2020��� 03��� 13��� ��������� 15:03:22 CST /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii /usr/local/freesurfer/bin/recon-all -s sub-123_ses-FU_T1w.nii -i sub-123_ses-FU_T1w.nii.gz -all -qcache subjid sub-123_ses-FU_T1w.nii setenv SUBJECTS_DIR /usr/local/freesurfer/subjects 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 test-QiTianM420-D166 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 16384 kbytes maxproc 31186 maxlocks unlimited maxsignal 31186 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 8032500 898452 5506360 107932 1627688 6708252 Swap: 2097148 899580 1197568 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:23-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:23-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:23-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/13-07:03:23-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:23-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:23-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/13-07:03:24-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/13-07:03:24-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/13-07:03:24-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/13-07:03:24-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/13-07:03:24-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/13-07:03:24-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:24-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:24-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/13-07:03:24-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:25-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:25-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:25-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:25-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:25-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:25-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/13-07:03:25-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:25-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:25-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:26-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/13-07:03:26-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:26-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2020/03/13-07:03:26-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:26-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:26-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:26-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:26-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:27-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:27-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:27-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:27-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:27-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:27-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2020/03/13-07:03:27-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: test Machine: test-QiTianM420-D166 Platform: Linux PlatformVersion: 5.3.0-40-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 ####################################### /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii mri_convert /home/test/Documents/houbu/sub-123_ses-FU_T1w.nii.gz /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri/orig/001.mgz mri_convert.bin /home/test/Documents/houbu/sub-123_ses-FU_T1w.nii.gz /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/test/Documents/houbu/sub-123_ses-FU_T1w.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0399549, -0.998896, -0.0247009) j_ras = (0.00148612, 0.02478, -0.999692) k_ras = (0.9992, 0.0399059, 0.00247457) writing to /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor 2020��� 03��� 13��� ��������� 15:03:30 CST Found 1 runs /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/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 /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri/orig/001.mgz /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri/rawavg.mgz /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii mri_convert /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri/rawavg.mgz /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri/orig.mgz --conform mri_convert.bin /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri/rawavg.mgz /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0399549, -0.998896, -0.0247009) j_ras = (0.00148612, 0.02478, -0.999692) k_ras = (0.9992, 0.0399059, 0.00247457) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri/orig.mgz /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach 2020��� 03��� 13��� ��������� 15:03:41 CST /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/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 test-QiTianM420-D166 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 2020��� 03��� 13��� ��������� 15:03:41 CST Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.4185 /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4185/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.4185/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (4.65661e-10, -1.53523e-09, -1) k_ras = (-3.72529e-09, 1, -3.20142e-10) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.4185/nu0.mnc... -------------------------------------------------------- Iteration 1 2020��� 03��� 13��� ��������� 15:03:44 CST nu_correct -clobber ./tmp.mri_nu_correct.mni.4185/nu0.mnc ./tmp.mri_nu_correct.mni.4185/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.4185/0/ -iterations 1000 -distance 50 [test@test-QiTianM420-D166:/usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri/] [2020-03-13 15:03:44] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.4185/0/ ./tmp.mri_nu_correct.mni.4185/nu0.mnc ./tmp.mri_nu_correct.mni.4185/nu1.imp 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Processing:.................................................................Done Number of iterations: 61 CV of field change: 0.000988845 mri_convert ./tmp.mri_nu_correct.mni.4185/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.4185/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.4185/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (4.65661e-10, -1.53523e-09, -1) k_ras = (-3.72529e-09, 1, -3.20142e-10) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... 2020��� 03��� 13��� ��������� 15:04:55 CST mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at 2020��� 03��� 13��� ��������� 15:04:55 CST Ended at 2020��� 03��� 13��� ��������� 15:05:24 CST talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection 2020��� 03��� 13��� ��������� 15:05:26 CST /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7448, pval=0.6675 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri/transforms/talairach_avi.log tal_QC_AZS /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri/transforms/talairach_avi.log TalAviQA: 0.97574 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction 2020��� 03��� 13��� ��������� 15:05:26 CST mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/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 test-QiTianM420-D166 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 2020��� 03��� 13��� ��������� 15:05:26 CST Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.10396 /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10396/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10396/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (4.65661e-10, -1.53523e-09, -1) k_ras = (-3.72529e-09, 1, -3.20142e-10) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.10396/nu0.mnc... -------------------------------------------------------- Iteration 1 2020��� 03��� 13��� ��������� 15:05:27 CST nu_correct -clobber ./tmp.mri_nu_correct.mni.10396/nu0.mnc ./tmp.mri_nu_correct.mni.10396/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10396/0/ [test@test-QiTianM420-D166:/usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri/] [2020-03-13 15:05:27] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.10396/0/ ./tmp.mri_nu_correct.mni.10396/nu0.mnc ./tmp.mri_nu_correct.mni.10396/nu1.imp 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Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.0014313 -------------------------------------------------------- Iteration 2 2020��� 03��� 13��� ��������� 15:06:13 CST nu_correct -clobber ./tmp.mri_nu_correct.mni.10396/nu1.mnc ./tmp.mri_nu_correct.mni.10396/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.10396/1/ [test@test-QiTianM420-D166:/usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri/] [2020-03-13 15:06:13] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.10396/1/ ./tmp.mri_nu_correct.mni.10396/nu1.mnc ./tmp.mri_nu_correct.mni.10396/nu2.imp Processing:.................................................................Done 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./tmp.mri_nu_correct.mni.10396/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10396/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.10396/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10396/ones.mgz sysname Linux hostname test-QiTianM420-D166 machine x86_64 user test input ./tmp.mri_nu_correct.mni.10396/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.10396/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.10396/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10396/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10396/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.10396/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10396/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10396/input.mean.dat sysname Linux hostname test-QiTianM420-D166 machine x86_64 user test UseRobust 0 Loading ./tmp.mri_nu_correct.mni.10396/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.10396/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10396/ones.mgz --i ./tmp.mri_nu_correct.mni.10396/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10396/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10396/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.10396/ones.mgz --i ./tmp.mri_nu_correct.mni.10396/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10396/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10396/output.mean.dat sysname Linux hostname test-QiTianM420-D166 machine x86_64 user test UseRobust 0 Loading ./tmp.mri_nu_correct.mni.10396/ones.mgz Loading ./tmp.mri_nu_correct.mni.10396/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.10396/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.10396/nu2.mnc ./tmp.mri_nu_correct.mni.10396/nu2.mnc mul 1.04184728065311578416 Saving result to './tmp.mri_nu_correct.mni.10396/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.10396/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.10396/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.10396/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (4.65661e-10, -1.53523e-09, -1) k_ras = (-3.72529e-09, 1, -3.20142e-10) 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 5 seconds. mapping (19, 120) to ( 3, 110) 2020��� 03��� 13��� ��������� 15:07:20 CST mri_nu_correct.mni done mri_add_xform_to_header -c /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization 2020��� 03��� 13��� ��������� 15:07:20 CST /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/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 1.05809 0.01198 -0.03868 1.35016; -0.00513 0.95013 0.16265 -13.52902; 0.01429 -0.14286 1.07702 -10.90392; 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 = 13 Starting OpenSpline(): npoints = 13 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 102 gm peak at 63 (63), valley at 50 (50) csf peak at 14, setting threshold to 46 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 59 (59), valley at 39 (39) csf peak at 30, setting threshold to 49 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 25 seconds. #-------------------------------------------- #@# Skull Stripping 2020��� 03��� 13��� ��������� 15:08:46 CST /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri mri_em_register -rusage /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/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=17.0 skull bounding box = (47, 36, 15) --> (210, 237, 223) using (101, 103, 119) as brain centroid... mean wm in atlas = 108, using box (81,78,93) --> (121, 127,144) to find MRI wm before smoothing, mri peak at 100 robust fit to distribution - 100 +- 9.6 distribution too broad for accurate scaling - disabling after smoothing, mri peak at 108, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.345 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.345348 @ (0.000, 0.000, 0.000) max log p = -4.115582 @ (-4.545, -4.545, -13.636) max log p = -4.115582 @ (0.000, 0.000, 0.000) max log p = -4.096274 @ (1.136, 1.136, 1.136) max log p = -4.059862 @ (0.568, -1.705, -0.568) max log p = -4.059862 @ (0.000, 0.000, 0.000) Found translation: (-2.8, -5.1, -13.1): log p = -4.060 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.949, old_max_log_p =-4.060 (thresh=-4.1) 1.07500 0.00000 0.00000 -12.41963; 0.00000 1.06580 0.14032 -24.70358; 0.00000 -0.12074 0.91709 14.99542; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.903, old_max_log_p =-3.949 (thresh=-3.9) 1.07500 0.00000 0.00000 -12.41963; 0.00000 1.14574 0.15084 -37.21942; 0.00000 -0.12074 0.91709 14.99542; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.903, old_max_log_p =-3.903 (thresh=-3.9) 1.07500 0.00000 0.00000 -12.41963; 0.00000 1.14574 0.15084 -37.21942; 0.00000 -0.12074 0.91709 14.99542; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.866, old_max_log_p =-3.903 (thresh=-3.9) 1.05428 0.00420 -0.03051 -6.60708; 0.00000 1.08304 0.13810 -28.72540; 0.03517 -0.13076 0.94994 5.99263; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.862, old_max_log_p =-3.866 (thresh=-3.9) 1.05430 -0.03552 -0.00394 -4.30603; 0.03516 1.10275 0.14064 -36.33127; 0.00065 -0.12838 0.93261 10.36153; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.862, old_max_log_p =-3.862 (thresh=-3.9) 1.05430 -0.03552 -0.00394 -4.30603; 0.03516 1.10275 0.14064 -36.33127; 0.00065 -0.12838 0.93261 10.36153; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.837, old_max_log_p =-3.862 (thresh=-3.9) 1.05719 -0.01027 0.01452 -11.07523; 0.00906 1.10047 0.13224 -32.06469; -0.01617 -0.11874 0.93367 11.01854; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.834, old_max_log_p =-3.837 (thresh=-3.8) 1.05472 -0.01024 0.01449 -10.75660; 0.00905 1.09918 0.13208 -31.86003; -0.01619 -0.11888 0.93476 10.90174; 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 1.05472 -0.01024 0.01449 -10.75660; 0.00905 1.09918 0.13208 -31.86003; -0.01619 -0.11888 0.93476 10.90174; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.05472 -0.01024 0.01449 -10.75660; 0.00905 1.09918 0.13208 -31.86003; -0.01619 -0.11888 0.93476 10.90174; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.05472 -0.01024 0.01449 -10.75660; 0.00905 1.09918 0.13208 -31.86003; -0.01619 -0.11888 0.93476 10.90174; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.834 (old=-4.345) transform before final EM align: 1.05472 -0.01024 0.01449 -10.75660; 0.00905 1.09918 0.13208 -31.86003; -0.01619 -0.11888 0.93476 10.90174; 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 1.05472 -0.01024 0.01449 -10.75660; 0.00905 1.09918 0.13208 -31.86003; -0.01619 -0.11888 0.93476 10.90174; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.05472 -0.01024 0.01449 -10.75660; 0.00905 1.09918 0.13208 -31.86003; -0.01619 -0.11888 0.93476 10.90174; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.2 tol 0.000000 final transform: 1.05472 -0.01024 0.01449 -10.75660; 0.00905 1.09918 0.13208 -31.86003; -0.01619 -0.11888 0.93476 10.90174; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 833.519246 mri_em_register stimesec 1.238732 mri_em_register ru_maxrss 614420 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 161772 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 16 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 0 mri_em_register ru_nivcsw 71472 registration took 13 minutes and 59 seconds. mri_watershed -rusage /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/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=117 z=126 r=86 first estimation of the main basin volume: 2751131 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=157, y=111, z=84, Imax=255 CSF=14, 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=1861003227 voxels, voxel volume =1.000 = 1861003227 mmm3 = 1861003.264 cm3 done. PostAnalyze...Basin Prior 245 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=120, z=117, r=10055 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 44252 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=37 , nb = -1038222789 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=33 , nb = -1048030036 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1026159606 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1065039774 OTHER CSF_MIN=0, CSF_intensity=7, CSF_MAX=50 , nb = 1077844314 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 5, 6, 24, 62 after analyzing : 5, 18, 25, 29 RIGHT_CER before analyzing : 37, 30, 23, 69 after analyzing : 17, 30, 30, 39 LEFT_CER before analyzing : 33, 29, 24, 65 after analyzing : 16, 29, 29, 38 RIGHT_BRAIN before analyzing : 4, 5, 26, 59 after analyzing : 4, 19, 26, 29 LEFT_BRAIN before analyzing : 4, 5, 25, 61 after analyzing : 4, 18, 25, 28 OTHER before analyzing : 50, 53, 57, 93 after analyzing : 50, 55, 57, 64 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...64 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.010 curvature mean = 73.798, std = 8.832 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.19, sigma = 3.29 after rotation: sse = 2.19, sigma = 3.29 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.23, its var is 2.61 before Erosion-Dilatation 0.00% 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...38 iterations mri_strip_skull: done peeling brain Brain Size = 1862053 voxels, voxel volume = 1.000 mm3 = 1862053 mmm3 = 1862.053 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 14.106380 mri_watershed stimesec 0.203112 mri_watershed ru_maxrss 836800 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 207425 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 3144 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 0 mri_watershed ru_nivcsw 3643 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration 2020��� 03��� 13��� ��������� 15:23:01 CST /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri mri_em_register -rusage /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/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=22.9 skull bounding box = (61, 61, 35) --> (194, 183, 213) using (105, 102, 124) as brain centroid... mean wm in atlas = 107, using box (89,87,102) --> (121, 116,145) to find MRI wm before smoothing, mri peak at 100 robust fit to distribution - 100 +- 8.7 after smoothing, mri peak at 100, scaling input intensities by 1.070 scaling channel 0 by 1.07 initial log_p = -4.152 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.186605 @ (0.000, 0.000, 0.000) max log p = -3.904677 @ (-4.545, -4.545, -13.636) max log p = -3.895897 @ (2.273, 2.273, -2.273) max log p = -3.819661 @ (1.136, 1.136, 3.409) max log p = -3.797394 @ (-0.568, 0.568, -0.568) max log p = -3.797394 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -0.6, -13.1): log p = -3.797 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.738, old_max_log_p =-3.797 (thresh=-3.8) 1.07500 0.00000 0.00000 -11.33768; 0.00000 1.06580 0.14032 -25.08441; 0.00000 -0.12074 0.91709 11.22939; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.738, old_max_log_p =-3.738 (thresh=-3.7) 1.07500 0.00000 0.00000 -11.33768; 0.00000 1.06580 0.14032 -25.08441; 0.00000 -0.12074 0.91709 11.22939; 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=-3.663, old_max_log_p =-3.738 (thresh=-3.7) 1.05428 -0.03422 -0.00450 -4.04101; 0.03517 1.06523 0.14024 -31.39979; 0.00000 -0.12526 0.95148 7.69633; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.662, old_max_log_p =-3.663 (thresh=-3.7) 1.05428 -0.03422 -0.00450 -4.04101; 0.03451 1.04526 0.13761 -28.57435; 0.00000 -0.12526 0.95148 7.69633; 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=-3.625, old_max_log_p =-3.662 (thresh=-3.7) 1.05551 -0.03426 -0.00451 -4.19391; 0.03455 1.04747 0.12999 -28.41267; 0.00028 -0.11655 0.95145 7.07205; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.625, old_max_log_p =-3.625 (thresh=-3.6) 1.05551 -0.03426 -0.00451 -4.19391; 0.03455 1.04747 0.12999 -28.41267; 0.00028 -0.11655 0.95145 7.07205; 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 1.05551 -0.03426 -0.00451 -4.19391; 0.03455 1.04747 0.12999 -28.41267; 0.00028 -0.11655 0.95145 7.07205; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.05551 -0.03426 -0.00451 -4.19391; 0.03455 1.04747 0.12999 -28.41267; 0.00028 -0.11655 0.95145 7.07205; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.05551 -0.03426 -0.00451 -4.19391; 0.03455 1.04747 0.12999 -28.41267; 0.00028 -0.11655 0.95145 7.07205; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.625 (old=-4.152) transform before final EM align: 1.05551 -0.03426 -0.00451 -4.19391; 0.03455 1.04747 0.12999 -28.41267; 0.00028 -0.11655 0.95145 7.07205; 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 1.05551 -0.03426 -0.00451 -4.19391; 0.03455 1.04747 0.12999 -28.41267; 0.00028 -0.11655 0.95145 7.07205; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.05551 -0.03426 -0.00451 -4.19391; 0.03455 1.04747 0.12999 -28.41267; 0.00028 -0.11655 0.95145 7.07205; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.1 tol 0.000000 final transform: 1.05551 -0.03426 -0.00451 -4.19391; 0.03455 1.04747 0.12999 -28.41267; 0.00028 -0.11655 0.95145 7.07205; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 528.519145 mri_em_register stimesec 1.011669 mri_em_register ru_maxrss 603408 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 162509 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 16 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 0 mri_em_register ru_nivcsw 25645 registration took 8 minutes and 52 seconds. #-------------------------------------- #@# CA Normalize 2020��� 03��� 13��� ��������� 15:31:52 CST /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/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=22.9 skull bounding box = (61, 61, 35) --> (194, 183, 213) using (105, 102, 124) as brain centroid... mean wm in atlas = 107, using box (89,87,102) --> (121, 116,145) to find MRI wm before smoothing, mri peak at 100 robust fit to distribution - 100 +- 8.7 after smoothing, mri peak at 100, scaling input intensities by 1.070 scaling channel 0 by 1.07 using 246344 sample points... INFO: compute sample coordinates transform 1.05551 -0.03426 -0.00451 -4.19391; 0.03455 1.04747 0.12999 -28.41267; 0.00028 -0.11655 0.95145 7.07205; 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, 58, 37) --> (191, 168, 211) Left_Cerebral_White_Matter: limiting intensities to 99.0 --> 132.0 0 of 45 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (67, 60, 36) --> (129, 171, 211) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 15 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 144, 63) --> (177, 183, 120) Left_Cerebellum_White_Matter: limiting intensities to 117.0 --> 132.0 1 of 7 (14.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (88, 144, 61) --> (129, 184, 122) Right_Cerebellum_White_Matter: limiting intensities to 105.0 --> 132.0 2 of 9 (22.2%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 132, 101) --> (146, 200, 132) Brain_Stem: limiting intensities to 97.0 --> 132.0 0 of 9 (0.0%) samples deleted using 85 total control points for intensity normalization... bias field = 0.875 +- 0.116 0 of 82 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 58, 37) --> (191, 168, 211) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 121 (0.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (67, 60, 36) --> (129, 171, 211) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 74 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 144, 63) --> (177, 183, 120) Left_Cerebellum_White_Matter: limiting intensities to 93.0 --> 132.0 19 of 51 (37.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (88, 144, 61) --> (129, 184, 122) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 9 of 35 (25.7%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 132, 101) --> (146, 200, 132) Brain_Stem: limiting intensities to 88.0 --> 132.0 7 of 48 (14.6%) samples deleted using 329 total control points for intensity normalization... bias field = 0.966 +- 0.099 0 of 287 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 58, 37) --> (191, 168, 211) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 6 of 213 (2.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (67, 60, 36) --> (129, 171, 211) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 8 of 202 (4.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 144, 63) --> (177, 183, 120) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 35 of 72 (48.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (88, 144, 61) --> (129, 184, 122) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 13 of 30 (43.3%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 132, 101) --> (146, 200, 132) Brain_Stem: limiting intensities to 88.0 --> 132.0 33 of 83 (39.8%) samples deleted using 600 total control points for intensity normalization... bias field = 1.000 +- 0.086 0 of 502 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 4 seconds. #-------------------------------------- #@# CA Reg 2020��� 03��� 13��� ��������� 15:32:56 CST /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/mri mri_ca_register -rusage /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/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) = 1.07 (predicted orig area = 7.5) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.866, neg=0, invalid=762 0001: dt=234.868837, rms=0.786 (9.169%), neg=0, invalid=762 0002: dt=221.952000, rms=0.769 (2.177%), neg=0, invalid=762 0003: dt=202.322581, rms=0.761 (1.037%), neg=0, invalid=762 0004: dt=166.956522, rms=0.757 (0.578%), neg=0, invalid=762 0005: dt=369.920000, rms=0.752 (0.649%), neg=0, invalid=762 0006: dt=129.472000, rms=0.749 (0.332%), neg=0, invalid=762 0007: dt=517.888000, rms=0.745 (0.524%), neg=0, invalid=762 0008: dt=110.976000, rms=0.744 (0.147%), neg=0, invalid=762 0009: dt=110.976000, rms=0.744 (0.092%), neg=0, invalid=762 0010: dt=110.976000, rms=0.742 (0.163%), neg=0, invalid=762 0011: dt=110.976000, rms=0.741 (0.210%), neg=0, invalid=762 0012: dt=110.976000, rms=0.739 (0.230%), neg=0, invalid=762 0013: dt=110.976000, rms=0.738 (0.225%), neg=0, invalid=762 0014: dt=110.976000, rms=0.736 (0.219%), neg=0, invalid=762 0015: dt=110.976000, rms=0.734 (0.196%), neg=0, invalid=762 0016: dt=110.976000, rms=0.733 (0.167%), neg=0, invalid=762 0017: dt=110.976000, rms=0.732 (0.149%), neg=0, invalid=762 0018: dt=110.976000, rms=0.731 (0.142%), neg=0, invalid=762 0019: dt=110.976000, rms=0.730 (0.141%), neg=0, invalid=762 0020: dt=110.976000, rms=0.729 (0.143%), neg=0, invalid=762 0021: dt=110.976000, rms=0.728 (0.137%), neg=0, invalid=762 0022: dt=110.976000, rms=0.727 (0.137%), neg=0, invalid=762 0023: dt=110.976000, rms=0.726 (0.136%), neg=0, invalid=762 0024: dt=110.976000, rms=0.725 (0.138%), neg=0, invalid=762 0025: dt=110.976000, rms=0.724 (0.130%), neg=0, invalid=762 0026: dt=110.976000, rms=0.723 (0.118%), neg=0, invalid=762 0027: dt=110.976000, rms=0.722 (0.108%), neg=0, invalid=762 0028: dt=517.888000, rms=0.722 (0.049%), neg=0, invalid=762 0029: dt=517.888000, rms=0.722 (0.001%), neg=0, invalid=762 0030: dt=517.888000, rms=0.722 (-0.254%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.723, neg=0, invalid=762 0031: dt=129.472000, rms=0.721 (0.288%), neg=0, invalid=762 0032: dt=369.920000, rms=0.720 (0.097%), neg=0, invalid=762 0033: dt=369.920000, rms=0.719 (0.123%), neg=0, invalid=762 0034: dt=369.920000, rms=0.718 (0.125%), neg=0, invalid=762 0035: dt=369.920000, rms=0.717 (0.129%), neg=0, invalid=762 0036: dt=369.920000, rms=0.716 (0.140%), neg=0, invalid=762 0037: dt=369.920000, rms=0.715 (0.143%), neg=0, invalid=762 0038: dt=369.920000, rms=0.714 (0.109%), neg=0, invalid=762 0039: dt=369.920000, rms=0.714 (0.085%), neg=0, invalid=762 0040: dt=443.904000, rms=0.714 (0.030%), neg=0, invalid=762 0041: dt=443.904000, rms=0.714 (-0.014%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.718, neg=0, invalid=762 0042: dt=132.266667, rms=0.712 (0.797%), neg=0, invalid=762 0043: dt=223.238095, rms=0.705 (1.045%), neg=0, invalid=762 0044: dt=62.208000, rms=0.700 (0.627%), neg=0, invalid=762 0045: dt=580.608000, rms=0.692 (1.167%), neg=0, invalid=762 0046: dt=74.796221, rms=0.687 (0.721%), neg=0, invalid=762 0047: dt=124.416000, rms=0.686 (0.180%), neg=0, invalid=762 0048: dt=124.416000, rms=0.685 (0.134%), neg=0, invalid=762 0049: dt=124.416000, rms=0.682 (0.395%), neg=0, invalid=762 0050: dt=124.416000, rms=0.680 (0.315%), neg=0, invalid=762 0051: dt=124.416000, rms=0.676 (0.599%), neg=0, invalid=762 0052: dt=124.416000, rms=0.673 (0.453%), neg=0, invalid=762 0053: dt=124.416000, rms=0.670 (0.379%), neg=0, invalid=762 0054: dt=124.416000, rms=0.667 (0.485%), neg=0, invalid=762 0055: dt=124.416000, rms=0.665 (0.377%), neg=0, invalid=762 0056: dt=124.416000, rms=0.663 (0.252%), neg=0, invalid=762 0057: dt=124.416000, rms=0.661 (0.290%), neg=0, invalid=762 0058: dt=124.416000, rms=0.659 (0.249%), neg=0, invalid=762 0059: dt=124.416000, rms=0.658 (0.139%), neg=0, invalid=762 0060: dt=124.416000, rms=0.658 (0.145%), neg=0, invalid=762 0061: dt=124.416000, rms=0.656 (0.209%), neg=0, invalid=762 0062: dt=124.416000, rms=0.655 (0.117%), neg=0, invalid=762 0063: dt=124.416000, rms=0.655 (0.066%), neg=0, invalid=762 0064: dt=82.944000, rms=0.654 (0.073%), neg=0, invalid=762 0065: dt=9.072000, rms=0.654 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.655, neg=0, invalid=762 0066: dt=103.680000, rms=0.653 (0.288%), neg=0, invalid=762 0067: dt=124.416000, rms=0.652 (0.132%), neg=0, invalid=762 0068: dt=124.416000, rms=0.652 (-0.052%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.676, neg=0, invalid=762 0069: dt=2.800000, rms=0.676 (0.095%), neg=0, invalid=762 0070: dt=1.600000, rms=0.676 (0.004%), neg=0, invalid=762 0071: dt=1.600000, rms=0.676 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.676, neg=0, invalid=762 0072: dt=0.700000, rms=0.676 (0.082%), neg=0, invalid=762 0073: dt=0.400000, rms=0.676 (-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=0.742, neg=0, invalid=762 0074: dt=5.693593, rms=0.719 (3.078%), neg=0, invalid=762 0075: dt=3.222222, rms=0.718 (0.147%), neg=0, invalid=762 0076: dt=3.222222, rms=0.718 (-0.044%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.719, neg=0, invalid=762 0077: dt=0.000000, rms=0.718 (0.083%), neg=0, invalid=762 0078: dt=0.000000, rms=0.718 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.775, neg=0, invalid=762 0079: dt=1.042071, rms=0.771 (0.456%), neg=0, invalid=762 0080: dt=1.891473, rms=0.767 (0.579%), neg=0, invalid=762 0081: dt=1.024000, rms=0.766 (0.072%), neg=0, invalid=762 0082: dt=1.024000, rms=0.765 (0.167%), neg=0, invalid=762 0083: dt=1.024000, rms=0.764 (0.107%), neg=0, invalid=762 0084: dt=1.024000, rms=0.764 (-0.101%), neg=0, invalid=762 0085: dt=0.320000, rms=0.764 (0.002%), neg=0, invalid=762 0086: dt=1.024000, rms=0.764 (0.015%), neg=0, invalid=762 0087: dt=3.072000, rms=0.763 (0.100%), neg=0, invalid=762 0088: dt=0.000000, rms=0.763 (0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.764, neg=0, invalid=762 0089: dt=1.024000, rms=0.763 (0.154%), neg=0, invalid=762 0090: dt=1.792000, rms=0.762 (0.046%), neg=0, invalid=762 0091: dt=1.792000, rms=0.762 (-0.050%), 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=0.734, neg=0, invalid=762 0092: dt=0.890063, rms=0.711 (3.112%), neg=0, invalid=762 0093: dt=0.080000, rms=0.710 (0.134%), neg=0, invalid=762 0094: dt=0.080000, rms=0.710 (-0.090%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.710, neg=0, invalid=762 0095: dt=0.028000, rms=0.710 (0.107%), neg=0, invalid=762 0096: dt=0.007000, rms=0.710 (0.002%), neg=0, invalid=762 0097: dt=0.007000, rms=0.710 (-0.000%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.10406 (17) Left_Lateral_Ventricle (4): linear fit = 0.61 x + 0.0 (508 voxels, overlap=0.324) Left_Lateral_Ventricle (4): linear fit = 0.61 x + 0.0 (508 voxels, peak = 12), gca=12.1 gca peak = 0.15565 (16) mri peak = 0.08937 (16) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (628 voxels, overlap=0.759) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (628 voxels, peak = 18), gca=17.5 gca peak = 0.26829 (96) mri peak = 0.06774 (89) Right_Pallidum (52): linear fit = 0.92 x + 0.0 (700 voxels, overlap=0.667) Right_Pallidum (52): linear fit = 0.92 x + 0.0 (700 voxels, peak = 88), gca=87.8 gca peak = 0.20183 (93) mri peak = 0.06593 (84) Left_Pallidum (13): linear fit = 0.92 x + 0.0 (696 voxels, overlap=1.019) Left_Pallidum (13): linear fit = 0.92 x + 0.0 (696 voxels, peak = 85), gca=85.1 gca peak = 0.21683 (55) mri peak = 0.05081 (71) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (493 voxels, overlap=0.179) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (493 voxels, peak = 67), gca=67.4 gca peak = 0.30730 (58) mri peak = 0.07692 (65) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (735 voxels, overlap=0.997) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (735 voxels, peak = 65), gca=64.7 gca peak = 0.11430 (101) mri peak = 0.05597 (102) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (64402 voxels, overlap=0.937) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (64402 voxels, peak = 105), gca=104.5 gca peak = 0.12076 (102) mri peak = 0.05655 (104) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (68015 voxels, overlap=0.914) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (68015 voxels, peak = 105), gca=104.5 gca peak = 0.14995 (59) mri peak = 0.02705 (62) Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (20722 voxels, overlap=0.112) Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (20722 voxels, peak = 66), gca=66.4 gca peak = 0.15082 (58) mri peak = 0.02808 (63) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (19109 voxels, overlap=0.264) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (19109 voxels, peak = 64), gca=63.5 gca peak = 0.14161 (67) mri peak = 0.06334 (79) Right_Caudate (50): linear fit = 1.22 x + 0.0 (997 voxels, overlap=0.059) Right_Caudate (50): linear fit = 1.22 x + 0.0 (997 voxels, peak = 81), gca=81.4 gca peak = 0.15243 (71) mri peak = 0.06019 (77) Left_Caudate (11): linear fit = 1.03 x + 0.0 (975 voxels, overlap=0.966) Left_Caudate (11): linear fit = 1.03 x + 0.0 (975 voxels, peak = 73), gca=73.5 gca peak = 0.13336 (57) mri peak = 0.03430 (53) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (17608 voxels, overlap=0.898) Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (17608 voxels, peak = 54), gca=53.9 gca peak = 0.13252 (56) mri peak = 0.03187 (53) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (17813 voxels, overlap=0.635) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (17813 voxels, peak = 54), gca=54.0 gca peak = 0.18181 (84) mri peak = 0.04589 (82) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (8085 voxels, overlap=0.958) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (8085 voxels, peak = 85), gca=85.3 gca peak = 0.20573 (83) mri peak = 0.04384 (83) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (6486 voxels, overlap=0.949) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (6486 voxels, peak = 82), gca=81.8 gca peak = 0.21969 (57) mri peak = 0.05476 (71) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (465 voxels, overlap=0.881) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (465 voxels, peak = 68), gca=67.5 gca peak = 0.39313 (56) mri peak = 0.05025 (68) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (476 voxels, overlap=1.013) Right_Amygdala (54): linear fit = 1.21 x + 0.0 (476 voxels, peak = 67), gca=67.5 gca peak = 0.14181 (85) mri peak = 0.06651 (88) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (6022 voxels, overlap=0.804) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (6022 voxels, peak = 87), gca=87.1 gca peak = 0.11978 (83) mri peak = 0.05444 (87) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4840 voxels, overlap=0.681) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4840 voxels, peak = 93), gca=92.5 gca peak = 0.13399 (79) mri peak = 0.05068 (76) Left_Putamen (12): linear fit = 0.98 x + 0.0 (2211 voxels, overlap=0.995) Left_Putamen (12): linear fit = 0.98 x + 0.0 (2211 voxels, peak = 77), gca=77.0 gca peak = 0.14159 (79) mri peak = 0.05773 (78) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2351 voxels, overlap=1.000) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2351 voxels, peak = 77), gca=77.0 gca peak = 0.10025 (80) mri peak = 0.06264 (87) Brain_Stem (16): linear fit = 1.12 x + 0.0 (9846 voxels, overlap=0.403) Brain_Stem (16): linear fit = 1.12 x + 0.0 (9846 voxels, peak = 89), gca=89.2 gca peak = 0.13281 (86) mri peak = 0.06775 (89) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (866 voxels, overlap=0.601) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (866 voxels, peak = 92), gca=92.5 gca peak = 0.12801 (89) mri peak = 0.06484 (93) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (996 voxels, overlap=0.852) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (996 voxels, peak = 95), gca=94.8 gca peak = 0.20494 (23) mri peak = 0.28583 (55) gca peak = 0.15061 (21) mri peak = 0.05998 ( 5) Fourth_Ventricle (15): linear fit = 0.93 x + 0.0 (191 voxels, overlap=0.587) Fourth_Ventricle (15): linear fit = 0.93 x + 0.0 (191 voxels, peak = 19), gca=19.4 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 1.16 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 0.88 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=0.704, neg=0, invalid=762 0098: dt=98.580645, rms=0.698 (0.809%), neg=0, invalid=762 0099: dt=129.472000, rms=0.696 (0.265%), neg=0, invalid=762 0100: dt=517.888000, rms=0.693 (0.452%), neg=0, invalid=762 0101: dt=369.920000, rms=0.691 (0.309%), neg=0, invalid=762 0102: dt=110.976000, rms=0.690 (0.146%), neg=0, invalid=762 0103: dt=295.936000, rms=0.689 (0.065%), neg=0, invalid=762 0104: dt=129.472000, rms=0.689 (0.076%), neg=0, invalid=762 0105: dt=129.472000, rms=0.689 (0.047%), neg=0, invalid=762 0106: dt=129.472000, rms=0.688 (0.042%), neg=0, invalid=762 0107: dt=129.472000, rms=0.688 (0.065%), neg=0, invalid=762 0108: dt=129.472000, rms=0.687 (0.086%), neg=0, invalid=762 0109: dt=129.472000, rms=0.687 (0.084%), neg=0, invalid=762 0110: dt=129.472000, rms=0.686 (0.080%), neg=0, invalid=762 0111: dt=129.472000, rms=0.686 (0.070%), neg=0, invalid=762 0112: dt=129.472000, rms=0.685 (0.065%), neg=0, invalid=762 0113: dt=129.472000, rms=0.685 (0.055%), neg=0, invalid=762 0114: dt=129.472000, rms=0.684 (0.053%), neg=0, invalid=762 0115: dt=129.472000, rms=0.684 (0.048%), neg=0, invalid=762 0116: dt=129.472000, rms=0.684 (0.050%), neg=0, invalid=762 0117: dt=129.472000, rms=0.683 (0.058%), neg=0, invalid=762 0118: dt=129.472000, rms=0.683 (0.059%), neg=0, invalid=762 0119: dt=129.472000, rms=0.682 (0.064%), neg=0, invalid=762 0120: dt=129.472000, rms=0.682 (0.072%), neg=0, invalid=762 0121: dt=129.472000, rms=0.682 (0.065%), neg=0, invalid=762 0122: dt=129.472000, rms=0.681 (0.064%), neg=0, invalid=762 0123: dt=129.472000, rms=0.681 (0.062%), neg=0, invalid=762 0124: dt=129.472000, rms=0.680 (0.063%), neg=0, invalid=762 0125: dt=129.472000, rms=0.680 (0.065%), neg=0, invalid=762 0126: dt=129.472000, rms=0.679 (0.060%), neg=0, invalid=762 0127: dt=129.472000, rms=0.679 (0.059%), neg=0, invalid=762 0128: dt=129.472000, rms=0.679 (0.059%), neg=0, invalid=762 0129: dt=129.472000, rms=0.678 (0.056%), neg=0, invalid=762 0130: dt=129.472000, rms=0.678 (0.052%), neg=0, invalid=762 0131: dt=129.472000, rms=0.678 (0.048%), neg=0, invalid=762 0132: dt=129.472000, rms=0.677 (0.046%), neg=0, invalid=762 0133: dt=129.472000, rms=0.677 (0.043%), neg=0, invalid=762 0134: dt=129.472000, rms=0.677 (0.043%), neg=0, invalid=762 0135: dt=129.472000, rms=0.676 (0.039%), neg=0, invalid=762 0136: dt=129.472000, rms=0.676 (0.039%), neg=0, invalid=762 0137: dt=129.472000, rms=0.676 (0.039%), neg=0, invalid=762 0138: dt=129.472000, rms=0.676 (0.036%), neg=0, invalid=762 0139: dt=129.472000, rms=0.675 (0.034%), neg=0, invalid=762 0140: dt=129.472000, rms=0.675 (0.029%), neg=0, invalid=762 0141: dt=129.472000, rms=0.675 (0.025%), neg=0, invalid=762 0142: dt=129.472000, rms=0.675 (0.028%), neg=0, invalid=762 0143: dt=129.472000, rms=0.675 (0.026%), neg=0, invalid=762 0144: dt=129.472000, rms=0.674 (0.025%), neg=0, invalid=762 0145: dt=129.472000, rms=0.674 (0.027%), neg=0, invalid=762 0146: dt=129.472000, rms=0.674 (0.027%), neg=0, invalid=762 0147: dt=129.472000, rms=0.674 (0.028%), neg=0, invalid=762 0148: dt=129.472000, rms=0.674 (0.025%), neg=0, invalid=762 0149: dt=129.472000, rms=0.674 (0.024%), neg=0, invalid=762 0150: dt=129.472000, rms=0.673 (0.024%), neg=0, invalid=762 0151: dt=517.888000, rms=0.673 (0.006%), neg=0, invalid=762 0152: dt=517.888000, rms=0.673 (-0.064%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.674, neg=0, invalid=762 0153: dt=369.920000, rms=0.672 (0.238%), neg=0, invalid=762 0154: dt=295.936000, rms=0.672 (0.098%), neg=0, invalid=762 0155: dt=92.480000, rms=0.671 (0.032%), neg=0, invalid=762 0156: dt=92.480000, rms=0.671 (0.015%), neg=0, invalid=762 0157: dt=92.480000, rms=0.671 (0.026%), neg=0, invalid=762 0158: dt=92.480000, rms=0.671 (0.032%), neg=0, invalid=762 0159: dt=92.480000, rms=0.671 (0.040%), neg=0, invalid=762 0160: dt=92.480000, rms=0.670 (0.037%), neg=0, invalid=762 0161: dt=92.480000, rms=0.670 (0.039%), neg=0, invalid=762 0162: dt=92.480000, rms=0.670 (0.035%), neg=0, invalid=762 0163: dt=92.480000, rms=0.670 (0.032%), neg=0, invalid=762 0164: dt=92.480000, rms=0.670 (0.030%), neg=0, invalid=762 0165: dt=92.480000, rms=0.669 (0.028%), neg=0, invalid=762 0166: dt=92.480000, rms=0.669 (0.025%), neg=0, invalid=762 0167: dt=92.480000, rms=0.669 (0.023%), neg=0, invalid=762 0168: dt=517.888000, rms=0.669 (0.013%), neg=0, invalid=762 0169: dt=517.888000, rms=0.669 (-0.005%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.670, neg=0, invalid=762 0170: dt=124.416000, rms=0.667 (0.471%), neg=0, invalid=762 0171: dt=145.152000, rms=0.662 (0.692%), neg=0, invalid=762 0172: dt=91.814346, rms=0.660 (0.321%), neg=0, invalid=762 0173: dt=117.213483, rms=0.658 (0.332%), neg=0, invalid=762 0174: dt=78.147368, rms=0.656 (0.316%), neg=0, invalid=762 0175: dt=124.416000, rms=0.654 (0.256%), neg=0, invalid=762 0176: dt=76.707581, rms=0.652 (0.291%), neg=0, invalid=762 0177: dt=103.680000, rms=0.651 (0.205%), neg=0, invalid=762 0178: dt=98.583851, rms=0.650 (0.245%), neg=0, invalid=762 0179: dt=80.326531, rms=0.648 (0.174%), neg=0, invalid=762 0180: dt=124.416000, rms=0.647 (0.236%), neg=0, invalid=762 0181: dt=71.890411, rms=0.646 (0.155%), neg=0, invalid=762 0182: dt=145.152000, rms=0.644 (0.251%), neg=0, invalid=762 0183: dt=68.139303, rms=0.643 (0.120%), neg=0, invalid=762 0184: dt=145.152000, rms=0.642 (0.223%), neg=0, invalid=762 0185: dt=65.391304, rms=0.641 (0.100%), neg=0, invalid=762 0186: dt=248.832000, rms=0.640 (0.270%), neg=0, invalid=762 0187: dt=36.288000, rms=0.639 (0.113%), neg=0, invalid=762 0188: dt=124.416000, rms=0.638 (0.110%), neg=0, invalid=762 0189: dt=82.000000, rms=0.637 (0.138%), neg=0, invalid=762 0190: dt=82.944000, rms=0.637 (0.065%), neg=0, invalid=762 0191: dt=103.680000, rms=0.636 (0.131%), neg=0, invalid=762 0192: dt=62.208000, rms=0.636 (0.062%), neg=0, invalid=762 0193: dt=497.664000, rms=0.634 (0.296%), neg=0, invalid=762 0194: dt=67.047619, rms=0.633 (0.162%), neg=0, invalid=762 0195: dt=103.680000, rms=0.632 (0.125%), neg=0, invalid=762 0196: dt=36.288000, rms=0.632 (0.033%), neg=0, invalid=762 0197: dt=36.288000, rms=0.632 (0.032%), neg=0, invalid=762 0198: dt=36.288000, rms=0.631 (0.047%), neg=0, invalid=762 0199: dt=36.288000, rms=0.631 (0.065%), neg=0, invalid=762 0200: dt=36.288000, rms=0.630 (0.089%), neg=0, invalid=762 0201: dt=36.288000, rms=0.630 (0.101%), neg=0, invalid=762 0202: dt=36.288000, rms=0.629 (0.111%), neg=0, invalid=762 0203: dt=36.288000, rms=0.628 (0.118%), neg=0, invalid=762 0204: dt=36.288000, rms=0.627 (0.126%), neg=0, invalid=762 0205: dt=36.288000, rms=0.627 (0.128%), neg=0, invalid=762 0206: dt=36.288000, rms=0.626 (0.133%), neg=0, invalid=762 0207: dt=36.288000, rms=0.625 (0.132%), neg=0, invalid=762 0208: dt=36.288000, rms=0.624 (0.132%), neg=0, invalid=762 0209: dt=36.288000, rms=0.623 (0.124%), neg=0, invalid=762 0210: dt=36.288000, rms=0.623 (0.119%), neg=0, invalid=762 0211: dt=36.288000, rms=0.622 (0.112%), neg=0, invalid=762 0212: dt=36.288000, rms=0.621 (0.107%), neg=0, invalid=762 0213: dt=36.288000, rms=0.621 (0.102%), neg=0, invalid=762 0214: dt=36.288000, rms=0.620 (0.101%), neg=0, invalid=762 0215: dt=36.288000, rms=0.619 (0.095%), neg=0, invalid=762 0216: dt=36.288000, rms=0.619 (0.089%), neg=0, invalid=762 0217: dt=36.288000, rms=0.618 (0.085%), neg=0, invalid=762 0218: dt=36.288000, rms=0.618 (0.083%), neg=0, invalid=762 0219: dt=36.288000, rms=0.617 (0.081%), neg=0, invalid=762 0220: dt=36.288000, rms=0.617 (0.085%), neg=0, invalid=762 0221: dt=36.288000, rms=0.616 (0.079%), neg=0, invalid=762 0222: dt=36.288000, rms=0.616 (0.074%), neg=0, invalid=762 0223: dt=36.288000, rms=0.615 (0.075%), neg=0, invalid=762 0224: dt=36.288000, rms=0.615 (0.068%), neg=0, invalid=762 0225: dt=36.288000, rms=0.615 (0.069%), neg=0, invalid=762 0226: dt=36.288000, rms=0.614 (0.062%), neg=0, invalid=762 0227: dt=36.288000, rms=0.614 (0.059%), neg=0, invalid=762 0228: dt=36.288000, rms=0.613 (0.057%), neg=0, invalid=762 0229: dt=36.288000, rms=0.613 (0.055%), neg=0, invalid=762 0230: dt=36.288000, rms=0.613 (0.055%), neg=0, invalid=762 0231: dt=36.288000, rms=0.612 (0.056%), neg=0, invalid=762 0232: dt=36.288000, rms=0.612 (0.006%), neg=0, invalid=762 0233: dt=36.288000, rms=0.612 (0.012%), neg=0, invalid=762 0234: dt=36.288000, rms=0.612 (0.016%), neg=0, invalid=762 0235: dt=36.288000, rms=0.612 (0.020%), neg=0, invalid=762 0236: dt=36.288000, rms=0.612 (0.021%), neg=0, invalid=762 0237: dt=36.288000, rms=0.612 (0.024%), neg=0, invalid=762 0238: dt=36.288000, rms=0.612 (0.026%), neg=0, invalid=762 0239: dt=36.288000, rms=0.612 (0.004%), neg=0, invalid=762 0240: dt=36.288000, rms=0.612 (0.006%), neg=0, invalid=762 0241: dt=18.144000, rms=0.612 (0.001%), neg=0, invalid=762 0242: dt=2.268000, rms=0.612 (0.000%), neg=0, invalid=762 0243: dt=2.268000, rms=0.612 (0.000%), neg=0, invalid=762 0244: dt=1.134000, rms=0.612 (0.000%), neg=0, invalid=762 0245: dt=0.141750, rms=0.612 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.612, neg=0, invalid=762 0246: dt=145.152000, rms=0.609 (0.473%), neg=0, invalid=762 0247: dt=145.152000, rms=0.608 (0.167%), neg=0, invalid=762 0248: dt=82.944000, rms=0.608 (0.093%), neg=0, invalid=762 0249: dt=124.416000, rms=0.607 (0.099%), neg=0, invalid=762 0250: dt=36.288000, rms=0.607 (0.040%), neg=0, invalid=762 0251: dt=36.288000, rms=0.607 (0.025%), neg=0, invalid=762 0252: dt=36.288000, rms=0.606 (0.038%), neg=0, invalid=762 0253: dt=36.288000, rms=0.606 (0.056%), neg=0, invalid=762 0254: dt=36.288000, rms=0.606 (0.064%), neg=0, invalid=762 0255: dt=36.288000, rms=0.605 (0.066%), neg=0, invalid=762 0256: dt=36.288000, rms=0.605 (0.065%), neg=0, invalid=762 0257: dt=36.288000, rms=0.604 (0.067%), neg=0, invalid=762 0258: dt=36.288000, rms=0.604 (0.067%), neg=0, invalid=762 0259: dt=36.288000, rms=0.604 (0.063%), neg=0, invalid=762 0260: dt=36.288000, rms=0.603 (0.062%), neg=0, invalid=762 0261: dt=36.288000, rms=0.603 (0.055%), neg=0, invalid=762 0262: dt=36.288000, rms=0.603 (0.053%), neg=0, invalid=762 0263: dt=36.288000, rms=0.602 (0.053%), neg=0, invalid=762 0264: dt=36.288000, rms=0.602 (0.058%), neg=0, invalid=762 0265: dt=36.288000, rms=0.602 (0.056%), neg=0, invalid=762 0266: dt=36.288000, rms=0.601 (0.056%), neg=0, invalid=762 0267: dt=36.288000, rms=0.601 (0.053%), neg=0, invalid=762 0268: dt=36.288000, rms=0.601 (0.049%), neg=0, invalid=762 0269: dt=36.288000, rms=0.601 (0.009%), neg=0, invalid=762 0270: dt=36.288000, rms=0.601 (0.012%), neg=0, invalid=762 0271: dt=36.288000, rms=0.601 (0.008%), neg=0, invalid=762 0272: dt=9.072000, rms=0.601 (0.002%), neg=0, invalid=762 0273: dt=9.072000, rms=0.601 (0.002%), neg=0, invalid=762 0274: dt=4.536000, rms=0.601 (0.000%), neg=0, invalid=762 0275: dt=1.134000, rms=0.601 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.608, neg=0, invalid=762 0276: dt=38.400000, rms=0.605 (0.541%), neg=0, invalid=762 0277: dt=44.800000, rms=0.601 (0.699%), neg=0, invalid=762 0278: dt=2.800000, rms=0.600 (0.043%), neg=0, invalid=762 0279: dt=0.350000, rms=0.600 (0.004%), neg=0, invalid=762 0280: dt=0.175000, rms=0.600 (0.002%), neg=0, invalid=762 0281: dt=0.087500, rms=0.600 (0.001%), neg=0, invalid=762 0282: dt=0.031250, rms=0.600 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.601, neg=0, invalid=762 0283: dt=0.010937, rms=0.600 (0.088%), neg=0, invalid=762 0284: dt=0.007812, rms=0.600 (0.000%), neg=0, invalid=762 0285: dt=0.000122, rms=0.600 (0.000%), neg=0, invalid=762 0286: dt=0.000061, rms=0.600 (0.000%), neg=0, invalid=762 0287: dt=0.000001, rms=0.600 (0.000%), neg=0, invalid=762 0288: dt=0.000000, rms=0.600 (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=0.621, neg=0, invalid=762 0289: dt=23.413333, rms=0.601 (3.206%), neg=0, invalid=762 0290: dt=20.435644, rms=0.593 (1.241%), neg=0, invalid=762 0291: dt=9.216000, rms=0.592 (0.242%), neg=0, invalid=762 0292: dt=16.128000, rms=0.590 (0.255%), neg=0, invalid=762 0293: dt=16.128000, rms=0.589 (0.144%), neg=0, invalid=762 0294: dt=32.800000, rms=0.588 (0.219%), neg=0, invalid=762 0295: dt=10.920635, rms=0.588 (0.032%), neg=0, invalid=762 0296: dt=10.920635, rms=0.587 (0.117%), neg=0, invalid=762 0297: dt=10.920635, rms=0.587 (0.102%), neg=0, invalid=762 0298: dt=10.920635, rms=0.586 (0.130%), neg=0, invalid=762 0299: dt=10.920635, rms=0.585 (0.163%), neg=0, invalid=762 0300: dt=10.920635, rms=0.584 (0.173%), neg=0, invalid=762 0301: dt=10.920635, rms=0.583 (0.148%), neg=0, invalid=762 0302: dt=10.920635, rms=0.582 (0.110%), neg=0, invalid=762 0303: dt=10.920635, rms=0.582 (0.092%), neg=0, invalid=762 0304: dt=10.920635, rms=0.581 (0.093%), neg=0, invalid=762 0305: dt=10.920635, rms=0.581 (0.087%), neg=0, invalid=762 0306: dt=10.920635, rms=0.580 (0.092%), neg=0, invalid=762 0307: dt=10.920635, rms=0.580 (0.084%), neg=0, invalid=762 0308: dt=10.920635, rms=0.579 (0.074%), neg=0, invalid=762 0309: dt=10.920635, rms=0.579 (0.060%), neg=0, invalid=762 0310: dt=10.920635, rms=0.579 (0.072%), neg=0, invalid=762 0311: dt=10.920635, rms=0.579 (0.002%), neg=0, invalid=762 0312: dt=10.920635, rms=0.579 (-0.015%), neg=0, invalid=762 0313: dt=0.000563, rms=0.579 (0.000%), neg=0, invalid=762 0314: dt=0.000000, rms=0.579 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.579, neg=0, invalid=762 0315: dt=0.000000, rms=0.579 (0.080%), neg=0, invalid=762 0316: dt=0.000000, rms=0.579 (0.000%), neg=0, invalid=762 0317: dt=0.150000, rms=0.579 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.601, neg=0, invalid=762 0318: dt=0.000000, rms=0.600 (0.075%), neg=0, invalid=762 0319: dt=0.000000, rms=0.600 (0.000%), neg=0, invalid=762 0320: dt=0.100000, rms=0.600 (-0.103%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.601, neg=0, invalid=762 0321: dt=0.000000, rms=0.600 (0.075%), neg=0, invalid=762 0322: dt=0.000000, rms=0.600 (0.000%), neg=0, invalid=762 0323: dt=0.100000, rms=0.600 (-0.068%), 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=0.564, neg=0, invalid=762 0324: dt=0.448000, rms=0.547 (3.036%), neg=0, invalid=762 0325: dt=0.384000, rms=0.544 (0.554%), neg=0, invalid=762 0326: dt=0.448000, rms=0.542 (0.396%), neg=0, invalid=762 0327: dt=0.448000, rms=0.541 (0.225%), neg=0, invalid=762 0328: dt=0.475000, rms=0.540 (0.177%), neg=0, invalid=762 0329: dt=0.448000, rms=0.539 (0.109%), neg=0, invalid=762 0330: dt=0.448000, rms=0.538 (0.099%), neg=0, invalid=762 0331: dt=0.448000, rms=0.538 (0.068%), neg=0, invalid=762 0332: dt=0.448000, rms=0.538 (0.068%), neg=0, invalid=762 0333: dt=0.448000, rms=0.537 (0.042%), neg=0, invalid=762 0334: dt=0.448000, rms=0.537 (0.051%), neg=0, invalid=762 0335: dt=0.448000, rms=0.537 (0.075%), neg=0, invalid=762 0336: dt=0.448000, rms=0.537 (0.024%), neg=0, invalid=762 0337: dt=0.448000, rms=0.536 (0.051%), neg=0, invalid=762 0338: dt=0.448000, rms=0.536 (0.025%), neg=0, invalid=762 0339: dt=0.448000, rms=0.536 (0.026%), neg=0, invalid=762 0340: dt=0.448000, rms=0.536 (0.020%), neg=0, invalid=762 0341: dt=0.448000, rms=0.536 (0.022%), neg=0, invalid=762 0342: dt=0.448000, rms=0.536 (0.011%), neg=0, invalid=762 0343: dt=0.320000, rms=0.536 (0.006%), neg=0, invalid=762 0344: dt=0.320000, rms=0.536 (0.013%), neg=0, invalid=762 0345: dt=0.320000, rms=0.536 (0.014%), neg=0, invalid=762 0346: dt=0.320000, rms=0.536 (0.011%), neg=0, invalid=762 0347: dt=0.320000, rms=0.536 (0.018%), neg=0, invalid=762 0348: dt=0.320000, rms=0.535 (0.024%), neg=0, invalid=762 0349: dt=0.320000, rms=0.535 (0.020%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.536, neg=0, invalid=762 0350: dt=0.320000, rms=0.530 (1.050%), neg=0, invalid=762 0351: dt=0.384000, rms=0.528 (0.429%), neg=0, invalid=762 0352: dt=0.384000, rms=0.527 (0.100%), neg=0, invalid=762 0353: dt=0.384000, rms=0.527 (0.030%), neg=0, invalid=762 0354: dt=0.384000, rms=0.527 (0.002%), neg=0, invalid=762 0355: dt=0.384000, rms=0.527 (0.006%), neg=0, invalid=762 0356: dt=0.384000, rms=0.527 (-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=0.525, neg=0, invalid=762 0357: dt=0.007902, rms=0.525 (0.105%), neg=0, invalid=762 0358: dt=0.000000, rms=0.525 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.525, neg=0, invalid=762 0359: dt=110.976000, rms=0.525 (0.152%), neg=0, invalid=762 0360: dt=295.936000, rms=0.524 (0.052%), neg=0, invalid=762 0361: dt=295.936000, rms=0.524 (-0.320%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.525, neg=0, invalid=762 0362: dt=36.288000, rms=0.524 (0.167%), neg=0, invalid=762 0363: dt=36.288000, rms=0.524 (0.035%), neg=0, invalid=762 0364: dt=36.288000, rms=0.524 (0.029%), neg=0, invalid=762 0365: dt=36.288000, rms=0.524 (0.010%), neg=0, invalid=762 0366: dt=36.288000, rms=0.524 (-0.031%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.524, neg=0, invalid=762 0367: dt=103.680000, rms=0.522 (0.504%), neg=0, invalid=762 0368: dt=36.288000, rms=0.521 (0.100%), neg=0, invalid=762 0369: dt=36.288000, rms=0.521 (0.056%), neg=0, invalid=762 0370: dt=36.288000, rms=0.520 (0.076%), neg=0, invalid=762 0371: dt=36.288000, rms=0.520 (0.089%), neg=0, invalid=762 0372: dt=36.288000, rms=0.519 (0.096%), neg=0, invalid=762 0373: dt=36.288000, rms=0.519 (0.098%), neg=0, invalid=762 0374: dt=36.288000, rms=0.518 (0.095%), neg=0, invalid=762 0375: dt=36.288000, rms=0.518 (0.089%), neg=0, invalid=762 0376: dt=82.944000, rms=0.518 (0.017%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.519, neg=0, invalid=762 0377: dt=32.000000, rms=0.516 (0.543%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0378: dt=63.640449, rms=0.514 (0.422%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0379: dt=25.600000, rms=0.513 (0.217%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0380: dt=25.600000, rms=0.511 (0.227%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0381: dt=25.600000, rms=0.510 (0.221%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 9 iterations, nbhd size=1, neg = 0 0382: dt=25.600000, rms=0.509 (0.207%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 9 iterations, nbhd size=1, neg = 0 0383: dt=25.600000, rms=0.508 (0.202%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 9 iterations, nbhd size=1, neg = 0 0384: dt=25.600000, rms=0.507 (0.154%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 3 iterations, nbhd size=0, neg = 0 0385: dt=25.600000, rms=0.507 (0.155%), neg=0, invalid=762 iter 0, gcam->neg = 16 after 4 iterations, nbhd size=0, neg = 0 0386: dt=25.600000, rms=0.506 (0.123%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 13 iterations, nbhd size=1, neg = 0 0387: dt=25.600000, rms=0.505 (0.090%), neg=0, invalid=762 0388: dt=32.000000, rms=0.505 (0.077%), neg=0, invalid=762 0389: dt=32.000000, rms=0.505 (0.036%), neg=0, invalid=762 0390: dt=32.000000, rms=0.504 (0.118%), neg=0, invalid=762 0391: dt=32.000000, rms=0.504 (0.075%), neg=0, invalid=762 0392: dt=32.000000, rms=0.504 (0.082%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 0393: dt=32.000000, rms=0.503 (0.051%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.504, neg=0, invalid=762 0394: dt=44.800000, rms=0.500 (0.866%), neg=0, invalid=762 0395: dt=25.600000, rms=0.498 (0.302%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0396: dt=32.000000, rms=0.497 (0.172%), neg=0, invalid=762 0397: dt=32.000000, rms=0.497 (0.116%), neg=0, invalid=762 0398: dt=32.000000, rms=0.496 (0.199%), neg=0, invalid=762 0399: dt=32.000000, rms=0.495 (0.080%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0400: dt=32.000000, rms=0.494 (0.159%), neg=0, invalid=762 0401: dt=32.000000, rms=0.494 (0.062%), neg=0, invalid=762 0402: dt=32.000000, rms=0.494 (0.078%), neg=0, invalid=762 0403: dt=32.000000, rms=0.494 (-0.011%), neg=0, invalid=762 0404: dt=11.200000, rms=0.493 (0.059%), neg=0, invalid=762 0405: dt=19.200000, rms=0.493 (0.042%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.498, neg=0, invalid=762 0406: dt=1.728000, rms=0.498 (0.134%), neg=0, invalid=762 0407: dt=0.576000, rms=0.498 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.498, neg=0, invalid=762 0408: dt=2.304000, rms=0.497 (0.126%), neg=0, invalid=762 0409: dt=1.008000, rms=0.497 (0.004%), neg=0, invalid=762 0410: dt=1.008000, rms=0.497 (0.001%), neg=0, invalid=762 0411: dt=1.008000, rms=0.497 (-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=0.506, neg=0, invalid=762 0412: dt=0.384000, rms=0.505 (0.121%), neg=0, invalid=762 0413: dt=0.064000, rms=0.505 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.505, neg=0, invalid=762 0414: dt=1.536000, rms=0.504 (0.323%), neg=0, invalid=762 0415: dt=1.280000, rms=0.504 (0.056%), neg=0, invalid=762 0416: dt=1.280000, rms=0.504 (-0.005%), 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=0.497, neg=0, invalid=762 iter 0, gcam->neg = 1137 after 13 iterations, nbhd size=1, neg = 0 0417: dt=2.300442, rms=0.466 (6.190%), neg=0, invalid=762 0418: dt=0.112000, rms=0.465 (0.171%), neg=0, invalid=762 0419: dt=0.112000, rms=0.465 (-0.055%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.466, neg=0, invalid=762 0420: dt=0.112000, rms=0.465 (0.261%), neg=0, invalid=762 0421: dt=0.028000, rms=0.465 (0.004%), neg=0, invalid=762 0422: dt=0.028000, rms=0.465 (-0.003%), 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=0.449, neg=0, invalid=762 0423: dt=8.092000, rms=0.449 (0.001%), neg=0, invalid=762 0424: dt=4.624000, rms=0.449 (0.000%), neg=0, invalid=762 0425: dt=4.624000, rms=0.449 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.449, neg=0, invalid=762 0426: dt=55.488000, rms=0.449 (0.005%), neg=0, invalid=762 0427: dt=73.984000, rms=0.449 (0.001%), neg=0, invalid=762 0428: dt=73.984000, rms=0.449 (0.001%), neg=0, invalid=762 0429: dt=73.984000, rms=0.449 (0.001%), neg=0, invalid=762 0430: dt=73.984000, rms=0.449 (-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=0.449, neg=0, invalid=762 0431: dt=0.567000, rms=0.449 (0.000%), neg=0, invalid=762 0432: dt=0.324000, rms=0.449 (0.000%), neg=0, invalid=762 0433: dt=0.324000, rms=0.449 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.449, neg=0, invalid=762 0434: dt=124.416000, rms=0.449 (0.053%), neg=0, invalid=762 0435: dt=145.152000, rms=0.448 (0.049%), neg=0, invalid=762 0436: dt=145.152000, rms=0.448 (-0.109%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.449, neg=0, invalid=762 0437: dt=11.200000, rms=0.449 (0.094%), neg=0, invalid=762 0438: dt=11.200000, rms=0.448 (0.031%), neg=0, invalid=762 0439: dt=11.200000, rms=0.448 (0.011%), neg=0, invalid=762 0440: dt=11.200000, rms=0.448 (-0.039%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.448, neg=0, invalid=762 0441: dt=44.800000, rms=0.446 (0.471%), neg=0, invalid=762 0442: dt=32.000000, rms=0.445 (0.191%), neg=0, invalid=762 0443: dt=32.000000, rms=0.445 (0.127%), neg=0, invalid=762 0444: dt=32.000000, rms=0.444 (0.179%), neg=0, invalid=762 0445: dt=32.000000, rms=0.443 (0.221%), neg=0, invalid=762 0446: dt=32.000000, rms=0.442 (0.188%), neg=0, invalid=762 0447: dt=32.000000, rms=0.441 (0.187%), neg=0, invalid=762 0448: dt=32.000000, rms=0.441 (0.155%), neg=0, invalid=762 0449: dt=32.000000, rms=0.440 (0.141%), neg=0, invalid=762 0450: dt=32.000000, rms=0.440 (0.117%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0451: dt=32.000000, rms=0.439 (0.114%), neg=0, invalid=762 0452: dt=25.600000, rms=0.439 (0.019%), neg=0, invalid=762 0453: dt=25.600000, rms=0.439 (0.010%), neg=0, invalid=762 0454: dt=25.600000, rms=0.439 (0.013%), neg=0, invalid=762 0455: dt=25.600000, rms=0.439 (0.016%), neg=0, invalid=762 0456: dt=25.600000, rms=0.439 (0.010%), neg=0, invalid=762 0457: dt=25.600000, rms=0.439 (0.010%), neg=0, invalid=762 0458: dt=25.600000, rms=0.439 (0.008%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.443, neg=0, invalid=762 0459: dt=0.000563, rms=0.443 (0.000%), neg=0, invalid=762 0460: dt=0.000000, rms=0.443 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.443, neg=0, invalid=762 0461: dt=2.304000, rms=0.443 (0.008%), neg=0, invalid=762 0462: dt=1.008000, rms=0.443 (0.002%), neg=0, invalid=762 0463: dt=1.008000, rms=0.443 (0.002%), neg=0, invalid=762 0464: dt=1.008000, rms=0.443 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.450, neg=0, invalid=762 0465: dt=0.000000, rms=0.450 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.450, neg=0, invalid=762 0466: dt=0.000000, rms=0.450 (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=0.437, neg=0, invalid=762 iter 0, gcam->neg = 514 after 13 iterations, nbhd size=1, neg = 0 0467: dt=1.419387, rms=0.426 (2.547%), neg=0, invalid=762 0468: dt=0.000013, rms=0.426 (0.000%), neg=0, invalid=762 0469: dt=0.000013, rms=0.426 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.426, neg=0, invalid=762 0470: dt=0.112000, rms=0.426 (0.126%), neg=0, invalid=762 0471: dt=0.096000, rms=0.426 (0.039%), neg=0, invalid=762 0472: dt=0.096000, rms=0.426 (0.014%), neg=0, invalid=762 0473: dt=0.096000, rms=0.426 (-0.061%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 3 hours, 34 minutes and 12 seconds. mri_ca_register utimesec 12519.218136 mri_ca_register stimesec 10.087305 mri_ca_register ru_maxrss 1284664 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4368550 mri_ca_register ru_majflt 29986 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 1116064 mri_ca_register ru_oublock 62944 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 32070 mri_ca_register ru_nivcsw 906649 FSRUNTIME@ mri_ca_register 3.5700 hours 1 threads #-------------------------------------- #@# SubCort Seg 2020��� 03��� 13��� ��������� 19:07:17 CST mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname test-QiTianM420-D166 machine x86_64 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/sub-123_ses-FU_T1w.nii/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 7.48 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 = 0.07590 (17) Left_Lateral_Ventricle (4): linear fit = 0.79 x + 0.0 (169 voxels, overlap=0.297) Left_Lateral_Ventricle (4): linear fit = 0.79 x + 0.0 (169 voxels, peak = 16), gca=15.7 gca peak = 0.17677 (13) mri peak = 0.08461 (16) Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (447 voxels, overlap=0.671) Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (447 voxels, peak = 15), gca=15.4 gca peak = 0.28129 (95) mri peak = 0.07967 (89) Right_Pallidum (52): linear fit = 0.93 x + 0.0 (736 voxels, overlap=1.020) Right_Pallidum (52): linear fit = 0.93 x + 0.0 (736 voxels, peak = 88), gca=87.9 gca peak = 0.16930 (96) mri peak = 0.07595 (91) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (672 voxels, overlap=1.018) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (672 voxels, peak = 95), gca=94.6 gca peak = 0.24553 (55) mri peak = 0.05096 (68) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (677 voxels, overlap=1.020) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (677 voxels, peak = 57), gca=57.5 gca peak = 0.30264 (59) mri peak = 0.07517 (65) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (901 voxels, overlap=1.015) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (901 voxels, peak = 67), gca=67.0 gca peak = 0.07580 (103) mri peak = 0.05756 (104) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (49576 voxels, overlap=0.824) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (49576 voxels, peak = 106), gca=105.6 gca peak = 0.07714 (104) mri peak = 0.05890 (104) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (49415 voxels, overlap=0.835) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (49415 voxels, peak = 106), gca=105.6 gca peak = 0.09712 (58) mri peak = 0.03117 (65) Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (24340 voxels, overlap=0.543) Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (24340 voxels, peak = 66), gca=65.8 gca peak = 0.11620 (58) mri peak = 0.03062 (65) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (22338 voxels, overlap=0.431) Right_Cerebral_Cortex (42): linear fit = 1.10 x + 0.0 (22338 voxels, peak = 64), gca=63.5 gca peak = 0.30970 (66) mri peak = 0.06818 (78) Right_Caudate (50): linear fit = 1.14 x + 0.0 (1052 voxels, overlap=0.038) Right_Caudate (50): linear fit = 1.14 x + 0.0 (1052 voxels, peak = 76), gca=75.6 gca peak = 0.15280 (69) mri peak = 0.06882 (78) Left_Caudate (11): linear fit = 1.02 x + 0.0 (965 voxels, overlap=0.929) Left_Caudate (11): linear fit = 1.02 x + 0.0 (965 voxels, peak = 71), gca=70.7 gca peak = 0.13902 (56) mri peak = 0.04042 (51) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (17463 voxels, overlap=0.999) Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (17463 voxels, peak = 54), gca=54.0 gca peak = 0.14777 (55) mri peak = 0.04124 (55) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (17571 voxels, overlap=0.990) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (17571 voxels, peak = 53), gca=53.1 gca peak = 0.16765 (84) mri peak = 0.05792 (82) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6094 voxels, overlap=0.976) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6094 voxels, peak = 85), gca=85.3 gca peak = 0.18739 (84) mri peak = 0.06021 (83) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (6021 voxels, overlap=0.984) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (6021 voxels, peak = 85), gca=85.3 gca peak = 0.29869 (57) mri peak = 0.07009 (69) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (463 voxels, overlap=0.854) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (463 voxels, peak = 66), gca=66.4 gca peak = 0.33601 (57) mri peak = 0.05417 (54) Right_Amygdala (54): linear fit = 0.93 x + 0.0 (546 voxels, overlap=1.042) Right_Amygdala (54): linear fit = 0.93 x + 0.0 (546 voxels, peak = 53), gca=52.7 gca peak = 0.11131 (90) mri peak = 0.07730 (88) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5595 voxels, overlap=0.908) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5595 voxels, peak = 90), gca=89.6 gca peak = 0.11793 (83) mri peak = 0.06056 (84) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4554 voxels, overlap=0.952) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (4554 voxels, peak = 87), gca=86.7 gca peak = 0.08324 (81) mri peak = 0.05686 (78) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1746 voxels, overlap=0.956) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1746 voxels, peak = 83), gca=83.0 gca peak = 0.10360 (77) mri peak = 0.05950 (76) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2281 voxels, overlap=0.985) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2281 voxels, peak = 77), gca=76.6 gca peak = 0.08424 (78) mri peak = 0.06053 (87) Brain_Stem (16): linear fit = 1.12 x + 0.0 (9998 voxels, overlap=0.477) Brain_Stem (16): linear fit = 1.12 x + 0.0 (9998 voxels, peak = 88), gca=87.8 gca peak = 0.12631 (89) mri peak = 0.07374 (93) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1306 voxels, overlap=0.808) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1306 voxels, peak = 97), gca=97.5 gca peak = 0.14500 (87) mri peak = 0.05546 (93) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1329 voxels, overlap=0.917) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1329 voxels, peak = 94), gca=93.5 gca peak = 0.14975 (24) mri peak = 1.00000 (40) gca peak = 0.19357 (14) mri peak = 0.07981 (17) Fourth_Ventricle (15): linear fit = 1.16 x + 0.0 (212 voxels, overlap=0.603) Fourth_Ventricle (15): linear fit = 1.16 x + 0.0 (212 voxels, peak = 16), gca=16.3 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.08 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.04 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.22675 (16) mri peak = 0.07590 (17) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (169 voxels, overlap=0.666) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (169 voxels, peak = 16), gca=16.4 gca peak = 0.18841 (15) mri peak = 0.08461 (16) Right_Lateral_Ventricle (43): linear fit = 0.98 x + 0.0 (447 voxels, overlap=0.656) Right_Lateral_Ventricle (43): linear fit = 0.98 x + 0.0 (447 voxels, peak = 15), gca=14.6 gca peak = 0.24278 (87) mri peak = 0.07967 (89) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (736 voxels, overlap=1.011) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (736 voxels, peak = 87), gca=86.6 gca peak = 0.20278 (95) mri peak = 0.07595 (91) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (672 voxels, overlap=1.016) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (672 voxels, peak = 95), gca=94.5 gca peak = 0.27932 (58) mri peak = 0.05096 (68) Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (677 voxels, overlap=1.014) Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (677 voxels, peak = 64), gca=63.5 gca peak = 0.28788 (64) mri peak = 0.07517 (65) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (901 voxels, overlap=1.013) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (901 voxels, peak = 64), gca=64.0 gca peak = 0.07610 (105) mri peak = 0.05756 (104) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (49576 voxels, overlap=0.898) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (49576 voxels, peak = 105), gca=105.0 gca peak = 0.07820 (106) mri peak = 0.05890 (104) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49415 voxels, overlap=0.888) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49415 voxels, peak = 106), gca=106.0 gca peak = 0.08637 (66) mri peak = 0.03117 (65) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (24340 voxels, overlap=0.736) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (24340 voxels, peak = 65), gca=65.0 gca peak = 0.10595 (64) mri peak = 0.03062 (65) Right_Cerebral_Cortex (42): linear fit = 1.05 x + 0.0 (22338 voxels, overlap=0.793) Right_Cerebral_Cortex (42): linear fit = 1.05 x + 0.0 (22338 voxels, peak = 68), gca=67.5 gca peak = 0.24438 (76) mri peak = 0.06818 (78) Right_Caudate (50): linear fit = 1.01 x + 0.0 (1052 voxels, overlap=1.010) Right_Caudate (50): linear fit = 1.01 x + 0.0 (1052 voxels, peak = 77), gca=77.1 gca peak = 0.15167 (70) mri peak = 0.06882 (78) Left_Caudate (11): linear fit = 1.00 x + 0.0 (965 voxels, overlap=1.005) Left_Caudate (11): linear fit = 1.00 x + 0.0 (965 voxels, peak = 70), gca=70.0 gca peak = 0.14774 (54) mri peak = 0.04042 (51) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (17463 voxels, overlap=0.990) Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (17463 voxels, peak = 56), gca=56.4 gca peak = 0.15505 (53) mri peak = 0.04124 (55) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (17571 voxels, overlap=0.998) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (17571 voxels, peak = 55), gca=55.4 gca peak = 0.16362 (86) mri peak = 0.05792 (82) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6094 voxels, overlap=0.987) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6094 voxels, peak = 86), gca=85.6 gca peak = 0.15132 (85) mri peak = 0.06021 (83) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6021 voxels, overlap=0.989) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6021 voxels, peak = 85), gca=84.6 gca peak = 0.30333 (68) mri peak = 0.07009 (69) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (463 voxels, overlap=1.020) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (463 voxels, peak = 67), gca=67.0 gca peak = 0.40129 (53) mri peak = 0.05417 (54) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (546 voxels, overlap=0.989) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (546 voxels, peak = 67), gca=66.5 gca peak = 0.09900 (89) mri peak = 0.07730 (88) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5595 voxels, overlap=0.900) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5595 voxels, peak = 89), gca=88.6 gca peak = 0.09489 (87) mri peak = 0.06056 (84) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (4554 voxels, overlap=0.996) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (4554 voxels, peak = 86), gca=85.7 gca peak = 0.09216 (77) mri peak = 0.05686 (78) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1746 voxels, overlap=0.992) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1746 voxels, peak = 77), gca=76.6 gca peak = 0.10883 (75) mri peak = 0.05950 (76) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2281 voxels, overlap=0.978) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2281 voxels, peak = 75), gca=74.6 gca peak = 0.07727 (88) mri peak = 0.06053 (87) Brain_Stem (16): linear fit = 1.01 x + 0.0 (9998 voxels, overlap=0.893) Brain_Stem (16): linear fit = 1.01 x + 0.0 (9998 voxels, peak = 89), gca=89.3 gca peak = 0.11481 (92) mri peak = 0.07374 (93) Right_VentralDC (60): linear fit = 0.98 x + 0.0 (1306 voxels, overlap=0.911) Right_VentralDC (60): linear fit = 0.98 x + 0.0 (1306 voxels, peak = 90), gca=89.7 gca peak = 0.16689 (92) mri peak = 0.05546 (93) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1329 voxels, overlap=0.975) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1329 voxels, peak = 91), gca=90.6 gca peak = 0.18627 (27) mri peak = 1.00000 (40) gca peak = 0.15840 (17) mri peak = 0.07981 (17) Fourth_Ventricle (15): linear fit = 0.92 x + 0.0 (212 voxels, overlap=0.646) Fourth_Ventricle (15): linear fit = 0.92 x + 0.0 (212 voxels, peak = 16), gca=15.6 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.15131 (30) gca peak Left_Thalamus = 1.00000 (102) gca peak Third_Ventricle = 0.18627 (27) gca peak CSF = 0.24163 (38) gca peak Left_Accumbens_area = 0.88917 (64) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.21972 (24) gca peak Right_Accumbens_area = 0.29775 (74) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.51881 (34) gca peak WM_hypointensities = 0.07618 (77) gca peak non_WM_hypointensities = 0.08683 (44) gca peak Optic_Chiasm = 0.70844 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.06 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.97 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt Killed Linux test-QiTianM420-D166 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-123_ses-FU_T1w.nii exited with ERRORS at 2020��� 03��� 13��� ��������� 19:44:17 CST To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting