0.023 49 5.9 postcentral 2164 1808 3561 2.187 1.092 0.156 0.037 31 3.7 posteriorcingulate 6852 5243 13020 2.647 0.582 0.111 0.020 70 5.7 precentral 6019 4665 10596 2.425 0.494 0.144 0.030 92 8.0 precuneus 861 832 2017 2.993 0.733 0.181 0.057 21 1.7 rostralanteriorcingulate 9578 8567 19019 2.475 0.529 0.159 0.032 120 13.9 rostralmiddlefrontal 9292 8020 20374 2.769 0.531 0.147 0.031 117 12.5 superiorfrontal 8037 6251 13279 2.313 0.414 0.131 0.026 97 8.5 superiorparietal 5218 4434 11356 2.856 0.604 0.129 0.024 50 5.7 superiortemporal 5021 3800 9502 2.632 0.476 0.125 0.028 54 6.1 supramarginal 477 575 1339 2.880 0.685 0.216 0.045 8 0.9 frontalpole 600 823 2605 4.073 0.528 0.189 0.039 7 1.1 temporalpole 599 459 967 2.431 0.363 0.135 0.030 5 0.8 transversetemporal 3307 2154 7449 3.258 0.777 0.135 0.039 72 5.7 insula #----------------------------------------- #@# Cortical Parc 2 lh Thu Sep 5 01:30:57 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 220 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 2.9 using min determinant for regularization = 0.086 0 singular and 762 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 32 labels changed using aseg relabeling using gibbs priors... 000: 8907 changed, 130488 examined... 001: 2071 changed, 34311 examined... 002: 655 changed, 10868 examined... 003: 272 changed, 3745 examined... 004: 136 changed, 1592 examined... 005: 56 changed, 754 examined... 006: 30 changed, 321 examined... 007: 12 changed, 159 examined... 008: 3 changed, 66 examined... 009: 0 changed, 18 examined... 7 labels changed using aseg 000: 286 total segments, 196 labels (2234 vertices) changed 001: 99 total segments, 11 labels (30 vertices) changed 002: 88 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 35 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1044 vertices marked for relabeling... 1044 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 11 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Thu Sep 5 01:31:08 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 220 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 719 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 19 labels changed using aseg relabeling using gibbs priors... 000: 8840 changed, 133815 examined... 001: 1925 changed, 34415 examined... 002: 541 changed, 10255 examined... 003: 233 changed, 3071 examined... 004: 105 changed, 1327 examined... 005: 57 changed, 604 examined... 006: 30 changed, 318 examined... 007: 19 changed, 176 examined... 008: 8 changed, 92 examined... 009: 1 changed, 38 examined... 010: 0 changed, 5 examined... 5 labels changed using aseg 000: 273 total segments, 182 labels (2612 vertices) changed 001: 101 total segments, 12 labels (42 vertices) changed 002: 91 total segments, 2 labels (9 vertices) changed 003: 90 total segments, 1 labels (3 vertices) changed 004: 89 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 32 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1383 vertices marked for relabeling... 1383 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 12 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Thu Sep 5 01:31:20 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 220 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/wm.mgz... reading input surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.white... reading input pial surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.pial... reading input white surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 248162 Total vertex volume 245116 (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) = 1373565 mm^3 (det: 1.418284 ) lhCtxGM: 244499.922 244288.000 diff= 211.9 pctdiff= 0.087 rhCtxGM: 244873.397 244419.000 diff= 454.4 pctdiff= 0.186 lhCtxWM: 214523.229 214464.000 diff= 59.2 pctdiff= 0.028 rhCtxWM: 212586.530 214152.000 diff=-1565.5 pctdiff=-0.736 SubCortGMVol 57045.000 SupraTentVol 984245.078 (981411.000) diff=2834.078 pctdiff=0.288 SupraTentVolNotVent 977208.078 (974374.000) diff=2834.078 pctdiff=0.290 BrainSegVol 1125586.000 (1123295.000) diff=2291.000 pctdiff=0.204 BrainSegVolNotVent 1115193.000 (1114279.078) diff=913.922 pctdiff=0.082 BrainSegVolNotVent 1115193.000 CerebellumVol 140745.000 VentChorVol 7037.000 3rd4th5thCSF 3356.000 CSFVol 1065.000, OptChiasmVol 74.000 MaskVol 1493038.000 1320 947 2516 2.329 0.590 0.141 0.031 22 1.9 G&S_frontomargin 1410 949 2869 2.604 0.592 0.130 0.026 19 1.3 G&S_occipital_inf 1568 1009 2890 2.378 0.553 0.113 0.018 16 1.1 G&S_paracentral 1391 903 3153 3.020 0.495 0.136 0.027 19 1.4 G&S_subcentral 665 484 1834 2.692 0.661 0.176 0.048 20 1.2 G&S_transv_frontopol 1734 1182 3744 2.952 0.659 0.113 0.023 17 1.6 G&S_cingul-Ant 940 657 1906 2.828 0.443 0.114 0.018 7 0.7 G&S_cingul-Mid-Ant 1331 924 2430 2.673 0.439 0.121 0.025 13 1.3 G&S_cingul-Mid-Post 757 488 2004 3.018 0.372 0.154 0.035 15 1.1 G_cingul-Post-dorsal 408 253 849 2.678 0.617 0.159 0.042 7 0.8 G_cingul-Post-ventral 2423 1510 3138 1.809 0.458 0.133 0.030 32 3.1 G_cuneus 1149 757 3335 3.191 0.475 0.126 0.023 16 1.1 G_front_inf-Opercular 443 300 1376 3.106 0.552 0.166 0.037 11 0.6 G_front_inf-Orbital 948 615 2339 2.763 0.493 0.149 0.037 19 1.4 G_front_inf-Triangul 4970 3300 12207 2.745 0.593 0.141 0.033 90 7.0 G_front_middle 7094 4819 18029 2.892 0.557 0.131 0.026 104 7.6 G_front_sup 653 403 1518 3.463 0.647 0.139 0.032 12 0.7 G_Ins_lg&S_cent_ins 664 416 2414 3.939 0.686 0.122 0.035 8 0.8 G_insular_short 2554 1627 6133 2.808 0.514 0.153 0.035 54 3.6 G_occipital_middle 1585 1024 2703 2.224 0.522 0.126 0.022 19 1.4 G_occipital_sup 2104 1367 4870 2.951 0.516 0.145 0.033 38 2.9 G_oc-temp_lat-fusifor 3409 2217 5338 2.112 0.623 0.158 0.041 60 5.6 G_oc-temp_med-Lingual 1106 710 2873 3.009 0.775 0.092 0.021 8 0.8 G_oc-temp_med-Parahip 2213 1492 6300 3.036 0.716 0.156 0.043 46 4.0 G_orbital 2796 1807 6741 2.809 0.496 0.147 0.029 54 3.3 G_pariet_inf-Angular 2340 1569 5204 2.668 0.533 0.138 0.029 42 2.6 G_pariet_inf-Supramar 2831 1945 5307 2.214 0.433 0.128 0.024 46 2.5 G_parietal_sup 2556 1612 4641 2.317 0.509 0.133 0.026 37 2.7 G_postcentral 2949 1824 7042 2.956 0.496 0.112 0.021 34 2.4 G_precentral 2574 1736 5847 2.610 0.574 0.140 0.027 49 2.9 G_precuneus 847 548 2227 2.730 0.870 0.139 0.049 19 1.9 G_rectus 573 335 633 1.776 1.161 0.129 0.078 47 1.7 G_subcallosal 573 363 990 2.407 0.560 0.156 0.029 10 0.6 G_temp_sup-G_T_transv 1925 1258 5987 3.252 0.700 0.144 0.030 38 2.2 G_temp_sup-Lateral 655 478 2090 3.440 0.585 0.095 0.015 5 0.4 G_temp_sup-Plan_polar 898 622 2163 2.921 0.481 0.125 0.028 12 1.1 G_temp_sup-Plan_tempo 2729 1810 7557 3.080 0.688 0.149 0.044 63 5.0 G_temporal_inf 2577 1720 7573 3.152 0.656 0.145 0.031 49 3.4 G_temporal_middle 213 158 313 2.178 0.364 0.102 0.011 1 0.1 Lat_Fis-ant-Horizont 225 158 359 2.412 0.395 0.128 0.016 2 0.1 Lat_Fis-ant-Vertical 965 647 1221 2.454 0.452 0.107 0.019 6 0.7 Lat_Fis-post 2170 1231 2864 2.053 0.535 0.131 0.029 31 2.6 Pole_occipital 1680 1179 6314 3.627 0.730 0.146 0.038 30 2.4 Pole_temporal 2965 2034 3245 1.846 0.594 0.128 0.025 30 3.1 S_calcarine 3114 2143 3815 1.969 0.533 0.098 0.015 17 1.9 S_central 1023 689 1351 2.171 0.452 0.103 0.016 7 0.7 S_cingul-Marginalis 489 328 846 2.943 0.485 0.097 0.017 2 0.3 S_circular_insula_ant 1496 1033 2472 2.867 0.502 0.088 0.012 6 0.7 S_circular_insula_inf 1521 1059 2288 2.640 0.423 0.106 0.018 8 1.2 S_circular_insula_sup 1000 693 1948 2.885 0.580 0.108 0.017 8 0.6 S_collat_transv_ant 421 303 695 2.381 0.445 0.138 0.020 4 0.4 S_collat_transv_post 1935 1331 2757 2.264 0.392 0.123 0.023 16 1.7 S_front_inf 1270 919 2004 2.309 0.411 0.130 0.023 14 1.1 S_front_middle 3289 2299 5424 2.414 0.432 0.105 0.018 24 2.2 S_front_sup 335 233 437 2.276 0.440 0.119 0.018 3 0.2 S_interm_prim-Jensen 2373 1636 3402 2.266 0.437 0.114 0.017 19 1.6 S_intrapariet&P_trans 1383 943 1806 2.282 0.304 0.132 0.025 12 1.4 S_oc_middle&Lunatus 1346 904 1915 2.285 0.356 0.113 0.017 10 0.9 S_oc_sup&transversal 939 685 1507 2.233 0.416 0.113 0.021 8 0.6 S_occipital_ant 842 618 1656 2.766 0.445 0.122 0.023 8 0.6 S_oc-temp_lat 1914 1387 2900 2.369 0.418 0.110 0.021 13 1.5 S_oc-temp_med&Lingual 279 211 441 2.098 0.426 0.141 0.019 2 0.2 S_orbital_lateral 653 452 1010 2.746 0.649 0.128 0.027 7 0.7 S_orbital_med-olfact 1280 895 2517 2.886 0.638 0.132 0.031 13 1.7 S_orbital-H_Shaped 2542 1728 3437 2.092 0.423 0.127 0.024 28 2.3 S_parieto_occipital 1061 705 1031 1.836 0.778 0.131 0.027 19 0.7 S_pericallosal 2538 1765 3636 2.247 0.408 0.107 0.018 19 1.8 S_postcentral 1629 1133 2617 2.474 0.442 0.124 0.019 15 1.2 S_precentral-inf-part 1661 1132 2620 2.536 0.326 0.122 0.023 16 1.4 S_precentral-sup-part 764 550 1289 2.530 0.617 0.122 0.021 7 0.7 S_suborbital 969 680 1358 2.334 0.331 0.112 0.019 6 0.7 S_subparietal 1531 1108 2716 2.826 0.624 0.117 0.020 12 1.2 S_temporal_inf 5676 3916 9373 2.544 0.419 0.109 0.021 44 4.5 S_temporal_sup 475 328 760 2.364 0.278 0.134 0.018 6 0.3 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Thu Sep 5 01:31:42 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 220 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/wm.mgz... reading input surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.white... reading input pial surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.pial... reading input white surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 249201 Total vertex volume 246094 (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) = 1373565 mm^3 (det: 1.418284 ) lhCtxGM: 244499.922 244288.000 diff= 211.9 pctdiff= 0.087 rhCtxGM: 244873.397 244419.000 diff= 454.4 pctdiff= 0.186 lhCtxWM: 214523.229 214464.000 diff= 59.2 pctdiff= 0.028 rhCtxWM: 212586.530 214152.000 diff=-1565.5 pctdiff=-0.736 SubCortGMVol 57045.000 SupraTentVol 984245.078 (981411.000) diff=2834.078 pctdiff=0.288 SupraTentVolNotVent 977208.078 (974374.000) diff=2834.078 pctdiff=0.290 BrainSegVol 1125586.000 (1123295.000) diff=2291.000 pctdiff=0.204 BrainSegVolNotVent 1115193.000 (1114279.078) diff=913.922 pctdiff=0.082 BrainSegVolNotVent 1115193.000 CerebellumVol 140745.000 VentChorVol 7037.000 3rd4th5thCSF 3356.000 CSFVol 1065.000, OptChiasmVol 74.000 MaskVol 1493038.000 935 628 1863 2.499 0.597 0.136 0.030 13 1.1 G&S_frontomargin 1468 948 3218 2.730 0.547 0.131 0.024 19 1.4 G&S_occipital_inf 1212 751 2286 2.422 0.571 0.104 0.019 9 1.0 G&S_paracentral 1639 1083 3437 2.756 0.526 0.121 0.022 19 1.3 G&S_subcentral 1208 820 2873 2.628 0.581 0.147 0.039 24 1.8 G&S_transv_frontopol 2863 1945 5813 2.719 0.649 0.123 0.027 31 2.9 G&S_cingul-Ant 1423 991 2970 2.818 0.614 0.133 0.025 16 1.6 G&S_cingul-Mid-Ant 1482 986 2893 2.719 0.527 0.135 0.032 19 1.9 G&S_cingul-Mid-Post 722 472 1781 2.978 0.684 0.162 0.044 16 1.2 G_cingul-Post-dorsal 398 231 899 2.827 0.604 0.130 0.039 6 0.6 G_cingul-Post-ventral 2341 1444 3382 2.005 0.433 0.148 0.035 39 3.1 G_cuneus 1339 852 3276 2.942 0.447 0.115 0.020 18 1.1 G_front_inf-Opercular 373 235 1173 3.183 0.391 0.168 0.038 8 0.6 G_front_inf-Orbital 863 559 2188 2.901 0.595 0.137 0.026 16 1.0 G_front_inf-Triangul 4544 2918 10935 2.732 0.519 0.142 0.032 83 5.9 G_front_middle 5862 3928 15291 2.940 0.531 0.137 0.028 91 6.7 G_front_sup 528 355 1634 3.829 0.661 0.125 0.031 7 0.6 G_Ins_lg&S_cent_ins 826 564 2462 3.385 0.903 0.124 0.034 13 0.9 G_insular_short 3172 2001 7151 2.721 0.527 0.145 0.029 56 3.6 G_occipital_middle 1718 1070 2982 2.318 0.465 0.139 0.027 27 1.9 G_occipital_sup 2094 1286 5000 2.924 0.583 0.141 0.033 36 2.9 G_oc-temp_lat-fusifor 3200 1995 4772 2.070 0.640 0.150 0.038 51 5.0 G_oc-temp_med-Lingual 1270 790 3856 3.515 0.814 0.109 0.039 18 2.4 G_oc-temp_med-Parahip 2664 1637 6364 2.827 0.755 0.140 0.047 55 5.3 G_orbital 2706 1759 6533 2.798 0.471 0.140 0.025 47 2.6 G_pariet_inf-Angular 2489 1607 5715 2.820 0.495 0.136 0.030 45 2.8 G_pariet_inf-Supramar 2498 1576 5003 2.412 0.405 0.130 0.026 41 2.5 G_parietal_sup 1999 1103 3176 2.212 0.554 0.100 0.023 22 2.0 G_postcentral 2549 1495 6109 2.977 0.505 0.098 0.017 24 1.6 G_precentral 2744 1817 5874 2.571 0.453 0.139 0.028 50 3.1 G_precuneus 776 538 2019 2.659 0.743 0.150 0.039 21 1.4 G_rectus 306 208 620 2.914 0.717 0.094 0.031 3 0.2 G_subcallosal 458 263 841 2.492 0.374 0.145 0.023 7 0.4 G_temp_sup-G_T_transv 1784 1081 4915 3.137 0.603 0.121 0.022 25 1.6 G_temp_sup-Lateral 967 650 2309 3.330 0.779 0.108 0.032 17 1.4 G_temp_sup-Plan_polar 771 525 1463 2.596 0.416 0.094 0.015 6 0.5 G_temp_sup-Plan_tempo 2800 1778 7948 3.178 0.776 0.141 0.037 58 4.0 G_temporal_inf 2778 1788 7430 3.104 0.587 0.127 0.027 47 2.7 G_temporal_middle 370 259 477 2.404 0.425 0.099 0.012 2 0.1 Lat_Fis-ant-Horizont 210 151 362 2.702 0.376 0.089 0.015 1 0.1 Lat_Fis-ant-Vertical 1436 962 2040 2.589 0.453 0.112 0.020 11 1.2 Lat_Fis-post 4048 2450 5268 1.912 0.564 0.136 0.033 56 5.6 Pole_occipital 1483 1040 5629 3.636 0.671 0.138 0.033 27 1.7 Pole_temporal 2817 1970 3552 2.054 0.580 0.129 0.026 29 2.8 S_calcarine 2891 1982 3237 1.873 0.542 0.100 0.015 16 1.8 S_central 1043 722 1644 2.285 0.440 0.102 0.015 7 0.6 S_cingul-Marginalis 502 338 821 3.022 0.554 0.097 0.022 2 0.4 S_circular_insula_ant 1114 746 1627 2.710 0.634 0.083 0.009 4 0.4 S_circular_insula_inf 1098 773 1707 2.706 0.517 0.103 0.018 5 0.9 S_circular_insula_sup 1049 723 2166 3.018 0.702 0.118 0.016 11 0.7 S_collat_transv_ant 371 251 513 2.292 0.305 0.147 0.025 4 0.5 S_collat_transv_post 2129 1449 2983 2.250 0.409 0.099 0.016 12 1.3 S_front_inf 2550 1780 4080 2.320 0.421 0.127 0.024 30 2.5 S_front_middle 2839 1976 4648 2.443 0.372 0.111 0.020 23 2.2 S_front_sup 350 239 526 2.512 0.399 0.103 0.014 2 0.3 S_interm_prim-Jensen 3586 2423 5005 2.288 0.386 0.111 0.017 30 2.4 S_intrapariet&P_trans 1104 785 1431 2.166 0.347 0.125 0.023 9 1.0 S_oc_middle&Lunatus 1198 832 1762 2.307 0.347 0.117 0.023 9 1.0 S_oc_sup&transversal 1074 722 1827 2.653 0.543 0.112 0.018 8 0.8 S_occipital_ant 1051 720 1759 2.614 0.543 0.116 0.023 8 0.9 S_oc-temp_lat 2011 1395 3068 2.423 0.464 0.103 0.016 12 1.4 S_oc-temp_med&Lingual 385 273 579 2.557 0.392 0.137 0.025 4 0.4 S_orbital_lateral 784 562 1109 2.326 0.549 0.118 0.021 6 0.8 S_orbital_med-olfact 1392 945 2627 2.910 0.560 0.122 0.029 12 1.6 S_orbital-H_Shaped 2348 1585 3161 2.168 0.411 0.124 0.018 22 1.8 S_parieto_occipital 1788 1168 1341 1.417 0.846 0.116 0.020 25 1.2 S_pericallosal 2400 1630 3189 2.177 0.406 0.108 0.018 19 1.7 S_postcentral 1696 1182 2714 2.437 0.340 0.093 0.011 12 0.8 S_precentral-inf-part 1223 879 1869 2.486 0.318 0.111 0.016 7 0.9 S_precentral-sup-part 111 80 234 3.342 0.526 0.171 0.024 2 0.1 S_suborbital 1209 817 1973 2.528 0.407 0.122 0.022 11 1.0 S_subparietal 1347 970 2134 2.691 0.547 0.114 0.016 9 1.0 S_temporal_inf 5975 4137 10073 2.649 0.441 0.107 0.016 47 3.8 S_temporal_sup 291 209 506 2.525 0.500 0.116 0.013 2 0.1 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Thu Sep 5 01:32:05 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 220 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1408 labels changed using aseg relabeling using gibbs priors... 000: 1905 changed, 130488 examined... 001: 459 changed, 8958 examined... 002: 128 changed, 2488 examined... 003: 58 changed, 731 examined... 004: 31 changed, 336 examined... 005: 19 changed, 174 examined... 006: 14 changed, 105 examined... 007: 7 changed, 80 examined... 008: 8 changed, 39 examined... 009: 6 changed, 41 examined... 010: 2 changed, 30 examined... 011: 1 changed, 13 examined... 012: 0 changed, 7 examined... 184 labels changed using aseg 000: 62 total segments, 29 labels (219 vertices) changed 001: 35 total segments, 2 labels (9 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 5 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 746 vertices marked for relabeling... 746 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 9 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Thu Sep 5 01:32:14 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 220 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1051 labels changed using aseg relabeling using gibbs priors... 000: 1873 changed, 133815 examined... 001: 436 changed, 8728 examined... 002: 136 changed, 2508 examined... 003: 55 changed, 871 examined... 004: 21 changed, 332 examined... 005: 11 changed, 136 examined... 006: 8 changed, 56 examined... 007: 5 changed, 41 examined... 008: 7 changed, 29 examined... 009: 10 changed, 35 examined... 010: 6 changed, 51 examined... 011: 6 changed, 27 examined... 012: 7 changed, 37 examined... 013: 5 changed, 35 examined... 014: 8 changed, 25 examined... 015: 3 changed, 31 examined... 016: 2 changed, 24 examined... 017: 1 changed, 11 examined... 018: 1 changed, 7 examined... 019: 0 changed, 7 examined... 113 labels changed using aseg 000: 47 total segments, 14 labels (105 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... 1260 vertices marked for relabeling... 1260 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 9 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Thu Sep 5 01:32:23 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 220 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/wm.mgz... reading input surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.white... reading input pial surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.pial... reading input white surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 248162 Total vertex volume 245116 (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) = 1373565 mm^3 (det: 1.418284 ) lhCtxGM: 244499.922 244288.000 diff= 211.9 pctdiff= 0.087 rhCtxGM: 244873.397 244419.000 diff= 454.4 pctdiff= 0.186 lhCtxWM: 214523.229 214464.000 diff= 59.2 pctdiff= 0.028 rhCtxWM: 212586.530 214152.000 diff=-1565.5 pctdiff=-0.736 SubCortGMVol 57045.000 SupraTentVol 984245.078 (981411.000) diff=2834.078 pctdiff=0.288 SupraTentVolNotVent 977208.078 (974374.000) diff=2834.078 pctdiff=0.290 BrainSegVol 1125586.000 (1123295.000) diff=2291.000 pctdiff=0.204 BrainSegVolNotVent 1115193.000 (1114279.078) diff=913.922 pctdiff=0.082 BrainSegVolNotVent 1115193.000 CerebellumVol 140745.000 VentChorVol 7037.000 3rd4th5thCSF 3356.000 CSFVol 1065.000, OptChiasmVol 74.000 MaskVol 1493038.000 1336 894 2730 2.832 0.555 0.132 0.021 17 1.0 caudalanteriorcingulate 4670 3176 9370 2.563 0.525 0.117 0.021 49 4.0 caudalmiddlefrontal 3494 2228 4603 1.894 0.419 0.130 0.027 44 3.8 cuneus 463 329 1672 3.510 0.844 0.096 0.021 4 0.3 entorhinal 4109 2807 8663 2.787 0.522 0.128 0.026 53 4.0 fusiform 7320 4909 14524 2.623 0.512 0.132 0.026 104 7.6 inferiorparietal 4858 3352 12337 3.090 0.679 0.137 0.034 78 6.8 inferiortemporal 1690 1134 3058 2.411 0.791 0.134 0.034 26 2.0 isthmuscingulate 7762 4962 12723 2.326 0.540 0.134 0.027 104 8.7 lateraloccipital 3771 2595 8723 2.960 0.739 0.148 0.038 66 6.0 lateralorbitofrontal 4777 3222 7146 2.095 0.597 0.144 0.035 69 6.7 lingual 2188 1444 4332 2.429 0.945 0.130 0.047 74 4.3 medialorbitofrontal 6274 4288 14965 2.918 0.642 0.130 0.027 89 6.8 middletemporal 959 606 1766 2.553 0.602 0.081 0.018 6 0.5 parahippocampal 2305 1514 4328 2.561 0.567 0.106 0.017 18 1.6 paracentral 1815 1200 4240 2.885 0.610 0.116 0.019 19 1.3 parsopercularis 859 569 2037 2.898 0.555 0.142 0.028 12 1.0 parsorbitalis 1962 1366 3991 2.462 0.532 0.137 0.027 28 2.2 parstriangularis 2402 1570 2322 1.670 0.474 0.134 0.027 27 2.7 pericalcarine 7089 4724 11456 2.222 0.630 0.119 0.022 77 6.2 postcentral 1856 1274 3394 2.526 0.621 0.143 0.028 28 2.1 posteriorcingulate 7392 4800 14405 2.717 0.526 0.114 0.021 72 5.8 precentral 5354 3665 9696 2.422 0.548 0.129 0.025 73 5.3 precuneus 1383 900 3016 3.115 0.736 0.130 0.031 19 1.8 rostralanteriorcingulate 5400 3699 11359 2.556 0.583 0.144 0.035 87 8.0 rostralmiddlefrontal 11339 7880 24946 2.677 0.568 0.124 0.024 148 10.8 superiorfrontal 5855 3984 9991 2.263 0.421 0.119 0.020 72 4.4 superiorparietal 7327 4971 17974 2.993 0.703 0.118 0.023 90 6.5 superiortemporal 4290 2930 8243 2.590 0.505 0.129 0.026 60 4.2 supramarginal 714 462 1084 2.284 0.402 0.148 0.027 11 0.6 transversetemporal 2615 1738 6020 3.235 0.708 0.114 0.024 26 2.3 insula #----------------------------------------- #@# Parcellation Stats 3 rh Thu Sep 5 01:32:45 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 220 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/wm.mgz... reading input surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.white... reading input pial surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.pial... reading input white surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 249201 Total vertex volume 246094 (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) = 1373565 mm^3 (det: 1.418284 ) lhCtxGM: 244499.922 244288.000 diff= 211.9 pctdiff= 0.087 rhCtxGM: 244873.397 244419.000 diff= 454.4 pctdiff= 0.186 lhCtxWM: 214523.229 214464.000 diff= 59.2 pctdiff= 0.028 rhCtxWM: 212586.530 214152.000 diff=-1565.5 pctdiff=-0.736 SubCortGMVol 57045.000 SupraTentVol 984245.078 (981411.000) diff=2834.078 pctdiff=0.288 SupraTentVolNotVent 977208.078 (974374.000) diff=2834.078 pctdiff=0.290 BrainSegVol 1125586.000 (1123295.000) diff=2291.000 pctdiff=0.204 BrainSegVolNotVent 1115193.000 (1114279.078) diff=913.922 pctdiff=0.082 BrainSegVolNotVent 1115193.000 CerebellumVol 140745.000 VentChorVol 7037.000 3rd4th5thCSF 3356.000 CSFVol 1065.000, OptChiasmVol 74.000 MaskVol 1493038.000 1354 905 2689 2.491 0.884 0.136 0.021 20 1.3 caudalanteriorcingulate 3357 2219 6189 2.625 0.421 0.113 0.020 34 2.8 caudalmiddlefrontal 3116 1952 4524 2.053 0.429 0.139 0.028 45 3.4 cuneus 526 353 1740 3.804 0.641 0.109 0.022 4 0.4 entorhinal 4337 2821 9534 2.833 0.669 0.131 0.027 59 4.8 fusiform 8430 5695 16769 2.608 0.479 0.131 0.024 109 8.1 inferiorparietal 5336 3565 13219 3.091 0.744 0.128 0.029 77 5.9 inferiortemporal 1690 1101 3265 2.581 0.885 0.134 0.036 26 2.3 isthmuscingulate 8201 5190 13584 2.312 0.580 0.134 0.027 109 8.9 lateraloccipital 4561 2995 9125 2.750 0.729 0.133 0.039 74 7.4 lateralorbitofrontal 4840 3143 7094 2.116 0.633 0.138 0.032 62 6.6 lingual 2094 1444 4837 2.744 0.716 0.135 0.035 42 3.1 medialorbitofrontal 6071 4037 13448 2.955 0.577 0.117 0.021 74 4.9 middletemporal 1164 738 2318 2.656 0.734 0.092 0.030 14 2.0 parahippocampal 1759 1156 3394 2.590 0.516 0.094 0.014 9 1.0 paracentral 2346 1572 4602 2.650 0.487 0.113 0.020 28 1.8 parsopercularis 811 500 1738 2.826 0.534 0.132 0.032 11 1.0 parsorbitalis 1834 1250 3685 2.679 0.562 0.130 0.023 24 1.7 parstriangularis 2534 1685 2801 1.793 0.454 0.138 0.032 31 3.3 pericalcarine 6360 4052 9657 2.141 0.628 0.104 0.019 57 4.9 postcentral 2220 1464 3697 2.206 1.097 0.135 0.030 34 2.6 posteriorcingulate 6557 4195 12664 2.660 0.590 0.101 0.016 48 4.0 precentral 6083 4102 10813 2.430 0.494 0.132 0.025 82 5.9 precuneus 1112 736 2443 2.905 0.718 0.128 0.027 16 1.1 rostralanteriorcingulate 7081 4790 14354 2.490 0.544 0.131 0.027 101 8.0 rostralmiddlefrontal 11931 8120 25271 2.689 0.544 0.129 0.027 152 12.6 superiorfrontal 6620 4299 10883 2.321 0.402 0.123 0.022 86 5.5 superiorparietal 6579 4343 15204 2.956 0.687 0.110 0.020 73 5.0 superiortemporal 4847 3206 9201 2.637 0.467 0.121 0.023 60 4.5 supramarginal 619 361 989 2.452 0.371 0.133 0.020 8 0.4 transversetemporal 2672 1817 6364 3.382 0.667 0.115 0.024 24 2.5 insula #----------------------------------------- #@# WM/GM Contrast lh Thu Sep 5 01:33:07 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts pctsurfcon --s 220 --lh-only Log file is /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts/pctsurfcon.log Thu Sep 5 01:33:07 CST 2019 setenv SUBJECTS_DIR /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217 cd /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux dell 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/tmp.pctsurfcon.3898/lh.wm.mgh --regheader 220 --cortex srcvol = /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 INFO: changing type to float Done loading volume Computing registration from header. Using /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/orig.mgz as target reference. -------- original matrix ----------- 0.00753 0.99997 -0.00000 -0.00004; -0.99937 0.00753 -0.03474 -0.00002; -0.03474 0.00026 0.99940 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/label/lh.cortex.label Reading surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 = 71243 Masking with /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/label/lh.cortex.label Writing to /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/tmp.pctsurfcon.3898/lh.wm.mgh Dim: 130488 1 1 mri_vol2surf --mov /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/tmp.pctsurfcon.3898/lh.gm.mgh --projfrac 0.3 --regheader 220 --cortex srcvol = /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 INFO: changing type to float Done loading volume Computing registration from header. Using /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/orig.mgz as target reference. -------- original matrix ----------- 0.00753 0.99997 -0.00000 -0.00004; -0.99937 0.00753 -0.03474 -0.00002; -0.03474 0.00026 0.99940 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/label/lh.cortex.label Reading surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.white Done reading source surface Reading thickness /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 = 86513 Masking with /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/label/lh.cortex.label Writing to /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/tmp.pctsurfcon.3898/lh.gm.mgh Dim: 130488 1 1 mri_concat /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/tmp.pctsurfcon.3898/lh.wm.mgh /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/tmp.pctsurfcon.3898/lh.gm.mgh --paired-diff-norm --mul 100 --o /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.w-g.pct.mgh mri_segstats --in /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.w-g.pct.mgh --annot 220 lh aparc --sum /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.w-g.pct.mgh --annot 220 lh aparc --sum /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/stats/lh.w-g.pct.stats --snr sysname Linux hostname dell machine x86_64 user dell UseRobust 0 Constructing seg from annotation Reading annotation /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.w-g.pct.mgh Vertex Area is 0.6734 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# WM/GM Contrast rh Thu Sep 5 01:33:11 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts pctsurfcon --s 220 --rh-only Log file is /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts/pctsurfcon.log Thu Sep 5 01:33:11 CST 2019 setenv SUBJECTS_DIR /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217 cd /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux dell 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/tmp.pctsurfcon.3956/rh.wm.mgh --regheader 220 --cortex srcvol = /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 INFO: changing type to float Done loading volume Computing registration from header. Using /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/orig.mgz as target reference. -------- original matrix ----------- 0.00753 0.99997 -0.00000 -0.00004; -0.99937 0.00753 -0.03474 -0.00002; -0.03474 0.00026 0.99940 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/label/rh.cortex.label Reading surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 = 71768 Masking with /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/label/rh.cortex.label Writing to /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/tmp.pctsurfcon.3956/rh.wm.mgh Dim: 133815 1 1 mri_vol2surf --mov /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/tmp.pctsurfcon.3956/rh.gm.mgh --projfrac 0.3 --regheader 220 --cortex srcvol = /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 INFO: changing type to float Done loading volume Computing registration from header. Using /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/orig.mgz as target reference. -------- original matrix ----------- 0.00753 0.99997 -0.00000 -0.00004; -0.99937 0.00753 -0.03474 -0.00002; -0.03474 0.00026 0.99940 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/label/rh.cortex.label Reading surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.white Done reading source surface Reading thickness /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 = 88024 Masking with /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/label/rh.cortex.label Writing to /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/tmp.pctsurfcon.3956/rh.gm.mgh Dim: 133815 1 1 mri_concat /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/tmp.pctsurfcon.3956/rh.wm.mgh /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/tmp.pctsurfcon.3956/rh.gm.mgh --paired-diff-norm --mul 100 --o /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.w-g.pct.mgh mri_segstats --in /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.w-g.pct.mgh --annot 220 rh aparc --sum /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.w-g.pct.mgh --annot 220 rh aparc --sum /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/stats/rh.w-g.pct.stats --snr sysname Linux hostname dell machine x86_64 user dell UseRobust 0 Constructing seg from annotation Reading annotation /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.w-g.pct.mgh Vertex Area is 0.660141 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# Relabel Hypointensities Thu Sep 5 01:33:15 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 1671 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 1758 voxels changed to hypointensity... 3456 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Thu Sep 5 01:33:28 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220 mri_aparc2aseg --s 220 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217 subject 220 outvol /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.white Reading lh pial surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.pial Loading lh annotations from /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.white Reading rh pial surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.pial Loading rh annotations from /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 6.26 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 109 rescaling Left_Cerebral_Cortex from 61 --> 64 rescaling Left_Lateral_Ventricle from 13 --> 30 rescaling Left_Inf_Lat_Vent from 34 --> 31 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 63 rescaling Left_Thalamus from 94 --> 106 rescaling Left_Thalamus_Proper from 84 --> 96 rescaling Left_Caudate from 75 --> 87 rescaling Left_Putamen from 80 --> 87 rescaling Left_Pallidum from 98 --> 104 rescaling Third_Ventricle from 25 --> 44 rescaling Fourth_Ventricle from 22 --> 26 rescaling Brain_Stem from 81 --> 86 rescaling Left_Hippocampus from 57 --> 65 rescaling Left_Amygdala from 56 --> 68 rescaling CSF from 32 --> 63 rescaling Left_Accumbens_area from 62 --> 70 rescaling Left_VentralDC from 87 --> 95 rescaling Right_Cerebral_White_Matter from 105 --> 106 rescaling Right_Cerebral_Cortex from 58 --> 66 rescaling Right_Lateral_Ventricle from 13 --> 27 rescaling Right_Inf_Lat_Vent from 25 --> 28 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 63 rescaling Right_Thalamus_Proper from 85 --> 91 rescaling Right_Caudate from 62 --> 81 rescaling Right_Putamen from 80 --> 89 rescaling Right_Pallidum from 97 --> 102 rescaling Right_Hippocampus from 53 --> 68 rescaling Right_Amygdala from 55 --> 67 rescaling Right_Accumbens_area from 65 --> 80 rescaling Right_VentralDC from 86 --> 93 rescaling Fifth_Ventricle from 40 --> 53 rescaling WM_hypointensities from 78 --> 79 rescaling non_WM_hypointensities from 40 --> 45 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 = 488836 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 119 changed. pass 2: 9 changed. pass 3: 3 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Thu Sep 5 01:36:29 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220 mri_aparc2aseg --s 220 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217 subject 220 outvol /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.white Reading lh pial surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.pial Loading lh annotations from /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.white Reading rh pial surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.pial Loading rh annotations from /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 6.26 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 109 rescaling Left_Cerebral_Cortex from 61 --> 64 rescaling Left_Lateral_Ventricle from 13 --> 30 rescaling Left_Inf_Lat_Vent from 34 --> 31 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 63 rescaling Left_Thalamus from 94 --> 106 rescaling Left_Thalamus_Proper from 84 --> 96 rescaling Left_Caudate from 75 --> 87 rescaling Left_Putamen from 80 --> 87 rescaling Left_Pallidum from 98 --> 104 rescaling Third_Ventricle from 25 --> 44 rescaling Fourth_Ventricle from 22 --> 26 rescaling Brain_Stem from 81 --> 86 rescaling Left_Hippocampus from 57 --> 65 rescaling Left_Amygdala from 56 --> 68 rescaling CSF from 32 --> 63 rescaling Left_Accumbens_area from 62 --> 70 rescaling Left_VentralDC from 87 --> 95 rescaling Right_Cerebral_White_Matter from 105 --> 106 rescaling Right_Cerebral_Cortex from 58 --> 66 rescaling Right_Lateral_Ventricle from 13 --> 27 rescaling Right_Inf_Lat_Vent from 25 --> 28 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 63 rescaling Right_Thalamus_Proper from 85 --> 91 rescaling Right_Caudate from 62 --> 81 rescaling Right_Putamen from 80 --> 89 rescaling Right_Pallidum from 97 --> 102 rescaling Right_Hippocampus from 53 --> 68 rescaling Right_Amygdala from 55 --> 67 rescaling Right_Accumbens_area from 65 --> 80 rescaling Right_VentralDC from 86 --> 93 rescaling Fifth_Ventricle from 40 --> 53 rescaling WM_hypointensities from 78 --> 79 rescaling non_WM_hypointensities from 40 --> 45 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 = 488826 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 119 changed. pass 2: 9 changed. pass 3: 3 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Thu Sep 5 01:39:32 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220 mri_aparc2aseg --s 220 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217 subject 220 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.white Reading lh pial surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.pial Loading lh annotations from /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.white Reading rh pial surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.pial Loading rh annotations from /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 6.26 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 109 rescaling Left_Cerebral_Cortex from 61 --> 64 rescaling Left_Lateral_Ventricle from 13 --> 30 rescaling Left_Inf_Lat_Vent from 34 --> 31 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 63 rescaling Left_Thalamus from 94 --> 106 rescaling Left_Thalamus_Proper from 84 --> 96 rescaling Left_Caudate from 75 --> 87 rescaling Left_Putamen from 80 --> 87 rescaling Left_Pallidum from 98 --> 104 rescaling Third_Ventricle from 25 --> 44 rescaling Fourth_Ventricle from 22 --> 26 rescaling Brain_Stem from 81 --> 86 rescaling Left_Hippocampus from 57 --> 65 rescaling Left_Amygdala from 56 --> 68 rescaling CSF from 32 --> 63 rescaling Left_Accumbens_area from 62 --> 70 rescaling Left_VentralDC from 87 --> 95 rescaling Right_Cerebral_White_Matter from 105 --> 106 rescaling Right_Cerebral_Cortex from 58 --> 66 rescaling Right_Lateral_Ventricle from 13 --> 27 rescaling Right_Inf_Lat_Vent from 25 --> 28 rescaling Right_Cerebellum_White_Matter from 87 --> 87 rescaling Right_Cerebellum_Cortex from 59 --> 63 rescaling Right_Thalamus_Proper from 85 --> 91 rescaling Right_Caudate from 62 --> 81 rescaling Right_Putamen from 80 --> 89 rescaling Right_Pallidum from 97 --> 102 rescaling Right_Hippocampus from 53 --> 68 rescaling Right_Amygdala from 55 --> 67 rescaling Right_Accumbens_area from 65 --> 80 rescaling Right_VentralDC from 86 --> 93 rescaling Fifth_Ventricle from 40 --> 53 rescaling WM_hypointensities from 78 --> 79 rescaling non_WM_hypointensities from 40 --> 45 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 = 488826 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 119 changed. pass 2: 9 changed. pass 3: 3 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Thu Sep 5 01:42:34 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Thu Sep 5 01:42:34 CST 2019 setenv SUBJECTS_DIR /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217 cd /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri /usr/local/freesurfer/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux dell 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 dell machine x86_64 user dell input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done Started at Thu Sep 5 01:42:34 CST 2019 Ended at Thu Sep 5 01:42:39 CST 2019 Apas2aseg-Run-Time-Sec 5 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Thu Sep 5 01:42:39 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject 220 $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject 220 sysname Linux hostname dell machine x86_64 user dell UseRobust 0 atlas_icv (eTIV) = 1373565 mm^3 (det: 1.418284 ) Computing euler number orig.nofix lheno = -32, rheno = -26 orig.nofix lhholes = 17, rhholes = 14 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 244499.922 244288.000 diff= 211.9 pctdiff= 0.087 rhCtxGM: 244873.397 244419.000 diff= 454.4 pctdiff= 0.186 lhCtxWM: 214523.229 214464.000 diff= 59.2 pctdiff= 0.028 rhCtxWM: 212586.530 214152.000 diff=-1565.5 pctdiff=-0.736 SubCortGMVol 57045.000 SupraTentVol 984245.078 (981411.000) diff=2834.078 pctdiff=0.288 SupraTentVolNotVent 977208.078 (974374.000) diff=2834.078 pctdiff=0.290 BrainSegVol 1125586.000 (1123295.000) diff=2291.000 pctdiff=0.204 BrainSegVolNotVent 1115193.000 (1114279.078) diff=913.922 pctdiff=0.082 BrainSegVolNotVent 1115193.000 CerebellumVol 140745.000 VentChorVol 7037.000 3rd4th5thCSF 3356.000 CSFVol 1065.000, OptChiasmVol 74.000 MaskVol 1493038.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Thu Sep 5 01:44:08 CST 2019 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220 mri_aparc2aseg --s 220 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217 subject 220 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/aparc+aseg.mgz Reading lh white surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.white Reading lh pial surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/lh.pial Loading lh annotations from /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.white Reading rh pial surface /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/surf/rh.pial Loading rh annotations from /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/ribbon.mgz Loading filled from /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 6882 vertices from left hemi Ripped 6780 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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/mri/aseg.mgz Loading Ctx Seg File /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/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 = 915051 Used brute-force search on 48 voxels Fixing Parahip LH WM Found 16 clusters 0 k 3.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 2.000000 6 k 1.000000 7 k 1.000000 8 k 2.000000 9 k 2.000000 10 k 1.000000 11 k 1144.000000 12 k 26.000000 13 k 1.000000 14 k 1.000000 15 k 1.000000 Fixing Parahip RH WM Found 14 clusters 0 k 1.000000 1 k 3.000000 2 k 1498.000000 3 k 2.000000 4 k 2.000000 5 k 28.000000 6 k 1.000000 7 k 2.000000 8 k 1.000000 9 k 5.000000 10 k 1.000000 11 k 1.000000 12 k 3.000000 13 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 220 --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 220 --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname dell machine x86_64 user dell UseRobust 0 atlas_icv (eTIV) = 1373565 mm^3 (det: 1.418284 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 244499.922 244288.000 diff= 211.9 pctdiff= 0.087 rhCtxGM: 244873.397 244419.000 diff= 454.4 pctdiff= 0.186 lhCtxWM: 214523.229 214464.000 diff= 59.2 pctdiff= 0.028 rhCtxWM: 212586.530 214152.000 diff=-1565.5 pctdiff=-0.736 SubCortGMVol 57045.000 SupraTentVol 984245.078 (981411.000) diff=2834.078 pctdiff=0.288 SupraTentVolNotVent 977208.078 (974374.000) diff=2834.078 pctdiff=0.290 BrainSegVol 1125586.000 (1123295.000) diff=2291.000 pctdiff=0.204 BrainSegVolNotVent 1115193.000 (1114279.078) diff=913.922 pctdiff=0.082 BrainSegVolNotVent 1115193.000 CerebellumVol 140745.000 VentChorVol 7037.000 3rd4th5thCSF 3356.000 CSFVol 1065.000, OptChiasmVol 74.000 MaskVol 1493038.000 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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/220/label INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217; ln -s /usr/local/freesurfer/subjects/fsaverage; cd - #-------------------------------------------- #@# BA_exvivo Labels lh Thu Sep 5 01:50:15 CST 2019 mri_label2label --srcsubject fsaverage --srclabel /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/fsaverage/label/lh.BA1_exvivo.label --trgsubject 220 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface No such file or directory mri_label2label.bin: could not open label file /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/fsaverage/label/lh.BA1_exvivo.label srclabel = /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 220 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 /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217 FREESURFER_HOME /usr/local/freesurfer Loading source label. Invalid argument ERROR reading /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/fsaverage/label/lh.BA1_exvivo.label Linux dell 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 220 exited with ERRORS at Thu Sep 5 01:50:15 CST 2019 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting