Fri May 5 16:15:25 EDT 2017 /usr/local/freesurfer/subjects/Sub01 /usr/local/freesurfer/bin/recon-all -i /home/amazinger/Public/share/fMRI/CrossModal/Imges/SPM_analysis/Preprocess/01/T1/T1.nii -s Sub01 subjid Sub01 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 X1 4.4.0-75-generic #96-Ubuntu SMP Thu Apr 20 09:56:33 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63148 maxlocks unlimited maxsignal 63148 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 16296464 2375828 418600 1189548 13502036 12289228 Swap: 16642044 6544 16635500 ######################################## 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: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-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: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-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: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-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: 2017/05/05-20:15:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-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: 2017/05/05-20:15:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:25-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-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/Sub01 mri_convert /home/amazinger/Public/share/fMRI/CrossModal/Imges/SPM_analysis/Preprocess/01/T1/T1.nii /usr/local/freesurfer/subjects/Sub01/mri/orig/001.mgz mri_convert.bin /home/amazinger/Public/share/fMRI/CrossModal/Imges/SPM_analysis/Preprocess/01/T1/T1.nii /usr/local/freesurfer/subjects/Sub01/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/amazinger/Public/share/fMRI/CrossModal/Imges/SPM_analysis/Preprocess/01/T1/T1.nii... TR=6.90, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999914, -0.0124993, 0.00396007) j_ras = (0.0124831, 0.999914, 0.00413877) k_ras = (-0.00401151, -0.00408912, 0.999984) writing to /usr/local/freesurfer/subjects/Sub01/mri/orig/001.mgz... Started at Fri May 5 16:15:25 EDT 2017 Ended at Fri May 5 16:15:30 EDT 2017 #@#%# recon-all-run-time-hours 0.001 recon-all -s Sub01 finished without error at Fri May 5 16:15:30 EDT 2017 New invocation of recon-all Fri May 5 16:15:48 EDT 2017 /usr/local/freesurfer/subjects/Sub01 /usr/local/freesurfer/bin/recon-all -autorecon1 -s Sub01 subjid Sub01 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 X1 4.4.0-75-generic #96-Ubuntu SMP Thu Apr 20 09:56:33 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63148 maxlocks unlimited maxsignal 63148 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 16296464 2381204 384096 1178892 13531164 12294492 Swap: 16642044 6544 16635500 ######################################## 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: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-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: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-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: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-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: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-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: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/05-20:15:48-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-75-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# MotionCor Fri May 5 16:15:48 EDT 2017 Found 1 runs /usr/local/freesurfer/subjects/Sub01/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/Sub01/mri/orig/001.mgz /usr/local/freesurfer/subjects/Sub01/mri/rawavg.mgz /usr/local/freesurfer/subjects/Sub01 mri_convert /usr/local/freesurfer/subjects/Sub01/mri/rawavg.mgz /usr/local/freesurfer/subjects/Sub01/mri/orig.mgz --conform mri_convert.bin /usr/local/freesurfer/subjects/Sub01/mri/rawavg.mgz /usr/local/freesurfer/subjects/Sub01/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/Sub01/mri/rawavg.mgz... TR=6.90, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999914, -0.0124993, 0.00396007) j_ras = (0.0124831, 0.999914, 0.00413877) k_ras = (-0.00401151, -0.00408912, 0.999984) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/Sub01/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/Sub01/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/Sub01/mri/orig.mgz /usr/local/freesurfer/subjects/Sub01/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri May 5 16:15:55 EDT 2017 /usr/local/freesurfer/subjects/Sub01/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/Sub01/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 X1 4.4.0-75-generic #96-Ubuntu SMP Thu Apr 20 09:56:33 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Fri May 5 16:15:55 EDT 2017 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.8783 /usr/local/freesurfer/subjects/Sub01/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.8783/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.8783/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=6.90, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -8.85848e-10, 0) j_ras = (4.65661e-10, 4.65661e-10, -1) k_ras = (1.46247e-09, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.8783/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri May 5 16:15:57 EDT 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.8783/nu0.mnc ./tmp.mri_nu_correct.mni.8783/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.8783/0/ -iterations 1000 -distance 50 [amazinger@X1:/usr/local/freesurfer/subjects/Sub01/mri/] [2017-05-05 16:15:57] 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.8783/0/ ./tmp.mri_nu_correct.mni.8783/nu0.mnc ./tmp.mri_nu_correct.mni.8783/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 41 CV of field change: 0.000992286 mri_convert ./tmp.mri_nu_correct.mni.8783/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.8783/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.8783/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -8.85848e-10, 0) j_ras = (4.65661e-10, 4.65661e-10, -1) k_ras = (1.46247e-09, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Fri May 5 16:16:48 EDT 2017 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 Fri May 5 16:16:48 EDT 2017 Ended at Fri May 5 16:17:23 EDT 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Fri May 5 16:17:25 EDT 2017 /usr/local/freesurfer/subjects/Sub01/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7255, pval=0.6675 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/Sub01/mri/transforms/talairach_avi.log tal_QC_AZS /usr/local/freesurfer/subjects/Sub01/mri/transforms/talairach_avi.log TalAviQA: 0.97462 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Fri May 5 16:17:25 EDT 2017 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /usr/local/freesurfer/subjects/Sub01/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 X1 4.4.0-75-generic #96-Ubuntu SMP Thu Apr 20 09:56:33 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Fri May 5 16:17:25 EDT 2017 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.9522 /usr/local/freesurfer/subjects/Sub01/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9522/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.9522/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=6.90, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -8.85848e-10, 0) j_ras = (4.65661e-10, 4.65661e-10, -1) k_ras = (1.46247e-09, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.9522/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri May 5 16:17:27 EDT 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.9522/nu0.mnc ./tmp.mri_nu_correct.mni.9522/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9522/0/ [amazinger@X1:/usr/local/freesurfer/subjects/Sub01/mri/] [2017-05-05 16:17:27] 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.9522/0/ ./tmp.mri_nu_correct.mni.9522/nu0.mnc ./tmp.mri_nu_correct.mni.9522/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 27 CV of field change: 0.000990588 -------------------------------------------------------- Iteration 2 Fri May 5 16:17:58 EDT 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.9522/nu1.mnc ./tmp.mri_nu_correct.mni.9522/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.9522/1/ [amazinger@X1:/usr/local/freesurfer/subjects/Sub01/mri/] [2017-05-05 16:17:58] 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.9522/1/ ./tmp.mri_nu_correct.mni.9522/nu1.mnc ./tmp.mri_nu_correct.mni.9522/nu2.imp Processing:.................................................................Done 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Processing:.................................................................Done Number of iterations: 26 CV of field change: 0.000970377 mri_binarize --i ./tmp.mri_nu_correct.mni.9522/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9522/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /usr/local/freesurfer/subjects/Sub01/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.9522/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9522/ones.mgz sysname Linux hostname X1 machine x86_64 user amazinger input ./tmp.mri_nu_correct.mni.9522/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.9522/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.9522/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9522/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9522/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.9522/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9522/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9522/input.mean.dat sysname Linux hostname X1 machine x86_64 user amazinger UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9522/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.9522/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9522/ones.mgz --i ./tmp.mri_nu_correct.mni.9522/nu2.mnc --sum ./tmp.mri_nu_correct.mni.9522/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9522/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.9522/ones.mgz --i ./tmp.mri_nu_correct.mni.9522/nu2.mnc --sum ./tmp.mri_nu_correct.mni.9522/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9522/output.mean.dat sysname Linux hostname X1 machine x86_64 user amazinger UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9522/ones.mgz Loading ./tmp.mri_nu_correct.mni.9522/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.9522/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.9522/nu2.mnc ./tmp.mri_nu_correct.mni.9522/nu2.mnc mul 1.08297298493435628021 Saving result to './tmp.mri_nu_correct.mni.9522/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.9522/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.9522/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.9522/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -8.85848e-10, 0) j_ras = (4.65661e-10, 4.65661e-10, -1) k_ras = (1.46247e-09, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 6 seconds. mapping ( 5, 105) to ( 3, 110) Fri May 5 16:18:57 EDT 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /usr/local/freesurfer/subjects/Sub01/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Fri May 5 16:18:58 EDT 2017 /usr/local/freesurfer/subjects/Sub01/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 1.06594 0.01684 0.01288 0.43982; -0.02069 1.11889 0.35837 -4.42801; -0.02022 -0.36412 1.16588 3.80107; 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 = 10 Starting OpenSpline(): npoints = 10 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 58 (58), valley at 37 (37) csf peak at 30, setting threshold to 48 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 22 (22) 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 Fri May 5 16:20:24 EDT 2017 /usr/local/freesurfer/subjects/Sub01/mri mri_em_register -rusage /usr/local/freesurfer/subjects/Sub01/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=9.0 skull bounding box = (47, 27, 27) --> (212, 222, 219) using (102, 92, 123) as brain centroid... mean wm in atlas = 108, using box (82,68,99) --> (122, 116,146) to find MRI wm before smoothing, mri peak at 122 robust fit to distribution - 97 +- 6.9 after smoothing, mri peak at 97, scaling input intensities by 1.113 scaling channel 0 by 1.1134 initial log_p = -4.581 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.596562 @ (-9.091, 9.091, -9.091) max log p = -4.530090 @ (4.545, 4.545, -4.545) max log p = -4.512497 @ (6.818, 2.273, -2.273) max log p = -4.494617 @ (-1.136, -1.136, -1.136) max log p = -4.486521 @ (1.705, 2.841, -0.568) max log p = -4.486521 @ (0.000, 0.000, 0.000) Found translation: (2.8, 17.6, -17.6): log p = -4.487 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.139, old_max_log_p =-4.487 (thresh=-4.5) 1.14737 0.00980 -0.07704 -14.96707; 0.01053 1.19695 0.30906 -36.39807; 0.07704 -0.28750 1.11081 9.04168; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.139, old_max_log_p =-4.139 (thresh=-4.1) 1.14737 0.00980 -0.07704 -14.96707; 0.01053 1.19695 0.30906 -36.39807; 0.07704 -0.28750 1.11081 9.04168; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.023, old_max_log_p =-4.139 (thresh=-4.1) 1.07924 0.12289 -0.04304 -19.82350; -0.10493 1.25823 0.33293 -33.54992; 0.07559 -0.28211 1.08999 7.27227; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.005, old_max_log_p =-4.023 (thresh=-4.0) 1.06173 0.08044 -0.05404 -11.28679; -0.06703 1.25168 0.36681 -39.61075; 0.08046 -0.32919 1.09873 11.24270; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.005, old_max_log_p =-4.005 (thresh=-4.0) 1.06173 0.08044 -0.05404 -11.28679; -0.06703 1.25168 0.36681 -39.61075; 0.08046 -0.32919 1.09873 11.24270; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.994, old_max_log_p =-4.005 (thresh=-4.0) 1.06300 0.08814 -0.04216 -13.74063; -0.07615 1.24926 0.35687 -37.49037; 0.07148 -0.32075 1.10597 10.53115; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.989, old_max_log_p =-3.994 (thresh=-4.0) 1.06340 0.10607 -0.02730 -18.11346; -0.09387 1.25208 0.35862 -36.27773; 0.06285 -0.32184 1.10757 11.55250; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.989, old_max_log_p =-3.989 (thresh=-4.0) 1.06340 0.10607 -0.02730 -18.11346; -0.09387 1.25208 0.35862 -36.27773; 0.06285 -0.32184 1.10757 11.55250; 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 1.06340 0.10607 -0.02730 -18.11346; -0.09387 1.25208 0.35862 -36.27773; 0.06285 -0.32184 1.10757 11.55250; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.06340 0.10607 -0.02730 -18.11346; -0.09387 1.25208 0.35862 -36.27773; 0.06285 -0.32184 1.10757 11.55250; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.06340 0.10607 -0.02730 -18.11346; -0.09387 1.25208 0.35862 -36.27773; 0.06285 -0.32184 1.10757 11.55250; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.989 (old=-4.581) transform before final EM align: 1.06340 0.10607 -0.02730 -18.11346; -0.09387 1.25208 0.35862 -36.27773; 0.06285 -0.32184 1.10757 11.55250; 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 1.06340 0.10607 -0.02730 -18.11346; -0.09387 1.25208 0.35862 -36.27773; 0.06285 -0.32184 1.10757 11.55250; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.06340 0.10607 -0.02730 -18.11346; -0.09387 1.25208 0.35862 -36.27773; 0.06285 -0.32184 1.10757 11.55250; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.4 tol 0.000000 final transform: 1.06340 0.10607 -0.02730 -18.11346; -0.09387 1.25208 0.35862 -36.27773; 0.06285 -0.32184 1.10757 11.55250; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 799.432000 mri_em_register stimesec 0.716000 mri_em_register ru_maxrss 614140 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 156666 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 139608 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 26 mri_em_register ru_nivcsw 1817 registration took 13 minutes and 20 seconds. mri_watershed -rusage /usr/local/freesurfer/subjects/Sub01/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=127 y=100 z=110 r=84 first estimation of the main basin volume: 2526857 voxels Looking for seedpoints 2 found in the cerebellum 14 found in the rest of the brain global maximum in x=147, y=95, z=77, Imax=255 CSF=20, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=628108205 voxels, voxel volume =1.000 = 628108205 mmm3 = 628108.224 cm3 done. PostAnalyze...Basin Prior 12 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=104, z=109, r=8755 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=14, CSF_MAX=57 , nb = 45027 RIGHT_CER CSF_MIN=0, CSF_intensity=5, CSF_MAX=28 , nb = -1030919246 LEFT_CER CSF_MIN=0, CSF_intensity=11, CSF_MAX=46 , nb = -1052448057 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=16, CSF_MAX=55 , nb = -1114580262 LEFT_BRAIN CSF_MIN=0, CSF_intensity=14, CSF_MAX=59 , nb = 1079043670 OTHER CSF_MIN=7, CSF_intensity=13, CSF_MAX=53 , nb = 1068150868 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 57, 41, 35, 55 after analyzing : 34, 41, 41, 44 RIGHT_CER before analyzing : 28, 29, 32, 60 after analyzing : 28, 31, 32, 38 LEFT_CER before analyzing : 46, 38, 33, 58 after analyzing : 31, 38, 38, 43 RIGHT_BRAIN before analyzing : 55, 41, 35, 55 after analyzing : 34, 41, 41, 44 LEFT_BRAIN before analyzing : 59, 42, 36, 54 after analyzing : 35, 42, 42, 45 OTHER before analyzing : 53, 63, 70, 94 after analyzing : 53, 67, 70, 73 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...75 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.013 curvature mean = 64.996, std = 6.835 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.75, sigma = 7.06 after rotation: sse = 4.75, sigma = 7.06 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 5.47, its var is 7.68 before Erosion-Dilatation 2.48% of inacurate vertices after Erosion-Dilatation 2.08% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...42 iterations mri_strip_skull: done peeling brain Brain Size = 1348609 voxels, voxel volume = 1.000 mm3 = 1348609 mmm3 = 1348.609 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 21.372000 mri_watershed stimesec 0.164000 mri_watershed ru_maxrss 838208 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 213041 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 7576 mri_watershed ru_oublock 2184 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 68 mri_watershed ru_nivcsw 112 mri_watershed done cp brainmask.auto.mgz brainmask.mgz Started at Fri May 5 16:15:48 EDT 2017 Ended at Fri May 5 16:34:07 EDT 2017 #@#%# recon-all-run-time-hours 0.305 recon-all -s Sub01 finished without error at Fri May 5 16:34:07 EDT 2017 New invocation of recon-all Sat May 6 18:06:57 EDT 2017 /usr/local/freesurfer/subjects/Sub01 /usr/local/freesurfer/bin/recon-all -autorecon1 -s Sub01 subjid Sub01 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 X1 4.4.0-77-generic #98-Ubuntu SMP Wed Apr 26 08:34:02 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63148 maxlocks unlimited maxsignal 63148 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 16296464 1647656 11148452 444792 3500356 13788296 Swap: 16642044 0 16642044 ######################################## 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: 2017/05/06-22:06:57-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-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: 2017/05/06-22:06:57-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-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: 2017/05/06-22:06:57-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:06:57-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:57-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:57-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:06:57-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:06:57-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:06:57-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:06:57-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:06:57-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:06:57-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:57-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:57-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:06:57-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:57-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:57-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-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: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-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: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:06:58-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# MotionCor Sat May 6 18:06:58 EDT 2017 Found 1 runs /usr/local/freesurfer/subjects/Sub01/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/Sub01/mri/orig/001.mgz /usr/local/freesurfer/subjects/Sub01/mri/rawavg.mgz /usr/local/freesurfer/subjects/Sub01 mri_convert /usr/local/freesurfer/subjects/Sub01/mri/rawavg.mgz /usr/local/freesurfer/subjects/Sub01/mri/orig.mgz --conform mri_convert.bin /usr/local/freesurfer/subjects/Sub01/mri/rawavg.mgz /usr/local/freesurfer/subjects/Sub01/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/Sub01/mri/rawavg.mgz... TR=6.90, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999914, -0.0124993, 0.00396007) j_ras = (0.0124831, 0.999914, 0.00413877) k_ras = (-0.00401151, -0.00408912, 0.999984) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/Sub01/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/Sub01/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/Sub01/mri/orig.mgz /usr/local/freesurfer/subjects/Sub01/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sat May 6 18:07:05 EDT 2017 /usr/local/freesurfer/subjects/Sub01/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/Sub01/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 X1 4.4.0-77-generic #98-Ubuntu SMP Wed Apr 26 08:34:02 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sat May 6 18:07:05 EDT 2017 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.5665 /usr/local/freesurfer/subjects/Sub01/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5665/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.5665/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=6.90, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -8.85848e-10, 0) j_ras = (4.65661e-10, 4.65661e-10, -1) k_ras = (1.46247e-09, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.5665/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat May 6 18:07:08 EDT 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.5665/nu0.mnc ./tmp.mri_nu_correct.mni.5665/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.5665/0/ -iterations 1000 -distance 50 [amazinger@X1:/usr/local/freesurfer/subjects/Sub01/mri/] [2017-05-06 18:07:08] 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.5665/0/ ./tmp.mri_nu_correct.mni.5665/nu0.mnc ./tmp.mri_nu_correct.mni.5665/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 41 CV of field change: 0.000992286 mri_convert ./tmp.mri_nu_correct.mni.5665/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.5665/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.5665/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -8.85848e-10, 0) j_ras = (4.65661e-10, 4.65661e-10, -1) k_ras = (1.46247e-09, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Sat May 6 18:08:00 EDT 2017 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 Sat May 6 18:08:00 EDT 2017 Ended at Sat May 6 18:08:35 EDT 2017 talairach_avi done INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sat May 6 18:08:35 EDT 2017 /usr/local/freesurfer/subjects/Sub01/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7255, pval=0.6675 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/Sub01/mri/transforms/talairach_avi.log tal_QC_AZS /usr/local/freesurfer/subjects/Sub01/mri/transforms/talairach_avi.log TalAviQA: 0.97462 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Sat May 6 18:08:35 EDT 2017 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /usr/local/freesurfer/subjects/Sub01/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 X1 4.4.0-77-generic #98-Ubuntu SMP Wed Apr 26 08:34:02 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sat May 6 18:08:35 EDT 2017 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.6405 /usr/local/freesurfer/subjects/Sub01/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.6405/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.6405/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=6.90, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -8.85848e-10, 0) j_ras = (4.65661e-10, 4.65661e-10, -1) k_ras = (1.46247e-09, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.6405/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat May 6 18:08:37 EDT 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.6405/nu0.mnc ./tmp.mri_nu_correct.mni.6405/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.6405/0/ [amazinger@X1:/usr/local/freesurfer/subjects/Sub01/mri/] [2017-05-06 18:08:37] 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.6405/0/ ./tmp.mri_nu_correct.mni.6405/nu0.mnc ./tmp.mri_nu_correct.mni.6405/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 27 CV of field change: 0.000990588 -------------------------------------------------------- Iteration 2 Sat May 6 18:09:09 EDT 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.6405/nu1.mnc ./tmp.mri_nu_correct.mni.6405/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.6405/1/ [amazinger@X1:/usr/local/freesurfer/subjects/Sub01/mri/] [2017-05-06 18:09:09] 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.6405/1/ ./tmp.mri_nu_correct.mni.6405/nu1.mnc ./tmp.mri_nu_correct.mni.6405/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 26 CV of field change: 0.000970377 mri_binarize --i ./tmp.mri_nu_correct.mni.6405/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.6405/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /usr/local/freesurfer/subjects/Sub01/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.6405/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.6405/ones.mgz sysname Linux hostname X1 machine x86_64 user amazinger input ./tmp.mri_nu_correct.mni.6405/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.6405/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.6405/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.6405/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6405/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.6405/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.6405/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6405/input.mean.dat sysname Linux hostname X1 machine x86_64 user amazinger UseRobust 0 Loading ./tmp.mri_nu_correct.mni.6405/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.6405/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.6405/ones.mgz --i ./tmp.mri_nu_correct.mni.6405/nu2.mnc --sum ./tmp.mri_nu_correct.mni.6405/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6405/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.6405/ones.mgz --i ./tmp.mri_nu_correct.mni.6405/nu2.mnc --sum ./tmp.mri_nu_correct.mni.6405/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6405/output.mean.dat sysname Linux hostname X1 machine x86_64 user amazinger UseRobust 0 Loading ./tmp.mri_nu_correct.mni.6405/ones.mgz Loading ./tmp.mri_nu_correct.mni.6405/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.6405/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.6405/nu2.mnc ./tmp.mri_nu_correct.mni.6405/nu2.mnc mul 1.08297298493435628021 Saving result to './tmp.mri_nu_correct.mni.6405/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.6405/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.6405/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.6405/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -8.85848e-10, 0) j_ras = (4.65661e-10, 4.65661e-10, -1) k_ras = (1.46247e-09, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 6 seconds. mapping ( 5, 105) to ( 3, 110) Sat May 6 18:10:08 EDT 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /usr/local/freesurfer/subjects/Sub01/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sat May 6 18:10:09 EDT 2017 /usr/local/freesurfer/subjects/Sub01/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 1.06594 0.01684 0.01288 0.43982; -0.02069 1.11889 0.35837 -4.42801; -0.02022 -0.36412 1.16588 3.80107; 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 = 10 Starting OpenSpline(): npoints = 10 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 58 (58), valley at 37 (37) csf peak at 30, setting threshold to 48 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 22 (22) 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 27 seconds. #-------------------------------------------- #@# Skull Stripping Sat May 6 18:11:37 EDT 2017 /usr/local/freesurfer/subjects/Sub01/mri mri_watershed -rusage /usr/local/freesurfer/subjects/Sub01/touch/rusage.mri_watershed.dat -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -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 Keeping brain edits brainmask.auto.mgz brainmask.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=127 y=100 z=110 r=84 first estimation of the main basin volume: 2526857 voxels Looking for seedpoints 2 found in the cerebellum 14 found in the rest of the brain global maximum in x=147, y=95, z=77, Imax=255 CSF=20, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=532159917 voxels, voxel volume =1.000 = 532159917 mmm3 = 532159.904 cm3 done. PostAnalyze...Basin Prior 12 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=104, z=109, r=8755 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=14, CSF_MAX=57 , nb = 45027 RIGHT_CER CSF_MIN=0, CSF_intensity=5, CSF_MAX=28 , nb = -1030919246 LEFT_CER CSF_MIN=0, CSF_intensity=11, CSF_MAX=46 , nb = -1052448057 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=16, CSF_MAX=55 , nb = -1114580262 LEFT_BRAIN CSF_MIN=0, CSF_intensity=14, CSF_MAX=59 , nb = 1079043670 OTHER CSF_MIN=7, CSF_intensity=13, CSF_MAX=53 , nb = 1068150868 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 57, 41, 35, 55 after analyzing : 34, 41, 41, 44 RIGHT_CER before analyzing : 28, 29, 32, 60 after analyzing : 28, 31, 32, 38 LEFT_CER before analyzing : 46, 38, 33, 58 after analyzing : 31, 38, 38, 43 RIGHT_BRAIN before analyzing : 55, 41, 35, 55 after analyzing : 34, 41, 41, 44 LEFT_BRAIN before analyzing : 59, 42, 36, 54 after analyzing : 35, 42, 42, 45 OTHER before analyzing : 53, 63, 70, 94 after analyzing : 53, 67, 70, 73 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...75 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.013 curvature mean = 64.996, std = 6.835 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.75, sigma = 7.06 after rotation: sse = 4.75, sigma = 7.06 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 5.47, its var is 7.68 before Erosion-Dilatation 2.48% of inacurate vertices after Erosion-Dilatation 2.08% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...42 iterations mri_strip_skull: done peeling brain Brain Size = 1348609 voxels, voxel volume = 1.000 mm3 = 1348609 mmm3 = 1348.609 cm3 ****************************** Saving brainmask.auto.mgz Keeping edits ... Saving kept edits to brainmask.mgz ..... done mri_watershed utimesec 26.052000 mri_watershed stimesec 0.212000 mri_watershed ru_maxrss 872020 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 221516 mri_watershed ru_majflt 9 mri_watershed ru_nswap 0 mri_watershed ru_inblock 162968 mri_watershed ru_oublock 4368 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 49 mri_watershed ru_nivcsw 56 mri_watershed done INFO: brainmask.mgz already exists! The new brainmask.auto.mgz will not be copied to brainmask.mgz. This is done to retain any edits made to brainmask.mgz. Add the -clean-bm flag to recon-all to overwrite brainmask.mgz. Started at Sat May 6 18:06:57 EDT 2017 Ended at Sat May 6 18:12:04 EDT 2017 #@#%# recon-all-run-time-hours 0.085 recon-all -s Sub01 finished without error at Sat May 6 18:12:04 EDT 2017 New invocation of recon-all Sat May 6 18:26:21 EDT 2017 /usr/local/freesurfer/subjects/Sub01 /usr/local/freesurfer/bin/recon-all -autorecon2 -s Sub01 subjid Sub01 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 X1 4.4.0-77-generic #98-Ubuntu SMP Wed Apr 26 08:34:02 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63148 maxlocks unlimited maxsignal 63148 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 16296464 1691852 10627376 447000 3977236 13741016 Swap: 16642044 0 16642044 ######################################## 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: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-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: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-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: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-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: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-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: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/06-22:26:21-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-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 ####################################### #------------------------------------- #@# EM Registration Sat May 6 18:26:21 EDT 2017 /usr/local/freesurfer/subjects/Sub01/mri mri_em_register -rusage /usr/local/freesurfer/subjects/Sub01/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=22.0 skull bounding box = (57, 45, 44) --> (197, 173, 188) using (104, 88, 116) as brain centroid... mean wm in atlas = 107, using box (87,72,98) --> (121, 103,133) to find MRI wm before smoothing, mri peak at 97 robust fit to distribution - 98 +- 5.7 after smoothing, mri peak at 98, scaling input intensities by 1.092 scaling channel 0 by 1.09184 initial log_p = -4.348 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.195919 @ (-9.091, 9.091, -9.091) max log p = -4.114071 @ (4.545, 13.636, -4.545) max log p = -4.039539 @ (2.273, -2.273, -2.273) max log p = -4.036994 @ (1.136, -7.955, 5.682) max log p = -4.029094 @ (0.568, 3.977, -0.568) max log p = -4.029094 @ (0.000, 0.000, 0.000) Found translation: (-0.6, 16.5, -10.8): log p = -4.029 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.745, old_max_log_p =-4.029 (thresh=-4.0) 1.00000 0.00000 0.00000 -0.56818; 0.00000 1.11081 0.29764 -29.51373; 0.00000 -0.29764 1.11081 14.42485; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.745, old_max_log_p =-3.745 (thresh=-3.7) 1.00000 0.00000 0.00000 -0.56818; 0.00000 1.11081 0.29764 -29.51373; 0.00000 -0.29764 1.11081 14.42485; 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=-3.634, old_max_log_p =-3.745 (thresh=-3.7) 1.03750 0.00000 0.00000 -7.21713; 0.00000 1.13127 0.37807 -38.62608; 0.00000 -0.36802 1.06630 28.29821; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.627, old_max_log_p =-3.634 (thresh=-3.6) 1.03750 0.00000 0.00000 -7.21713; 0.00000 1.14270 0.34298 -34.14238; 0.00000 -0.33701 1.09831 21.63006; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.627, old_max_log_p =-3.627 (thresh=-3.6) 1.03750 0.00000 0.00000 -7.21713; 0.00000 1.14270 0.34298 -34.14238; 0.00000 -0.33701 1.09831 21.63006; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.574, old_max_log_p =-3.627 (thresh=-3.6) 1.03625 0.00297 -0.00859 -5.94888; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30078; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.571, old_max_log_p =-3.574 (thresh=-3.6) 1.03746 0.00297 -0.00860 -6.10401; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30078; 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 1.03746 0.00297 -0.00860 -6.10401; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30078; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.03746 0.00297 -0.00860 -6.10401; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30078; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03746 0.00297 -0.00860 -6.10401; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30078; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.571 (old=-4.348) transform before final EM align: 1.03746 0.00297 -0.00860 -6.10401; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30078; 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 1.03746 0.00297 -0.00860 -6.10401; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30078; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.03746 0.00297 -0.00860 -6.10401; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30078; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.0 tol 0.000000 final transform: 1.03746 0.00297 -0.00860 -6.10401; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30078; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 731.608000 mri_em_register stimesec 0.596000 mri_em_register ru_maxrss 603016 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 158410 mri_em_register ru_majflt 6 mri_em_register ru_nswap 0 mri_em_register ru_inblock 141536 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 9 mri_em_register ru_nivcsw 2007 registration took 12 minutes and 12 seconds. #-------------------------------------- #@# CA Normalize Sat May 6 18:38:34 EDT 2017 /usr/local/freesurfer/subjects/Sub01/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=22.0 skull bounding box = (57, 45, 44) --> (197, 173, 188) using (104, 88, 116) as brain centroid... mean wm in atlas = 107, using box (87,72,98) --> (121, 103,133) to find MRI wm before smoothing, mri peak at 97 robust fit to distribution - 98 +- 5.7 after smoothing, mri peak at 98, scaling input intensities by 1.092 scaling channel 0 by 1.09184 using 246344 sample points... INFO: compute sample coordinates transform 1.03746 0.00297 -0.00860 -6.10401; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30078; 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 (127, 46, 43) --> (192, 147, 186) Left_Cerebral_White_Matter: limiting intensities to 99.0 --> 132.0 8 of 507 (1.6%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 46, 42) --> (130, 140, 186) Right_Cerebral_White_Matter: limiting intensities to 115.0 --> 132.0 106 of 571 (18.6%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 125, 70) --> (176, 161, 117) Left_Cerebellum_White_Matter: limiting intensities to 103.0 --> 132.0 4 of 12 (33.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 125, 68) --> (128, 160, 117) Right_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 8 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 112, 100) --> (145, 171, 126) Brain_Stem: limiting intensities to 88.0 --> 132.0 0 of 19 (0.0%) samples deleted using 1117 total control points for intensity normalization... bias field = 0.888 +- 0.054 0 of 999 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (127, 46, 43) --> (192, 147, 186) Left_Cerebral_White_Matter: limiting intensities to 109.0 --> 132.0 772 of 1097 (70.4%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 46, 42) --> (130, 140, 186) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 58 of 1565 (3.7%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 125, 70) --> (176, 161, 117) Left_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0 65 of 73 (89.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 125, 68) --> (128, 160, 117) Right_Cerebellum_White_Matter: limiting intensities to 94.0 --> 132.0 33 of 72 (45.8%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 112, 100) --> (145, 171, 126) Brain_Stem: limiting intensities to 88.0 --> 132.0 95 of 114 (83.3%) samples deleted using 2921 total control points for intensity normalization... bias field = 1.017 +- 0.089 0 of 1889 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (127, 46, 43) --> (192, 147, 186) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 51 of 1266 (4.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 46, 42) --> (130, 140, 186) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 35 of 1657 (2.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 125, 70) --> (176, 161, 117) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 116 of 134 (86.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 125, 68) --> (128, 160, 117) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 49 of 88 (55.7%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 112, 100) --> (145, 171, 126) Brain_Stem: limiting intensities to 88.0 --> 132.0 216 of 226 (95.6%) samples deleted using 3371 total control points for intensity normalization... bias field = 1.066 +- 0.068 0 of 2831 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 10 seconds. #-------------------------------------- #@# CA Reg Sat May 6 18:39:44 EDT 2017 /usr/local/freesurfer/subjects/Sub01/mri mri_ca_register -rusage /usr/local/freesurfer/subjects/Sub01/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) = 1.42 (predicted orig area = 5.6) 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=0.831, neg=0, invalid=762 0001: dt=197.271318, rms=0.759 (8.647%), neg=0, invalid=762 0002: dt=206.961039, rms=0.741 (2.371%), neg=0, invalid=762 0003: dt=156.220472, rms=0.734 (0.896%), neg=0, invalid=762 0004: dt=369.920000, rms=0.727 (0.955%), neg=0, invalid=762 0005: dt=129.472000, rms=0.723 (0.564%), neg=0, invalid=762 0006: dt=517.888000, rms=0.717 (0.798%), neg=0, invalid=762 0007: dt=110.976000, rms=0.715 (0.369%), neg=0, invalid=762 0008: dt=2071.552000, rms=0.704 (1.475%), neg=0, invalid=762 0009: dt=92.480000, rms=0.701 (0.462%), neg=0, invalid=762 0010: dt=517.888000, rms=0.700 (0.152%), neg=0, invalid=762 0011: dt=517.888000, rms=0.700 (-0.489%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.700, neg=0, invalid=762 0012: dt=129.472000, rms=0.698 (0.299%), neg=0, invalid=762 0013: dt=517.888000, rms=0.695 (0.387%), neg=0, invalid=762 0014: dt=129.472000, rms=0.695 (0.070%), neg=0, invalid=762 0015: dt=129.472000, rms=0.694 (0.050%), neg=0, invalid=762 0016: dt=129.472000, rms=0.694 (0.086%), neg=0, invalid=762 0017: dt=129.472000, rms=0.693 (0.111%), neg=0, invalid=762 0018: dt=129.472000, rms=0.692 (0.138%), neg=0, invalid=762 0019: dt=129.472000, rms=0.691 (0.156%), neg=0, invalid=762 0020: dt=129.472000, rms=0.690 (0.173%), neg=0, invalid=762 0021: dt=129.472000, rms=0.689 (0.184%), neg=0, invalid=762 0022: dt=129.472000, rms=0.687 (0.181%), neg=0, invalid=762 0023: dt=129.472000, rms=0.686 (0.184%), neg=0, invalid=762 0024: dt=129.472000, rms=0.685 (0.185%), neg=0, invalid=762 0025: dt=129.472000, rms=0.684 (0.185%), neg=0, invalid=762 0026: dt=129.472000, rms=0.682 (0.178%), neg=0, invalid=762 0027: dt=129.472000, rms=0.681 (0.163%), neg=0, invalid=762 0028: dt=129.472000, rms=0.680 (0.148%), neg=0, invalid=762 0029: dt=129.472000, rms=0.679 (0.138%), neg=0, invalid=762 0030: dt=129.472000, rms=0.678 (0.137%), neg=0, invalid=762 0031: dt=129.472000, rms=0.677 (0.138%), neg=0, invalid=762 0032: dt=129.472000, rms=0.677 (0.131%), neg=0, invalid=762 0033: dt=129.472000, rms=0.676 (0.117%), neg=0, invalid=762 0034: dt=129.472000, rms=0.675 (0.102%), neg=0, invalid=762 0035: dt=887.808000, rms=0.675 (0.046%), neg=0, invalid=762 0036: dt=887.808000, rms=0.675 (-0.724%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.679, neg=0, invalid=762 0037: dt=169.539623, rms=0.671 (1.115%), neg=0, invalid=762 0038: dt=258.359447, rms=0.658 (1.938%), neg=0, invalid=762 0039: dt=65.021277, rms=0.653 (0.828%), neg=0, invalid=762 0040: dt=145.152000, rms=0.650 (0.449%), neg=0, invalid=762 0041: dt=78.125341, rms=0.647 (0.389%), neg=0, invalid=762 0042: dt=122.181818, rms=0.645 (0.458%), neg=0, invalid=762 0043: dt=36.288000, rms=0.643 (0.248%), neg=0, invalid=762 0044: dt=36.288000, rms=0.642 (0.129%), neg=0, invalid=762 0045: dt=36.288000, rms=0.641 (0.212%), neg=0, invalid=762 0046: dt=36.288000, rms=0.639 (0.304%), neg=0, invalid=762 0047: dt=36.288000, rms=0.636 (0.393%), neg=0, invalid=762 0048: dt=36.288000, rms=0.634 (0.431%), neg=0, invalid=762 0049: dt=36.288000, rms=0.631 (0.444%), neg=0, invalid=762 0050: dt=36.288000, rms=0.628 (0.441%), neg=0, invalid=762 0051: dt=36.288000, rms=0.625 (0.414%), neg=0, invalid=762 0052: dt=36.288000, rms=0.623 (0.386%), neg=0, invalid=762 0053: dt=36.288000, rms=0.621 (0.370%), neg=0, invalid=762 0054: dt=36.288000, rms=0.618 (0.346%), neg=0, invalid=762 0055: dt=36.288000, rms=0.617 (0.308%), neg=0, invalid=762 0056: dt=36.288000, rms=0.615 (0.272%), neg=0, invalid=762 0057: dt=36.288000, rms=0.613 (0.237%), neg=0, invalid=762 0058: dt=36.288000, rms=0.612 (0.206%), neg=0, invalid=762 0059: dt=36.288000, rms=0.611 (0.183%), neg=0, invalid=762 0060: dt=36.288000, rms=0.610 (0.165%), neg=0, invalid=762 0061: dt=36.288000, rms=0.609 (0.145%), neg=0, invalid=762 0062: dt=36.288000, rms=0.608 (0.135%), neg=0, invalid=762 0063: dt=36.288000, rms=0.608 (0.124%), neg=0, invalid=762 0064: dt=36.288000, rms=0.607 (0.116%), neg=0, invalid=762 0065: dt=580.608000, rms=0.606 (0.143%), neg=0, invalid=762 0066: dt=31.104000, rms=0.606 (0.014%), neg=0, invalid=762 0067: dt=31.104000, rms=0.606 (0.004%), neg=0, invalid=762 0068: dt=31.104000, rms=0.606 (0.002%), neg=0, invalid=762 0069: dt=31.104000, rms=0.606 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.606, neg=0, invalid=762 0070: dt=124.416000, rms=0.604 (0.464%), neg=0, invalid=762 0071: dt=62.208000, rms=0.603 (0.081%), neg=0, invalid=762 0072: dt=62.208000, rms=0.603 (0.020%), neg=0, invalid=762 0073: dt=62.208000, rms=0.603 (0.020%), neg=0, invalid=762 0074: dt=62.208000, rms=0.603 (0.012%), neg=0, invalid=762 0075: dt=62.208000, rms=0.603 (-0.028%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.625, neg=0, invalid=762 0076: dt=0.700000, rms=0.625 (0.078%), neg=0, invalid=762 0077: dt=0.700000, rms=0.625 (0.002%), neg=0, invalid=762 0078: dt=0.700000, rms=0.625 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.625, neg=0, invalid=762 0079: dt=0.150000, rms=0.625 (0.077%), neg=0, invalid=762 0080: dt=0.043750, rms=0.625 (0.000%), neg=0, invalid=762 0081: dt=0.043750, rms=0.625 (-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=0.690, neg=0, invalid=762 0082: dt=5.435897, rms=0.670 (2.924%), neg=0, invalid=762 0083: dt=2.245614, rms=0.669 (0.071%), neg=0, invalid=762 0084: dt=2.245614, rms=0.669 (-0.041%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.669, neg=0, invalid=762 0085: dt=0.000000, rms=0.669 (0.050%), neg=0, invalid=762 0086: dt=0.000000, rms=0.669 (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=0.732, neg=0, invalid=762 0087: dt=1.280000, rms=0.728 (0.524%), neg=0, invalid=762 0088: dt=1.921569, rms=0.723 (0.720%), neg=0, invalid=762 0089: dt=0.320000, rms=0.723 (0.014%), neg=0, invalid=762 0090: dt=0.320000, rms=0.723 (0.013%), neg=0, invalid=762 0091: dt=0.320000, rms=0.723 (0.009%), neg=0, invalid=762 0092: dt=0.320000, rms=0.723 (-0.016%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.723, neg=0, invalid=762 0093: dt=1.792000, rms=0.721 (0.299%), neg=0, invalid=762 0094: dt=0.000000, rms=0.721 (0.001%), neg=0, invalid=762 0095: dt=0.100000, rms=0.721 (-0.002%), 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=0.676, neg=0, invalid=762 0096: dt=0.981271, rms=0.653 (3.478%), neg=0, invalid=762 0097: dt=0.096000, rms=0.652 (0.189%), neg=0, invalid=762 0098: dt=0.096000, rms=0.652 (-0.135%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.652, neg=0, invalid=762 0099: dt=0.028000, rms=0.652 (0.064%), neg=0, invalid=762 0100: dt=0.000000, rms=0.652 (0.000%), neg=0, invalid=762 0101: dt=0.050000, rms=0.652 (-0.034%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.14577 ( 9) Left_Lateral_Ventricle (4): linear fit = 0.34 x + 0.0 (805 voxels, overlap=0.018) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (805 voxels, peak = 7), gca=8.0 gca peak = 0.15565 (16) mri peak = 0.12992 ( 9) Right_Lateral_Ventricle (43): linear fit = 0.56 x + 0.0 (807 voxels, overlap=0.147) Right_Lateral_Ventricle (43): linear fit = 0.56 x + 0.0 (807 voxels, peak = 9), gca=8.9 gca peak = 0.26829 (96) mri peak = 0.08429 (92) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (734 voxels, overlap=0.763) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (734 voxels, peak = 91), gca=90.7 gca peak = 0.20183 (93) mri peak = 0.07164 (83) Left_Pallidum (13): linear fit = 0.89 x + 0.0 (581 voxels, overlap=0.592) Left_Pallidum (13): linear fit = 0.89 x + 0.0 (581 voxels, peak = 83), gca=83.2 gca peak = 0.21683 (55) mri peak = 0.11339 (57) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (647 voxels, overlap=0.992) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (647 voxels, peak = 56), gca=56.4 gca peak = 0.30730 (58) mri peak = 0.09939 (57) Left_Hippocampus (17): linear fit = 0.96 x + 0.0 (737 voxels, overlap=0.963) Left_Hippocampus (17): linear fit = 0.96 x + 0.0 (737 voxels, peak = 56), gca=56.0 gca peak = 0.11430 (101) mri peak = 0.06410 (98) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (49953 voxels, overlap=0.902) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (49953 voxels, peak = 103), gca=102.5 gca peak = 0.12076 (102) mri peak = 0.06625 (98) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (47716 voxels, overlap=0.943) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (47716 voxels, peak = 103), gca=102.5 gca peak = 0.14995 (59) mri peak = 0.04310 (53) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (16052 voxels, overlap=0.988) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (16052 voxels, peak = 54), gca=54.0 gca peak = 0.15082 (58) mri peak = 0.04323 (56) Right_Cerebral_Cortex (42): linear fit = 0.94 x + 0.0 (15841 voxels, overlap=0.981) Right_Cerebral_Cortex (42): linear fit = 0.94 x + 0.0 (15841 voxels, peak = 55), gca=54.8 gca peak = 0.14161 (67) mri peak = 0.09622 (61) Right_Caudate (50): linear fit = 0.93 x + 0.0 (712 voxels, overlap=0.798) Right_Caudate (50): linear fit = 0.93 x + 0.0 (712 voxels, peak = 62), gca=62.0 gca peak = 0.15243 (71) mri peak = 0.07775 (67) Left_Caudate (11): linear fit = 0.90 x + 0.0 (833 voxels, overlap=0.430) Left_Caudate (11): linear fit = 0.90 x + 0.0 (833 voxels, peak = 64), gca=64.3 gca peak = 0.13336 (57) mri peak = 0.04909 (48) Left_Cerebellum_Cortex (8): linear fit = 0.89 x + 0.0 (26052 voxels, overlap=0.557) Left_Cerebellum_Cortex (8): linear fit = 0.89 x + 0.0 (26052 voxels, peak = 51), gca=51.0 gca peak = 0.13252 (56) mri peak = 0.03657 (54) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (22345 voxels, overlap=0.979) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (22345 voxels, peak = 54), gca=54.0 gca peak = 0.18181 (84) mri peak = 0.05988 (84) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7487 voxels, overlap=0.975) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7487 voxels, peak = 84), gca=84.0 gca peak = 0.20573 (83) mri peak = 0.06153 (86) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (6032 voxels, overlap=0.872) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (6032 voxels, peak = 85), gca=85.1 gca peak = 0.21969 (57) mri peak = 0.08440 (55) Left_Amygdala (18): linear fit = 0.94 x + 0.0 (306 voxels, overlap=0.999) Left_Amygdala (18): linear fit = 0.94 x + 0.0 (306 voxels, peak = 54), gca=53.9 gca peak = 0.39313 (56) mri peak = 0.11905 (53) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (378 voxels, overlap=1.003) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (378 voxels, peak = 52), gca=52.4 gca peak = 0.14181 (85) mri peak = 0.06373 (75) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (4738 voxels, overlap=0.913) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (4738 voxels, peak = 81), gca=81.2 gca peak = 0.11978 (83) mri peak = 0.08175 (77) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3972 voxels, overlap=0.926) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3972 voxels, peak = 83), gca=82.6 gca peak = 0.13399 (79) mri peak = 0.06204 (82) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1815 voxels, overlap=0.996) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1815 voxels, peak = 79), gca=79.0 gca peak = 0.14159 (79) mri peak = 0.06078 (75) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1770 voxels, overlap=0.993) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1770 voxels, peak = 79), gca=79.0 gca peak = 0.10025 (80) mri peak = 0.21641 (80) Brain_Stem (16): linear fit = 1.05 x + 0.0 (9913 voxels, overlap=0.401) Brain_Stem (16): linear fit = 1.05 x + 0.0 (9913 voxels, peak = 84), gca=84.4 gca peak = 0.13281 (86) mri peak = 0.10758 (84) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (903 voxels, overlap=0.725) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (903 voxels, peak = 92), gca=92.5 gca peak = 0.12801 (89) mri peak = 0.09424 (83) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1076 voxels, overlap=0.814) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1076 voxels, peak = 90), gca=90.3 gca peak = 0.20494 (23) mri peak = 0.22232 (11) gca peak = 0.15061 (21) mri peak = 0.09684 (10) Fourth_Ventricle (15): linear fit = 0.44 x + 0.0 (283 voxels, overlap=0.287) Fourth_Ventricle (15): linear fit = 0.44 x + 0.0 (283 voxels, peak = 9), gca=9.1 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 0.95 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.48 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.652, neg=0, invalid=762 0102: dt=129.472000, rms=0.649 (0.533%), neg=0, invalid=762 0103: dt=295.936000, rms=0.646 (0.490%), neg=0, invalid=762 0104: dt=73.984000, rms=0.645 (0.121%), neg=0, invalid=762 0105: dt=517.888000, rms=0.642 (0.488%), neg=0, invalid=762 0106: dt=73.984000, rms=0.641 (0.037%), neg=0, invalid=762 0107: dt=73.984000, rms=0.641 (0.034%), neg=0, invalid=762 0108: dt=73.984000, rms=0.641 (0.060%), neg=0, invalid=762 0109: dt=73.984000, rms=0.640 (0.074%), neg=0, invalid=762 0110: dt=73.984000, rms=0.640 (0.089%), neg=0, invalid=762 0111: dt=73.984000, rms=0.639 (0.099%), neg=0, invalid=762 0112: dt=73.984000, rms=0.639 (0.105%), neg=0, invalid=762 0113: dt=73.984000, rms=0.638 (0.097%), neg=0, invalid=762 0114: dt=73.984000, rms=0.637 (0.082%), neg=0, invalid=762 0115: dt=73.984000, rms=0.637 (0.065%), neg=0, invalid=762 0116: dt=73.984000, rms=0.637 (0.048%), neg=0, invalid=762 0117: dt=73.984000, rms=0.636 (0.041%), neg=0, invalid=762 0118: dt=73.984000, rms=0.636 (0.030%), neg=0, invalid=762 0119: dt=73.984000, rms=0.636 (0.026%), neg=0, invalid=762 0120: dt=73.984000, rms=0.636 (0.029%), neg=0, invalid=762 0121: dt=73.984000, rms=0.636 (0.033%), neg=0, invalid=762 0122: dt=73.984000, rms=0.635 (0.042%), neg=0, invalid=762 0123: dt=73.984000, rms=0.635 (0.041%), neg=0, invalid=762 0124: dt=73.984000, rms=0.635 (0.032%), neg=0, invalid=762 0125: dt=73.984000, rms=0.635 (0.023%), neg=0, invalid=762 0126: dt=73.984000, rms=0.635 (0.020%), neg=0, invalid=762 0127: dt=2071.552000, rms=0.633 (0.205%), neg=0, invalid=762 0128: dt=32.368000, rms=0.633 (0.049%), neg=0, invalid=762 0129: dt=32.368000, rms=0.633 (0.001%), neg=0, invalid=762 0130: dt=32.368000, rms=0.633 (-0.024%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.633, neg=0, invalid=762 0131: dt=295.936000, rms=0.631 (0.348%), neg=0, invalid=762 0132: dt=221.952000, rms=0.630 (0.202%), neg=0, invalid=762 0133: dt=129.472000, rms=0.630 (0.035%), neg=0, invalid=762 0134: dt=129.472000, rms=0.629 (0.042%), neg=0, invalid=762 0135: dt=129.472000, rms=0.629 (0.071%), neg=0, invalid=762 0136: dt=129.472000, rms=0.628 (0.088%), neg=0, invalid=762 0137: dt=129.472000, rms=0.628 (0.088%), neg=0, invalid=762 0138: dt=129.472000, rms=0.627 (0.085%), neg=0, invalid=762 0139: dt=129.472000, rms=0.627 (0.079%), neg=0, invalid=762 0140: dt=129.472000, rms=0.626 (0.073%), neg=0, invalid=762 0141: dt=129.472000, rms=0.626 (0.064%), neg=0, invalid=762 0142: dt=129.472000, rms=0.626 (0.054%), neg=0, invalid=762 0143: dt=129.472000, rms=0.625 (0.048%), neg=0, invalid=762 0144: dt=129.472000, rms=0.625 (0.039%), neg=0, invalid=762 0145: dt=129.472000, rms=0.625 (0.035%), neg=0, invalid=762 0146: dt=129.472000, rms=0.625 (0.027%), neg=0, invalid=762 0147: dt=129.472000, rms=0.625 (0.028%), neg=0, invalid=762 0148: dt=129.472000, rms=0.624 (0.034%), neg=0, invalid=762 0149: dt=129.472000, rms=0.624 (0.037%), neg=0, invalid=762 0150: dt=129.472000, rms=0.624 (0.034%), neg=0, invalid=762 0151: dt=129.472000, rms=0.624 (0.032%), neg=0, invalid=762 0152: dt=129.472000, rms=0.624 (0.031%), neg=0, invalid=762 0153: dt=129.472000, rms=0.623 (0.036%), neg=0, invalid=762 0154: dt=129.472000, rms=0.623 (0.036%), neg=0, invalid=762 0155: dt=129.472000, rms=0.623 (0.031%), neg=0, invalid=762 0156: dt=129.472000, rms=0.623 (0.029%), neg=0, invalid=762 0157: dt=129.472000, rms=0.623 (0.025%), neg=0, invalid=762 0158: dt=129.472000, rms=0.622 (0.026%), neg=0, invalid=762 0159: dt=129.472000, rms=0.622 (0.019%), neg=0, invalid=762 0160: dt=129.472000, rms=0.622 (0.019%), neg=0, invalid=762 0161: dt=517.888000, rms=0.622 (0.015%), neg=0, invalid=762 0162: dt=517.888000, rms=0.622 (-0.285%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.623, neg=0, invalid=762 0163: dt=72.681388, rms=0.621 (0.388%), neg=0, invalid=762 0164: dt=145.152000, rms=0.618 (0.468%), neg=0, invalid=762 0165: dt=65.084746, rms=0.615 (0.406%), neg=0, invalid=762 0166: dt=85.333333, rms=0.613 (0.317%), neg=0, invalid=762 0167: dt=62.208000, rms=0.611 (0.353%), neg=0, invalid=762 0168: dt=80.202532, rms=0.610 (0.235%), neg=0, invalid=762 0169: dt=77.528455, rms=0.608 (0.310%), neg=0, invalid=762 0170: dt=62.208000, rms=0.606 (0.198%), neg=0, invalid=762 0171: dt=103.680000, rms=0.605 (0.277%), neg=0, invalid=762 0172: dt=36.288000, rms=0.604 (0.167%), neg=0, invalid=762 0173: dt=124.416000, rms=0.602 (0.322%), neg=0, invalid=762 0174: dt=25.920000, rms=0.601 (0.072%), neg=0, invalid=762 0175: dt=0.141750, rms=0.601 (0.000%), neg=0, invalid=762 0176: dt=0.008859, rms=0.601 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.602, neg=0, invalid=762 0177: dt=0.007594, rms=0.601 (0.084%), neg=0, invalid=762 0178: dt=0.000000, rms=0.601 (0.000%), neg=0, invalid=762 0179: dt=0.000439, rms=0.601 (0.000%), neg=0, invalid=762 0180: dt=0.000110, rms=0.601 (0.000%), neg=0, invalid=762 0181: dt=0.000055, 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=0.604, neg=0, invalid=762 0182: dt=0.000000, rms=0.604 (0.084%), neg=0, invalid=762 0183: dt=0.000000, rms=0.604 (0.000%), neg=0, invalid=762 0184: dt=0.000031, rms=0.604 (0.000%), neg=0, invalid=762 0185: dt=0.000008, rms=0.604 (0.000%), neg=0, invalid=762 0186: dt=0.000000, rms=0.604 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.604, neg=0, invalid=762 0187: dt=0.000000, rms=0.604 (0.084%), neg=0, invalid=762 0188: dt=0.000000, rms=0.604 (0.000%), neg=0, invalid=762 0189: dt=0.000000, rms=0.604 (0.000%), neg=0, invalid=762 0190: dt=0.000000, rms=0.604 (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=0.612, neg=0, invalid=762 0191: dt=4.032000, rms=0.595 (2.781%), neg=0, invalid=762 0192: dt=4.032000, rms=0.582 (2.109%), neg=0, invalid=762 0193: dt=4.032000, rms=0.573 (1.633%), neg=0, invalid=762 0194: dt=4.032000, rms=0.566 (1.271%), neg=0, invalid=762 0195: dt=4.032000, rms=0.560 (0.995%), neg=0, invalid=762 0196: dt=4.032000, rms=0.556 (0.785%), neg=0, invalid=762 0197: dt=1.008000, rms=0.555 (0.156%), neg=0, invalid=762 0198: dt=0.063000, rms=0.555 (0.009%), neg=0, invalid=762 0199: dt=0.031500, rms=0.555 (0.005%), neg=0, invalid=762 0200: dt=0.015750, rms=0.555 (0.002%), neg=0, invalid=762 0201: dt=0.003938, rms=0.555 (0.000%), neg=0, invalid=762 0202: dt=0.000984, rms=0.555 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.555, neg=0, invalid=762 0203: dt=16.128000, rms=0.542 (2.307%), neg=0, invalid=762 0204: dt=11.520000, rms=0.539 (0.552%), neg=0, invalid=762 0205: dt=16.128000, rms=0.536 (0.536%), neg=0, invalid=762 0206: dt=4.032000, rms=0.536 (0.107%), neg=0, invalid=762 0207: dt=4.032000, rms=0.535 (0.095%), neg=0, invalid=762 0208: dt=16.128000, rms=0.534 (0.294%), neg=0, invalid=762 0209: dt=16.128000, rms=0.533 (0.216%), neg=0, invalid=762 0210: dt=4.032000, rms=0.532 (0.059%), neg=0, invalid=762 0211: dt=11.520000, rms=0.532 (0.135%), neg=0, invalid=762 0212: dt=26.105263, rms=0.531 (0.151%), neg=0, invalid=762 0213: dt=11.520000, rms=0.530 (0.166%), neg=0, invalid=762 0214: dt=13.824000, rms=0.529 (0.087%), neg=0, invalid=762 0215: dt=12.952381, rms=0.529 (0.079%), neg=0, invalid=762 0216: dt=11.520000, rms=0.529 (0.072%), neg=0, invalid=762 0217: dt=11.520000, rms=0.528 (0.055%), neg=0, invalid=762 0218: dt=11.428571, rms=0.528 (0.059%), neg=0, invalid=762 0219: dt=9.756098, rms=0.528 (0.040%), neg=0, invalid=762 0220: dt=9.756098, rms=0.527 (0.053%), neg=0, invalid=762 0221: dt=9.756098, rms=0.527 (0.074%), neg=0, invalid=762 0222: dt=9.756098, rms=0.527 (0.092%), neg=0, invalid=762 0223: dt=9.756098, rms=0.526 (0.127%), neg=0, invalid=762 0224: dt=9.756098, rms=0.525 (0.129%), neg=0, invalid=762 0225: dt=9.756098, rms=0.525 (0.139%), neg=0, invalid=762 0226: dt=9.756098, rms=0.524 (0.112%), neg=0, invalid=762 0227: dt=9.756098, rms=0.523 (0.127%), neg=0, invalid=762 0228: dt=9.756098, rms=0.523 (0.115%), neg=0, invalid=762 0229: dt=9.756098, rms=0.522 (0.101%), neg=0, invalid=762 0230: dt=9.756098, rms=0.522 (0.091%), neg=0, invalid=762 0231: dt=9.756098, rms=0.521 (0.088%), neg=0, invalid=762 0232: dt=9.756098, rms=0.521 (0.080%), neg=0, invalid=762 0233: dt=9.756098, rms=0.520 (0.065%), neg=0, invalid=762 0234: dt=9.756098, rms=0.520 (0.055%), neg=0, invalid=762 0235: dt=9.756098, rms=0.520 (0.045%), neg=0, invalid=762 0236: dt=9.756098, rms=0.520 (0.049%), neg=0, invalid=762 0237: dt=9.756098, rms=0.519 (0.050%), neg=0, invalid=762 0238: dt=9.756098, rms=0.519 (0.034%), neg=0, invalid=762 0239: dt=9.756098, rms=0.519 (0.048%), neg=0, invalid=762 0240: dt=9.756098, rms=0.519 (0.022%), neg=0, invalid=762 0241: dt=9.756098, rms=0.519 (0.031%), neg=0, invalid=762 0242: dt=9.756098, rms=0.519 (0.014%), neg=0, invalid=762 0243: dt=9.756098, rms=0.518 (0.033%), neg=0, invalid=762 0244: dt=9.756098, rms=0.518 (0.023%), neg=0, invalid=762 0245: dt=9.756098, rms=0.518 (0.029%), neg=0, invalid=762 0246: dt=9.756098, rms=0.518 (0.021%), neg=0, invalid=762 0247: dt=9.756098, rms=0.518 (0.015%), neg=0, invalid=762 0248: dt=7.794872, rms=0.518 (0.028%), neg=0, invalid=762 0249: dt=2.304000, rms=0.518 (0.004%), neg=0, invalid=762 0250: dt=2.304000, rms=0.518 (-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=0.533, neg=0, invalid=762 0251: dt=0.000000, rms=0.532 (0.098%), neg=0, invalid=762 0252: dt=0.000000, rms=0.532 (0.000%), neg=0, invalid=762 0253: dt=0.100000, rms=0.532 (-0.173%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.533, neg=0, invalid=762 0254: dt=0.000000, rms=0.532 (0.098%), neg=0, invalid=762 0255: dt=0.000000, rms=0.532 (0.000%), neg=0, invalid=762 0256: dt=0.100000, rms=0.532 (-0.162%), 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=0.509, neg=0, invalid=762 0257: dt=0.320000, rms=0.497 (2.174%), neg=0, invalid=762 0258: dt=0.384000, rms=0.492 (1.135%), neg=0, invalid=762 0259: dt=0.384000, rms=0.489 (0.482%), neg=0, invalid=762 0260: dt=0.384000, rms=0.488 (0.286%), neg=0, invalid=762 0261: dt=0.384000, rms=0.487 (0.201%), neg=0, invalid=762 0262: dt=0.384000, rms=0.486 (0.148%), neg=0, invalid=762 0263: dt=0.384000, rms=0.486 (0.121%), neg=0, invalid=762 0264: dt=0.384000, rms=0.485 (0.088%), neg=0, invalid=762 0265: dt=0.384000, rms=0.485 (0.081%), neg=0, invalid=762 0266: dt=0.384000, rms=0.485 (0.059%), neg=0, invalid=762 0267: dt=0.384000, rms=0.484 (0.060%), neg=0, invalid=762 0268: dt=0.384000, rms=0.484 (0.042%), neg=0, invalid=762 0269: dt=0.384000, rms=0.484 (0.043%), neg=0, invalid=762 0270: dt=0.384000, rms=0.484 (0.067%), neg=0, invalid=762 0271: dt=0.192000, rms=0.484 (0.020%), neg=0, invalid=762 0272: dt=0.192000, rms=0.483 (0.024%), neg=0, invalid=762 0273: dt=0.192000, rms=0.483 (0.033%), neg=0, invalid=762 0274: dt=0.192000, rms=0.483 (0.027%), neg=0, invalid=762 0275: dt=0.192000, rms=0.483 (0.032%), neg=0, invalid=762 0276: dt=0.192000, rms=0.483 (0.040%), neg=0, invalid=762 0277: dt=0.192000, rms=0.483 (0.038%), neg=0, invalid=762 0278: dt=0.192000, rms=0.482 (0.033%), neg=0, invalid=762 0279: dt=0.192000, rms=0.482 (0.026%), neg=0, invalid=762 0280: dt=0.192000, rms=0.482 (0.024%), neg=0, invalid=762 0281: dt=0.192000, rms=0.482 (0.021%), neg=0, invalid=762 0282: dt=-0.000061, rms=0.482 (-0.007%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.483, neg=0, invalid=762 0283: dt=0.258929, rms=0.479 (0.685%), neg=0, invalid=762 0284: dt=0.320000, rms=0.478 (0.312%), neg=0, invalid=762 0285: dt=0.320000, rms=0.477 (0.102%), neg=0, invalid=762 0286: dt=0.320000, rms=0.477 (0.032%), neg=0, invalid=762 0287: dt=0.320000, rms=0.477 (0.004%), neg=0, invalid=762 0288: dt=0.320000, rms=0.477 (0.003%), neg=0, invalid=762 0289: dt=0.320000, rms=0.477 (-0.003%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.476, neg=0, invalid=762 0290: dt=0.000000, rms=0.475 (0.139%), neg=0, invalid=762 0291: dt=0.000000, rms=0.475 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.476, neg=0, invalid=762 0292: dt=129.472000, rms=0.475 (0.173%), neg=0, invalid=762 0293: dt=129.472000, rms=0.475 (0.013%), neg=0, invalid=762 0294: dt=129.472000, rms=0.475 (0.012%), neg=0, invalid=762 0295: dt=129.472000, rms=0.475 (0.022%), neg=0, invalid=762 0296: dt=129.472000, rms=0.474 (0.015%), neg=0, invalid=762 0297: dt=129.472000, rms=0.474 (0.013%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.475, neg=0, invalid=762 0298: dt=2.268000, rms=0.474 (0.136%), neg=0, invalid=762 0299: dt=0.405000, rms=0.474 (0.001%), neg=0, invalid=762 0300: dt=0.405000, rms=0.474 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.475, neg=0, invalid=762 0301: dt=145.152000, rms=0.473 (0.435%), neg=0, invalid=762 0302: dt=36.288000, rms=0.473 (0.075%), neg=0, invalid=762 0303: dt=36.288000, rms=0.472 (0.048%), neg=0, invalid=762 0304: dt=36.288000, rms=0.472 (0.070%), neg=0, invalid=762 0305: dt=36.288000, rms=0.472 (0.090%), neg=0, invalid=762 0306: dt=36.288000, rms=0.471 (0.088%), neg=0, invalid=762 0307: dt=36.288000, rms=0.471 (0.084%), neg=0, invalid=762 0308: dt=82.944000, rms=0.471 (0.035%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.472, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0309: dt=21.393768, rms=0.470 (0.442%), neg=0, invalid=762 0310: dt=24.744186, rms=0.469 (0.172%), neg=0, invalid=762 0311: dt=24.744186, rms=0.468 (0.127%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0312: dt=24.744186, rms=0.467 (0.198%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 9 iterations, nbhd size=1, neg = 0 0313: dt=24.744186, rms=0.467 (0.011%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 9 iterations, nbhd size=1, neg = 0 0314: dt=24.744186, rms=0.467 (0.087%), neg=0, invalid=762 iter 0, gcam->neg = 29 after 11 iterations, nbhd size=1, neg = 0 0315: dt=24.744186, rms=0.467 (-0.007%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0316: dt=38.400000, rms=0.465 (0.317%), neg=0, invalid=762 0317: dt=25.600000, rms=0.464 (0.277%), neg=0, invalid=762 0318: dt=11.200000, rms=0.463 (0.109%), neg=0, invalid=762 0319: dt=11.200000, rms=0.463 (0.057%), neg=0, invalid=762 0320: dt=11.200000, rms=0.463 (0.087%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0321: dt=11.200000, rms=0.462 (0.115%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0322: dt=11.200000, rms=0.462 (0.127%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0323: dt=11.200000, rms=0.461 (0.126%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 0324: dt=11.200000, rms=0.460 (0.119%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0325: dt=11.200000, rms=0.460 (0.116%), neg=0, invalid=762 0326: dt=44.800000, rms=0.460 (0.034%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 8 iterations, nbhd size=1, neg = 0 0327: dt=44.800000, rms=0.460 (-0.086%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.460, neg=0, invalid=762 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0328: dt=50.947368, rms=0.454 (1.294%), neg=0, invalid=762 0329: dt=22.000000, rms=0.453 (0.400%), neg=0, invalid=762 0330: dt=32.000000, rms=0.452 (0.214%), neg=0, invalid=762 0331: dt=32.000000, rms=0.452 (0.009%), neg=0, invalid=762 0332: dt=32.000000, rms=0.450 (0.376%), neg=0, invalid=762 0333: dt=32.000000, rms=0.450 (-0.019%), neg=0, invalid=762 0334: dt=11.200000, rms=0.450 (0.058%), neg=0, invalid=762 0335: dt=44.800000, rms=0.449 (0.088%), neg=0, invalid=762 0336: dt=25.600000, rms=0.449 (0.056%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 0337: dt=3.636364, rms=0.454 (0.212%), neg=0, invalid=762 0338: dt=1.846154, rms=0.454 (0.012%), neg=0, invalid=762 0339: dt=1.846154, rms=0.454 (0.003%), neg=0, invalid=762 0340: dt=1.846154, rms=0.454 (-0.024%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.454, neg=0, invalid=762 0341: dt=10.873786, rms=0.452 (0.435%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 10 iterations, nbhd size=1, neg = 0 0342: dt=20.444444, rms=0.451 (0.267%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0343: dt=18.793651, rms=0.450 (0.279%), neg=0, invalid=762 0344: dt=11.377778, rms=0.449 (0.212%), neg=0, invalid=762 0345: dt=11.377778, rms=0.448 (0.147%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0346: dt=11.377778, rms=0.448 (0.190%), neg=0, invalid=762 0347: dt=11.377778, rms=0.446 (0.273%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0348: dt=11.377778, rms=0.445 (0.227%), neg=0, invalid=762 0349: dt=11.377778, rms=0.444 (0.250%), neg=0, invalid=762 0350: dt=11.377778, rms=0.443 (0.230%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0351: dt=11.377778, rms=0.442 (0.196%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0352: dt=11.377778, rms=0.442 (0.088%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0353: dt=11.377778, rms=0.442 (0.086%), neg=0, invalid=762 0354: dt=9.216000, rms=0.441 (0.045%), neg=0, invalid=762 0355: dt=9.216000, rms=0.441 (-0.033%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.447, neg=0, invalid=762 0356: dt=0.000000, rms=0.447 (0.168%), neg=0, invalid=762 0357: dt=0.000000, rms=0.447 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.447, neg=0, invalid=762 0358: dt=0.000000, rms=0.447 (0.168%), neg=0, invalid=762 0359: dt=0.000000, rms=0.447 (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=0.439, neg=0, invalid=762 iter 0, gcam->neg = 1086 after 12 iterations, nbhd size=1, neg = 0 0360: dt=1.756311, rms=0.418 (4.640%), neg=0, invalid=762 0361: dt=0.000013, rms=0.418 (0.001%), neg=0, invalid=762 0362: dt=0.000013, rms=0.418 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.419, neg=0, invalid=762 0363: dt=0.064000, rms=0.418 (0.215%), neg=0, invalid=762 0364: dt=0.001500, rms=0.418 (-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=0.408, neg=0, invalid=762 0365: dt=0.000000, rms=0.408 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0366: dt=18.496000, rms=0.408 (0.002%), neg=0, invalid=762 0367: dt=1.734000, rms=0.408 (0.000%), neg=0, invalid=762 0368: dt=1.734000, rms=0.408 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0369: dt=0.000000, rms=0.408 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0370: dt=36.288000, rms=0.408 (0.022%), neg=0, invalid=762 0371: dt=36.288000, rms=0.408 (0.011%), neg=0, invalid=762 0372: dt=36.288000, rms=0.408 (0.008%), neg=0, invalid=762 0373: dt=36.288000, rms=0.408 (0.004%), neg=0, invalid=762 0374: dt=36.288000, rms=0.408 (-0.010%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0375: dt=8.000000, rms=0.408 (0.050%), neg=0, invalid=762 0376: dt=2.800000, rms=0.408 (0.004%), neg=0, invalid=762 0377: dt=2.800000, rms=0.408 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 iter 0, gcam->neg = 27 after 10 iterations, nbhd size=1, neg = 0 0378: dt=79.085714, rms=0.406 (0.597%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0379: dt=24.555102, rms=0.405 (0.246%), neg=0, invalid=762 0380: dt=24.555102, rms=0.404 (0.093%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 2 iterations, nbhd size=0, neg = 0 0381: dt=24.555102, rms=0.404 (0.117%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0382: dt=24.555102, rms=0.403 (0.128%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 8 iterations, nbhd size=1, neg = 0 0383: dt=24.555102, rms=0.403 (0.121%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 9 iterations, nbhd size=1, neg = 0 0384: dt=24.555102, rms=0.402 (0.145%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 8 iterations, nbhd size=1, neg = 0 0385: dt=24.555102, rms=0.402 (0.066%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 2 iterations, nbhd size=0, neg = 0 0386: dt=24.555102, rms=0.402 (0.110%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 11 iterations, nbhd size=1, neg = 0 0387: dt=24.555102, rms=0.401 (0.077%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0388: dt=44.800000, rms=0.401 (0.047%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0389: dt=44.800000, rms=0.401 (-0.012%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.405, neg=0, invalid=762 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 0390: dt=4.111111, rms=0.405 (0.034%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0391: dt=2.500000, rms=0.405 (0.002%), neg=0, invalid=762 0392: dt=2.500000, rms=0.405 (-0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.405, neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0393: dt=14.296296, rms=0.403 (0.324%), neg=0, invalid=762 iter 0, gcam->neg = 19 after 13 iterations, nbhd size=1, neg = 0 0394: dt=26.153846, rms=0.402 (0.250%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 9 iterations, nbhd size=1, neg = 0 0395: dt=11.520000, rms=0.402 (0.141%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 0396: dt=11.520000, rms=0.401 (0.086%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0397: dt=11.520000, rms=0.401 (0.104%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 12 iterations, nbhd size=1, neg = 0 0398: dt=11.520000, rms=0.400 (0.131%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 3 iterations, nbhd size=0, neg = 0 0399: dt=11.520000, rms=0.400 (0.138%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 3 iterations, nbhd size=0, neg = 0 0400: dt=11.520000, rms=0.399 (0.127%), neg=0, invalid=762 iter 0, gcam->neg = 25 after 13 iterations, nbhd size=1, neg = 0 0401: dt=11.520000, rms=0.399 (0.039%), neg=0, invalid=762 iter 0, gcam->neg = 27 after 5 iterations, nbhd size=0, neg = 0 0402: dt=11.520000, rms=0.399 (0.080%), neg=0, invalid=762 iter 0, gcam->neg = 28 after 6 iterations, nbhd size=0, neg = 0 0403: dt=11.520000, rms=0.399 (0.054%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 0 iterations, nbhd size=0, neg = 0 0404: dt=7.000000, rms=0.399 (0.013%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=0, neg = 0 0405: dt=7.000000, rms=0.399 (0.011%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0406: dt=7.000000, rms=0.399 (0.014%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 6 iterations, nbhd size=0, neg = 0 0407: dt=7.000000, rms=0.399 (-0.007%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.404, neg=0, invalid=762 0408: dt=0.000060, rms=0.404 (0.000%), neg=0, invalid=762 0409: dt=0.000000, rms=0.404 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.404, neg=0, invalid=762 0410: dt=0.000000, rms=0.404 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.395, neg=0, invalid=762 iter 0, gcam->neg = 617 after 16 iterations, nbhd size=1, neg = 0 0411: dt=1.082869, rms=0.388 (1.682%), neg=0, invalid=762 0412: dt=0.000023, rms=0.388 (0.000%), neg=0, invalid=762 0413: dt=0.000023, rms=0.388 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.388, neg=0, invalid=762 0414: dt=0.112000, rms=0.388 (0.082%), neg=0, invalid=762 0415: dt=0.112000, rms=0.388 (0.045%), neg=0, invalid=762 0416: dt=0.112000, rms=0.388 (0.042%), neg=0, invalid=762 0417: dt=0.112000, rms=0.388 (0.027%), neg=0, invalid=762 0418: dt=0.112000, rms=0.388 (-0.033%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 47 minutes and 46 seconds. mri_ca_register utimesec 6461.944000 mri_ca_register stimesec 3.764000 mri_ca_register ru_maxrss 1341288 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 3818934 mri_ca_register ru_majflt 8 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 1696 mri_ca_register ru_oublock 62952 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 20 mri_ca_register ru_nivcsw 10803 FSRUNTIME@ mri_ca_register 1.7961 hours 1 threads #-------------------------------------- #@# SubCort Seg Sat May 6 20:27:30 EDT 2017 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 X1 machine x86_64 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/Sub01/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 5.65 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 = 0.12075 ( 9) Left_Lateral_Ventricle (4): linear fit = 0.38 x + 0.0 (852 voxels, overlap=0.014) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (852 voxels, peak = 8), gca=8.0 gca peak = 0.17677 (13) mri peak = 0.14076 ( 9) Right_Lateral_Ventricle (43): linear fit = 0.58 x + 0.0 (943 voxels, overlap=0.421) Right_Lateral_Ventricle (43): linear fit = 0.58 x + 0.0 (943 voxels, peak = 8), gca=7.6 gca peak = 0.28129 (95) mri peak = 0.10228 (92) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (630 voxels, overlap=0.656) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (630 voxels, peak = 89), gca=88.8 gca peak = 0.16930 (96) mri peak = 0.09084 (87) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (644 voxels, overlap=0.408) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (644 voxels, peak = 90), gca=89.8 gca peak = 0.24553 (55) mri peak = 0.10100 (58) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (868 voxels, overlap=1.006) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (868 voxels, peak = 56), gca=56.4 gca peak = 0.30264 (59) mri peak = 0.10464 (53) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (836 voxels, overlap=1.009) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (836 voxels, peak = 56), gca=55.8 gca peak = 0.07580 (103) mri peak = 0.06064 (101) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (35246 voxels, overlap=0.824) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (35246 voxels, peak = 105), gca=104.5 gca peak = 0.07714 (104) mri peak = 0.05895 (98) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35444 voxels, overlap=0.857) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35444 voxels, peak = 103), gca=103.5 gca peak = 0.09712 (58) mri peak = 0.04529 (52) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (18991 voxels, overlap=0.978) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (18991 voxels, peak = 53), gca=53.1 gca peak = 0.11620 (58) mri peak = 0.04512 (55) Right_Cerebral_Cortex (42): linear fit = 0.94 x + 0.0 (19544 voxels, overlap=0.992) Right_Cerebral_Cortex (42): linear fit = 0.94 x + 0.0 (19544 voxels, peak = 55), gca=54.8 gca peak = 0.30970 (66) mri peak = 0.09357 (63) Right_Caudate (50): linear fit = 0.92 x + 0.0 (1227 voxels, overlap=0.998) Right_Caudate (50): linear fit = 0.92 x + 0.0 (1227 voxels, peak = 60), gca=60.4 gca peak = 0.15280 (69) mri peak = 0.08834 (66) Left_Caudate (11): linear fit = 0.88 x + 0.0 (1092 voxels, overlap=0.449) Left_Caudate (11): linear fit = 0.88 x + 0.0 (1092 voxels, peak = 61), gca=61.1 gca peak = 0.13902 (56) mri peak = 0.05976 (48) Left_Cerebellum_Cortex (8): linear fit = 0.89 x + 0.0 (24454 voxels, overlap=0.782) Left_Cerebellum_Cortex (8): linear fit = 0.89 x + 0.0 (24454 voxels, peak = 50), gca=50.1 gca peak = 0.14777 (55) mri peak = 0.04900 (51) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (22068 voxels, overlap=0.998) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (22068 voxels, peak = 53), gca=53.1 gca peak = 0.16765 (84) mri peak = 0.08456 (84) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5147 voxels, overlap=0.976) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5147 voxels, peak = 84), gca=84.0 gca peak = 0.18739 (84) mri peak = 0.07970 (86) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5109 voxels, overlap=0.862) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5109 voxels, peak = 89), gca=89.5 gca peak = 0.29869 (57) mri peak = 0.09278 (54) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (328 voxels, overlap=1.024) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (328 voxels, peak = 58), gca=57.9 gca peak = 0.33601 (57) mri peak = 0.09196 (53) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (370 voxels, overlap=1.021) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (370 voxels, peak = 58), gca=57.9 gca peak = 0.11131 (90) mri peak = 0.09368 (75) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (4051 voxels, overlap=0.722) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (4051 voxels, peak = 86), gca=85.9 gca peak = 0.11793 (83) mri peak = 0.10149 (76) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3828 voxels, overlap=0.974) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3828 voxels, peak = 81), gca=80.9 gca peak = 0.08324 (81) mri peak = 0.06159 (78) Left_Putamen (12): linear fit = 0.98 x + 0.0 (1962 voxels, overlap=0.932) Left_Putamen (12): linear fit = 0.98 x + 0.0 (1962 voxels, peak = 79), gca=79.0 gca peak = 0.10360 (77) mri peak = 0.07428 (75) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1845 voxels, overlap=0.968) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1845 voxels, peak = 76), gca=75.8 gca peak = 0.08424 (78) mri peak = 0.19527 (80) Brain_Stem: unreasonable value (79.2/80.0), not in range [80, 110] - rejecting gca peak = 0.12631 (89) mri peak = 0.08304 (92) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1090 voxels, overlap=0.824) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1090 voxels, peak = 91), gca=91.2 gca peak = 0.14500 (87) mri peak = 0.08795 (89) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1101 voxels, overlap=0.916) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1101 voxels, peak = 89), gca=89.2 gca peak = 0.14975 (24) mri peak = 0.13636 (11) gca peak = 0.19357 (14) mri peak = 0.12820 (10) Fourth_Ventricle (15): linear fit = 0.51 x + 0.0 (100 voxels, overlap=0.459) Fourth_Ventricle (15): linear fit = 0.51 x + 0.0 (100 voxels, peak = 7), gca=7.2 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak Brain_Stem = 0.08424 (78) 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 0.98 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.49 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.31512 ( 7) mri peak = 0.12075 ( 9) Left_Lateral_Ventricle (4): linear fit = 1.08 x + 0.0 (852 voxels, overlap=0.935) Left_Lateral_Ventricle (4): linear fit = 1.08 x + 0.0 (852 voxels, peak = 8), gca=7.5 gca peak = 0.23922 ( 8) mri peak = 0.14076 ( 9) Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (943 voxels, overlap=0.835) Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (943 voxels, peak = 8), gca=8.4 gca peak = 0.27946 (88) mri peak = 0.10228 (92) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (630 voxels, overlap=1.013) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (630 voxels, peak = 89), gca=89.3 gca peak = 0.16174 (90) mri peak = 0.09084 (87) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (644 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (644 voxels, peak = 91), gca=91.3 gca peak = 0.29677 (57) mri peak = 0.10100 (58) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (868 voxels, overlap=0.982) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (868 voxels, peak = 57), gca=57.0 gca peak = 0.30421 (53) mri peak = 0.10464 (53) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (836 voxels, overlap=1.009) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (836 voxels, peak = 52), gca=51.7 gca peak = 0.07772 (104) mri peak = 0.06064 (101) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (35246 voxels, overlap=0.867) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (35246 voxels, peak = 103), gca=103.5 gca peak = 0.08055 (104) mri peak = 0.05895 (98) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35444 voxels, overlap=0.851) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35444 voxels, peak = 103), gca=103.5 gca peak = 0.10695 (53) mri peak = 0.04529 (52) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (18991 voxels, overlap=1.000) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (18991 voxels, peak = 52), gca=52.2 gca peak = 0.12393 (55) mri peak = 0.04512 (55) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (19544 voxels, overlap=0.995) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (19544 voxels, peak = 54), gca=54.2 gca peak = 0.27303 (61) mri peak = 0.09357 (63) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1227 voxels, overlap=1.007) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1227 voxels, peak = 61), gca=61.0 gca peak = 0.14698 (61) mri peak = 0.08834 (66) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1092 voxels, overlap=1.000) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1092 voxels, peak = 61), gca=61.0 gca peak = 0.15858 (50) mri peak = 0.05976 (48) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (24454 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (24454 voxels, peak = 49), gca=48.8 gca peak = 0.15521 (53) mri peak = 0.04900 (51) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (22068 voxels, overlap=0.999) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (22068 voxels, peak = 52), gca=52.2 gca peak = 0.16765 (84) mri peak = 0.08456 (84) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5147 voxels, overlap=0.976) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5147 voxels, peak = 84), gca=84.0 gca peak = 0.15003 (90) mri peak = 0.07970 (86) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5109 voxels, overlap=0.988) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5109 voxels, peak = 89), gca=88.7 gca peak = 0.28044 (59) mri peak = 0.09278 (54) Left_Amygdala (18): linear fit = 0.92 x + 0.0 (328 voxels, overlap=1.012) Left_Amygdala (18): linear fit = 0.92 x + 0.0 (328 voxels, peak = 54), gca=54.0 gca peak = 0.36965 (58) mri peak = 0.09196 (53) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (370 voxels, overlap=1.018) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (370 voxels, peak = 58), gca=58.0 gca peak = 0.11511 (86) mri peak = 0.09368 (75) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (4051 voxels, overlap=0.948) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (4051 voxels, peak = 85), gca=84.7 gca peak = 0.11482 (79) mri peak = 0.10149 (76) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3828 voxels, overlap=0.921) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3828 voxels, peak = 79), gca=79.0 gca peak = 0.08312 (79) mri peak = 0.06159 (78) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1962 voxels, overlap=0.999) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1962 voxels, peak = 79), gca=79.0 gca peak = 0.09873 (76) mri peak = 0.07428 (75) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1845 voxels, overlap=1.001) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1845 voxels, peak = 76), gca=76.0 gca peak = 0.08505 (79) mri peak = 0.19527 (80) Brain_Stem (16): linear fit = 1.01 x + 0.0 (11370 voxels, overlap=0.516) Brain_Stem (16): linear fit = 1.01 x + 0.0 (11370 voxels, peak = 80), gca=80.2 gca peak = 0.11494 (86) mri peak = 0.08304 (92) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1090 voxels, overlap=0.862) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1090 voxels, peak = 86), gca=85.6 gca peak = 0.13378 (89) mri peak = 0.08795 (89) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1101 voxels, overlap=0.943) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1101 voxels, peak = 88), gca=87.7 gca peak = 0.29156 (13) mri peak = 0.13636 (11) gca peak = 0.37683 ( 7) mri peak = 0.12820 (10) Fourth_Ventricle (15): linear fit = 1.08 x + 0.0 (100 voxels, overlap=0.968) Fourth_Ventricle (15): linear fit = 1.08 x + 0.0 (100 voxels, peak = 8), gca=7.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18199 (30) gca peak Left_Thalamus = 1.00000 (92) gca peak Third_Ventricle = 0.29156 (13) gca peak CSF = 0.34711 (18) gca peak Left_Accumbens_area = 0.81154 (55) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.74619 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.20983 (24) gca peak Right_Accumbens_area = 0.41190 (59) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65358 (16) gca peak WM_hypointensities = 0.07080 (76) gca peak non_WM_hypointensities = 0.07897 (44) gca peak Optic_Chiasm = 0.70931 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.98 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.07 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 48110 voxels changed in iteration 0 of unlikely voxel relabeling 173 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 23891 gm and wm labels changed (%23 to gray, %77 to white out of all changed labels) 217 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 57766 changed. image ll: -2.081, PF=0.500 pass 2: 16431 changed. image ll: -2.080, PF=0.500 pass 3: 5462 changed. pass 4: 2082 changed. 29076 voxels changed in iteration 0 of unlikely voxel relabeling 166 voxels changed in iteration 1 of unlikely voxel relabeling 9 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6091 voxels changed in iteration 0 of unlikely voxel relabeling 37 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 5501 voxels changed in iteration 0 of unlikely voxel relabeling 71 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4354 voxels changed in iteration 0 of unlikely voxel relabeling 20 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 2153.268000 mri_ca_label stimesec 0.644000 mri_ca_label ru_maxrss 2098016 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 661541 mri_ca_label ru_majflt 8 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 1616 mri_ca_label ru_oublock 432 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 88 mri_ca_label ru_nivcsw 3997 auto-labeling took 35 minutes and 54 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /usr/local/freesurfer/subjects/Sub01/mri/transforms/cc_up.lta Sub01 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /usr/local/freesurfer/subjects/Sub01/mri/transforms/cc_up.lta reading aseg from /usr/local/freesurfer/subjects/Sub01/mri/aseg.auto_noCCseg.mgz reading norm from /usr/local/freesurfer/subjects/Sub01/mri/norm.mgz 28191 voxels in left wm, 29693 in right wm, xrange [125, 133] searching rotation angles z=[-8 6], y=[-8 6] searching scale 1 Z rot -8.2 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 global minimum found at slice 128.5, rotations (-1.11, -1.25) final transformation (x=128.5, yr=-1.112, zr=-1.245): 0.99958 0.02173 -0.01940 -0.10770; -0.02173 0.99976 0.00042 45.76429; 0.01940 0.00000 0.99981 12.52828; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 132] in xformed coordinates best xformed slice 128 cc center is found at 128 85 113 eigenvectors: 0.00022 0.00008 1.00000; -0.16497 -0.98630 0.00011; 0.98630 -0.16497 -0.00020; writing aseg with callosum to /usr/local/freesurfer/subjects/Sub01/mri/aseg.auto.mgz... corpus callosum segmentation took 0.6 minutes #-------------------------------------- #@# Merge ASeg Sat May 6 21:03:57 EDT 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sat May 6 21:03:57 EDT 2017 /usr/local/freesurfer/subjects/Sub01/mri mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 470 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 57 (57), valley at 24 (24) csf peak at 29, setting threshold to 47 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 26 (26) csf peak at 30, setting threshold to 49 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 40 seconds. #-------------------------------------------- #@# Mask BFS Sat May 6 21:06:39 EDT 2017 /usr/local/freesurfer/subjects/Sub01/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1341432 voxels in mask (pct= 8.00) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sat May 6 21:06:41 EDT 2017 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (105.0): 106.0 +- 5.4 [79.0 --> 125.0] GM (68.0) : 66.7 +- 9.6 [30.0 --> 95.0] setting bottom of white matter range to 76.3 setting top of gray matter range to 85.9 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 3967 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4556 filled 763 bright non-wm voxels segmented. 2574 diagonally connected voxels added... white matter segmentation took 1.0 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.39 minutes reading wm segmentation from wm.seg.mgz... 63 voxels added to wm to prevent paths from MTL structures to cortex 2271 additional wm voxels added 0 additional wm voxels added SEG EDIT: 38344 voxels turned on, 34771 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 14 found - 14 modified | TOTAL: 14 pass 2 (xy+): 0 found - 14 modified | TOTAL: 14 pass 1 (xy-): 24 found - 24 modified | TOTAL: 38 pass 2 (xy-): 0 found - 24 modified | TOTAL: 38 pass 1 (yz+): 31 found - 31 modified | TOTAL: 69 pass 2 (yz+): 0 found - 31 modified | TOTAL: 69 pass 1 (yz-): 19 found - 19 modified | TOTAL: 88 pass 2 (yz-): 0 found - 19 modified | TOTAL: 88 pass 1 (xz+): 23 found - 23 modified | TOTAL: 111 pass 2 (xz+): 0 found - 23 modified | TOTAL: 111 pass 1 (xz-): 16 found - 16 modified | TOTAL: 127 pass 2 (xz-): 0 found - 16 modified | TOTAL: 127 Iteration Number : 1 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 12 found - 12 modified | TOTAL: 18 pass 2 (+++): 0 found - 12 modified | TOTAL: 18 pass 1 (+++): 16 found - 16 modified | TOTAL: 34 pass 2 (+++): 0 found - 16 modified | TOTAL: 34 pass 1 (+++): 8 found - 8 modified | TOTAL: 42 pass 2 (+++): 0 found - 8 modified | TOTAL: 42 Iteration Number : 1 pass 1 (++): 111 found - 111 modified | TOTAL: 111 pass 2 (++): 0 found - 111 modified | TOTAL: 111 pass 1 (+-): 107 found - 107 modified | TOTAL: 218 pass 2 (+-): 0 found - 107 modified | TOTAL: 218 pass 1 (--): 76 found - 76 modified | TOTAL: 294 pass 2 (--): 0 found - 76 modified | TOTAL: 294 pass 1 (-+): 129 found - 129 modified | TOTAL: 423 pass 2 (-+): 0 found - 129 modified | TOTAL: 423 Iteration Number : 2 pass 1 (xy+): 7 found - 7 modified | TOTAL: 7 pass 2 (xy+): 0 found - 7 modified | TOTAL: 7 pass 1 (xy-): 5 found - 5 modified | TOTAL: 12 pass 2 (xy-): 0 found - 5 modified | TOTAL: 12 pass 1 (yz+): 5 found - 5 modified | TOTAL: 17 pass 2 (yz+): 0 found - 5 modified | TOTAL: 17 pass 1 (yz-): 0 found - 0 modified | TOTAL: 17 pass 1 (xz+): 4 found - 4 modified | TOTAL: 21 pass 2 (xz+): 0 found - 4 modified | TOTAL: 21 pass 1 (xz-): 1 found - 1 modified | TOTAL: 22 pass 2 (xz-): 0 found - 1 modified | TOTAL: 22 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 2 found - 2 modified | TOTAL: 5 pass 2 (-+): 0 found - 2 modified | TOTAL: 5 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 619 (out of 458471: 0.135014) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sat May 6 21:08:04 EDT 2017 /usr/local/freesurfer/subjects/Sub01/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.03746 0.00297 -0.00860 -6.10400; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30077; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.03746 0.00297 -0.00860 -6.10400; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30077; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1054 (min = 350, max = 1400), aspect = 0.53 (min = 0.10, max = 0.75) no need to search using seed (127, 113, 123), TAL = (1.0, -5.0, 15.0) talairach voxel to voxel transform 0.96383 -0.00025 0.00764 5.71925; 0.00219 0.80223 -0.25092 32.69804; -0.00653 0.24628 0.83561 -8.53304; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (127, 113, 123) --> (1.0, -5.0, 15.0) done. writing output to filled.mgz... filling took 0.6 minutes talairach cc position changed to (1.00, -5.00, 15.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, -5.00, 15.00) SRC: (111.69, 92.73, 121.36) search lh wm seed point around talairach space (-17.00, -5.00, 15.00), SRC: (146.39, 92.80, 121.13) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Sat May 6 21:08:40 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 3 found - 3 modified | TOTAL: 6 pass 2 (xy-): 0 found - 3 modified | TOTAL: 6 pass 1 (yz+): 3 found - 3 modified | TOTAL: 9 pass 2 (yz+): 0 found - 3 modified | TOTAL: 9 pass 1 (yz-): 4 found - 4 modified | TOTAL: 13 pass 2 (yz-): 0 found - 4 modified | TOTAL: 13 pass 1 (xz+): 1 found - 1 modified | TOTAL: 14 pass 2 (xz+): 0 found - 1 modified | TOTAL: 14 pass 1 (xz-): 0 found - 0 modified | TOTAL: 14 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 2 found - 2 modified | TOTAL: 4 pass 2 (--): 0 found - 2 modified | TOTAL: 4 pass 1 (-+): 2 found - 2 modified | TOTAL: 6 pass 2 (-+): 0 found - 2 modified | TOTAL: 6 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 20 (out of 218237: 0.009164) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 1349 vertices, 1498 faces slice 60: 8732 vertices, 9092 faces slice 70: 19762 vertices, 20127 faces slice 80: 30408 vertices, 30791 faces slice 90: 41692 vertices, 42040 faces slice 100: 52774 vertices, 53171 faces slice 110: 63455 vertices, 63851 faces slice 120: 74164 vertices, 74537 faces slice 130: 84574 vertices, 84973 faces slice 140: 94686 vertices, 95038 faces slice 150: 103172 vertices, 103543 faces slice 160: 110183 vertices, 110437 faces slice 170: 115666 vertices, 115872 faces slice 180: 119399 vertices, 119525 faces slice 190: 119952 vertices, 120002 faces slice 200: 119952 vertices, 120002 faces slice 210: 119952 vertices, 120002 faces slice 220: 119952 vertices, 120002 faces slice 230: 119952 vertices, 120002 faces slice 240: 119952 vertices, 120002 faces slice 250: 119952 vertices, 120002 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 119952 voxel in cpt #1: X=-50 [v=119952,e=360006,f=240004] located at (-27.871365, -20.728607, 31.213120) For the whole surface: X=-50 [v=119952,e=360006,f=240004] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Sat May 6 21:08:44 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 4 found - 4 modified | TOTAL: 7 pass 2 (xy-): 0 found - 4 modified | TOTAL: 7 pass 1 (yz+): 3 found - 3 modified | TOTAL: 10 pass 2 (yz+): 0 found - 3 modified | TOTAL: 10 pass 1 (yz-): 8 found - 8 modified | TOTAL: 18 pass 2 (yz-): 0 found - 8 modified | TOTAL: 18 pass 1 (xz+): 0 found - 0 modified | TOTAL: 18 pass 1 (xz-): 0 found - 0 modified | TOTAL: 18 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 21 (out of 221675: 0.009473) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 608 vertices, 708 faces slice 60: 6820 vertices, 7105 faces slice 70: 17156 vertices, 17555 faces slice 80: 28207 vertices, 28581 faces slice 90: 39077 vertices, 39435 faces slice 100: 50687 vertices, 51106 faces slice 110: 61678 vertices, 62060 faces slice 120: 72608 vertices, 73025 faces slice 130: 83151 vertices, 83563 faces slice 140: 93102 vertices, 93470 faces slice 150: 101999 vertices, 102339 faces slice 160: 109563 vertices, 109843 faces slice 170: 115639 vertices, 115879 faces slice 180: 119735 vertices, 119929 faces slice 190: 120862 vertices, 120916 faces slice 200: 120862 vertices, 120916 faces slice 210: 120862 vertices, 120916 faces slice 220: 120862 vertices, 120916 faces slice 230: 120862 vertices, 120916 faces slice 240: 120862 vertices, 120916 faces slice 250: 120862 vertices, 120916 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 120862 voxel in cpt #1: X=-54 [v=120862,e=362748,f=241832] located at (27.571899, -18.461262, 33.167397) For the whole surface: X=-54 [v=120862,e=362748,f=241832] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sat May 6 21:08:49 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh Sat May 6 21:08:53 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Sat May 6 21:08:57 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 43.4 mm, total surface area = 63302 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.5 minutes step 000: RMS=0.157 (target=0.015) step 005: RMS=0.118 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.056 (target=0.015) step 030: RMS=0.051 (target=0.015) step 035: RMS=0.046 (target=0.015) step 040: RMS=0.042 (target=0.015) step 045: RMS=0.040 (target=0.015) step 050: RMS=0.039 (target=0.015) step 055: RMS=0.038 (target=0.015) step 060: RMS=0.037 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 31.560000 mris_inflate stimesec 0.032000 mris_inflate ru_maxrss 158952 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 19202 mris_inflate ru_majflt 5 mris_inflate ru_nswap 0 mris_inflate ru_inblock 1048 mris_inflate ru_oublock 8440 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 5 mris_inflate ru_nivcsw 53 #-------------------------------------------- #@# Inflation1 rh Sat May 6 21:09:28 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 43.0 mm, total surface area = 63627 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.5 minutes step 000: RMS=0.155 (target=0.015) step 005: RMS=0.117 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.055 (target=0.015) step 030: RMS=0.049 (target=0.015) step 035: RMS=0.043 (target=0.015) step 040: RMS=0.040 (target=0.015) step 045: RMS=0.037 (target=0.015) step 050: RMS=0.034 (target=0.015) step 055: RMS=0.034 (target=0.015) step 060: RMS=0.033 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 31.728000 mris_inflate stimesec 0.024000 mris_inflate ru_maxrss 159948 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 19521 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8504 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 46 #-------------------------------------------- #@# QSphere lh Sat May 6 21:10:00 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.07 +- 0.59 (0.00-->6.69) (max @ vno 89466 --> 89486) face area 0.04 +- 0.04 (-0.20-->0.82) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.366... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.556, avgs=0 005/300: dt: 0.9000, rms radial error=174.298, avgs=0 010/300: dt: 0.9000, rms radial error=173.747, avgs=0 015/300: dt: 0.9000, rms radial error=173.029, avgs=0 020/300: dt: 0.9000, rms radial error=172.211, avgs=0 025/300: dt: 0.9000, rms radial error=171.337, avgs=0 030/300: dt: 0.9000, rms radial error=170.431, avgs=0 035/300: dt: 0.9000, rms radial error=169.508, avgs=0 040/300: dt: 0.9000, rms radial error=168.577, avgs=0 045/300: dt: 0.9000, rms radial error=167.644, avgs=0 050/300: dt: 0.9000, rms radial error=166.711, avgs=0 055/300: dt: 0.9000, rms radial error=165.780, avgs=0 060/300: dt: 0.9000, rms radial error=164.853, avgs=0 065/300: dt: 0.9000, rms radial error=163.931, avgs=0 070/300: dt: 0.9000, rms radial error=163.012, avgs=0 075/300: dt: 0.9000, rms radial error=162.098, avgs=0 080/300: dt: 0.9000, rms radial error=161.189, avgs=0 085/300: dt: 0.9000, rms radial error=160.285, avgs=0 090/300: dt: 0.9000, rms radial error=159.386, avgs=0 095/300: dt: 0.9000, rms radial error=158.492, avgs=0 100/300: dt: 0.9000, rms radial error=157.602, avgs=0 105/300: dt: 0.9000, rms radial error=156.717, avgs=0 110/300: dt: 0.9000, rms radial error=155.836, avgs=0 115/300: dt: 0.9000, rms radial error=154.960, avgs=0 120/300: dt: 0.9000, rms radial error=154.089, avgs=0 125/300: dt: 0.9000, rms radial error=153.222, avgs=0 130/300: dt: 0.9000, rms radial error=152.360, avgs=0 135/300: dt: 0.9000, rms radial error=151.502, avgs=0 140/300: dt: 0.9000, rms radial error=150.650, avgs=0 145/300: dt: 0.9000, rms radial error=149.802, avgs=0 150/300: dt: 0.9000, rms radial error=148.958, avgs=0 155/300: dt: 0.9000, rms radial error=148.119, avgs=0 160/300: dt: 0.9000, rms radial error=147.284, avgs=0 165/300: dt: 0.9000, rms radial error=146.454, avgs=0 170/300: dt: 0.9000, rms radial error=145.629, avgs=0 175/300: dt: 0.9000, rms radial error=144.808, avgs=0 180/300: dt: 0.9000, rms radial error=143.991, avgs=0 185/300: dt: 0.9000, rms radial error=143.179, avgs=0 190/300: dt: 0.9000, rms radial error=142.371, avgs=0 195/300: dt: 0.9000, rms radial error=141.568, avgs=0 200/300: dt: 0.9000, rms radial error=140.769, avgs=0 205/300: dt: 0.9000, rms radial error=139.975, avgs=0 210/300: dt: 0.9000, rms radial error=139.185, avgs=0 215/300: dt: 0.9000, rms radial error=138.400, avgs=0 220/300: dt: 0.9000, rms radial error=137.619, avgs=0 225/300: dt: 0.9000, rms radial error=136.842, avgs=0 230/300: dt: 0.9000, rms radial error=136.070, avgs=0 235/300: dt: 0.9000, rms radial error=135.301, avgs=0 240/300: dt: 0.9000, rms radial error=134.537, avgs=0 245/300: dt: 0.9000, rms radial error=133.778, avgs=0 250/300: dt: 0.9000, rms radial error=133.022, avgs=0 255/300: dt: 0.9000, rms radial error=132.271, avgs=0 260/300: dt: 0.9000, rms radial error=131.524, avgs=0 265/300: dt: 0.9000, rms radial error=130.781, avgs=0 270/300: dt: 0.9000, rms radial error=130.042, avgs=0 275/300: dt: 0.9000, rms radial error=129.307, avgs=0 280/300: dt: 0.9000, rms radial error=128.577, avgs=0 285/300: dt: 0.9000, rms radial error=127.850, avgs=0 290/300: dt: 0.9000, rms radial error=127.128, avgs=0 295/300: dt: 0.9000, rms radial error=126.410, avgs=0 300/300: dt: 0.9000, rms radial error=125.696, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 13185.69 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 2 (K=40.0), pass 1, starting sse = 1951.34 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00075 epoch 3 (K=160.0), pass 1, starting sse = 155.50 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/10 = 0.00597 epoch 4 (K=640.0), pass 1, starting sse = 10.73 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/13 = 0.00699 final distance error %23.02 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.05 hours mris_sphere utimesec 165.220000 mris_sphere stimesec 0.024000 mris_sphere ru_maxrss 159432 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 19215 mris_sphere ru_majflt 7 mris_sphere ru_nswap 0 mris_sphere ru_inblock 1304 mris_sphere ru_oublock 8440 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 7 mris_sphere ru_nivcsw 243 FSRUNTIME@ mris_sphere 0.0459 hours 1 threads #-------------------------------------------- #@# QSphere rh Sat May 6 21:12:46 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.07 +- 0.57 (0.00-->8.42) (max @ vno 53875 --> 53887) face area 0.03 +- 0.04 (-0.15-->1.15) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.364... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.664, avgs=0 005/300: dt: 0.9000, rms radial error=174.408, avgs=0 010/300: dt: 0.9000, rms radial error=173.857, avgs=0 015/300: dt: 0.9000, rms radial error=173.132, avgs=0 020/300: dt: 0.9000, rms radial error=172.305, avgs=0 025/300: dt: 0.9000, rms radial error=171.421, avgs=0 030/300: dt: 0.9000, rms radial error=170.511, avgs=0 035/300: dt: 0.9000, rms radial error=169.587, avgs=0 040/300: dt: 0.9000, rms radial error=168.655, avgs=0 045/300: dt: 0.9000, rms radial error=167.720, avgs=0 050/300: dt: 0.9000, rms radial error=166.786, avgs=0 055/300: dt: 0.9000, rms radial error=165.854, avgs=0 060/300: dt: 0.9000, rms radial error=164.926, avgs=0 065/300: dt: 0.9000, rms radial error=164.002, avgs=0 070/300: dt: 0.9000, rms radial error=163.082, avgs=0 075/300: dt: 0.9000, rms radial error=162.167, avgs=0 080/300: dt: 0.9000, rms radial error=161.256, avgs=0 085/300: dt: 0.9000, rms radial error=160.351, avgs=0 090/300: dt: 0.9000, rms radial error=159.450, avgs=0 095/300: dt: 0.9000, rms radial error=158.554, avgs=0 100/300: dt: 0.9000, rms radial error=157.662, avgs=0 105/300: dt: 0.9000, rms radial error=156.776, avgs=0 110/300: dt: 0.9000, rms radial error=155.894, avgs=0 115/300: dt: 0.9000, rms radial error=155.017, avgs=0 120/300: dt: 0.9000, rms radial error=154.145, avgs=0 125/300: dt: 0.9000, rms radial error=153.277, avgs=0 130/300: dt: 0.9000, rms radial error=152.415, avgs=0 135/300: dt: 0.9000, rms radial error=151.557, avgs=0 140/300: dt: 0.9000, rms radial error=150.704, avgs=0 145/300: dt: 0.9000, rms radial error=149.856, avgs=0 150/300: dt: 0.9000, rms radial error=149.012, avgs=0 155/300: dt: 0.9000, rms radial error=148.174, avgs=0 160/300: dt: 0.9000, rms radial error=147.341, avgs=0 165/300: dt: 0.9000, rms radial error=146.512, avgs=0 170/300: dt: 0.9000, rms radial error=145.688, avgs=0 175/300: dt: 0.9000, rms radial error=144.868, avgs=0 180/300: dt: 0.9000, rms radial error=144.053, avgs=0 185/300: dt: 0.9000, rms radial error=143.242, avgs=0 190/300: dt: 0.9000, rms radial error=142.436, avgs=0 195/300: dt: 0.9000, rms radial error=141.634, avgs=0 200/300: dt: 0.9000, rms radial error=140.836, avgs=0 205/300: dt: 0.9000, rms radial error=140.044, avgs=0 210/300: dt: 0.9000, rms radial error=139.255, avgs=0 215/300: dt: 0.9000, rms radial error=138.471, avgs=0 220/300: dt: 0.9000, rms radial error=137.691, avgs=0 225/300: dt: 0.9000, rms radial error=136.916, avgs=0 230/300: dt: 0.9000, rms radial error=136.145, avgs=0 235/300: dt: 0.9000, rms radial error=135.378, avgs=0 240/300: dt: 0.9000, rms radial error=134.616, avgs=0 245/300: dt: 0.9000, rms radial error=133.857, avgs=0 250/300: dt: 0.9000, rms radial error=133.103, avgs=0 255/300: dt: 0.9000, rms radial error=132.353, avgs=0 260/300: dt: 0.9000, rms radial error=131.607, avgs=0 265/300: dt: 0.9000, rms radial error=130.865, avgs=0 270/300: dt: 0.9000, rms radial error=130.128, avgs=0 275/300: dt: 0.9000, rms radial error=129.394, avgs=0 280/300: dt: 0.9000, rms radial error=128.665, avgs=0 285/300: dt: 0.9000, rms radial error=127.939, avgs=0 290/300: dt: 0.9000, rms radial error=127.218, avgs=0 295/300: dt: 0.9000, rms radial error=126.501, avgs=0 300/300: dt: 0.9000, rms radial error=125.788, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 13294.97 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 2 (K=40.0), pass 1, starting sse = 1948.99 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00037 epoch 3 (K=160.0), pass 1, starting sse = 156.98 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00630 epoch 4 (K=640.0), pass 1, starting sse = 10.44 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.17/16 = 0.01039 final distance error %22.74 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.05 hours mris_sphere utimesec 177.640000 mris_sphere stimesec 0.032000 mris_sphere ru_maxrss 160312 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 19535 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 8504 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 0 mris_sphere ru_nivcsw 249 FSRUNTIME@ mris_sphere 0.0494 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Sat May 6 21:15:43 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Sat May 6 21:15:43 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Sat May 6 21:15:43 EDT 2017 mris_fix_topology -rusage /usr/local/freesurfer/subjects/Sub01/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 Sub01 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-50 (nv=119952, nf=240004, ne=360006, g=26) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 6 iterations marking ambiguous vertices... 4009 ambiguous faces found in tessellation segmenting defects... 33 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 33 defects to be corrected 0 vertices coincident reading input surface /usr/local/freesurfer/subjects/Sub01/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.6978 (-4.8489) -vertex loglikelihood: -6.7075 (-3.3538) -normal dot loglikelihood: -3.6204 (-3.6204) -quad curv loglikelihood: -6.3526 (-3.1763) Total Loglikelihood : -26.3784 CORRECTING DEFECT 0 (vertices=79, convex hull=87, v0=0) After retessellation of defect 0 (v0=0), euler #=-30 (117504,351568,234034) : difference with theory (-30) = 0 CORRECTING DEFECT 1 (vertices=20, convex hull=38, v0=336) After retessellation of defect 1 (v0=336), euler #=-29 (117505,351585,234051) : difference with theory (-29) = 0 CORRECTING DEFECT 2 (vertices=27, convex hull=34, v0=1590) After retessellation of defect 2 (v0=1590), euler #=-28 (117507,351601,234066) : difference with theory (-28) = 0 CORRECTING DEFECT 3 (vertices=27, convex hull=34, v0=2304) After retessellation of defect 3 (v0=2304), euler #=-27 (117511,351626,234088) : difference with theory (-27) = 0 CORRECTING DEFECT 4 (vertices=12, convex hull=27, v0=2333) After retessellation of defect 4 (v0=2333), euler #=-26 (117513,351640,234101) : difference with theory (-26) = 0 CORRECTING DEFECT 5 (vertices=6, convex hull=26, v0=2335) After retessellation of defect 5 (v0=2335), euler #=-25 (117514,351650,234111) : difference with theory (-25) = 0 CORRECTING DEFECT 6 (vertices=12, convex hull=36, v0=2937) After retessellation of defect 6 (v0=2937), euler #=-24 (117515,351666,234127) : difference with theory (-24) = 0 CORRECTING DEFECT 7 (vertices=55, convex hull=110, v0=4116) After retessellation of defect 7 (v0=4116), euler #=-23 (117538,351784,234223) : difference with theory (-23) = 0 CORRECTING DEFECT 8 (vertices=114, convex hull=45, v0=10473) After retessellation of defect 8 (v0=10473), euler #=-22 (117552,351845,234271) : difference with theory (-22) = 0 CORRECTING DEFECT 9 (vertices=105, convex hull=87, v0=17353) After retessellation of defect 9 (v0=17353), euler #=-21 (117569,351932,234342) : difference with theory (-21) = 0 CORRECTING DEFECT 10 (vertices=10, convex hull=27, v0=22941) After retessellation of defect 10 (v0=22941), euler #=-20 (117571,351947,234356) : difference with theory (-20) = 0 CORRECTING DEFECT 11 (vertices=38, convex hull=91, v0=31927) After retessellation of defect 11 (v0=31927), euler #=-19 (117592,352045,234434) : difference with theory (-19) = 0 CORRECTING DEFECT 12 (vertices=32, convex hull=66, v0=34506) After retessellation of defect 12 (v0=34506), euler #=-18 (117603,352103,234482) : difference with theory (-18) = 0 CORRECTING DEFECT 13 (vertices=45, convex hull=97, v0=44030) After retessellation of defect 13 (v0=44030), euler #=-17 (117631,352225,234577) : difference with theory (-17) = 0 CORRECTING DEFECT 14 (vertices=89, convex hull=93, v0=48780) After retessellation of defect 14 (v0=48780), euler #=-16 (117652,352329,234661) : difference with theory (-16) = 0 CORRECTING DEFECT 15 (vertices=55, convex hull=89, v0=52870) After retessellation of defect 15 (v0=52870), euler #=-15 (117665,352405,234725) : difference with theory (-15) = 0 CORRECTING DEFECT 16 (vertices=28, convex hull=59, v0=63220) After retessellation of defect 16 (v0=63220), euler #=-14 (117675,352461,234772) : difference with theory (-14) = 0 CORRECTING DEFECT 17 (vertices=53, convex hull=69, v0=65630) After retessellation of defect 17 (v0=65630), euler #=-13 (117703,352578,234862) : difference with theory (-13) = 0 CORRECTING DEFECT 18 (vertices=83, convex hull=66, v0=65672) After retessellation of defect 18 (v0=65672), euler #=-12 (117714,352640,234914) : difference with theory (-12) = 0 CORRECTING DEFECT 19 (vertices=23, convex hull=23, v0=67635) After retessellation of defect 19 (v0=67635), euler #=-11 (117715,352650,234924) : difference with theory (-11) = 0 CORRECTING DEFECT 20 (vertices=28, convex hull=18, v0=75675) After retessellation of defect 20 (v0=75675), euler #=-10 (117720,352671,234941) : difference with theory (-10) = 0 CORRECTING DEFECT 21 (vertices=12, convex hull=25, v0=75929) After retessellation of defect 21 (v0=75929), euler #=-9 (117725,352694,234960) : difference with theory (-9) = 0 CORRECTING DEFECT 22 (vertices=18, convex hull=33, v0=83182) After retessellation of defect 22 (v0=83182), euler #=-8 (117735,352733,234990) : difference with theory (-8) = 0 CORRECTING DEFECT 23 (vertices=52, convex hull=89, v0=83850) After retessellation of defect 23 (v0=83850), euler #=-7 (117770,352872,235095) : difference with theory (-7) = 0 CORRECTING DEFECT 24 (vertices=106, convex hull=84, v0=84335) After retessellation of defect 24 (v0=84335), euler #=-6 (117814,353040,235220) : difference with theory (-6) = 0 CORRECTING DEFECT 25 (vertices=897, convex hull=437, v0=86248) L defect detected... After retessellation of defect 25 (v0=86248), euler #=-5 (118008,353855,235842) : difference with theory (-5) = 0 CORRECTING DEFECT 26 (vertices=69, convex hull=91, v0=86531) After retessellation of defect 26 (v0=86531), euler #=-4 (118045,354004,235955) : difference with theory (-4) = 0 CORRECTING DEFECT 27 (vertices=125, convex hull=89, v0=96186) After retessellation of defect 27 (v0=96186), euler #=-3 (118077,354139,236059) : difference with theory (-3) = 0 CORRECTING DEFECT 28 (vertices=50, convex hull=93, v0=99518) After retessellation of defect 28 (v0=99518), euler #=-2 (118101,354251,236148) : difference with theory (-2) = 0 CORRECTING DEFECT 29 (vertices=21, convex hull=27, v0=102661) After retessellation of defect 29 (v0=102661), euler #=-1 (118106,354273,236166) : difference with theory (-1) = 0 CORRECTING DEFECT 30 (vertices=21, convex hull=20, v0=105423) After retessellation of defect 30 (v0=105423), euler #=0 (118112,354298,236186) : difference with theory (0) = 0 CORRECTING DEFECT 31 (vertices=122, convex hull=68, v0=113113) After retessellation of defect 31 (v0=113113), euler #=1 (118134,354391,236258) : difference with theory (1) = 0 CORRECTING DEFECT 32 (vertices=24, convex hull=17, v0=118802) After retessellation of defect 32 (v0=118802), euler #=2 (118136,354402,236268) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.09-->11.94) (max @ vno 98501 --> 104413) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.09-->11.94) (max @ vno 98501 --> 104413) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 112 mutations (36.0%), 199 crossovers (64.0%), 191 vertices were eliminated building final representation... 1816 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=118136, nf=236268, ne=354402, g=0) writing corrected surface to /usr/local/freesurfer/subjects/Sub01/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 14.8 minutes 0 defective edges removing intersecting faces 000: 288 intersecting 001: 20 intersecting 002: 2 intersecting mris_fix_topology utimesec 886.892000 mris_fix_topology stimesec 0.076000 mris_fix_topology ru_maxrss 387880 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 50088 mris_fix_topology ru_majflt 8 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 1464 mris_fix_topology ru_oublock 11144 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 9 mris_fix_topology ru_nivcsw 1262 FSRUNTIME@ mris_fix_topology lh 0.2464 hours 1 threads #@# Fix Topology rh Sat May 6 21:30:30 EDT 2017 mris_fix_topology -rusage /usr/local/freesurfer/subjects/Sub01/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 Sub01 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-54 (nv=120862, nf=241832, ne=362748, g=28) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 7 iterations marking ambiguous vertices... 3455 ambiguous faces found in tessellation segmenting defects... 32 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 32 defects to be corrected 0 vertices coincident reading input surface /usr/local/freesurfer/subjects/Sub01/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5720 (-4.7860) -vertex loglikelihood: -6.6484 (-3.3242) -normal dot loglikelihood: -3.5968 (-3.5968) -quad curv loglikelihood: -6.4565 (-3.2282) Total Loglikelihood : -26.2737 CORRECTING DEFECT 0 (vertices=5, convex hull=22, v0=315) After retessellation of defect 0 (v0=315), euler #=-29 (118749,355360,236582) : difference with theory (-29) = 0 CORRECTING DEFECT 1 (vertices=61, convex hull=91, v0=489) After retessellation of defect 1 (v0=489), euler #=-28 (118771,355465,236666) : difference with theory (-28) = 0 CORRECTING DEFECT 2 (vertices=86, convex hull=71, v0=7372) After retessellation of defect 2 (v0=7372), euler #=-27 (118787,355540,236726) : difference with theory (-27) = 0 CORRECTING DEFECT 3 (vertices=17, convex hull=44, v0=10049) After retessellation of defect 3 (v0=10049), euler #=-26 (118795,355582,236761) : difference with theory (-26) = 0 CORRECTING DEFECT 4 (vertices=37, convex hull=39, v0=16745) After retessellation of defect 4 (v0=16745), euler #=-25 (118799,355607,236783) : difference with theory (-25) = 0 CORRECTING DEFECT 5 (vertices=28, convex hull=57, v0=16880) After retessellation of defect 5 (v0=16880), euler #=-24 (118810,355662,236828) : difference with theory (-24) = 0 CORRECTING DEFECT 6 (vertices=36, convex hull=80, v0=22202) After retessellation of defect 6 (v0=22202), euler #=-23 (118828,355747,236896) : difference with theory (-23) = 0 CORRECTING DEFECT 7 (vertices=32, convex hull=65, v0=23424) After retessellation of defect 7 (v0=23424), euler #=-22 (118845,355824,236957) : difference with theory (-22) = 0 CORRECTING DEFECT 8 (vertices=53, convex hull=65, v0=26923) After retessellation of defect 8 (v0=26923), euler #=-21 (118866,355913,237026) : difference with theory (-21) = 0 CORRECTING DEFECT 9 (vertices=5, convex hull=14, v0=35503) After retessellation of defect 9 (v0=35503), euler #=-20 (118867,355918,237031) : difference with theory (-20) = 0 CORRECTING DEFECT 10 (vertices=52, convex hull=72, v0=38678) After retessellation of defect 10 (v0=38678), euler #=-19 (118902,356053,237132) : difference with theory (-19) = 0 CORRECTING DEFECT 11 (vertices=26, convex hull=40, v0=38758) After retessellation of defect 11 (v0=38758), euler #=-18 (118911,356094,237165) : difference with theory (-18) = 0 CORRECTING DEFECT 12 (vertices=32, convex hull=77, v0=41481) After retessellation of defect 12 (v0=41481), euler #=-17 (118925,356166,237224) : difference with theory (-17) = 0 CORRECTING DEFECT 13 (vertices=253, convex hull=191, v0=44060) normal vector of length zero at vertex 119357 with 3 faces normal vector of length zero at vertex 119417 with 4 faces After retessellation of defect 13 (v0=44060), euler #=-16 (118994,356462,237452) : difference with theory (-16) = 0 CORRECTING DEFECT 14 (vertices=32, convex hull=73, v0=46705) After retessellation of defect 14 (v0=46705), euler #=-15 (119007,356528,237506) : difference with theory (-15) = 0 CORRECTING DEFECT 15 (vertices=28, convex hull=44, v0=46725) After retessellation of defect 15 (v0=46725), euler #=-14 (119017,356573,237542) : difference with theory (-14) = 0 CORRECTING DEFECT 16 (vertices=16, convex hull=16, v0=55585) After retessellation of defect 16 (v0=55585), euler #=-13 (119018,356579,237548) : difference with theory (-13) = 0 CORRECTING DEFECT 17 (vertices=101, convex hull=32, v0=66732) After retessellation of defect 17 (v0=66732), euler #=-12 (119028,356619,237579) : difference with theory (-12) = 0 CORRECTING DEFECT 18 (vertices=31, convex hull=72, v0=73713) After retessellation of defect 18 (v0=73713), euler #=-11 (119049,356710,237650) : difference with theory (-11) = 0 CORRECTING DEFECT 19 (vertices=63, convex hull=73, v0=75136) After retessellation of defect 19 (v0=75136), euler #=-10 (119082,356844,237752) : difference with theory (-10) = 0 CORRECTING DEFECT 20 (vertices=48, convex hull=63, v0=80969) After retessellation of defect 20 (v0=80969), euler #=-9 (119101,356927,237817) : difference with theory (-9) = 0 CORRECTING DEFECT 21 (vertices=35, convex hull=32, v0=83957) After retessellation of defect 21 (v0=83957), euler #=-8 (119110,356963,237845) : difference with theory (-8) = 0 CORRECTING DEFECT 22 (vertices=46, convex hull=65, v0=84562) After retessellation of defect 22 (v0=84562), euler #=-7 (119134,357061,237920) : difference with theory (-7) = 0 CORRECTING DEFECT 23 (vertices=654, convex hull=390, v0=84882) After retessellation of defect 23 (v0=84882), euler #=-6 (119274,357670,238390) : difference with theory (-6) = 0 CORRECTING DEFECT 24 (vertices=25, convex hull=62, v0=86039) After retessellation of defect 24 (v0=86039), euler #=-5 (119288,357735,238442) : difference with theory (-5) = 0 CORRECTING DEFECT 25 (vertices=62, convex hull=67, v0=86939) After retessellation of defect 25 (v0=86939), euler #=-4 (119296,357789,238489) : difference with theory (-4) = 0 CORRECTING DEFECT 26 (vertices=28, convex hull=47, v0=92766) After retessellation of defect 26 (v0=92766), euler #=-3 (119312,357856,238541) : difference with theory (-3) = 0 CORRECTING DEFECT 27 (vertices=118, convex hull=42, v0=96471) After retessellation of defect 27 (v0=96471), euler #=-2 (119323,357904,238579) : difference with theory (-2) = 0 CORRECTING DEFECT 28 (vertices=44, convex hull=31, v0=100197) After retessellation of defect 28 (v0=100197), euler #=-1 (119336,357952,238615) : difference with theory (-1) = 0 CORRECTING DEFECT 29 (vertices=11, convex hull=27, v0=100695) After retessellation of defect 29 (v0=100695), euler #=0 (119338,357966,238628) : difference with theory (0) = 0 CORRECTING DEFECT 30 (vertices=17, convex hull=56, v0=107175) After retessellation of defect 30 (v0=107175), euler #=1 (119347,358012,238666) : difference with theory (1) = 0 CORRECTING DEFECT 31 (vertices=30, convex hull=57, v0=118754) After retessellation of defect 31 (v0=118754), euler #=2 (119358,358068,238712) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.07-->9.37) (max @ vno 43637 --> 49622) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.07-->9.37) (max @ vno 43637 --> 49622) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 102 mutations (34.7%), 192 crossovers (65.3%), 161 vertices were eliminated building final representation... 1504 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=119358, nf=238712, ne=358068, g=0) writing corrected surface to /usr/local/freesurfer/subjects/Sub01/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 12.0 minutes 0 defective edges removing intersecting faces 000: 202 intersecting 001: 12 intersecting mris_fix_topology utimesec 717.812000 mris_fix_topology stimesec 0.060000 mris_fix_topology ru_maxrss 387724 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 48433 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 11256 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 0 mris_fix_topology ru_nivcsw 1269 FSRUNTIME@ mris_fix_topology rh 0.1994 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 118136 - 354402 + 236268 = 2 --> 0 holes F =2V-4: 236268 = 236272-4 (0) 2E=3F: 708804 = 708804 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 119358 - 358068 + 238712 = 2 --> 0 holes F =2V-4: 238712 = 238716-4 (0) 2E=3F: 716136 = 716136 (0) total defect index = 0 /usr/local/freesurfer/subjects/Sub01/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 45 intersecting 001: 9 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /usr/local/freesurfer/subjects/Sub01/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 48 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Sat May 6 21:42:35 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -mgz -T1 brain.finalsurfs Sub01 lh using white.preaparc as white matter name... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /usr/local/freesurfer/subjects/Sub01/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/Sub01/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/Sub01/mri/../mri/aseg.presurf.mgz... reading volume /usr/local/freesurfer/subjects/Sub01/mri/wm.mgz... 17673 bright wm thresholded. 1364 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/Sub01/surf/lh.orig... computing class statistics... border white: 222774 voxels (1.33%) border gray 251817 voxels (1.50%) WM (97.0): 96.9 +- 9.6 [70.0 --> 110.0] GM (65.0) : 65.2 +- 10.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 47.2 (was 70) setting MAX_BORDER_WHITE to 112.6 (was 105) setting MIN_BORDER_WHITE to 58.0 (was 85) setting MAX_CSF to 36.3 (was 40) setting MAX_GRAY to 93.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 47.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 25.5 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->3.90) (max @ vno 107384 --> 107904) face area 0.28 +- 0.12 (0.00-->3.46) mean absolute distance = 0.65 +- 0.77 3805 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-7.8, GM=58+-9.6 mean inside = 91.8, mean outside = 68.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=73.4, 38 (38) missing vertices, mean dist 0.4 [0.4 (%32.9)->0.8 (%67.1))] %75 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.25 (0.07-->4.28) (max @ vno 117852 --> 91217) face area 0.28 +- 0.13 (0.00-->3.59) mean absolute distance = 0.32 +- 0.50 3045 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4090675.5, rms=12.686 001: dt: 0.5000, sse=2294039.5, rms=9.035 (28.784%) 002: dt: 0.5000, sse=1522238.0, rms=6.886 (23.782%) 003: dt: 0.5000, sse=1138900.9, rms=5.511 (19.970%) 004: dt: 0.5000, sse=970453.1, rms=4.779 (13.276%) 005: dt: 0.5000, sse=893794.9, rms=4.402 (7.896%) 006: dt: 0.5000, sse=865733.9, rms=4.255 (3.344%) 007: dt: 0.5000, sse=850786.4, rms=4.169 (2.025%) rms = 4.14, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=845261.6, rms=4.136 (0.780%) 009: dt: 0.2500, sse=625879.1, rms=2.622 (36.605%) 010: dt: 0.2500, sse=579396.3, rms=2.178 (16.948%) 011: dt: 0.2500, sse=568392.6, rms=2.059 (5.455%) 012: dt: 0.2500, sse=560745.9, rms=1.970 (4.299%) rms = 1.93, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=558090.1, rms=1.932 (1.936%) 014: dt: 0.1250, sse=538964.6, rms=1.692 (12.442%) rms = 1.66, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=537393.8, rms=1.661 (1.808%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=77.3, 52 (14) missing vertices, mean dist -0.2 [0.3 (%77.3)->0.2 (%22.7))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= X1, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.05-->4.58) (max @ vno 117852 --> 91217) face area 0.36 +- 0.16 (0.00-->4.45) mean absolute distance = 0.22 +- 0.36 2565 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1300295.6, rms=5.576 016: dt: 0.5000, sse=940429.3, rms=3.883 (30.373%) rms = 4.16, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=779283.4, rms=2.808 (27.689%) 018: dt: 0.2500, sse=707061.1, rms=2.150 (23.407%) 019: dt: 0.2500, sse=676100.7, rms=1.811 (15.764%) 020: dt: 0.2500, sse=667032.4, rms=1.694 (6.463%) 021: dt: 0.2500, sse=660675.8, rms=1.607 (5.174%) rms = 1.57, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=657699.2, rms=1.567 (2.443%) 023: dt: 0.1250, sse=647684.8, rms=1.408 (10.191%) rms = 1.39, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=646302.3, rms=1.388 (1.391%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=79.7, 55 (13) missing vertices, mean dist -0.1 [0.2 (%70.7)->0.2 (%29.3))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= X1, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.11-->4.72) (max @ vno 117852 --> 91217) face area 0.34 +- 0.16 (0.00-->4.31) mean absolute distance = 0.19 +- 0.31 2217 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=829475.1, rms=3.329 rms = 3.54, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=696465.2, rms=2.263 (32.015%) 026: dt: 0.2500, sse=631873.7, rms=1.474 (34.873%) 027: dt: 0.2500, sse=626210.7, rms=1.363 (7.526%) rms = 1.33, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=622867.7, rms=1.334 (2.102%) 029: dt: 0.1250, sse=615683.2, rms=1.224 (8.298%) rms = 1.22, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=615566.3, rms=1.219 (0.385%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group mean border=80.5, 82 (10) missing vertices, mean dist -0.0 [0.2 (%55.6)->0.2 (%44.4))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= X1, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /usr/local/freesurfer/subjects/Sub01/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=632689.8, rms=1.601 rms = 2.22, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=600624.2, rms=1.069 (33.209%) 032: dt: 0.2500, sse=602623.7, rms=0.910 (14.879%) rms = 0.92, time step reduction 2 of 3 to 0.125... rms = 0.90, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=593795.4, rms=0.904 (0.688%) positioning took 0.3 minutes generating cortex label... 3 non-cortical segments detected only using segment with 7224 vertices erasing segment 1 (vno[0] = 82241) erasing segment 2 (vno[0] = 99066) writing cortex label to /usr/local/freesurfer/subjects/Sub01/label/lh.cortex.label... writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/lh.curv writing smoothed area to lh.area writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/lh.area vertex spacing 0.90 +- 0.25 (0.03-->4.80) (max @ vno 91217 --> 117852) face area 0.34 +- 0.16 (0.00-->4.17) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group smoothing surface for 5 iterations... mean border=45.7, 47 (47) missing vertices, mean dist 1.7 [0.0 (%0.0)->2.7 (%100.0))] %10 local maxima, %50 large gradients and %35 min vals, 287 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=27057996.0, rms=34.400 001: dt: 0.0500, sse=23668240.0, rms=32.130 (6.600%) 002: dt: 0.0500, sse=21054154.0, rms=30.263 (5.811%) 003: dt: 0.0500, sse=19034418.0, rms=28.737 (5.042%) 004: dt: 0.0500, sse=17431726.0, rms=27.466 (4.423%) 005: dt: 0.0500, sse=16122471.0, rms=26.382 (3.947%) 006: dt: 0.0500, sse=15019515.0, rms=25.433 (3.597%) 007: dt: 0.0500, sse=14072009.0, rms=24.588 (3.321%) 008: dt: 0.0500, sse=13242651.0, rms=23.824 (3.107%) 009: dt: 0.0500, sse=12509235.0, rms=23.128 (2.924%) 010: dt: 0.0500, sse=11852547.0, rms=22.486 (2.777%) positioning took 0.7 minutes mean border=45.4, 55 (20) missing vertices, mean dist 1.4 [0.1 (%0.2)->2.2 (%99.8))] %12 local maxima, %49 large gradients and %33 min vals, 271 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=12639914.0, rms=23.220 011: dt: 0.0500, sse=12039650.0, rms=22.636 (2.515%) 012: dt: 0.0500, sse=11495572.0, rms=22.093 (2.397%) 013: dt: 0.0500, sse=11000243.0, rms=21.587 (2.290%) 014: dt: 0.0500, sse=10547969.0, rms=21.115 (2.189%) 015: dt: 0.0500, sse=10133829.0, rms=20.672 (2.095%) 016: dt: 0.0500, sse=9753066.0, rms=20.257 (2.009%) 017: dt: 0.0500, sse=9400427.0, rms=19.865 (1.937%) 018: dt: 0.0500, sse=9073173.0, rms=19.493 (1.869%) 019: dt: 0.0500, sse=8768803.0, rms=19.141 (1.805%) 020: dt: 0.0500, sse=8484376.0, rms=18.807 (1.749%) positioning took 0.7 minutes mean border=45.3, 82 (16) missing vertices, mean dist 1.2 [0.1 (%3.7)->1.9 (%96.3))] %13 local maxima, %49 large gradients and %33 min vals, 260 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=8569341.0, rms=18.902 021: dt: 0.0500, sse=8297795.5, rms=18.578 (1.713%) 022: dt: 0.0500, sse=8044499.5, rms=18.271 (1.654%) 023: dt: 0.0500, sse=7805242.0, rms=17.976 (1.615%) 024: dt: 0.0500, sse=7581314.5, rms=17.695 (1.561%) 025: dt: 0.0500, sse=7371067.5, rms=17.428 (1.513%) 026: dt: 0.0500, sse=7173442.0, rms=17.172 (1.466%) 027: dt: 0.0500, sse=6985968.5, rms=16.926 (1.433%) 028: dt: 0.0500, sse=6807010.5, rms=16.688 (1.408%) 029: dt: 0.0500, sse=6635959.0, rms=16.456 (1.385%) 030: dt: 0.0500, sse=6472221.0, rms=16.232 (1.364%) positioning took 0.7 minutes mean border=45.3, 94 (14) missing vertices, mean dist 1.0 [0.1 (%13.0)->1.8 (%87.0))] %13 local maxima, %49 large gradients and %33 min vals, 207 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=6533289.0, rms=16.303 031: dt: 0.5000, sse=5404370.0, rms=14.672 (10.008%) 032: dt: 0.5000, sse=4604236.5, rms=13.389 (8.746%) 033: dt: 0.5000, sse=3967876.0, rms=12.273 (8.329%) 034: dt: 0.5000, sse=3440283.0, rms=11.261 (8.251%) 035: dt: 0.5000, sse=2968423.2, rms=10.273 (8.774%) 036: dt: 0.5000, sse=2533947.0, rms=9.270 (9.759%) 037: dt: 0.5000, sse=2142699.2, rms=8.268 (10.810%) 038: dt: 0.5000, sse=1822631.5, rms=7.346 (11.154%) 039: dt: 0.5000, sse=1574461.2, rms=6.546 (10.889%) 040: dt: 0.5000, sse=1403961.0, rms=5.930 (9.413%) 041: dt: 0.5000, sse=1290128.0, rms=5.485 (7.510%) 042: dt: 0.5000, sse=1228263.9, rms=5.222 (4.790%) 043: dt: 0.5000, sse=1187572.6, rms=5.046 (3.374%) 044: dt: 0.5000, sse=1168114.0, rms=4.955 (1.805%) 045: dt: 0.5000, sse=1150202.5, rms=4.874 (1.623%) rms = 4.84, time step reduction 1 of 3 to 0.250... 046: dt: 0.5000, sse=1143082.2, rms=4.838 (0.739%) 047: dt: 0.2500, sse=1036316.9, rms=4.262 (11.907%) 048: dt: 0.2500, sse=1006854.1, rms=4.102 (3.756%) rms = 4.09, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=1005550.4, rms=4.092 (0.256%) 050: dt: 0.1250, sse=987068.9, rms=3.983 (2.657%) rms = 3.97, time step reduction 3 of 3 to 0.062... 051: dt: 0.1250, sse=984745.4, rms=3.970 (0.334%) positioning took 1.8 minutes mean border=44.5, 1649 (6) missing vertices, mean dist 0.1 [0.2 (%52.8)->0.5 (%47.2))] %24 local maxima, %39 large gradients and %30 min vals, 99 gradients ignored tol=1.0e-04, sigma=1.0, host= X1, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1244827.6, rms=4.226 052: dt: 0.5000, sse=1225210.5, rms=4.140 (2.037%) rms = 4.17, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1127828.6, rms=3.542 (14.448%) 054: dt: 0.2500, sse=1097096.9, rms=3.340 (5.682%) rms = 3.29, time step reduction 2 of 3 to 0.125... 055: dt: 0.2500, sse=1089815.5, rms=3.292 (1.439%) 056: dt: 0.1250, sse=1070847.0, rms=3.151 (4.294%) rms = 3.13, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1067278.6, rms=3.128 (0.740%) positioning took 0.6 minutes mean border=43.8, 1631 (6) missing vertices, mean dist 0.1 [0.1 (%52.5)->0.4 (%47.5))] %38 local maxima, %26 large gradients and %30 min vals, 120 gradients ignored tol=1.0e-04, sigma=0.5, host= X1, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1114048.4, rms=3.450 rms = 3.82, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1085189.1, rms=3.252 (5.752%) 059: dt: 0.2500, sse=1074821.4, rms=3.188 (1.970%) rms = 3.19, time step reduction 2 of 3 to 0.125... rms = 3.16, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1070764.2, rms=3.156 (0.983%) positioning took 0.4 minutes mean border=43.1, 3370 (5) missing vertices, mean dist 0.1 [0.1 (%50.2)->0.3 (%49.8))] %44 local maxima, %20 large gradients and %29 min vals, 143 gradients ignored tol=1.0e-04, sigma=0.2, host= X1, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /usr/local/freesurfer/subjects/Sub01/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1095495.0, rms=3.329 rms = 3.68, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1073989.8, rms=3.174 (4.646%) 062: dt: 0.2500, sse=1060324.8, rms=3.092 (2.598%) rms = 3.08, time step reduction 2 of 3 to 0.125... 063: dt: 0.2500, sse=1056746.6, rms=3.077 (0.478%) 064: dt: 0.1250, sse=1040895.6, rms=2.956 (3.942%) rms = 2.93, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=1036681.9, rms=2.928 (0.923%) positioning took 0.5 minutes writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/lh.area.pial vertex spacing 1.05 +- 0.45 (0.10-->8.15) (max @ vno 80200 --> 80185) face area 0.43 +- 0.33 (0.00-->5.01) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 118136 vertices processed 25000 of 118136 vertices processed 50000 of 118136 vertices processed 75000 of 118136 vertices processed 100000 of 118136 vertices processed 0 of 118136 vertices processed 25000 of 118136 vertices processed 50000 of 118136 vertices processed 75000 of 118136 vertices processed 100000 of 118136 vertices processed thickness calculation complete, 549:974 truncations. 24298 vertices at 0 distance 75378 vertices at 1 distance 75394 vertices at 2 distance 33647 vertices at 3 distance 10729 vertices at 4 distance 3170 vertices at 5 distance 981 vertices at 6 distance 340 vertices at 7 distance 154 vertices at 8 distance 94 vertices at 9 distance 58 vertices at 10 distance 47 vertices at 11 distance 39 vertices at 12 distance 39 vertices at 13 distance 32 vertices at 14 distance 15 vertices at 15 distance 12 vertices at 16 distance 12 vertices at 17 distance 10 vertices at 18 distance 16 vertices at 19 distance 23 vertices at 20 distance writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/lh.thickness positioning took 10.6 minutes #-------------------------------------------- #@# Make White Surf rh Sat May 6 21:53:11 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -mgz -T1 brain.finalsurfs Sub01 rh using white.preaparc as white matter name... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /usr/local/freesurfer/subjects/Sub01/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/Sub01/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/Sub01/mri/../mri/aseg.presurf.mgz... reading volume /usr/local/freesurfer/subjects/Sub01/mri/wm.mgz... 17673 bright wm thresholded. 1364 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/Sub01/surf/rh.orig... computing class statistics... border white: 222774 voxels (1.33%) border gray 251817 voxels (1.50%) WM (97.0): 96.9 +- 9.6 [70.0 --> 110.0] GM (65.0) : 65.2 +- 10.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.2 (was 70) setting MAX_BORDER_WHITE to 113.6 (was 105) setting MIN_BORDER_WHITE to 60.0 (was 85) setting MAX_CSF to 38.3 (was 40) setting MAX_GRAY to 94.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 49.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 27.5 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->4.28) (max @ vno 105402 --> 119254) face area 0.28 +- 0.12 (0.00-->5.45) mean absolute distance = 0.64 +- 0.77 3630 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104+-7.8, GM=60+-8.7 mean inside = 92.3, mean outside = 69.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=74.5, 34 (34) missing vertices, mean dist 0.3 [0.5 (%34.4)->0.7 (%65.6))] %72 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.09-->5.49) (max @ vno 105402 --> 119254) face area 0.28 +- 0.13 (0.00-->6.27) mean absolute distance = 0.31 +- 0.52 2788 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3907435.5, rms=12.281 001: dt: 0.5000, sse=2161425.2, rms=8.633 (29.708%) 002: dt: 0.5000, sse=1438393.5, rms=6.543 (24.204%) 003: dt: 0.5000, sse=1088252.8, rms=5.249 (19.774%) 004: dt: 0.5000, sse=940924.1, rms=4.590 (12.563%) 005: dt: 0.5000, sse=876071.8, rms=4.263 (7.128%) 006: dt: 0.5000, sse=855029.1, rms=4.148 (2.704%) 007: dt: 0.5000, sse=841759.8, rms=4.073 (1.805%) rms = 4.05, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=838603.6, rms=4.052 (0.516%) 009: dt: 0.2500, sse=622969.3, rms=2.542 (37.270%) 010: dt: 0.2500, sse=576734.9, rms=2.090 (17.754%) 011: dt: 0.2500, sse=565862.7, rms=1.965 (6.012%) 012: dt: 0.2500, sse=558960.2, rms=1.882 (4.229%) rms = 1.84, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=555855.8, rms=1.840 (2.210%) 014: dt: 0.1250, sse=540810.2, rms=1.642 (10.773%) rms = 1.62, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=539137.4, rms=1.618 (1.473%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=78.3, 29 (6) missing vertices, mean dist -0.2 [0.3 (%76.3)->0.2 (%23.7))] %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= X1, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.10-->5.54) (max @ vno 105402 --> 119254) face area 0.35 +- 0.16 (0.00-->8.29) mean absolute distance = 0.22 +- 0.37 2406 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1279218.4, rms=5.453 016: dt: 0.5000, sse=924037.9, rms=3.759 (31.072%) rms = 4.04, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=770845.0, rms=2.710 (27.915%) 018: dt: 0.2500, sse=701373.6, rms=2.064 (23.827%) 019: dt: 0.2500, sse=672128.7, rms=1.722 (16.556%) 020: dt: 0.2500, sse=664964.6, rms=1.619 (5.998%) 021: dt: 0.2500, sse=658624.1, rms=1.539 (4.964%) rms = 1.51, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=658020.1, rms=1.509 (1.946%) 023: dt: 0.1250, sse=648861.3, rms=1.378 (8.651%) rms = 1.36, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=647692.2, rms=1.363 (1.112%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.8, 31 (3) missing vertices, mean dist -0.1 [0.2 (%70.8)->0.2 (%29.2))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= X1, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.07-->5.49) (max @ vno 105402 --> 119254) face area 0.34 +- 0.16 (0.00-->7.88) mean absolute distance = 0.19 +- 0.30 2176 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=839662.9, rms=3.356 rms = 3.48, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=705897.5, rms=2.311 (31.137%) 026: dt: 0.2500, sse=637411.3, rms=1.489 (35.559%) 027: dt: 0.2500, sse=627275.6, rms=1.345 (9.669%) rms = 1.30, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=623747.9, rms=1.296 (3.681%) 029: dt: 0.1250, sse=617677.2, rms=1.197 (7.649%) rms = 1.19, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=618672.6, rms=1.193 (0.273%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=81.5, 45 (3) missing vertices, mean dist -0.0 [0.2 (%55.6)->0.2 (%44.4))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= X1, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /usr/local/freesurfer/subjects/Sub01/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=635093.0, rms=1.567 rms = 2.14, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=602919.2, rms=1.045 (33.291%) 032: dt: 0.2500, sse=596603.2, rms=0.882 (15.638%) rms = 0.89, time step reduction 2 of 3 to 0.125... rms = 0.88, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=595744.9, rms=0.877 (0.533%) positioning took 0.3 minutes generating cortex label... 8 non-cortical segments detected only using segment with 6973 vertices erasing segment 1 (vno[0] = 48310) erasing segment 2 (vno[0] = 84732) erasing segment 3 (vno[0] = 84899) erasing segment 4 (vno[0] = 85863) erasing segment 5 (vno[0] = 86804) erasing segment 6 (vno[0] = 94238) erasing segment 7 (vno[0] = 99798) writing cortex label to /usr/local/freesurfer/subjects/Sub01/label/rh.cortex.label... writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/rh.curv writing smoothed area to rh.area writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/rh.area vertex spacing 0.90 +- 0.25 (0.04-->5.51) (max @ vno 105402 --> 119254) face area 0.34 +- 0.16 (0.00-->7.86) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group smoothing surface for 5 iterations... mean border=47.3, 57 (57) missing vertices, mean dist 1.8 [0.2 (%0.0)->2.6 (%100.0))] %12 local maxima, %52 large gradients and %31 min vals, 330 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=26398372.0, rms=33.777 001: dt: 0.0500, sse=23090802.0, rms=31.546 (6.605%) 002: dt: 0.0500, sse=20550192.0, rms=29.719 (5.792%) 003: dt: 0.0500, sse=18582602.0, rms=28.222 (5.036%) 004: dt: 0.0500, sse=17019540.0, rms=26.974 (4.422%) 005: dt: 0.0500, sse=15736022.0, rms=25.904 (3.966%) 006: dt: 0.0500, sse=14653095.0, rms=24.966 (3.623%) 007: dt: 0.0500, sse=13720388.0, rms=24.128 (3.355%) 008: dt: 0.0500, sse=12904517.0, rms=23.371 (3.139%) 009: dt: 0.0500, sse=12180810.0, rms=22.678 (2.965%) 010: dt: 0.0500, sse=11532293.0, rms=22.038 (2.820%) positioning took 0.7 minutes mean border=47.1, 43 (17) missing vertices, mean dist 1.5 [0.1 (%0.2)->2.1 (%99.8))] %14 local maxima, %52 large gradients and %29 min vals, 292 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=12316312.0, rms=22.774 011: dt: 0.0500, sse=11723101.0, rms=22.192 (2.554%) 012: dt: 0.0500, sse=11185353.0, rms=21.651 (2.437%) 013: dt: 0.0500, sse=10694495.0, rms=21.146 (2.336%) 014: dt: 0.0500, sse=10245862.0, rms=20.672 (2.238%) 015: dt: 0.0500, sse=9835072.0, rms=20.229 (2.144%) 016: dt: 0.0500, sse=9457711.0, rms=19.813 (2.056%) 017: dt: 0.0500, sse=9107882.0, rms=19.420 (1.986%) 018: dt: 0.0500, sse=8783490.0, rms=19.048 (1.917%) 019: dt: 0.0500, sse=8481931.0, rms=18.695 (1.852%) 020: dt: 0.0500, sse=8200460.0, rms=18.359 (1.795%) positioning took 0.7 minutes mean border=46.9, 57 (12) missing vertices, mean dist 1.2 [0.1 (%3.9)->1.8 (%96.1))] %15 local maxima, %52 large gradients and %29 min vals, 280 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=8277230.0, rms=18.446 021: dt: 0.0500, sse=8006744.0, rms=18.119 (1.772%) 022: dt: 0.0500, sse=7754499.5, rms=17.809 (1.712%) 023: dt: 0.0500, sse=7515908.0, rms=17.510 (1.676%) 024: dt: 0.0500, sse=7292802.5, rms=17.226 (1.621%) 025: dt: 0.0500, sse=7083465.5, rms=16.956 (1.572%) 026: dt: 0.0500, sse=6886530.5, rms=16.697 (1.526%) 027: dt: 0.0500, sse=6699643.0, rms=16.447 (1.494%) 028: dt: 0.0500, sse=6520985.0, rms=16.205 (1.472%) 029: dt: 0.0500, sse=6350140.0, rms=15.970 (1.451%) 030: dt: 0.0500, sse=6186575.5, rms=15.742 (1.430%) positioning took 0.7 minutes mean border=46.9, 93 (10) missing vertices, mean dist 1.0 [0.1 (%14.1)->1.7 (%85.9))] %15 local maxima, %52 large gradients and %28 min vals, 231 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=6269682.0, rms=15.844 031: dt: 0.5000, sse=5127860.5, rms=14.161 (10.623%) 032: dt: 0.5000, sse=4326705.5, rms=12.841 (9.317%) 033: dt: 0.5000, sse=3699238.8, rms=11.706 (8.841%) 034: dt: 0.5000, sse=3193173.8, rms=10.696 (8.628%) 035: dt: 0.5000, sse=2754381.8, rms=9.740 (8.935%) 036: dt: 0.5000, sse=2367965.8, rms=8.810 (9.550%) 037: dt: 0.5000, sse=2022077.0, rms=7.890 (10.438%) 038: dt: 0.5000, sse=1743439.9, rms=7.061 (10.512%) 039: dt: 0.5000, sse=1532220.8, rms=6.365 (9.864%) 040: dt: 0.5000, sse=1397723.4, rms=5.874 (7.710%) 041: dt: 0.5000, sse=1297742.6, rms=5.486 (6.600%) 042: dt: 0.5000, sse=1243880.4, rms=5.259 (4.132%) 043: dt: 0.5000, sse=1199758.8, rms=5.072 (3.569%) 044: dt: 0.5000, sse=1179206.2, rms=4.978 (1.846%) 045: dt: 0.5000, sse=1158601.4, rms=4.887 (1.841%) rms = 4.87, time step reduction 1 of 3 to 0.250... 046: dt: 0.5000, sse=1154445.1, rms=4.865 (0.432%) 047: dt: 0.2500, sse=1038447.1, rms=4.249 (12.661%) 048: dt: 0.2500, sse=1006287.9, rms=4.077 (4.066%) rms = 4.08, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=1006734.2, rms=4.076 (0.020%) 050: dt: 0.1250, sse=986161.9, rms=3.956 (2.940%) rms = 3.94, time step reduction 3 of 3 to 0.062... 051: dt: 0.1250, sse=983624.9, rms=3.941 (0.378%) positioning took 1.8 minutes mean border=45.9, 1478 (7) missing vertices, mean dist 0.1 [0.2 (%50.6)->0.5 (%49.4))] %27 local maxima, %40 large gradients and %27 min vals, 78 gradients ignored tol=1.0e-04, sigma=1.0, host= X1, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1260335.1, rms=4.281 052: dt: 0.5000, sse=1227867.0, rms=4.125 (3.641%) rms = 4.12, time step reduction 1 of 3 to 0.250... 053: dt: 0.5000, sse=1219679.4, rms=4.122 (0.077%) 054: dt: 0.2500, sse=1099904.8, rms=3.342 (18.929%) 055: dt: 0.2500, sse=1070267.1, rms=3.141 (5.991%) rms = 3.12, time step reduction 2 of 3 to 0.125... 056: dt: 0.2500, sse=1067748.2, rms=3.122 (0.631%) 057: dt: 0.1250, sse=1040890.4, rms=2.914 (6.658%) rms = 2.88, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1036046.1, rms=2.878 (1.211%) positioning took 0.6 minutes mean border=45.0, 1494 (6) missing vertices, mean dist 0.1 [0.1 (%50.1)->0.3 (%49.9))] %43 local maxima, %25 large gradients and %26 min vals, 108 gradients ignored tol=1.0e-04, sigma=0.5, host= X1, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1095903.2, rms=3.301 rms = 3.72, time step reduction 1 of 3 to 0.250... 059: dt: 0.2500, sse=1057159.4, rms=3.021 (8.463%) 060: dt: 0.2500, sse=1043928.9, rms=2.925 (3.175%) rms = 2.95, time step reduction 2 of 3 to 0.125... rms = 2.89, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=1039152.4, rms=2.886 (1.343%) positioning took 0.4 minutes mean border=44.3, 2877 (6) missing vertices, mean dist 0.1 [0.1 (%49.3)->0.3 (%50.7))] %48 local maxima, %19 large gradients and %25 min vals, 115 gradients ignored tol=1.0e-04, sigma=0.2, host= X1, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /usr/local/freesurfer/subjects/Sub01/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1063255.2, rms=3.074 rms = 3.54, time step reduction 1 of 3 to 0.250... 062: dt: 0.2500, sse=1040745.4, rms=2.900 (5.662%) 063: dt: 0.2500, sse=1030769.9, rms=2.837 (2.162%) rms = 2.86, time step reduction 2 of 3 to 0.125... rms = 2.80, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=1026285.9, rms=2.799 (1.356%) positioning took 0.4 minutes writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/rh.area.pial vertex spacing 1.04 +- 0.45 (0.03-->9.44) (max @ vno 79640 --> 78609) face area 0.43 +- 0.33 (0.00-->8.89) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 119358 vertices processed 25000 of 119358 vertices processed 50000 of 119358 vertices processed 75000 of 119358 vertices processed 100000 of 119358 vertices processed 0 of 119358 vertices processed 25000 of 119358 vertices processed 50000 of 119358 vertices processed 75000 of 119358 vertices processed 100000 of 119358 vertices processed thickness calculation complete, 548:1091 truncations. 25143 vertices at 0 distance 78286 vertices at 1 distance 75079 vertices at 2 distance 33745 vertices at 3 distance 10407 vertices at 4 distance 2791 vertices at 5 distance 876 vertices at 6 distance 288 vertices at 7 distance 115 vertices at 8 distance 59 vertices at 9 distance 39 vertices at 10 distance 46 vertices at 11 distance 38 vertices at 12 distance 24 vertices at 13 distance 33 vertices at 14 distance 23 vertices at 15 distance 15 vertices at 16 distance 9 vertices at 17 distance 20 vertices at 18 distance 15 vertices at 19 distance 13 vertices at 20 distance writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/rh.thickness positioning took 10.4 minutes #-------------------------------------------- #@# Smooth2 lh Sat May 6 22:03:35 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth2 rh Sat May 6 22:03:39 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Sat May 6 22:03:42 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_inflate -rusage /usr/local/freesurfer/subjects/Sub01/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 43.4 mm, total surface area = 72564 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.179 (target=0.015) step 005: RMS=0.125 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 0.5 minutes mris_inflate utimesec 31.160000 mris_inflate stimesec 0.020000 mris_inflate ru_maxrss 156416 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 19671 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 232 mris_inflate ru_oublock 9240 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 1 mris_inflate ru_nivcsw 63 #-------------------------------------------- #@# Inflation2 rh Sat May 6 22:04:14 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_inflate -rusage /usr/local/freesurfer/subjects/Sub01/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 43.2 mm, total surface area = 72808 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.179 (target=0.015) step 005: RMS=0.124 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.076 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 0.5 minutes mris_inflate utimesec 31.412000 mris_inflate stimesec 0.032000 mris_inflate ru_maxrss 158052 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 19051 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9336 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 58 #-------------------------------------------- #@# Curv .H and .K lh Sat May 6 22:04:45 EDT 2017 /usr/local/freesurfer/subjects/Sub01/surf mris_curvature -w lh.white.preaparc total integrated curvature = 7.791*4pi (97.908) --> -7 handles ICI = 140.6, FI = 1539.7, variation=23903.960 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 161 vertices thresholded to be in k1 ~ [-0.18 0.90], k2 ~ [-0.09 0.04] total integrated curvature = 0.581*4pi (7.298) --> 0 handles ICI = 1.4, FI = 8.2, variation=141.235 85 vertices thresholded to be in [-0.03 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 114 vertices thresholded to be in [-0.12 0.25] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.022 done. #-------------------------------------------- #@# Curv .H and .K rh Sat May 6 22:05:34 EDT 2017 /usr/local/freesurfer/subjects/Sub01/surf mris_curvature -w rh.white.preaparc total integrated curvature = -1.021*4pi (-12.828) --> 2 handles ICI = 138.6, FI = 1538.5, variation=23970.827 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 190 vertices thresholded to be in k1 ~ [-0.19 0.38], k2 ~ [-0.10 0.05] total integrated curvature = 0.579*4pi (7.275) --> 0 handles ICI = 1.4, FI = 7.9, variation=138.062 108 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 133 vertices thresholded to be in [-0.12 0.19] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.022 done. #----------------------------------------- #@# Curvature Stats lh Sat May 6 22:06:22 EDT 2017 /usr/local/freesurfer/subjects/Sub01/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm Sub01 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ Sub01/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 200 ] Gb_filter = 0 WARN: S lookup min: -0.503639 WARN: S explicit min: 0.000000 vertex = 970 #----------------------------------------- #@# Curvature Stats rh Sat May 6 22:06:25 EDT 2017 /usr/local/freesurfer/subjects/Sub01/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm Sub01 rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ Sub01/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 209 ] Gb_filter = 0 WARN: S lookup min: -0.400908 WARN: S explicit min: 0.000000 vertex = 909 Started at Sat May 6 18:26:21 EDT 2017 Ended at Sat May 6 22:06:27 EDT 2017 #@#%# recon-all-run-time-hours 3.668 recon-all -s Sub01 finished without error at Sat May 6 22:06:27 EDT 2017 New invocation of recon-all Sat May 20 17:02:04 EDT 2017 /usr/local/freesurfer/subjects/Sub01 /usr/local/freesurfer/bin/recon-all -autorecon2 -s Sub01 subjid Sub01 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 X1 4.4.0-77-generic #98-Ubuntu SMP Wed Apr 26 08:34:02 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63057 maxlocks unlimited maxsignal 63057 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 16284648 927368 13305100 341548 2052180 14659468 Swap: 16642044 0 16642044 ######################################## 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: 2017/05/20-21:02:04-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-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: 2017/05/20-21:02:04-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-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: 2017/05/20-21:02:04-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/20-21:02:04-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:04-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:04-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/20-21:02:04-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/20-21:02:04-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/20-21:02:04-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/20-21:02:04-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/20-21:02:04-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/20-21:02:04-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:04-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-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: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-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: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/05/20-21:02:05-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-77-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 ####################################### #------------------------------------- #@# EM Registration Sat May 20 17:02:05 EDT 2017 /usr/local/freesurfer/subjects/Sub01/mri mri_em_register -rusage /usr/local/freesurfer/subjects/Sub01/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=22.0 skull bounding box = (57, 45, 44) --> (197, 173, 188) using (104, 88, 116) as brain centroid... mean wm in atlas = 107, using box (87,72,98) --> (121, 103,133) to find MRI wm before smoothing, mri peak at 97 robust fit to distribution - 98 +- 5.7 after smoothing, mri peak at 98, scaling input intensities by 1.092 scaling channel 0 by 1.09184 initial log_p = -4.348 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.195919 @ (-9.091, 9.091, -9.091) max log p = -4.114071 @ (4.545, 13.636, -4.545) max log p = -4.039539 @ (2.273, -2.273, -2.273) max log p = -4.036994 @ (1.136, -7.955, 5.682) max log p = -4.029094 @ (0.568, 3.977, -0.568) max log p = -4.029094 @ (0.000, 0.000, 0.000) Found translation: (-0.6, 16.5, -10.8): log p = -4.029 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.745, old_max_log_p =-4.029 (thresh=-4.0) 1.00000 0.00000 0.00000 -0.56818; 0.00000 1.11081 0.29764 -29.51373; 0.00000 -0.29764 1.11081 14.42485; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.745, old_max_log_p =-3.745 (thresh=-3.7) 1.00000 0.00000 0.00000 -0.56818; 0.00000 1.11081 0.29764 -29.51373; 0.00000 -0.29764 1.11081 14.42485; 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=-3.634, old_max_log_p =-3.745 (thresh=-3.7) 1.03750 0.00000 0.00000 -7.21713; 0.00000 1.13127 0.37807 -38.62608; 0.00000 -0.36802 1.06630 28.29821; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.627, old_max_log_p =-3.634 (thresh=-3.6) 1.03750 0.00000 0.00000 -7.21713; 0.00000 1.14270 0.34298 -34.14238; 0.00000 -0.33701 1.09831 21.63006; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.627, old_max_log_p =-3.627 (thresh=-3.6) 1.03750 0.00000 0.00000 -7.21713; 0.00000 1.14270 0.34298 -34.14238; 0.00000 -0.33701 1.09831 21.63006; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.574, old_max_log_p =-3.627 (thresh=-3.6) 1.03625 0.00297 -0.00859 -5.94888; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30078; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.571, old_max_log_p =-3.574 (thresh=-3.6) 1.03746 0.00297 -0.00860 -6.10401; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30078; 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 1.03746 0.00297 -0.00860 -6.10401; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30078; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.03746 0.00297 -0.00860 -6.10401; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30078; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03746 0.00297 -0.00860 -6.10401; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30078; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.571 (old=-4.348) transform before final EM align: 1.03746 0.00297 -0.00860 -6.10401; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30078; 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 1.03746 0.00297 -0.00860 -6.10401; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30078; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.03746 0.00297 -0.00860 -6.10401; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30078; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.0 tol 0.000000 final transform: 1.03746 0.00297 -0.00860 -6.10401; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30078; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 600.320000 mri_em_register stimesec 0.680000 mri_em_register ru_maxrss 605144 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 158386 mri_em_register ru_majflt 6 mri_em_register ru_nswap 0 mri_em_register ru_inblock 152312 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 13 mri_em_register ru_nivcsw 1537 registration took 10 minutes and 1 seconds. #-------------------------------------- #@# CA Normalize Sat May 20 17:12:06 EDT 2017 /usr/local/freesurfer/subjects/Sub01/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=22.0 skull bounding box = (57, 45, 44) --> (197, 173, 188) using (104, 88, 116) as brain centroid... mean wm in atlas = 107, using box (87,72,98) --> (121, 103,133) to find MRI wm before smoothing, mri peak at 97 robust fit to distribution - 98 +- 5.7 after smoothing, mri peak at 98, scaling input intensities by 1.092 scaling channel 0 by 1.09184 using 246344 sample points... INFO: compute sample coordinates transform 1.03746 0.00297 -0.00860 -6.10401; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30078; 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 (127, 46, 43) --> (192, 147, 186) Left_Cerebral_White_Matter: limiting intensities to 99.0 --> 132.0 8 of 507 (1.6%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 46, 42) --> (130, 140, 186) Right_Cerebral_White_Matter: limiting intensities to 115.0 --> 132.0 106 of 571 (18.6%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 125, 70) --> (176, 161, 117) Left_Cerebellum_White_Matter: limiting intensities to 103.0 --> 132.0 4 of 12 (33.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 125, 68) --> (128, 160, 117) Right_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 8 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 112, 100) --> (145, 171, 126) Brain_Stem: limiting intensities to 88.0 --> 132.0 0 of 19 (0.0%) samples deleted using 1117 total control points for intensity normalization... bias field = 0.888 +- 0.054 0 of 999 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (127, 46, 43) --> (192, 147, 186) Left_Cerebral_White_Matter: limiting intensities to 109.0 --> 132.0 772 of 1097 (70.4%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 46, 42) --> (130, 140, 186) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 58 of 1565 (3.7%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 125, 70) --> (176, 161, 117) Left_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0 65 of 73 (89.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 125, 68) --> (128, 160, 117) Right_Cerebellum_White_Matter: limiting intensities to 94.0 --> 132.0 33 of 72 (45.8%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 112, 100) --> (145, 171, 126) Brain_Stem: limiting intensities to 88.0 --> 132.0 95 of 114 (83.3%) samples deleted using 2921 total control points for intensity normalization... bias field = 1.017 +- 0.089 0 of 1889 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (127, 46, 43) --> (192, 147, 186) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 51 of 1266 (4.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 46, 42) --> (130, 140, 186) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 35 of 1657 (2.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 125, 70) --> (176, 161, 117) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 116 of 134 (86.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 125, 68) --> (128, 160, 117) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 49 of 88 (55.7%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (112, 112, 100) --> (145, 171, 126) Brain_Stem: limiting intensities to 88.0 --> 132.0 216 of 226 (95.6%) samples deleted using 3371 total control points for intensity normalization... bias field = 1.066 +- 0.068 0 of 2831 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 9 seconds. #-------------------------------------- #@# CA Reg Sat May 20 17:13:15 EDT 2017 /usr/local/freesurfer/subjects/Sub01/mri mri_ca_register -rusage /usr/local/freesurfer/subjects/Sub01/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) = 1.42 (predicted orig area = 5.6) 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=0.831, neg=0, invalid=762 0001: dt=197.271318, rms=0.759 (8.647%), neg=0, invalid=762 0002: dt=206.961039, rms=0.741 (2.371%), neg=0, invalid=762 0003: dt=156.220472, rms=0.734 (0.896%), neg=0, invalid=762 0004: dt=369.920000, rms=0.727 (0.955%), neg=0, invalid=762 0005: dt=129.472000, rms=0.723 (0.564%), neg=0, invalid=762 0006: dt=517.888000, rms=0.717 (0.798%), neg=0, invalid=762 0007: dt=110.976000, rms=0.715 (0.369%), neg=0, invalid=762 0008: dt=2071.552000, rms=0.704 (1.475%), neg=0, invalid=762 0009: dt=92.480000, rms=0.701 (0.462%), neg=0, invalid=762 0010: dt=517.888000, rms=0.700 (0.152%), neg=0, invalid=762 0011: dt=517.888000, rms=0.700 (-0.489%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.700, neg=0, invalid=762 0012: dt=129.472000, rms=0.698 (0.299%), neg=0, invalid=762 0013: dt=517.888000, rms=0.695 (0.387%), neg=0, invalid=762 0014: dt=129.472000, rms=0.695 (0.070%), neg=0, invalid=762 0015: dt=129.472000, rms=0.694 (0.050%), neg=0, invalid=762 0016: dt=129.472000, rms=0.694 (0.086%), neg=0, invalid=762 0017: dt=129.472000, rms=0.693 (0.111%), neg=0, invalid=762 0018: dt=129.472000, rms=0.692 (0.138%), neg=0, invalid=762 0019: dt=129.472000, rms=0.691 (0.156%), neg=0, invalid=762 0020: dt=129.472000, rms=0.690 (0.173%), neg=0, invalid=762 0021: dt=129.472000, rms=0.689 (0.184%), neg=0, invalid=762 0022: dt=129.472000, rms=0.687 (0.181%), neg=0, invalid=762 0023: dt=129.472000, rms=0.686 (0.184%), neg=0, invalid=762 0024: dt=129.472000, rms=0.685 (0.185%), neg=0, invalid=762 0025: dt=129.472000, rms=0.684 (0.185%), neg=0, invalid=762 0026: dt=129.472000, rms=0.682 (0.178%), neg=0, invalid=762 0027: dt=129.472000, rms=0.681 (0.163%), neg=0, invalid=762 0028: dt=129.472000, rms=0.680 (0.148%), neg=0, invalid=762 0029: dt=129.472000, rms=0.679 (0.138%), neg=0, invalid=762 0030: dt=129.472000, rms=0.678 (0.137%), neg=0, invalid=762 0031: dt=129.472000, rms=0.677 (0.138%), neg=0, invalid=762 0032: dt=129.472000, rms=0.677 (0.131%), neg=0, invalid=762 0033: dt=129.472000, rms=0.676 (0.117%), neg=0, invalid=762 0034: dt=129.472000, rms=0.675 (0.102%), neg=0, invalid=762 0035: dt=887.808000, rms=0.675 (0.046%), neg=0, invalid=762 0036: dt=887.808000, rms=0.675 (-0.724%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.679, neg=0, invalid=762 0037: dt=169.539623, rms=0.671 (1.115%), neg=0, invalid=762 0038: dt=258.359447, rms=0.658 (1.938%), neg=0, invalid=762 0039: dt=65.021277, rms=0.653 (0.828%), neg=0, invalid=762 0040: dt=145.152000, rms=0.650 (0.449%), neg=0, invalid=762 0041: dt=78.125341, rms=0.647 (0.389%), neg=0, invalid=762 0042: dt=122.181818, rms=0.645 (0.458%), neg=0, invalid=762 0043: dt=36.288000, rms=0.643 (0.248%), neg=0, invalid=762 0044: dt=36.288000, rms=0.642 (0.129%), neg=0, invalid=762 0045: dt=36.288000, rms=0.641 (0.212%), neg=0, invalid=762 0046: dt=36.288000, rms=0.639 (0.304%), neg=0, invalid=762 0047: dt=36.288000, rms=0.636 (0.393%), neg=0, invalid=762 0048: dt=36.288000, rms=0.634 (0.431%), neg=0, invalid=762 0049: dt=36.288000, rms=0.631 (0.444%), neg=0, invalid=762 0050: dt=36.288000, rms=0.628 (0.441%), neg=0, invalid=762 0051: dt=36.288000, rms=0.625 (0.414%), neg=0, invalid=762 0052: dt=36.288000, rms=0.623 (0.386%), neg=0, invalid=762 0053: dt=36.288000, rms=0.621 (0.370%), neg=0, invalid=762 0054: dt=36.288000, rms=0.618 (0.346%), neg=0, invalid=762 0055: dt=36.288000, rms=0.617 (0.308%), neg=0, invalid=762 0056: dt=36.288000, rms=0.615 (0.272%), neg=0, invalid=762 0057: dt=36.288000, rms=0.613 (0.237%), neg=0, invalid=762 0058: dt=36.288000, rms=0.612 (0.206%), neg=0, invalid=762 0059: dt=36.288000, rms=0.611 (0.183%), neg=0, invalid=762 0060: dt=36.288000, rms=0.610 (0.165%), neg=0, invalid=762 0061: dt=36.288000, rms=0.609 (0.145%), neg=0, invalid=762 0062: dt=36.288000, rms=0.608 (0.135%), neg=0, invalid=762 0063: dt=36.288000, rms=0.608 (0.124%), neg=0, invalid=762 0064: dt=36.288000, rms=0.607 (0.116%), neg=0, invalid=762 0065: dt=580.608000, rms=0.606 (0.143%), neg=0, invalid=762 0066: dt=31.104000, rms=0.606 (0.014%), neg=0, invalid=762 0067: dt=31.104000, rms=0.606 (0.004%), neg=0, invalid=762 0068: dt=31.104000, rms=0.606 (0.002%), neg=0, invalid=762 0069: dt=31.104000, rms=0.606 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.606, neg=0, invalid=762 0070: dt=124.416000, rms=0.604 (0.464%), neg=0, invalid=762 0071: dt=62.208000, rms=0.603 (0.081%), neg=0, invalid=762 0072: dt=62.208000, rms=0.603 (0.020%), neg=0, invalid=762 0073: dt=62.208000, rms=0.603 (0.020%), neg=0, invalid=762 0074: dt=62.208000, rms=0.603 (0.012%), neg=0, invalid=762 0075: dt=62.208000, rms=0.603 (-0.028%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.625, neg=0, invalid=762 0076: dt=0.700000, rms=0.625 (0.078%), neg=0, invalid=762 0077: dt=0.700000, rms=0.625 (0.002%), neg=0, invalid=762 0078: dt=0.700000, rms=0.625 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.625, neg=0, invalid=762 0079: dt=0.150000, rms=0.625 (0.077%), neg=0, invalid=762 0080: dt=0.043750, rms=0.625 (0.000%), neg=0, invalid=762 0081: dt=0.043750, rms=0.625 (-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=0.690, neg=0, invalid=762 0082: dt=5.435897, rms=0.670 (2.924%), neg=0, invalid=762 0083: dt=2.245614, rms=0.669 (0.071%), neg=0, invalid=762 0084: dt=2.245614, rms=0.669 (-0.041%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.669, neg=0, invalid=762 0085: dt=0.000000, rms=0.669 (0.050%), neg=0, invalid=762 0086: dt=0.000000, rms=0.669 (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=0.732, neg=0, invalid=762 0087: dt=1.280000, rms=0.728 (0.524%), neg=0, invalid=762 0088: dt=1.921569, rms=0.723 (0.720%), neg=0, invalid=762 0089: dt=0.320000, rms=0.723 (0.014%), neg=0, invalid=762 0090: dt=0.320000, rms=0.723 (0.013%), neg=0, invalid=762 0091: dt=0.320000, rms=0.723 (0.009%), neg=0, invalid=762 0092: dt=0.320000, rms=0.723 (-0.016%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.723, neg=0, invalid=762 0093: dt=1.792000, rms=0.721 (0.299%), neg=0, invalid=762 0094: dt=0.000000, rms=0.721 (0.001%), neg=0, invalid=762 0095: dt=0.100000, rms=0.721 (-0.002%), 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=0.676, neg=0, invalid=762 0096: dt=0.981271, rms=0.653 (3.478%), neg=0, invalid=762 0097: dt=0.096000, rms=0.652 (0.189%), neg=0, invalid=762 0098: dt=0.096000, rms=0.652 (-0.135%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.652, neg=0, invalid=762 0099: dt=0.028000, rms=0.652 (0.064%), neg=0, invalid=762 0100: dt=0.000000, rms=0.652 (0.000%), neg=0, invalid=762 0101: dt=0.050000, rms=0.652 (-0.034%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.14577 ( 9) Left_Lateral_Ventricle (4): linear fit = 0.34 x + 0.0 (805 voxels, overlap=0.018) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (805 voxels, peak = 7), gca=8.0 gca peak = 0.15565 (16) mri peak = 0.12992 ( 9) Right_Lateral_Ventricle (43): linear fit = 0.56 x + 0.0 (807 voxels, overlap=0.147) Right_Lateral_Ventricle (43): linear fit = 0.56 x + 0.0 (807 voxels, peak = 9), gca=8.9 gca peak = 0.26829 (96) mri peak = 0.08429 (92) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (734 voxels, overlap=0.763) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (734 voxels, peak = 91), gca=90.7 gca peak = 0.20183 (93) mri peak = 0.07164 (83) Left_Pallidum (13): linear fit = 0.89 x + 0.0 (581 voxels, overlap=0.592) Left_Pallidum (13): linear fit = 0.89 x + 0.0 (581 voxels, peak = 83), gca=83.2 gca peak = 0.21683 (55) mri peak = 0.11339 (57) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (647 voxels, overlap=0.992) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (647 voxels, peak = 56), gca=56.4 gca peak = 0.30730 (58) mri peak = 0.09939 (57) Left_Hippocampus (17): linear fit = 0.96 x + 0.0 (737 voxels, overlap=0.963) Left_Hippocampus (17): linear fit = 0.96 x + 0.0 (737 voxels, peak = 56), gca=56.0 gca peak = 0.11430 (101) mri peak = 0.06410 (98) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (49953 voxels, overlap=0.902) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (49953 voxels, peak = 103), gca=102.5 gca peak = 0.12076 (102) mri peak = 0.06625 (98) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (47716 voxels, overlap=0.943) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (47716 voxels, peak = 103), gca=102.5 gca peak = 0.14995 (59) mri peak = 0.04310 (53) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (16052 voxels, overlap=0.988) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (16052 voxels, peak = 54), gca=54.0 gca peak = 0.15082 (58) mri peak = 0.04323 (56) Right_Cerebral_Cortex (42): linear fit = 0.94 x + 0.0 (15841 voxels, overlap=0.981) Right_Cerebral_Cortex (42): linear fit = 0.94 x + 0.0 (15841 voxels, peak = 55), gca=54.8 gca peak = 0.14161 (67) mri peak = 0.09622 (61) Right_Caudate (50): linear fit = 0.93 x + 0.0 (712 voxels, overlap=0.798) Right_Caudate (50): linear fit = 0.93 x + 0.0 (712 voxels, peak = 62), gca=62.0 gca peak = 0.15243 (71) mri peak = 0.07775 (67) Left_Caudate (11): linear fit = 0.90 x + 0.0 (833 voxels, overlap=0.430) Left_Caudate (11): linear fit = 0.90 x + 0.0 (833 voxels, peak = 64), gca=64.3 gca peak = 0.13336 (57) mri peak = 0.04909 (48) Left_Cerebellum_Cortex (8): linear fit = 0.89 x + 0.0 (26052 voxels, overlap=0.557) Left_Cerebellum_Cortex (8): linear fit = 0.89 x + 0.0 (26052 voxels, peak = 51), gca=51.0 gca peak = 0.13252 (56) mri peak = 0.03657 (54) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (22345 voxels, overlap=0.979) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (22345 voxels, peak = 54), gca=54.0 gca peak = 0.18181 (84) mri peak = 0.05988 (84) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7487 voxels, overlap=0.975) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7487 voxels, peak = 84), gca=84.0 gca peak = 0.20573 (83) mri peak = 0.06153 (86) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (6032 voxels, overlap=0.872) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (6032 voxels, peak = 85), gca=85.1 gca peak = 0.21969 (57) mri peak = 0.08440 (55) Left_Amygdala (18): linear fit = 0.94 x + 0.0 (306 voxels, overlap=0.999) Left_Amygdala (18): linear fit = 0.94 x + 0.0 (306 voxels, peak = 54), gca=53.9 gca peak = 0.39313 (56) mri peak = 0.11905 (53) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (378 voxels, overlap=1.003) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (378 voxels, peak = 52), gca=52.4 gca peak = 0.14181 (85) mri peak = 0.06373 (75) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (4738 voxels, overlap=0.913) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (4738 voxels, peak = 81), gca=81.2 gca peak = 0.11978 (83) mri peak = 0.08175 (77) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3972 voxels, overlap=0.926) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3972 voxels, peak = 83), gca=82.6 gca peak = 0.13399 (79) mri peak = 0.06204 (82) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1815 voxels, overlap=0.996) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1815 voxels, peak = 79), gca=79.0 gca peak = 0.14159 (79) mri peak = 0.06078 (75) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1770 voxels, overlap=0.993) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1770 voxels, peak = 79), gca=79.0 gca peak = 0.10025 (80) mri peak = 0.21641 (80) Brain_Stem (16): linear fit = 1.05 x + 0.0 (9913 voxels, overlap=0.401) Brain_Stem (16): linear fit = 1.05 x + 0.0 (9913 voxels, peak = 84), gca=84.4 gca peak = 0.13281 (86) mri peak = 0.10758 (84) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (903 voxels, overlap=0.725) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (903 voxels, peak = 92), gca=92.5 gca peak = 0.12801 (89) mri peak = 0.09424 (83) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1076 voxels, overlap=0.814) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1076 voxels, peak = 90), gca=90.3 gca peak = 0.20494 (23) mri peak = 0.22232 (11) gca peak = 0.15061 (21) mri peak = 0.09684 (10) Fourth_Ventricle (15): linear fit = 0.44 x + 0.0 (283 voxels, overlap=0.287) Fourth_Ventricle (15): linear fit = 0.44 x + 0.0 (283 voxels, peak = 9), gca=9.1 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 0.95 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.48 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.652, neg=0, invalid=762 0102: dt=129.472000, rms=0.649 (0.533%), neg=0, invalid=762 0103: dt=295.936000, rms=0.646 (0.490%), neg=0, invalid=762 0104: dt=73.984000, rms=0.645 (0.121%), neg=0, invalid=762 0105: dt=517.888000, rms=0.642 (0.488%), neg=0, invalid=762 0106: dt=73.984000, rms=0.641 (0.037%), neg=0, invalid=762 0107: dt=73.984000, rms=0.641 (0.034%), neg=0, invalid=762 0108: dt=73.984000, rms=0.641 (0.060%), neg=0, invalid=762 0109: dt=73.984000, rms=0.640 (0.074%), neg=0, invalid=762 0110: dt=73.984000, rms=0.640 (0.089%), neg=0, invalid=762 0111: dt=73.984000, rms=0.639 (0.099%), neg=0, invalid=762 0112: dt=73.984000, rms=0.639 (0.105%), neg=0, invalid=762 0113: dt=73.984000, rms=0.638 (0.097%), neg=0, invalid=762 0114: dt=73.984000, rms=0.637 (0.082%), neg=0, invalid=762 0115: dt=73.984000, rms=0.637 (0.065%), neg=0, invalid=762 0116: dt=73.984000, rms=0.637 (0.048%), neg=0, invalid=762 0117: dt=73.984000, rms=0.636 (0.041%), neg=0, invalid=762 0118: dt=73.984000, rms=0.636 (0.030%), neg=0, invalid=762 0119: dt=73.984000, rms=0.636 (0.026%), neg=0, invalid=762 0120: dt=73.984000, rms=0.636 (0.029%), neg=0, invalid=762 0121: dt=73.984000, rms=0.636 (0.033%), neg=0, invalid=762 0122: dt=73.984000, rms=0.635 (0.042%), neg=0, invalid=762 0123: dt=73.984000, rms=0.635 (0.041%), neg=0, invalid=762 0124: dt=73.984000, rms=0.635 (0.032%), neg=0, invalid=762 0125: dt=73.984000, rms=0.635 (0.023%), neg=0, invalid=762 0126: dt=73.984000, rms=0.635 (0.020%), neg=0, invalid=762 0127: dt=2071.552000, rms=0.633 (0.205%), neg=0, invalid=762 0128: dt=32.368000, rms=0.633 (0.049%), neg=0, invalid=762 0129: dt=32.368000, rms=0.633 (0.001%), neg=0, invalid=762 0130: dt=32.368000, rms=0.633 (-0.024%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.633, neg=0, invalid=762 0131: dt=295.936000, rms=0.631 (0.348%), neg=0, invalid=762 0132: dt=221.952000, rms=0.630 (0.202%), neg=0, invalid=762 0133: dt=129.472000, rms=0.630 (0.035%), neg=0, invalid=762 0134: dt=129.472000, rms=0.629 (0.042%), neg=0, invalid=762 0135: dt=129.472000, rms=0.629 (0.071%), neg=0, invalid=762 0136: dt=129.472000, rms=0.628 (0.088%), neg=0, invalid=762 0137: dt=129.472000, rms=0.628 (0.088%), neg=0, invalid=762 0138: dt=129.472000, rms=0.627 (0.085%), neg=0, invalid=762 0139: dt=129.472000, rms=0.627 (0.079%), neg=0, invalid=762 0140: dt=129.472000, rms=0.626 (0.073%), neg=0, invalid=762 0141: dt=129.472000, rms=0.626 (0.064%), neg=0, invalid=762 0142: dt=129.472000, rms=0.626 (0.054%), neg=0, invalid=762 0143: dt=129.472000, rms=0.625 (0.048%), neg=0, invalid=762 0144: dt=129.472000, rms=0.625 (0.039%), neg=0, invalid=762 0145: dt=129.472000, rms=0.625 (0.035%), neg=0, invalid=762 0146: dt=129.472000, rms=0.625 (0.027%), neg=0, invalid=762 0147: dt=129.472000, rms=0.625 (0.028%), neg=0, invalid=762 0148: dt=129.472000, rms=0.624 (0.034%), neg=0, invalid=762 0149: dt=129.472000, rms=0.624 (0.037%), neg=0, invalid=762 0150: dt=129.472000, rms=0.624 (0.034%), neg=0, invalid=762 0151: dt=129.472000, rms=0.624 (0.032%), neg=0, invalid=762 0152: dt=129.472000, rms=0.624 (0.031%), neg=0, invalid=762 0153: dt=129.472000, rms=0.623 (0.036%), neg=0, invalid=762 0154: dt=129.472000, rms=0.623 (0.036%), neg=0, invalid=762 0155: dt=129.472000, rms=0.623 (0.031%), neg=0, invalid=762 0156: dt=129.472000, rms=0.623 (0.029%), neg=0, invalid=762 0157: dt=129.472000, rms=0.623 (0.025%), neg=0, invalid=762 0158: dt=129.472000, rms=0.622 (0.026%), neg=0, invalid=762 0159: dt=129.472000, rms=0.622 (0.019%), neg=0, invalid=762 0160: dt=129.472000, rms=0.622 (0.019%), neg=0, invalid=762 0161: dt=517.888000, rms=0.622 (0.015%), neg=0, invalid=762 0162: dt=517.888000, rms=0.622 (-0.285%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.623, neg=0, invalid=762 0163: dt=72.681388, rms=0.621 (0.388%), neg=0, invalid=762 0164: dt=145.152000, rms=0.618 (0.468%), neg=0, invalid=762 0165: dt=65.084746, rms=0.615 (0.406%), neg=0, invalid=762 0166: dt=85.333333, rms=0.613 (0.317%), neg=0, invalid=762 0167: dt=62.208000, rms=0.611 (0.353%), neg=0, invalid=762 0168: dt=80.202532, rms=0.610 (0.235%), neg=0, invalid=762 0169: dt=77.528455, rms=0.608 (0.310%), neg=0, invalid=762 0170: dt=62.208000, rms=0.606 (0.198%), neg=0, invalid=762 0171: dt=103.680000, rms=0.605 (0.277%), neg=0, invalid=762 0172: dt=36.288000, rms=0.604 (0.167%), neg=0, invalid=762 0173: dt=124.416000, rms=0.602 (0.322%), neg=0, invalid=762 0174: dt=25.920000, rms=0.601 (0.072%), neg=0, invalid=762 0175: dt=0.141750, rms=0.601 (0.000%), neg=0, invalid=762 0176: dt=0.008859, rms=0.601 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.602, neg=0, invalid=762 0177: dt=0.007594, rms=0.601 (0.084%), neg=0, invalid=762 0178: dt=0.000000, rms=0.601 (0.000%), neg=0, invalid=762 0179: dt=0.000439, rms=0.601 (0.000%), neg=0, invalid=762 0180: dt=0.000110, rms=0.601 (0.000%), neg=0, invalid=762 0181: dt=0.000055, 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=0.604, neg=0, invalid=762 0182: dt=0.000000, rms=0.604 (0.084%), neg=0, invalid=762 0183: dt=0.000000, rms=0.604 (0.000%), neg=0, invalid=762 0184: dt=0.000031, rms=0.604 (0.000%), neg=0, invalid=762 0185: dt=0.000008, rms=0.604 (0.000%), neg=0, invalid=762 0186: dt=0.000000, rms=0.604 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.604, neg=0, invalid=762 0187: dt=0.000000, rms=0.604 (0.084%), neg=0, invalid=762 0188: dt=0.000000, rms=0.604 (0.000%), neg=0, invalid=762 0189: dt=0.000000, rms=0.604 (0.000%), neg=0, invalid=762 0190: dt=0.000000, rms=0.604 (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=0.612, neg=0, invalid=762 0191: dt=4.032000, rms=0.595 (2.781%), neg=0, invalid=762 0192: dt=4.032000, rms=0.582 (2.109%), neg=0, invalid=762 0193: dt=4.032000, rms=0.573 (1.633%), neg=0, invalid=762 0194: dt=4.032000, rms=0.566 (1.271%), neg=0, invalid=762 0195: dt=4.032000, rms=0.560 (0.995%), neg=0, invalid=762 0196: dt=4.032000, rms=0.556 (0.785%), neg=0, invalid=762 0197: dt=1.008000, rms=0.555 (0.156%), neg=0, invalid=762 0198: dt=0.063000, rms=0.555 (0.009%), neg=0, invalid=762 0199: dt=0.031500, rms=0.555 (0.005%), neg=0, invalid=762 0200: dt=0.015750, rms=0.555 (0.002%), neg=0, invalid=762 0201: dt=0.003938, rms=0.555 (0.000%), neg=0, invalid=762 0202: dt=0.000984, rms=0.555 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.555, neg=0, invalid=762 0203: dt=16.128000, rms=0.542 (2.307%), neg=0, invalid=762 0204: dt=11.520000, rms=0.539 (0.552%), neg=0, invalid=762 0205: dt=16.128000, rms=0.536 (0.536%), neg=0, invalid=762 0206: dt=4.032000, rms=0.536 (0.107%), neg=0, invalid=762 0207: dt=4.032000, rms=0.535 (0.095%), neg=0, invalid=762 0208: dt=16.128000, rms=0.534 (0.294%), neg=0, invalid=762 0209: dt=16.128000, rms=0.533 (0.216%), neg=0, invalid=762 0210: dt=4.032000, rms=0.532 (0.059%), neg=0, invalid=762 0211: dt=11.520000, rms=0.532 (0.135%), neg=0, invalid=762 0212: dt=26.105263, rms=0.531 (0.151%), neg=0, invalid=762 0213: dt=11.520000, rms=0.530 (0.166%), neg=0, invalid=762 0214: dt=13.824000, rms=0.529 (0.087%), neg=0, invalid=762 0215: dt=12.952381, rms=0.529 (0.079%), neg=0, invalid=762 0216: dt=11.520000, rms=0.529 (0.072%), neg=0, invalid=762 0217: dt=11.520000, rms=0.528 (0.055%), neg=0, invalid=762 0218: dt=11.428571, rms=0.528 (0.059%), neg=0, invalid=762 0219: dt=9.756098, rms=0.528 (0.040%), neg=0, invalid=762 0220: dt=9.756098, rms=0.527 (0.053%), neg=0, invalid=762 0221: dt=9.756098, rms=0.527 (0.074%), neg=0, invalid=762 0222: dt=9.756098, rms=0.527 (0.092%), neg=0, invalid=762 0223: dt=9.756098, rms=0.526 (0.127%), neg=0, invalid=762 0224: dt=9.756098, rms=0.525 (0.129%), neg=0, invalid=762 0225: dt=9.756098, rms=0.525 (0.139%), neg=0, invalid=762 0226: dt=9.756098, rms=0.524 (0.112%), neg=0, invalid=762 0227: dt=9.756098, rms=0.523 (0.127%), neg=0, invalid=762 0228: dt=9.756098, rms=0.523 (0.115%), neg=0, invalid=762 0229: dt=9.756098, rms=0.522 (0.101%), neg=0, invalid=762 0230: dt=9.756098, rms=0.522 (0.091%), neg=0, invalid=762 0231: dt=9.756098, rms=0.521 (0.088%), neg=0, invalid=762 0232: dt=9.756098, rms=0.521 (0.080%), neg=0, invalid=762 0233: dt=9.756098, rms=0.520 (0.065%), neg=0, invalid=762 0234: dt=9.756098, rms=0.520 (0.055%), neg=0, invalid=762 0235: dt=9.756098, rms=0.520 (0.045%), neg=0, invalid=762 0236: dt=9.756098, rms=0.520 (0.049%), neg=0, invalid=762 0237: dt=9.756098, rms=0.519 (0.050%), neg=0, invalid=762 0238: dt=9.756098, rms=0.519 (0.034%), neg=0, invalid=762 0239: dt=9.756098, rms=0.519 (0.048%), neg=0, invalid=762 0240: dt=9.756098, rms=0.519 (0.022%), neg=0, invalid=762 0241: dt=9.756098, rms=0.519 (0.031%), neg=0, invalid=762 0242: dt=9.756098, rms=0.519 (0.014%), neg=0, invalid=762 0243: dt=9.756098, rms=0.518 (0.033%), neg=0, invalid=762 0244: dt=9.756098, rms=0.518 (0.023%), neg=0, invalid=762 0245: dt=9.756098, rms=0.518 (0.029%), neg=0, invalid=762 0246: dt=9.756098, rms=0.518 (0.021%), neg=0, invalid=762 0247: dt=9.756098, rms=0.518 (0.015%), neg=0, invalid=762 0248: dt=7.794872, rms=0.518 (0.028%), neg=0, invalid=762 0249: dt=2.304000, rms=0.518 (0.004%), neg=0, invalid=762 0250: dt=2.304000, rms=0.518 (-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=0.533, neg=0, invalid=762 0251: dt=0.000000, rms=0.532 (0.098%), neg=0, invalid=762 0252: dt=0.000000, rms=0.532 (0.000%), neg=0, invalid=762 0253: dt=0.100000, rms=0.532 (-0.173%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.533, neg=0, invalid=762 0254: dt=0.000000, rms=0.532 (0.098%), neg=0, invalid=762 0255: dt=0.000000, rms=0.532 (0.000%), neg=0, invalid=762 0256: dt=0.100000, rms=0.532 (-0.162%), 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=0.509, neg=0, invalid=762 0257: dt=0.320000, rms=0.497 (2.174%), neg=0, invalid=762 0258: dt=0.384000, rms=0.492 (1.135%), neg=0, invalid=762 0259: dt=0.384000, rms=0.489 (0.482%), neg=0, invalid=762 0260: dt=0.384000, rms=0.488 (0.286%), neg=0, invalid=762 0261: dt=0.384000, rms=0.487 (0.201%), neg=0, invalid=762 0262: dt=0.384000, rms=0.486 (0.148%), neg=0, invalid=762 0263: dt=0.384000, rms=0.486 (0.121%), neg=0, invalid=762 0264: dt=0.384000, rms=0.485 (0.088%), neg=0, invalid=762 0265: dt=0.384000, rms=0.485 (0.081%), neg=0, invalid=762 0266: dt=0.384000, rms=0.485 (0.059%), neg=0, invalid=762 0267: dt=0.384000, rms=0.484 (0.060%), neg=0, invalid=762 0268: dt=0.384000, rms=0.484 (0.042%), neg=0, invalid=762 0269: dt=0.384000, rms=0.484 (0.043%), neg=0, invalid=762 0270: dt=0.384000, rms=0.484 (0.067%), neg=0, invalid=762 0271: dt=0.192000, rms=0.484 (0.020%), neg=0, invalid=762 0272: dt=0.192000, rms=0.483 (0.024%), neg=0, invalid=762 0273: dt=0.192000, rms=0.483 (0.033%), neg=0, invalid=762 0274: dt=0.192000, rms=0.483 (0.027%), neg=0, invalid=762 0275: dt=0.192000, rms=0.483 (0.032%), neg=0, invalid=762 0276: dt=0.192000, rms=0.483 (0.040%), neg=0, invalid=762 0277: dt=0.192000, rms=0.483 (0.038%), neg=0, invalid=762 0278: dt=0.192000, rms=0.482 (0.033%), neg=0, invalid=762 0279: dt=0.192000, rms=0.482 (0.026%), neg=0, invalid=762 0280: dt=0.192000, rms=0.482 (0.024%), neg=0, invalid=762 0281: dt=0.192000, rms=0.482 (0.021%), neg=0, invalid=762 0282: dt=-0.000061, rms=0.482 (-0.007%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.483, neg=0, invalid=762 0283: dt=0.258929, rms=0.479 (0.685%), neg=0, invalid=762 0284: dt=0.320000, rms=0.478 (0.312%), neg=0, invalid=762 0285: dt=0.320000, rms=0.477 (0.102%), neg=0, invalid=762 0286: dt=0.320000, rms=0.477 (0.032%), neg=0, invalid=762 0287: dt=0.320000, rms=0.477 (0.004%), neg=0, invalid=762 0288: dt=0.320000, rms=0.477 (0.003%), neg=0, invalid=762 0289: dt=0.320000, rms=0.477 (-0.003%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.476, neg=0, invalid=762 0290: dt=0.000000, rms=0.475 (0.139%), neg=0, invalid=762 0291: dt=0.000000, rms=0.475 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.476, neg=0, invalid=762 0292: dt=129.472000, rms=0.475 (0.173%), neg=0, invalid=762 0293: dt=129.472000, rms=0.475 (0.013%), neg=0, invalid=762 0294: dt=129.472000, rms=0.475 (0.012%), neg=0, invalid=762 0295: dt=129.472000, rms=0.475 (0.022%), neg=0, invalid=762 0296: dt=129.472000, rms=0.474 (0.015%), neg=0, invalid=762 0297: dt=129.472000, rms=0.474 (0.013%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.475, neg=0, invalid=762 0298: dt=2.268000, rms=0.474 (0.136%), neg=0, invalid=762 0299: dt=0.405000, rms=0.474 (0.001%), neg=0, invalid=762 0300: dt=0.405000, rms=0.474 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.475, neg=0, invalid=762 0301: dt=145.152000, rms=0.473 (0.435%), neg=0, invalid=762 0302: dt=36.288000, rms=0.473 (0.075%), neg=0, invalid=762 0303: dt=36.288000, rms=0.472 (0.048%), neg=0, invalid=762 0304: dt=36.288000, rms=0.472 (0.070%), neg=0, invalid=762 0305: dt=36.288000, rms=0.472 (0.090%), neg=0, invalid=762 0306: dt=36.288000, rms=0.471 (0.088%), neg=0, invalid=762 0307: dt=36.288000, rms=0.471 (0.084%), neg=0, invalid=762 0308: dt=82.944000, rms=0.471 (0.035%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.472, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0309: dt=21.393768, rms=0.470 (0.442%), neg=0, invalid=762 0310: dt=24.744186, rms=0.469 (0.172%), neg=0, invalid=762 0311: dt=24.744186, rms=0.468 (0.127%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0312: dt=24.744186, rms=0.467 (0.198%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 9 iterations, nbhd size=1, neg = 0 0313: dt=24.744186, rms=0.467 (0.011%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 9 iterations, nbhd size=1, neg = 0 0314: dt=24.744186, rms=0.467 (0.087%), neg=0, invalid=762 iter 0, gcam->neg = 29 after 11 iterations, nbhd size=1, neg = 0 0315: dt=24.744186, rms=0.467 (-0.007%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0316: dt=38.400000, rms=0.465 (0.317%), neg=0, invalid=762 0317: dt=25.600000, rms=0.464 (0.277%), neg=0, invalid=762 0318: dt=11.200000, rms=0.463 (0.109%), neg=0, invalid=762 0319: dt=11.200000, rms=0.463 (0.057%), neg=0, invalid=762 0320: dt=11.200000, rms=0.463 (0.087%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0321: dt=11.200000, rms=0.462 (0.115%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0322: dt=11.200000, rms=0.462 (0.127%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0323: dt=11.200000, rms=0.461 (0.126%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 0324: dt=11.200000, rms=0.460 (0.119%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0325: dt=11.200000, rms=0.460 (0.116%), neg=0, invalid=762 0326: dt=44.800000, rms=0.460 (0.034%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 8 iterations, nbhd size=1, neg = 0 0327: dt=44.800000, rms=0.460 (-0.086%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.460, neg=0, invalid=762 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0328: dt=50.947368, rms=0.454 (1.294%), neg=0, invalid=762 0329: dt=22.000000, rms=0.453 (0.400%), neg=0, invalid=762 0330: dt=32.000000, rms=0.452 (0.214%), neg=0, invalid=762 0331: dt=32.000000, rms=0.452 (0.009%), neg=0, invalid=762 0332: dt=32.000000, rms=0.450 (0.376%), neg=0, invalid=762 0333: dt=32.000000, rms=0.450 (-0.019%), neg=0, invalid=762 0334: dt=11.200000, rms=0.450 (0.058%), neg=0, invalid=762 0335: dt=44.800000, rms=0.449 (0.088%), neg=0, invalid=762 0336: dt=25.600000, rms=0.449 (0.056%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 0337: dt=3.636364, rms=0.454 (0.212%), neg=0, invalid=762 0338: dt=1.846154, rms=0.454 (0.012%), neg=0, invalid=762 0339: dt=1.846154, rms=0.454 (0.003%), neg=0, invalid=762 0340: dt=1.846154, rms=0.454 (-0.024%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.454, neg=0, invalid=762 0341: dt=10.873786, rms=0.452 (0.435%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 10 iterations, nbhd size=1, neg = 0 0342: dt=20.444444, rms=0.451 (0.267%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0343: dt=18.793651, rms=0.450 (0.279%), neg=0, invalid=762 0344: dt=11.377778, rms=0.449 (0.212%), neg=0, invalid=762 0345: dt=11.377778, rms=0.448 (0.147%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0346: dt=11.377778, rms=0.448 (0.190%), neg=0, invalid=762 0347: dt=11.377778, rms=0.446 (0.273%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0348: dt=11.377778, rms=0.445 (0.227%), neg=0, invalid=762 0349: dt=11.377778, rms=0.444 (0.250%), neg=0, invalid=762 0350: dt=11.377778, rms=0.443 (0.230%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0351: dt=11.377778, rms=0.442 (0.196%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0352: dt=11.377778, rms=0.442 (0.088%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0353: dt=11.377778, rms=0.442 (0.086%), neg=0, invalid=762 0354: dt=9.216000, rms=0.441 (0.045%), neg=0, invalid=762 0355: dt=9.216000, rms=0.441 (-0.033%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.447, neg=0, invalid=762 0356: dt=0.000000, rms=0.447 (0.168%), neg=0, invalid=762 0357: dt=0.000000, rms=0.447 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.447, neg=0, invalid=762 0358: dt=0.000000, rms=0.447 (0.168%), neg=0, invalid=762 0359: dt=0.000000, rms=0.447 (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=0.439, neg=0, invalid=762 iter 0, gcam->neg = 1086 after 12 iterations, nbhd size=1, neg = 0 0360: dt=1.756311, rms=0.418 (4.640%), neg=0, invalid=762 0361: dt=0.000013, rms=0.418 (0.001%), neg=0, invalid=762 0362: dt=0.000013, rms=0.418 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.419, neg=0, invalid=762 0363: dt=0.064000, rms=0.418 (0.215%), neg=0, invalid=762 0364: dt=0.001500, rms=0.418 (-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=0.408, neg=0, invalid=762 0365: dt=0.000000, rms=0.408 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0366: dt=18.496000, rms=0.408 (0.002%), neg=0, invalid=762 0367: dt=1.734000, rms=0.408 (0.000%), neg=0, invalid=762 0368: dt=1.734000, rms=0.408 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0369: dt=0.000000, rms=0.408 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0370: dt=36.288000, rms=0.408 (0.022%), neg=0, invalid=762 0371: dt=36.288000, rms=0.408 (0.011%), neg=0, invalid=762 0372: dt=36.288000, rms=0.408 (0.008%), neg=0, invalid=762 0373: dt=36.288000, rms=0.408 (0.004%), neg=0, invalid=762 0374: dt=36.288000, rms=0.408 (-0.010%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 0375: dt=8.000000, rms=0.408 (0.050%), neg=0, invalid=762 0376: dt=2.800000, rms=0.408 (0.004%), neg=0, invalid=762 0377: dt=2.800000, rms=0.408 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 iter 0, gcam->neg = 27 after 10 iterations, nbhd size=1, neg = 0 0378: dt=79.085714, rms=0.406 (0.597%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0379: dt=24.555102, rms=0.405 (0.246%), neg=0, invalid=762 0380: dt=24.555102, rms=0.404 (0.093%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 2 iterations, nbhd size=0, neg = 0 0381: dt=24.555102, rms=0.404 (0.117%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0382: dt=24.555102, rms=0.403 (0.128%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 8 iterations, nbhd size=1, neg = 0 0383: dt=24.555102, rms=0.403 (0.121%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 9 iterations, nbhd size=1, neg = 0 0384: dt=24.555102, rms=0.402 (0.145%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 8 iterations, nbhd size=1, neg = 0 0385: dt=24.555102, rms=0.402 (0.066%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 2 iterations, nbhd size=0, neg = 0 0386: dt=24.555102, rms=0.402 (0.110%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 11 iterations, nbhd size=1, neg = 0 0387: dt=24.555102, rms=0.401 (0.077%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0388: dt=44.800000, rms=0.401 (0.047%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0389: dt=44.800000, rms=0.401 (-0.012%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.405, neg=0, invalid=762 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 0390: dt=4.111111, rms=0.405 (0.034%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0391: dt=2.500000, rms=0.405 (0.002%), neg=0, invalid=762 0392: dt=2.500000, rms=0.405 (-0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.405, neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0393: dt=14.296296, rms=0.403 (0.324%), neg=0, invalid=762 iter 0, gcam->neg = 19 after 13 iterations, nbhd size=1, neg = 0 0394: dt=26.153846, rms=0.402 (0.250%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 9 iterations, nbhd size=1, neg = 0 0395: dt=11.520000, rms=0.402 (0.141%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 0396: dt=11.520000, rms=0.401 (0.086%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0397: dt=11.520000, rms=0.401 (0.104%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 12 iterations, nbhd size=1, neg = 0 0398: dt=11.520000, rms=0.400 (0.131%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 3 iterations, nbhd size=0, neg = 0 0399: dt=11.520000, rms=0.400 (0.138%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 3 iterations, nbhd size=0, neg = 0 0400: dt=11.520000, rms=0.399 (0.127%), neg=0, invalid=762 iter 0, gcam->neg = 25 after 13 iterations, nbhd size=1, neg = 0 0401: dt=11.520000, rms=0.399 (0.039%), neg=0, invalid=762 iter 0, gcam->neg = 27 after 5 iterations, nbhd size=0, neg = 0 0402: dt=11.520000, rms=0.399 (0.080%), neg=0, invalid=762 iter 0, gcam->neg = 28 after 6 iterations, nbhd size=0, neg = 0 0403: dt=11.520000, rms=0.399 (0.054%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 0 iterations, nbhd size=0, neg = 0 0404: dt=7.000000, rms=0.399 (0.013%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=0, neg = 0 0405: dt=7.000000, rms=0.399 (0.011%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0406: dt=7.000000, rms=0.399 (0.014%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 6 iterations, nbhd size=0, neg = 0 0407: dt=7.000000, rms=0.399 (-0.007%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.404, neg=0, invalid=762 0408: dt=0.000060, rms=0.404 (0.000%), neg=0, invalid=762 0409: dt=0.000000, rms=0.404 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.404, neg=0, invalid=762 0410: dt=0.000000, rms=0.404 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.395, neg=0, invalid=762 iter 0, gcam->neg = 617 after 16 iterations, nbhd size=1, neg = 0 0411: dt=1.082869, rms=0.388 (1.682%), neg=0, invalid=762 0412: dt=0.000023, rms=0.388 (0.000%), neg=0, invalid=762 0413: dt=0.000023, rms=0.388 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.388, neg=0, invalid=762 0414: dt=0.112000, rms=0.388 (0.082%), neg=0, invalid=762 0415: dt=0.112000, rms=0.388 (0.045%), neg=0, invalid=762 0416: dt=0.112000, rms=0.388 (0.042%), neg=0, invalid=762 0417: dt=0.112000, rms=0.388 (0.027%), neg=0, invalid=762 0418: dt=0.112000, rms=0.388 (-0.033%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 43 minutes and 4 seconds. mri_ca_register utimesec 6179.248000 mri_ca_register stimesec 3.596000 mri_ca_register ru_maxrss 1341200 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 3818926 mri_ca_register ru_majflt 8 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 1696 mri_ca_register ru_oublock 62952 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 15 mri_ca_register ru_nivcsw 9465 FSRUNTIME@ mri_ca_register 1.7177 hours 1 threads #-------------------------------------- #@# SubCort Seg Sat May 20 18:56:19 EDT 2017 mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.presurf.mgz --diff aseg.manedit.mgz $Id: mri_seg_diff.c,v 1.5 2011/03/02 00:04:24 nicks Exp $ cwd /usr/local/freesurfer/subjects/Sub01/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.presurf.mgz --diff aseg.manedit.mgz sysname Linux hostname X1 machine x86_64 user amazinger Seg1 aseg.auto.mgz Seg2 aseg.presurf.mgz Diff aseg.manedit.mgz InDiff (null) Merged (null) ForceDiff 0 Computing difference between segmentations No difference found. 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 X1 machine x86_64 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/Sub01/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 5.65 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 = 0.12075 ( 9) Left_Lateral_Ventricle (4): linear fit = 0.38 x + 0.0 (852 voxels, overlap=0.014) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (852 voxels, peak = 8), gca=8.0 gca peak = 0.17677 (13) mri peak = 0.14076 ( 9) Right_Lateral_Ventricle (43): linear fit = 0.58 x + 0.0 (943 voxels, overlap=0.421) Right_Lateral_Ventricle (43): linear fit = 0.58 x + 0.0 (943 voxels, peak = 8), gca=7.6 gca peak = 0.28129 (95) mri peak = 0.10228 (92) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (630 voxels, overlap=0.656) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (630 voxels, peak = 89), gca=88.8 gca peak = 0.16930 (96) mri peak = 0.09084 (87) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (644 voxels, overlap=0.408) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (644 voxels, peak = 90), gca=89.8 gca peak = 0.24553 (55) mri peak = 0.10100 (58) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (868 voxels, overlap=1.006) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (868 voxels, peak = 56), gca=56.4 gca peak = 0.30264 (59) mri peak = 0.10464 (53) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (836 voxels, overlap=1.009) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (836 voxels, peak = 56), gca=55.8 gca peak = 0.07580 (103) mri peak = 0.06064 (101) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (35246 voxels, overlap=0.824) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (35246 voxels, peak = 105), gca=104.5 gca peak = 0.07714 (104) mri peak = 0.05895 (98) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35444 voxels, overlap=0.857) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35444 voxels, peak = 103), gca=103.5 gca peak = 0.09712 (58) mri peak = 0.04529 (52) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (18991 voxels, overlap=0.978) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (18991 voxels, peak = 53), gca=53.1 gca peak = 0.11620 (58) mri peak = 0.04512 (55) Right_Cerebral_Cortex (42): linear fit = 0.94 x + 0.0 (19544 voxels, overlap=0.992) Right_Cerebral_Cortex (42): linear fit = 0.94 x + 0.0 (19544 voxels, peak = 55), gca=54.8 gca peak = 0.30970 (66) mri peak = 0.09357 (63) Right_Caudate (50): linear fit = 0.92 x + 0.0 (1227 voxels, overlap=0.998) Right_Caudate (50): linear fit = 0.92 x + 0.0 (1227 voxels, peak = 60), gca=60.4 gca peak = 0.15280 (69) mri peak = 0.08834 (66) Left_Caudate (11): linear fit = 0.88 x + 0.0 (1092 voxels, overlap=0.449) Left_Caudate (11): linear fit = 0.88 x + 0.0 (1092 voxels, peak = 61), gca=61.1 gca peak = 0.13902 (56) mri peak = 0.05976 (48) Left_Cerebellum_Cortex (8): linear fit = 0.89 x + 0.0 (24454 voxels, overlap=0.782) Left_Cerebellum_Cortex (8): linear fit = 0.89 x + 0.0 (24454 voxels, peak = 50), gca=50.1 gca peak = 0.14777 (55) mri peak = 0.04900 (51) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (22068 voxels, overlap=0.998) Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (22068 voxels, peak = 53), gca=53.1 gca peak = 0.16765 (84) mri peak = 0.08456 (84) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5147 voxels, overlap=0.976) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5147 voxels, peak = 84), gca=84.0 gca peak = 0.18739 (84) mri peak = 0.07970 (86) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5109 voxels, overlap=0.862) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5109 voxels, peak = 89), gca=89.5 gca peak = 0.29869 (57) mri peak = 0.09278 (54) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (328 voxels, overlap=1.024) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (328 voxels, peak = 58), gca=57.9 gca peak = 0.33601 (57) mri peak = 0.09196 (53) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (370 voxels, overlap=1.021) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (370 voxels, peak = 58), gca=57.9 gca peak = 0.11131 (90) mri peak = 0.09368 (75) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (4051 voxels, overlap=0.722) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (4051 voxels, peak = 86), gca=85.9 gca peak = 0.11793 (83) mri peak = 0.10149 (76) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3828 voxels, overlap=0.974) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3828 voxels, peak = 81), gca=80.9 gca peak = 0.08324 (81) mri peak = 0.06159 (78) Left_Putamen (12): linear fit = 0.98 x + 0.0 (1962 voxels, overlap=0.932) Left_Putamen (12): linear fit = 0.98 x + 0.0 (1962 voxels, peak = 79), gca=79.0 gca peak = 0.10360 (77) mri peak = 0.07428 (75) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1845 voxels, overlap=0.968) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1845 voxels, peak = 76), gca=75.8 gca peak = 0.08424 (78) mri peak = 0.19527 (80) Brain_Stem: unreasonable value (79.2/80.0), not in range [80, 110] - rejecting gca peak = 0.12631 (89) mri peak = 0.08304 (92) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1090 voxels, overlap=0.824) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1090 voxels, peak = 91), gca=91.2 gca peak = 0.14500 (87) mri peak = 0.08795 (89) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1101 voxels, overlap=0.916) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1101 voxels, peak = 89), gca=89.2 gca peak = 0.14975 (24) mri peak = 0.13636 (11) gca peak = 0.19357 (14) mri peak = 0.12820 (10) Fourth_Ventricle (15): linear fit = 0.51 x + 0.0 (100 voxels, overlap=0.459) Fourth_Ventricle (15): linear fit = 0.51 x + 0.0 (100 voxels, peak = 7), gca=7.2 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak Brain_Stem = 0.08424 (78) 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 0.98 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.49 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.31512 ( 7) mri peak = 0.12075 ( 9) Left_Lateral_Ventricle (4): linear fit = 1.08 x + 0.0 (852 voxels, overlap=0.935) Left_Lateral_Ventricle (4): linear fit = 1.08 x + 0.0 (852 voxels, peak = 8), gca=7.5 gca peak = 0.23922 ( 8) mri peak = 0.14076 ( 9) Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (943 voxels, overlap=0.835) Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (943 voxels, peak = 8), gca=8.4 gca peak = 0.27946 (88) mri peak = 0.10228 (92) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (630 voxels, overlap=1.013) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (630 voxels, peak = 89), gca=89.3 gca peak = 0.16174 (90) mri peak = 0.09084 (87) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (644 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (644 voxels, peak = 91), gca=91.3 gca peak = 0.29677 (57) mri peak = 0.10100 (58) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (868 voxels, overlap=0.982) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (868 voxels, peak = 57), gca=57.0 gca peak = 0.30421 (53) mri peak = 0.10464 (53) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (836 voxels, overlap=1.009) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (836 voxels, peak = 52), gca=51.7 gca peak = 0.07772 (104) mri peak = 0.06064 (101) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (35246 voxels, overlap=0.867) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (35246 voxels, peak = 103), gca=103.5 gca peak = 0.08055 (104) mri peak = 0.05895 (98) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35444 voxels, overlap=0.851) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35444 voxels, peak = 103), gca=103.5 gca peak = 0.10695 (53) mri peak = 0.04529 (52) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (18991 voxels, overlap=1.000) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (18991 voxels, peak = 52), gca=52.2 gca peak = 0.12393 (55) mri peak = 0.04512 (55) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (19544 voxels, overlap=0.995) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (19544 voxels, peak = 54), gca=54.2 gca peak = 0.27303 (61) mri peak = 0.09357 (63) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1227 voxels, overlap=1.007) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1227 voxels, peak = 61), gca=61.0 gca peak = 0.14698 (61) mri peak = 0.08834 (66) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1092 voxels, overlap=1.000) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1092 voxels, peak = 61), gca=61.0 gca peak = 0.15858 (50) mri peak = 0.05976 (48) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (24454 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (24454 voxels, peak = 49), gca=48.8 gca peak = 0.15521 (53) mri peak = 0.04900 (51) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (22068 voxels, overlap=0.999) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (22068 voxels, peak = 52), gca=52.2 gca peak = 0.16765 (84) mri peak = 0.08456 (84) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5147 voxels, overlap=0.976) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5147 voxels, peak = 84), gca=84.0 gca peak = 0.15003 (90) mri peak = 0.07970 (86) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5109 voxels, overlap=0.988) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5109 voxels, peak = 89), gca=88.7 gca peak = 0.28044 (59) mri peak = 0.09278 (54) Left_Amygdala (18): linear fit = 0.92 x + 0.0 (328 voxels, overlap=1.012) Left_Amygdala (18): linear fit = 0.92 x + 0.0 (328 voxels, peak = 54), gca=54.0 gca peak = 0.36965 (58) mri peak = 0.09196 (53) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (370 voxels, overlap=1.018) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (370 voxels, peak = 58), gca=58.0 gca peak = 0.11511 (86) mri peak = 0.09368 (75) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (4051 voxels, overlap=0.948) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (4051 voxels, peak = 85), gca=84.7 gca peak = 0.11482 (79) mri peak = 0.10149 (76) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3828 voxels, overlap=0.921) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3828 voxels, peak = 79), gca=79.0 gca peak = 0.08312 (79) mri peak = 0.06159 (78) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1962 voxels, overlap=0.999) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1962 voxels, peak = 79), gca=79.0 gca peak = 0.09873 (76) mri peak = 0.07428 (75) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1845 voxels, overlap=1.001) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1845 voxels, peak = 76), gca=76.0 gca peak = 0.08505 (79) mri peak = 0.19527 (80) Brain_Stem (16): linear fit = 1.01 x + 0.0 (11370 voxels, overlap=0.516) Brain_Stem (16): linear fit = 1.01 x + 0.0 (11370 voxels, peak = 80), gca=80.2 gca peak = 0.11494 (86) mri peak = 0.08304 (92) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1090 voxels, overlap=0.862) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1090 voxels, peak = 86), gca=85.6 gca peak = 0.13378 (89) mri peak = 0.08795 (89) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1101 voxels, overlap=0.943) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1101 voxels, peak = 88), gca=87.7 gca peak = 0.29156 (13) mri peak = 0.13636 (11) gca peak = 0.37683 ( 7) mri peak = 0.12820 (10) Fourth_Ventricle (15): linear fit = 1.08 x + 0.0 (100 voxels, overlap=0.968) Fourth_Ventricle (15): linear fit = 1.08 x + 0.0 (100 voxels, peak = 8), gca=7.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18199 (30) gca peak Left_Thalamus = 1.00000 (92) gca peak Third_Ventricle = 0.29156 (13) gca peak CSF = 0.34711 (18) gca peak Left_Accumbens_area = 0.81154 (55) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.74619 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.20983 (24) gca peak Right_Accumbens_area = 0.41190 (59) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65358 (16) gca peak WM_hypointensities = 0.07080 (76) gca peak non_WM_hypointensities = 0.07897 (44) gca peak Optic_Chiasm = 0.70931 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.98 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.07 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 48110 voxels changed in iteration 0 of unlikely voxel relabeling 173 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 23891 gm and wm labels changed (%23 to gray, %77 to white out of all changed labels) 217 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 57766 changed. image ll: -2.081, PF=0.500 pass 2: 16431 changed. image ll: -2.080, PF=0.500 pass 3: 5462 changed. pass 4: 2082 changed. 29076 voxels changed in iteration 0 of unlikely voxel relabeling 166 voxels changed in iteration 1 of unlikely voxel relabeling 9 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6091 voxels changed in iteration 0 of unlikely voxel relabeling 37 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 5501 voxels changed in iteration 0 of unlikely voxel relabeling 71 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4354 voxels changed in iteration 0 of unlikely voxel relabeling 20 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 1993.924000 mri_ca_label stimesec 0.544000 mri_ca_label ru_maxrss 2098064 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 669160 mri_ca_label ru_majflt 8 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 1616 mri_ca_label ru_oublock 432 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 152 mri_ca_label ru_nivcsw 3328 auto-labeling took 33 minutes and 15 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /usr/local/freesurfer/subjects/Sub01/mri/transforms/cc_up.lta Sub01 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /usr/local/freesurfer/subjects/Sub01/mri/transforms/cc_up.lta reading aseg from /usr/local/freesurfer/subjects/Sub01/mri/aseg.auto_noCCseg.mgz reading norm from /usr/local/freesurfer/subjects/Sub01/mri/norm.mgz 28191 voxels in left wm, 29693 in right wm, xrange [125, 133] searching rotation angles z=[-8 6], y=[-8 6] searching scale 1 Z rot -8.2 searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 global minimum found at slice 128.5, rotations (-1.11, -1.25) final transformation (x=128.5, yr=-1.112, zr=-1.245): 0.99958 0.02173 -0.01940 -0.10770; -0.02173 0.99976 0.00042 45.76429; 0.01940 0.00000 0.99981 12.52828; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 132] in xformed coordinates best xformed slice 128 cc center is found at 128 85 113 eigenvectors: 0.00022 0.00008 1.00000; -0.16497 -0.98630 0.00011; 0.98630 -0.16497 -0.00020; writing aseg with callosum to /usr/local/freesurfer/subjects/Sub01/mri/aseg.auto.mgz... corpus callosum segmentation took 0.5 minutes #-------------------------------------- #@# Merge ASeg Sat May 20 19:30:07 EDT 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sat May 20 19:30:07 EDT 2017 /usr/local/freesurfer/subjects/Sub01/mri mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 470 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 57 (57), valley at 24 (24) csf peak at 29, setting threshold to 47 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 26 (26) csf peak at 30, setting threshold to 49 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 33 seconds. #-------------------------------------------- #@# Mask BFS Sat May 20 19:32:42 EDT 2017 /usr/local/freesurfer/subjects/Sub01/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1341432 voxels in mask (pct= 8.00) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sat May 20 19:32:44 EDT 2017 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /usr/local/freesurfer/subjects/Sub01/mri cmdline mri_binarize.bin --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname X1 machine x86_64 user amazinger input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /usr/local/freesurfer/subjects/Sub01/mri cmdline mri_binarize.bin --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname X1 machine x86_64 user amazinger input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done rm wm1.mgz wm255.mgz mri_segment -keep -mprage brain.mgz wm.seg.mgz preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (105.0): 106.0 +- 5.4 [79.0 --> 125.0] GM (68.0) : 66.7 +- 9.6 [30.0 --> 95.0] setting bottom of white matter range to 76.3 setting top of gray matter range to 85.9 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 3967 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4556 filled 763 bright non-wm voxels segmented. 2574 diagonally connected voxels added... white matter segmentation took 0.9 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.38 minutes reading wm segmentation from wm.seg.mgz... 63 voxels added to wm to prevent paths from MTL structures to cortex 2271 additional wm voxels added 0 additional wm voxels added SEG EDIT: 38344 voxels turned on, 34771 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 14 found - 14 modified | TOTAL: 14 pass 2 (xy+): 0 found - 14 modified | TOTAL: 14 pass 1 (xy-): 24 found - 24 modified | TOTAL: 38 pass 2 (xy-): 0 found - 24 modified | TOTAL: 38 pass 1 (yz+): 31 found - 31 modified | TOTAL: 69 pass 2 (yz+): 0 found - 31 modified | TOTAL: 69 pass 1 (yz-): 19 found - 19 modified | TOTAL: 88 pass 2 (yz-): 0 found - 19 modified | TOTAL: 88 pass 1 (xz+): 23 found - 23 modified | TOTAL: 111 pass 2 (xz+): 0 found - 23 modified | TOTAL: 111 pass 1 (xz-): 16 found - 16 modified | TOTAL: 127 pass 2 (xz-): 0 found - 16 modified | TOTAL: 127 Iteration Number : 1 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 12 found - 12 modified | TOTAL: 18 pass 2 (+++): 0 found - 12 modified | TOTAL: 18 pass 1 (+++): 16 found - 16 modified | TOTAL: 34 pass 2 (+++): 0 found - 16 modified | TOTAL: 34 pass 1 (+++): 8 found - 8 modified | TOTAL: 42 pass 2 (+++): 0 found - 8 modified | TOTAL: 42 Iteration Number : 1 pass 1 (++): 111 found - 111 modified | TOTAL: 111 pass 2 (++): 0 found - 111 modified | TOTAL: 111 pass 1 (+-): 107 found - 107 modified | TOTAL: 218 pass 2 (+-): 0 found - 107 modified | TOTAL: 218 pass 1 (--): 76 found - 76 modified | TOTAL: 294 pass 2 (--): 0 found - 76 modified | TOTAL: 294 pass 1 (-+): 129 found - 129 modified | TOTAL: 423 pass 2 (-+): 0 found - 129 modified | TOTAL: 423 Iteration Number : 2 pass 1 (xy+): 7 found - 7 modified | TOTAL: 7 pass 2 (xy+): 0 found - 7 modified | TOTAL: 7 pass 1 (xy-): 5 found - 5 modified | TOTAL: 12 pass 2 (xy-): 0 found - 5 modified | TOTAL: 12 pass 1 (yz+): 5 found - 5 modified | TOTAL: 17 pass 2 (yz+): 0 found - 5 modified | TOTAL: 17 pass 1 (yz-): 0 found - 0 modified | TOTAL: 17 pass 1 (xz+): 4 found - 4 modified | TOTAL: 21 pass 2 (xz+): 0 found - 4 modified | TOTAL: 21 pass 1 (xz-): 1 found - 1 modified | TOTAL: 22 pass 2 (xz-): 0 found - 1 modified | TOTAL: 22 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 2 found - 2 modified | TOTAL: 5 pass 2 (-+): 0 found - 2 modified | TOTAL: 5 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 619 (out of 458471: 0.135014) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels mri_pretess done #-------------------------------------------- #@# Fill Sat May 20 19:34:11 EDT 2017 /usr/local/freesurfer/subjects/Sub01/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.03746 0.00297 -0.00860 -6.10400; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30077; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.03746 0.00297 -0.00860 -6.10400; -0.00027 1.14131 0.34273 -34.39264; 0.00819 -0.33636 1.09566 20.30077; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1054 (min = 350, max = 1400), aspect = 0.53 (min = 0.10, max = 0.75) no need to search using seed (127, 113, 123), TAL = (1.0, -5.0, 15.0) talairach voxel to voxel transform 0.96383 -0.00025 0.00764 5.71925; 0.00219 0.80223 -0.25092 32.69804; -0.00653 0.24628 0.83561 -8.53304; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (127, 113, 123) --> (1.0, -5.0, 15.0) done. writing output to filled.mgz... filling took 0.5 minutes talairach cc position changed to (1.00, -5.00, 15.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, -5.00, 15.00) SRC: (111.69, 92.73, 121.36) search lh wm seed point around talairach space (-17.00, -5.00, 15.00), SRC: (146.39, 92.80, 121.13) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Sat May 20 19:34:44 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 3 found - 3 modified | TOTAL: 6 pass 2 (xy-): 0 found - 3 modified | TOTAL: 6 pass 1 (yz+): 3 found - 3 modified | TOTAL: 9 pass 2 (yz+): 0 found - 3 modified | TOTAL: 9 pass 1 (yz-): 4 found - 4 modified | TOTAL: 13 pass 2 (yz-): 0 found - 4 modified | TOTAL: 13 pass 1 (xz+): 1 found - 1 modified | TOTAL: 14 pass 2 (xz+): 0 found - 1 modified | TOTAL: 14 pass 1 (xz-): 0 found - 0 modified | TOTAL: 14 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 2 found - 2 modified | TOTAL: 4 pass 2 (--): 0 found - 2 modified | TOTAL: 4 pass 1 (-+): 2 found - 2 modified | TOTAL: 6 pass 2 (-+): 0 found - 2 modified | TOTAL: 6 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 20 (out of 218237: 0.009164) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 1349 vertices, 1498 faces slice 60: 8732 vertices, 9092 faces slice 70: 19762 vertices, 20127 faces slice 80: 30408 vertices, 30791 faces slice 90: 41692 vertices, 42040 faces slice 100: 52774 vertices, 53171 faces slice 110: 63455 vertices, 63851 faces slice 120: 74164 vertices, 74537 faces slice 130: 84574 vertices, 84973 faces slice 140: 94686 vertices, 95038 faces slice 150: 103172 vertices, 103543 faces slice 160: 110183 vertices, 110437 faces slice 170: 115666 vertices, 115872 faces slice 180: 119399 vertices, 119525 faces slice 190: 119952 vertices, 120002 faces slice 200: 119952 vertices, 120002 faces slice 210: 119952 vertices, 120002 faces slice 220: 119952 vertices, 120002 faces slice 230: 119952 vertices, 120002 faces slice 240: 119952 vertices, 120002 faces slice 250: 119952 vertices, 120002 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 119952 voxel in cpt #1: X=-50 [v=119952,e=360006,f=240004] located at (-27.871365, -20.728607, 31.213120) For the whole surface: X=-50 [v=119952,e=360006,f=240004] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Sat May 20 19:34:49 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 4 found - 4 modified | TOTAL: 7 pass 2 (xy-): 0 found - 4 modified | TOTAL: 7 pass 1 (yz+): 3 found - 3 modified | TOTAL: 10 pass 2 (yz+): 0 found - 3 modified | TOTAL: 10 pass 1 (yz-): 8 found - 8 modified | TOTAL: 18 pass 2 (yz-): 0 found - 8 modified | TOTAL: 18 pass 1 (xz+): 0 found - 0 modified | TOTAL: 18 pass 1 (xz-): 0 found - 0 modified | TOTAL: 18 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 21 (out of 221675: 0.009473) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 608 vertices, 708 faces slice 60: 6820 vertices, 7105 faces slice 70: 17156 vertices, 17555 faces slice 80: 28207 vertices, 28581 faces slice 90: 39077 vertices, 39435 faces slice 100: 50687 vertices, 51106 faces slice 110: 61678 vertices, 62060 faces slice 120: 72608 vertices, 73025 faces slice 130: 83151 vertices, 83563 faces slice 140: 93102 vertices, 93470 faces slice 150: 101999 vertices, 102339 faces slice 160: 109563 vertices, 109843 faces slice 170: 115639 vertices, 115879 faces slice 180: 119735 vertices, 119929 faces slice 190: 120862 vertices, 120916 faces slice 200: 120862 vertices, 120916 faces slice 210: 120862 vertices, 120916 faces slice 220: 120862 vertices, 120916 faces slice 230: 120862 vertices, 120916 faces slice 240: 120862 vertices, 120916 faces slice 250: 120862 vertices, 120916 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 120862 voxel in cpt #1: X=-54 [v=120862,e=362748,f=241832] located at (27.571899, -18.461262, 33.167397) For the whole surface: X=-54 [v=120862,e=362748,f=241832] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sat May 20 19:34:53 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh Sat May 20 19:34:57 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Sat May 20 19:35:01 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 43.4 mm, total surface area = 63302 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.5 minutes step 000: RMS=0.157 (target=0.015) step 005: RMS=0.118 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.056 (target=0.015) step 030: RMS=0.051 (target=0.015) step 035: RMS=0.046 (target=0.015) step 040: RMS=0.042 (target=0.015) step 045: RMS=0.040 (target=0.015) step 050: RMS=0.039 (target=0.015) step 055: RMS=0.038 (target=0.015) step 060: RMS=0.037 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 30.364000 mris_inflate stimesec 0.024000 mris_inflate ru_maxrss 158880 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 19714 mris_inflate ru_majflt 5 mris_inflate ru_nswap 0 mris_inflate ru_inblock 1048 mris_inflate ru_oublock 8440 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 5 mris_inflate ru_nivcsw 27 #-------------------------------------------- #@# Inflation1 rh Sat May 20 19:35:31 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 43.0 mm, total surface area = 63627 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.5 minutes step 000: RMS=0.155 (target=0.015) step 005: RMS=0.117 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.055 (target=0.015) step 030: RMS=0.049 (target=0.015) step 035: RMS=0.043 (target=0.015) step 040: RMS=0.040 (target=0.015) step 045: RMS=0.037 (target=0.015) step 050: RMS=0.034 (target=0.015) step 055: RMS=0.034 (target=0.015) step 060: RMS=0.033 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 30.564000 mris_inflate stimesec 0.028000 mris_inflate ru_maxrss 160112 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 20035 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 8504 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 57 #-------------------------------------------- #@# QSphere lh Sat May 20 19:36:02 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.07 +- 0.59 (0.00-->6.69) (max @ vno 89466 --> 89486) face area 0.04 +- 0.04 (-0.20-->0.82) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.366... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.556, avgs=0 005/300: dt: 0.9000, rms radial error=174.298, avgs=0 010/300: dt: 0.9000, rms radial error=173.747, avgs=0 015/300: dt: 0.9000, rms radial error=173.029, avgs=0 020/300: dt: 0.9000, rms radial error=172.211, avgs=0 025/300: dt: 0.9000, rms radial error=171.337, avgs=0 030/300: dt: 0.9000, rms radial error=170.431, avgs=0 035/300: dt: 0.9000, rms radial error=169.508, avgs=0 040/300: dt: 0.9000, rms radial error=168.577, avgs=0 045/300: dt: 0.9000, rms radial error=167.644, avgs=0 050/300: dt: 0.9000, rms radial error=166.711, avgs=0 055/300: dt: 0.9000, rms radial error=165.780, avgs=0 060/300: dt: 0.9000, rms radial error=164.853, avgs=0 065/300: dt: 0.9000, rms radial error=163.931, avgs=0 070/300: dt: 0.9000, rms radial error=163.012, avgs=0 075/300: dt: 0.9000, rms radial error=162.098, avgs=0 080/300: dt: 0.9000, rms radial error=161.189, avgs=0 085/300: dt: 0.9000, rms radial error=160.285, avgs=0 090/300: dt: 0.9000, rms radial error=159.386, avgs=0 095/300: dt: 0.9000, rms radial error=158.492, avgs=0 100/300: dt: 0.9000, rms radial error=157.602, avgs=0 105/300: dt: 0.9000, rms radial error=156.717, avgs=0 110/300: dt: 0.9000, rms radial error=155.836, avgs=0 115/300: dt: 0.9000, rms radial error=154.960, avgs=0 120/300: dt: 0.9000, rms radial error=154.089, avgs=0 125/300: dt: 0.9000, rms radial error=153.222, avgs=0 130/300: dt: 0.9000, rms radial error=152.360, avgs=0 135/300: dt: 0.9000, rms radial error=151.502, avgs=0 140/300: dt: 0.9000, rms radial error=150.650, avgs=0 145/300: dt: 0.9000, rms radial error=149.802, avgs=0 150/300: dt: 0.9000, rms radial error=148.958, avgs=0 155/300: dt: 0.9000, rms radial error=148.119, avgs=0 160/300: dt: 0.9000, rms radial error=147.284, avgs=0 165/300: dt: 0.9000, rms radial error=146.454, avgs=0 170/300: dt: 0.9000, rms radial error=145.629, avgs=0 175/300: dt: 0.9000, rms radial error=144.808, avgs=0 180/300: dt: 0.9000, rms radial error=143.991, avgs=0 185/300: dt: 0.9000, rms radial error=143.179, avgs=0 190/300: dt: 0.9000, rms radial error=142.371, avgs=0 195/300: dt: 0.9000, rms radial error=141.568, avgs=0 200/300: dt: 0.9000, rms radial error=140.769, avgs=0 205/300: dt: 0.9000, rms radial error=139.975, avgs=0 210/300: dt: 0.9000, rms radial error=139.185, avgs=0 215/300: dt: 0.9000, rms radial error=138.400, avgs=0 220/300: dt: 0.9000, rms radial error=137.619, avgs=0 225/300: dt: 0.9000, rms radial error=136.842, avgs=0 230/300: dt: 0.9000, rms radial error=136.070, avgs=0 235/300: dt: 0.9000, rms radial error=135.301, avgs=0 240/300: dt: 0.9000, rms radial error=134.537, avgs=0 245/300: dt: 0.9000, rms radial error=133.778, avgs=0 250/300: dt: 0.9000, rms radial error=133.022, avgs=0 255/300: dt: 0.9000, rms radial error=132.271, avgs=0 260/300: dt: 0.9000, rms radial error=131.524, avgs=0 265/300: dt: 0.9000, rms radial error=130.781, avgs=0 270/300: dt: 0.9000, rms radial error=130.042, avgs=0 275/300: dt: 0.9000, rms radial error=129.307, avgs=0 280/300: dt: 0.9000, rms radial error=128.577, avgs=0 285/300: dt: 0.9000, rms radial error=127.850, avgs=0 290/300: dt: 0.9000, rms radial error=127.128, avgs=0 295/300: dt: 0.9000, rms radial error=126.410, avgs=0 300/300: dt: 0.9000, rms radial error=125.696, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 13185.69 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 2 (K=40.0), pass 1, starting sse = 1951.34 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00075 epoch 3 (K=160.0), pass 1, starting sse = 155.50 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/10 = 0.00597 epoch 4 (K=640.0), pass 1, starting sse = 10.73 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/13 = 0.00699 final distance error %23.02 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.04 hours mris_sphere utimesec 160.544000 mris_sphere stimesec 0.028000 mris_sphere ru_maxrss 159436 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 19729 mris_sphere ru_majflt 7 mris_sphere ru_nswap 0 mris_sphere ru_inblock 1304 mris_sphere ru_oublock 8440 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 7 mris_sphere ru_nivcsw 98 FSRUNTIME@ mris_sphere 0.0446 hours 1 threads #-------------------------------------------- #@# QSphere rh Sat May 20 19:38:42 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.07 +- 0.57 (0.00-->8.42) (max @ vno 53875 --> 53887) face area 0.03 +- 0.04 (-0.15-->1.15) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.364... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.664, avgs=0 005/300: dt: 0.9000, rms radial error=174.408, avgs=0 010/300: dt: 0.9000, rms radial error=173.857, avgs=0 015/300: dt: 0.9000, rms radial error=173.132, avgs=0 020/300: dt: 0.9000, rms radial error=172.305, avgs=0 025/300: dt: 0.9000, rms radial error=171.421, avgs=0 030/300: dt: 0.9000, rms radial error=170.511, avgs=0 035/300: dt: 0.9000, rms radial error=169.587, avgs=0 040/300: dt: 0.9000, rms radial error=168.655, avgs=0 045/300: dt: 0.9000, rms radial error=167.720, avgs=0 050/300: dt: 0.9000, rms radial error=166.786, avgs=0 055/300: dt: 0.9000, rms radial error=165.854, avgs=0 060/300: dt: 0.9000, rms radial error=164.926, avgs=0 065/300: dt: 0.9000, rms radial error=164.002, avgs=0 070/300: dt: 0.9000, rms radial error=163.082, avgs=0 075/300: dt: 0.9000, rms radial error=162.167, avgs=0 080/300: dt: 0.9000, rms radial error=161.256, avgs=0 085/300: dt: 0.9000, rms radial error=160.351, avgs=0 090/300: dt: 0.9000, rms radial error=159.450, avgs=0 095/300: dt: 0.9000, rms radial error=158.554, avgs=0 100/300: dt: 0.9000, rms radial error=157.662, avgs=0 105/300: dt: 0.9000, rms radial error=156.776, avgs=0 110/300: dt: 0.9000, rms radial error=155.894, avgs=0 115/300: dt: 0.9000, rms radial error=155.017, avgs=0 120/300: dt: 0.9000, rms radial error=154.145, avgs=0 125/300: dt: 0.9000, rms radial error=153.277, avgs=0 130/300: dt: 0.9000, rms radial error=152.415, avgs=0 135/300: dt: 0.9000, rms radial error=151.557, avgs=0 140/300: dt: 0.9000, rms radial error=150.704, avgs=0 145/300: dt: 0.9000, rms radial error=149.856, avgs=0 150/300: dt: 0.9000, rms radial error=149.012, avgs=0 155/300: dt: 0.9000, rms radial error=148.174, avgs=0 160/300: dt: 0.9000, rms radial error=147.341, avgs=0 165/300: dt: 0.9000, rms radial error=146.512, avgs=0 170/300: dt: 0.9000, rms radial error=145.688, avgs=0 175/300: dt: 0.9000, rms radial error=144.868, avgs=0 180/300: dt: 0.9000, rms radial error=144.053, avgs=0 185/300: dt: 0.9000, rms radial error=143.242, avgs=0 190/300: dt: 0.9000, rms radial error=142.436, avgs=0 195/300: dt: 0.9000, rms radial error=141.634, avgs=0 200/300: dt: 0.9000, rms radial error=140.836, avgs=0 205/300: dt: 0.9000, rms radial error=140.044, avgs=0 210/300: dt: 0.9000, rms radial error=139.255, avgs=0 215/300: dt: 0.9000, rms radial error=138.471, avgs=0 220/300: dt: 0.9000, rms radial error=137.691, avgs=0 225/300: dt: 0.9000, rms radial error=136.916, avgs=0 230/300: dt: 0.9000, rms radial error=136.145, avgs=0 235/300: dt: 0.9000, rms radial error=135.378, avgs=0 240/300: dt: 0.9000, rms radial error=134.616, avgs=0 245/300: dt: 0.9000, rms radial error=133.857, avgs=0 250/300: dt: 0.9000, rms radial error=133.103, avgs=0 255/300: dt: 0.9000, rms radial error=132.353, avgs=0 260/300: dt: 0.9000, rms radial error=131.607, avgs=0 265/300: dt: 0.9000, rms radial error=130.865, avgs=0 270/300: dt: 0.9000, rms radial error=130.128, avgs=0 275/300: dt: 0.9000, rms radial error=129.394, avgs=0 280/300: dt: 0.9000, rms radial error=128.665, avgs=0 285/300: dt: 0.9000, rms radial error=127.939, avgs=0 290/300: dt: 0.9000, rms radial error=127.218, avgs=0 295/300: dt: 0.9000, rms radial error=126.501, avgs=0 300/300: dt: 0.9000, rms radial error=125.788, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 13294.97 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 2 (K=40.0), pass 1, starting sse = 1948.99 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00037 epoch 3 (K=160.0), pass 1, starting sse = 156.98 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00630 epoch 4 (K=640.0), pass 1, starting sse = 10.44 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.17/16 = 0.01039 final distance error %22.74 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.05 hours mris_sphere utimesec 171.160000 mris_sphere stimesec 0.020000 mris_sphere ru_maxrss 160292 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 19537 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 8504 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 0 mris_sphere ru_nivcsw 164 FSRUNTIME@ mris_sphere 0.0475 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Sat May 20 19:41:34 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Sat May 20 19:41:34 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Sat May 20 19:41:34 EDT 2017 mris_fix_topology -rusage /usr/local/freesurfer/subjects/Sub01/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 Sub01 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-50 (nv=119952, nf=240004, ne=360006, g=26) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 6 iterations marking ambiguous vertices... 4009 ambiguous faces found in tessellation segmenting defects... 33 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 33 defects to be corrected 0 vertices coincident reading input surface /usr/local/freesurfer/subjects/Sub01/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.6978 (-4.8489) -vertex loglikelihood: -6.7075 (-3.3538) -normal dot loglikelihood: -3.6204 (-3.6204) -quad curv loglikelihood: -6.3526 (-3.1763) Total Loglikelihood : -26.3784 CORRECTING DEFECT 0 (vertices=79, convex hull=87, v0=0) After retessellation of defect 0 (v0=0), euler #=-30 (117504,351568,234034) : difference with theory (-30) = 0 CORRECTING DEFECT 1 (vertices=20, convex hull=38, v0=336) After retessellation of defect 1 (v0=336), euler #=-29 (117505,351585,234051) : difference with theory (-29) = 0 CORRECTING DEFECT 2 (vertices=27, convex hull=34, v0=1590) After retessellation of defect 2 (v0=1590), euler #=-28 (117507,351601,234066) : difference with theory (-28) = 0 CORRECTING DEFECT 3 (vertices=27, convex hull=34, v0=2304) After retessellation of defect 3 (v0=2304), euler #=-27 (117511,351626,234088) : difference with theory (-27) = 0 CORRECTING DEFECT 4 (vertices=12, convex hull=27, v0=2333) After retessellation of defect 4 (v0=2333), euler #=-26 (117513,351640,234101) : difference with theory (-26) = 0 CORRECTING DEFECT 5 (vertices=6, convex hull=26, v0=2335) After retessellation of defect 5 (v0=2335), euler #=-25 (117514,351650,234111) : difference with theory (-25) = 0 CORRECTING DEFECT 6 (vertices=12, convex hull=36, v0=2937) After retessellation of defect 6 (v0=2937), euler #=-24 (117515,351666,234127) : difference with theory (-24) = 0 CORRECTING DEFECT 7 (vertices=55, convex hull=110, v0=4116) After retessellation of defect 7 (v0=4116), euler #=-23 (117538,351784,234223) : difference with theory (-23) = 0 CORRECTING DEFECT 8 (vertices=114, convex hull=45, v0=10473) After retessellation of defect 8 (v0=10473), euler #=-22 (117552,351845,234271) : difference with theory (-22) = 0 CORRECTING DEFECT 9 (vertices=105, convex hull=87, v0=17353) After retessellation of defect 9 (v0=17353), euler #=-21 (117569,351932,234342) : difference with theory (-21) = 0 CORRECTING DEFECT 10 (vertices=10, convex hull=27, v0=22941) After retessellation of defect 10 (v0=22941), euler #=-20 (117571,351947,234356) : difference with theory (-20) = 0 CORRECTING DEFECT 11 (vertices=38, convex hull=91, v0=31927) After retessellation of defect 11 (v0=31927), euler #=-19 (117592,352045,234434) : difference with theory (-19) = 0 CORRECTING DEFECT 12 (vertices=32, convex hull=66, v0=34506) After retessellation of defect 12 (v0=34506), euler #=-18 (117603,352103,234482) : difference with theory (-18) = 0 CORRECTING DEFECT 13 (vertices=45, convex hull=97, v0=44030) After retessellation of defect 13 (v0=44030), euler #=-17 (117631,352225,234577) : difference with theory (-17) = 0 CORRECTING DEFECT 14 (vertices=89, convex hull=93, v0=48780) After retessellation of defect 14 (v0=48780), euler #=-16 (117652,352329,234661) : difference with theory (-16) = 0 CORRECTING DEFECT 15 (vertices=55, convex hull=89, v0=52870) After retessellation of defect 15 (v0=52870), euler #=-15 (117665,352405,234725) : difference with theory (-15) = 0 CORRECTING DEFECT 16 (vertices=28, convex hull=59, v0=63220) After retessellation of defect 16 (v0=63220), euler #=-14 (117675,352461,234772) : difference with theory (-14) = 0 CORRECTING DEFECT 17 (vertices=53, convex hull=69, v0=65630) After retessellation of defect 17 (v0=65630), euler #=-13 (117703,352578,234862) : difference with theory (-13) = 0 CORRECTING DEFECT 18 (vertices=83, convex hull=66, v0=65672) After retessellation of defect 18 (v0=65672), euler #=-12 (117714,352640,234914) : difference with theory (-12) = 0 CORRECTING DEFECT 19 (vertices=23, convex hull=23, v0=67635) After retessellation of defect 19 (v0=67635), euler #=-11 (117715,352650,234924) : difference with theory (-11) = 0 CORRECTING DEFECT 20 (vertices=28, convex hull=18, v0=75675) After retessellation of defect 20 (v0=75675), euler #=-10 (117720,352671,234941) : difference with theory (-10) = 0 CORRECTING DEFECT 21 (vertices=12, convex hull=25, v0=75929) After retessellation of defect 21 (v0=75929), euler #=-9 (117725,352694,234960) : difference with theory (-9) = 0 CORRECTING DEFECT 22 (vertices=18, convex hull=33, v0=83182) After retessellation of defect 22 (v0=83182), euler #=-8 (117735,352733,234990) : difference with theory (-8) = 0 CORRECTING DEFECT 23 (vertices=52, convex hull=89, v0=83850) After retessellation of defect 23 (v0=83850), euler #=-7 (117770,352872,235095) : difference with theory (-7) = 0 CORRECTING DEFECT 24 (vertices=106, convex hull=84, v0=84335) After retessellation of defect 24 (v0=84335), euler #=-6 (117814,353040,235220) : difference with theory (-6) = 0 CORRECTING DEFECT 25 (vertices=897, convex hull=437, v0=86248) L defect detected... After retessellation of defect 25 (v0=86248), euler #=-5 (118008,353855,235842) : difference with theory (-5) = 0 CORRECTING DEFECT 26 (vertices=69, convex hull=91, v0=86531) After retessellation of defect 26 (v0=86531), euler #=-4 (118045,354004,235955) : difference with theory (-4) = 0 CORRECTING DEFECT 27 (vertices=125, convex hull=89, v0=96186) After retessellation of defect 27 (v0=96186), euler #=-3 (118077,354139,236059) : difference with theory (-3) = 0 CORRECTING DEFECT 28 (vertices=50, convex hull=93, v0=99518) After retessellation of defect 28 (v0=99518), euler #=-2 (118101,354251,236148) : difference with theory (-2) = 0 CORRECTING DEFECT 29 (vertices=21, convex hull=27, v0=102661) After retessellation of defect 29 (v0=102661), euler #=-1 (118106,354273,236166) : difference with theory (-1) = 0 CORRECTING DEFECT 30 (vertices=21, convex hull=20, v0=105423) After retessellation of defect 30 (v0=105423), euler #=0 (118112,354298,236186) : difference with theory (0) = 0 CORRECTING DEFECT 31 (vertices=122, convex hull=68, v0=113113) After retessellation of defect 31 (v0=113113), euler #=1 (118134,354391,236258) : difference with theory (1) = 0 CORRECTING DEFECT 32 (vertices=24, convex hull=17, v0=118802) After retessellation of defect 32 (v0=118802), euler #=2 (118136,354402,236268) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.09-->11.94) (max @ vno 98501 --> 104413) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.09-->11.94) (max @ vno 98501 --> 104413) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 112 mutations (36.0%), 199 crossovers (64.0%), 191 vertices were eliminated building final representation... 1816 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=118136, nf=236268, ne=354402, g=0) writing corrected surface to /usr/local/freesurfer/subjects/Sub01/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 14.3 minutes 0 defective edges removing intersecting faces 000: 288 intersecting 001: 20 intersecting 002: 2 intersecting mris_fix_topology utimesec 856.204000 mris_fix_topology stimesec 0.072000 mris_fix_topology ru_maxrss 387896 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 50084 mris_fix_topology ru_majflt 8 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 1464 mris_fix_topology ru_oublock 11144 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 9 mris_fix_topology ru_nivcsw 776 FSRUNTIME@ mris_fix_topology lh 0.2379 hours 1 threads #@# Fix Topology rh Sat May 20 19:55:50 EDT 2017 mris_fix_topology -rusage /usr/local/freesurfer/subjects/Sub01/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 Sub01 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-54 (nv=120862, nf=241832, ne=362748, g=28) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 7 iterations marking ambiguous vertices... 3455 ambiguous faces found in tessellation segmenting defects... 32 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 32 defects to be corrected 0 vertices coincident reading input surface /usr/local/freesurfer/subjects/Sub01/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5720 (-4.7860) -vertex loglikelihood: -6.6484 (-3.3242) -normal dot loglikelihood: -3.5968 (-3.5968) -quad curv loglikelihood: -6.4565 (-3.2282) Total Loglikelihood : -26.2737 CORRECTING DEFECT 0 (vertices=5, convex hull=22, v0=315) After retessellation of defect 0 (v0=315), euler #=-29 (118749,355360,236582) : difference with theory (-29) = 0 CORRECTING DEFECT 1 (vertices=61, convex hull=91, v0=489) After retessellation of defect 1 (v0=489), euler #=-28 (118771,355465,236666) : difference with theory (-28) = 0 CORRECTING DEFECT 2 (vertices=86, convex hull=71, v0=7372) After retessellation of defect 2 (v0=7372), euler #=-27 (118787,355540,236726) : difference with theory (-27) = 0 CORRECTING DEFECT 3 (vertices=17, convex hull=44, v0=10049) After retessellation of defect 3 (v0=10049), euler #=-26 (118795,355582,236761) : difference with theory (-26) = 0 CORRECTING DEFECT 4 (vertices=37, convex hull=39, v0=16745) After retessellation of defect 4 (v0=16745), euler #=-25 (118799,355607,236783) : difference with theory (-25) = 0 CORRECTING DEFECT 5 (vertices=28, convex hull=57, v0=16880) After retessellation of defect 5 (v0=16880), euler #=-24 (118810,355662,236828) : difference with theory (-24) = 0 CORRECTING DEFECT 6 (vertices=36, convex hull=80, v0=22202) After retessellation of defect 6 (v0=22202), euler #=-23 (118828,355747,236896) : difference with theory (-23) = 0 CORRECTING DEFECT 7 (vertices=32, convex hull=65, v0=23424) After retessellation of defect 7 (v0=23424), euler #=-22 (118845,355824,236957) : difference with theory (-22) = 0 CORRECTING DEFECT 8 (vertices=53, convex hull=65, v0=26923) After retessellation of defect 8 (v0=26923), euler #=-21 (118866,355913,237026) : difference with theory (-21) = 0 CORRECTING DEFECT 9 (vertices=5, convex hull=14, v0=35503) After retessellation of defect 9 (v0=35503), euler #=-20 (118867,355918,237031) : difference with theory (-20) = 0 CORRECTING DEFECT 10 (vertices=52, convex hull=72, v0=38678) After retessellation of defect 10 (v0=38678), euler #=-19 (118902,356053,237132) : difference with theory (-19) = 0 CORRECTING DEFECT 11 (vertices=26, convex hull=40, v0=38758) After retessellation of defect 11 (v0=38758), euler #=-18 (118911,356094,237165) : difference with theory (-18) = 0 CORRECTING DEFECT 12 (vertices=32, convex hull=77, v0=41481) After retessellation of defect 12 (v0=41481), euler #=-17 (118925,356166,237224) : difference with theory (-17) = 0 CORRECTING DEFECT 13 (vertices=253, convex hull=191, v0=44060) normal vector of length zero at vertex 119357 with 3 faces normal vector of length zero at vertex 119417 with 4 faces After retessellation of defect 13 (v0=44060), euler #=-16 (118994,356462,237452) : difference with theory (-16) = 0 CORRECTING DEFECT 14 (vertices=32, convex hull=73, v0=46705) After retessellation of defect 14 (v0=46705), euler #=-15 (119007,356528,237506) : difference with theory (-15) = 0 CORRECTING DEFECT 15 (vertices=28, convex hull=44, v0=46725) After retessellation of defect 15 (v0=46725), euler #=-14 (119017,356573,237542) : difference with theory (-14) = 0 CORRECTING DEFECT 16 (vertices=16, convex hull=16, v0=55585) After retessellation of defect 16 (v0=55585), euler #=-13 (119018,356579,237548) : difference with theory (-13) = 0 CORRECTING DEFECT 17 (vertices=101, convex hull=32, v0=66732) After retessellation of defect 17 (v0=66732), euler #=-12 (119028,356619,237579) : difference with theory (-12) = 0 CORRECTING DEFECT 18 (vertices=31, convex hull=72, v0=73713) After retessellation of defect 18 (v0=73713), euler #=-11 (119049,356710,237650) : difference with theory (-11) = 0 CORRECTING DEFECT 19 (vertices=63, convex hull=73, v0=75136) After retessellation of defect 19 (v0=75136), euler #=-10 (119082,356844,237752) : difference with theory (-10) = 0 CORRECTING DEFECT 20 (vertices=48, convex hull=63, v0=80969) After retessellation of defect 20 (v0=80969), euler #=-9 (119101,356927,237817) : difference with theory (-9) = 0 CORRECTING DEFECT 21 (vertices=35, convex hull=32, v0=83957) After retessellation of defect 21 (v0=83957), euler #=-8 (119110,356963,237845) : difference with theory (-8) = 0 CORRECTING DEFECT 22 (vertices=46, convex hull=65, v0=84562) After retessellation of defect 22 (v0=84562), euler #=-7 (119134,357061,237920) : difference with theory (-7) = 0 CORRECTING DEFECT 23 (vertices=654, convex hull=390, v0=84882) After retessellation of defect 23 (v0=84882), euler #=-6 (119274,357670,238390) : difference with theory (-6) = 0 CORRECTING DEFECT 24 (vertices=25, convex hull=62, v0=86039) After retessellation of defect 24 (v0=86039), euler #=-5 (119288,357735,238442) : difference with theory (-5) = 0 CORRECTING DEFECT 25 (vertices=62, convex hull=67, v0=86939) After retessellation of defect 25 (v0=86939), euler #=-4 (119296,357789,238489) : difference with theory (-4) = 0 CORRECTING DEFECT 26 (vertices=28, convex hull=47, v0=92766) After retessellation of defect 26 (v0=92766), euler #=-3 (119312,357856,238541) : difference with theory (-3) = 0 CORRECTING DEFECT 27 (vertices=118, convex hull=42, v0=96471) After retessellation of defect 27 (v0=96471), euler #=-2 (119323,357904,238579) : difference with theory (-2) = 0 CORRECTING DEFECT 28 (vertices=44, convex hull=31, v0=100197) After retessellation of defect 28 (v0=100197), euler #=-1 (119336,357952,238615) : difference with theory (-1) = 0 CORRECTING DEFECT 29 (vertices=11, convex hull=27, v0=100695) After retessellation of defect 29 (v0=100695), euler #=0 (119338,357966,238628) : difference with theory (0) = 0 CORRECTING DEFECT 30 (vertices=17, convex hull=56, v0=107175) After retessellation of defect 30 (v0=107175), euler #=1 (119347,358012,238666) : difference with theory (1) = 0 CORRECTING DEFECT 31 (vertices=30, convex hull=57, v0=118754) After retessellation of defect 31 (v0=118754), euler #=2 (119358,358068,238712) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.07-->9.37) (max @ vno 43637 --> 49622) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.07-->9.37) (max @ vno 43637 --> 49622) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 102 mutations (34.7%), 192 crossovers (65.3%), 161 vertices were eliminated building final representation... 1504 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=119358, nf=238712, ne=358068, g=0) writing corrected surface to /usr/local/freesurfer/subjects/Sub01/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 11.6 minutes 0 defective edges removing intersecting faces 000: 202 intersecting 001: 12 intersecting mris_fix_topology utimesec 694.840000 mris_fix_topology stimesec 0.040000 mris_fix_topology ru_maxrss 387700 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 47924 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 11256 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 0 mris_fix_topology ru_nivcsw 711 FSRUNTIME@ mris_fix_topology rh 0.1930 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 118136 - 354402 + 236268 = 2 --> 0 holes F =2V-4: 236268 = 236272-4 (0) 2E=3F: 708804 = 708804 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 119358 - 358068 + 238712 = 2 --> 0 holes F =2V-4: 238712 = 238716-4 (0) 2E=3F: 716136 = 716136 (0) total defect index = 0 /usr/local/freesurfer/subjects/Sub01/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 45 intersecting 001: 9 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /usr/local/freesurfer/subjects/Sub01/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 48 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Sat May 20 20:07:31 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -mgz -T1 brain.finalsurfs Sub01 lh using white.preaparc as white matter name... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /usr/local/freesurfer/subjects/Sub01/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/Sub01/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/Sub01/mri/../mri/aseg.presurf.mgz... reading volume /usr/local/freesurfer/subjects/Sub01/mri/wm.mgz... 17673 bright wm thresholded. 1364 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/Sub01/surf/lh.orig... computing class statistics... border white: 222774 voxels (1.33%) border gray 251817 voxels (1.50%) WM (97.0): 96.9 +- 9.6 [70.0 --> 110.0] GM (65.0) : 65.2 +- 10.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 47.2 (was 70) setting MAX_BORDER_WHITE to 112.6 (was 105) setting MIN_BORDER_WHITE to 58.0 (was 85) setting MAX_CSF to 36.3 (was 40) setting MAX_GRAY to 93.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 47.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 25.5 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->3.90) (max @ vno 107384 --> 107904) face area 0.28 +- 0.12 (0.00-->3.46) mean absolute distance = 0.65 +- 0.77 3805 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-7.8, GM=58+-9.6 mean inside = 91.8, mean outside = 68.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=73.4, 38 (38) missing vertices, mean dist 0.4 [0.4 (%32.9)->0.8 (%67.1))] %75 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.25 (0.07-->4.28) (max @ vno 117852 --> 91217) face area 0.28 +- 0.13 (0.00-->3.59) mean absolute distance = 0.32 +- 0.50 3045 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4090675.5, rms=12.686 001: dt: 0.5000, sse=2294039.5, rms=9.035 (28.784%) 002: dt: 0.5000, sse=1522238.0, rms=6.886 (23.782%) 003: dt: 0.5000, sse=1138900.9, rms=5.511 (19.970%) 004: dt: 0.5000, sse=970453.1, rms=4.779 (13.276%) 005: dt: 0.5000, sse=893794.9, rms=4.402 (7.896%) 006: dt: 0.5000, sse=865733.9, rms=4.255 (3.344%) 007: dt: 0.5000, sse=850786.4, rms=4.169 (2.025%) rms = 4.14, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=845261.6, rms=4.136 (0.780%) 009: dt: 0.2500, sse=625879.1, rms=2.622 (36.605%) 010: dt: 0.2500, sse=579396.3, rms=2.178 (16.948%) 011: dt: 0.2500, sse=568392.6, rms=2.059 (5.455%) 012: dt: 0.2500, sse=560745.9, rms=1.970 (4.299%) rms = 1.93, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=558090.1, rms=1.932 (1.936%) 014: dt: 0.1250, sse=538964.6, rms=1.692 (12.442%) rms = 1.66, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=537393.8, rms=1.661 (1.808%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=77.3, 52 (14) missing vertices, mean dist -0.2 [0.3 (%77.3)->0.2 (%22.7))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= X1, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.05-->4.58) (max @ vno 117852 --> 91217) face area 0.36 +- 0.16 (0.00-->4.45) mean absolute distance = 0.22 +- 0.36 2565 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1300295.6, rms=5.576 016: dt: 0.5000, sse=940429.3, rms=3.883 (30.373%) rms = 4.16, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=779283.4, rms=2.808 (27.689%) 018: dt: 0.2500, sse=707061.1, rms=2.150 (23.407%) 019: dt: 0.2500, sse=676100.7, rms=1.811 (15.764%) 020: dt: 0.2500, sse=667032.4, rms=1.694 (6.463%) 021: dt: 0.2500, sse=660675.8, rms=1.607 (5.174%) rms = 1.57, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=657699.2, rms=1.567 (2.443%) 023: dt: 0.1250, sse=647684.8, rms=1.408 (10.191%) rms = 1.39, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=646302.3, rms=1.388 (1.391%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=79.7, 55 (13) missing vertices, mean dist -0.1 [0.2 (%70.7)->0.2 (%29.3))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= X1, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.11-->4.72) (max @ vno 117852 --> 91217) face area 0.34 +- 0.16 (0.00-->4.31) mean absolute distance = 0.19 +- 0.31 2217 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=829475.1, rms=3.329 rms = 3.54, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=696465.2, rms=2.263 (32.015%) 026: dt: 0.2500, sse=631873.7, rms=1.474 (34.873%) 027: dt: 0.2500, sse=626210.7, rms=1.363 (7.526%) rms = 1.33, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=622867.7, rms=1.334 (2.102%) 029: dt: 0.1250, sse=615683.2, rms=1.224 (8.298%) rms = 1.22, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=615566.3, rms=1.219 (0.385%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group mean border=80.5, 82 (10) missing vertices, mean dist -0.0 [0.2 (%55.6)->0.2 (%44.4))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= X1, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /usr/local/freesurfer/subjects/Sub01/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=632689.8, rms=1.601 rms = 2.22, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=600624.2, rms=1.069 (33.209%) 032: dt: 0.2500, sse=602623.7, rms=0.910 (14.879%) rms = 0.92, time step reduction 2 of 3 to 0.125... rms = 0.90, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=593795.4, rms=0.904 (0.688%) positioning took 0.3 minutes generating cortex label... 3 non-cortical segments detected only using segment with 7224 vertices erasing segment 1 (vno[0] = 82241) erasing segment 2 (vno[0] = 99066) writing cortex label to /usr/local/freesurfer/subjects/Sub01/label/lh.cortex.label... writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/lh.curv writing smoothed area to lh.area writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/lh.area vertex spacing 0.90 +- 0.25 (0.03-->4.80) (max @ vno 91217 --> 117852) face area 0.34 +- 0.16 (0.00-->4.17) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group smoothing surface for 5 iterations... mean border=45.7, 47 (47) missing vertices, mean dist 1.7 [0.0 (%0.0)->2.7 (%100.0))] %10 local maxima, %50 large gradients and %35 min vals, 287 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=27057996.0, rms=34.400 001: dt: 0.0500, sse=23668240.0, rms=32.130 (6.600%) 002: dt: 0.0500, sse=21054154.0, rms=30.263 (5.811%) 003: dt: 0.0500, sse=19034418.0, rms=28.737 (5.042%) 004: dt: 0.0500, sse=17431726.0, rms=27.466 (4.423%) 005: dt: 0.0500, sse=16122471.0, rms=26.382 (3.947%) 006: dt: 0.0500, sse=15019515.0, rms=25.433 (3.597%) 007: dt: 0.0500, sse=14072009.0, rms=24.588 (3.321%) 008: dt: 0.0500, sse=13242651.0, rms=23.824 (3.107%) 009: dt: 0.0500, sse=12509235.0, rms=23.128 (2.924%) 010: dt: 0.0500, sse=11852547.0, rms=22.486 (2.777%) positioning took 0.7 minutes mean border=45.4, 55 (20) missing vertices, mean dist 1.4 [0.1 (%0.2)->2.2 (%99.8))] %12 local maxima, %49 large gradients and %33 min vals, 271 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=12639914.0, rms=23.220 011: dt: 0.0500, sse=12039650.0, rms=22.636 (2.515%) 012: dt: 0.0500, sse=11495572.0, rms=22.093 (2.397%) 013: dt: 0.0500, sse=11000243.0, rms=21.587 (2.290%) 014: dt: 0.0500, sse=10547969.0, rms=21.115 (2.189%) 015: dt: 0.0500, sse=10133829.0, rms=20.672 (2.095%) 016: dt: 0.0500, sse=9753066.0, rms=20.257 (2.009%) 017: dt: 0.0500, sse=9400427.0, rms=19.865 (1.937%) 018: dt: 0.0500, sse=9073173.0, rms=19.493 (1.869%) 019: dt: 0.0500, sse=8768803.0, rms=19.141 (1.805%) 020: dt: 0.0500, sse=8484376.0, rms=18.807 (1.749%) positioning took 0.7 minutes mean border=45.3, 82 (16) missing vertices, mean dist 1.2 [0.1 (%3.7)->1.9 (%96.3))] %13 local maxima, %49 large gradients and %33 min vals, 260 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=8569341.0, rms=18.902 021: dt: 0.0500, sse=8297795.5, rms=18.578 (1.713%) 022: dt: 0.0500, sse=8044499.5, rms=18.271 (1.654%) 023: dt: 0.0500, sse=7805242.0, rms=17.976 (1.615%) 024: dt: 0.0500, sse=7581314.5, rms=17.695 (1.561%) 025: dt: 0.0500, sse=7371067.5, rms=17.428 (1.513%) 026: dt: 0.0500, sse=7173442.0, rms=17.172 (1.466%) 027: dt: 0.0500, sse=6985968.5, rms=16.926 (1.433%) 028: dt: 0.0500, sse=6807010.5, rms=16.688 (1.408%) 029: dt: 0.0500, sse=6635959.0, rms=16.456 (1.385%) 030: dt: 0.0500, sse=6472221.0, rms=16.232 (1.364%) positioning took 0.7 minutes mean border=45.3, 94 (14) missing vertices, mean dist 1.0 [0.1 (%13.0)->1.8 (%87.0))] %13 local maxima, %49 large gradients and %33 min vals, 207 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=6533289.0, rms=16.303 031: dt: 0.5000, sse=5404370.0, rms=14.672 (10.008%) 032: dt: 0.5000, sse=4604236.5, rms=13.389 (8.746%) 033: dt: 0.5000, sse=3967876.0, rms=12.273 (8.329%) 034: dt: 0.5000, sse=3440283.0, rms=11.261 (8.251%) 035: dt: 0.5000, sse=2968423.2, rms=10.273 (8.774%) 036: dt: 0.5000, sse=2533947.0, rms=9.270 (9.759%) 037: dt: 0.5000, sse=2142699.2, rms=8.268 (10.810%) 038: dt: 0.5000, sse=1822631.5, rms=7.346 (11.154%) 039: dt: 0.5000, sse=1574461.2, rms=6.546 (10.889%) 040: dt: 0.5000, sse=1403961.0, rms=5.930 (9.413%) 041: dt: 0.5000, sse=1290128.0, rms=5.485 (7.510%) 042: dt: 0.5000, sse=1228263.9, rms=5.222 (4.790%) 043: dt: 0.5000, sse=1187572.6, rms=5.046 (3.374%) 044: dt: 0.5000, sse=1168114.0, rms=4.955 (1.805%) 045: dt: 0.5000, sse=1150202.5, rms=4.874 (1.623%) rms = 4.84, time step reduction 1 of 3 to 0.250... 046: dt: 0.5000, sse=1143082.2, rms=4.838 (0.739%) 047: dt: 0.2500, sse=1036316.9, rms=4.262 (11.907%) 048: dt: 0.2500, sse=1006854.1, rms=4.102 (3.756%) rms = 4.09, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=1005550.4, rms=4.092 (0.256%) 050: dt: 0.1250, sse=987068.9, rms=3.983 (2.657%) rms = 3.97, time step reduction 3 of 3 to 0.062... 051: dt: 0.1250, sse=984745.4, rms=3.970 (0.334%) positioning took 1.7 minutes mean border=44.5, 1649 (6) missing vertices, mean dist 0.1 [0.2 (%52.8)->0.5 (%47.2))] %24 local maxima, %39 large gradients and %30 min vals, 99 gradients ignored tol=1.0e-04, sigma=1.0, host= X1, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1244827.6, rms=4.226 052: dt: 0.5000, sse=1225210.5, rms=4.140 (2.037%) rms = 4.17, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1127828.6, rms=3.542 (14.448%) 054: dt: 0.2500, sse=1097096.9, rms=3.340 (5.682%) rms = 3.29, time step reduction 2 of 3 to 0.125... 055: dt: 0.2500, sse=1089815.5, rms=3.292 (1.439%) 056: dt: 0.1250, sse=1070847.0, rms=3.151 (4.294%) rms = 3.13, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1067278.6, rms=3.128 (0.740%) positioning took 0.5 minutes mean border=43.8, 1631 (6) missing vertices, mean dist 0.1 [0.1 (%52.5)->0.4 (%47.5))] %38 local maxima, %26 large gradients and %30 min vals, 120 gradients ignored tol=1.0e-04, sigma=0.5, host= X1, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1114048.4, rms=3.450 rms = 3.82, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1085189.1, rms=3.252 (5.752%) 059: dt: 0.2500, sse=1074821.4, rms=3.188 (1.970%) rms = 3.19, time step reduction 2 of 3 to 0.125... rms = 3.16, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1070764.2, rms=3.156 (0.983%) positioning took 0.4 minutes mean border=43.1, 3370 (5) missing vertices, mean dist 0.1 [0.1 (%50.2)->0.3 (%49.8))] %44 local maxima, %20 large gradients and %29 min vals, 143 gradients ignored tol=1.0e-04, sigma=0.2, host= X1, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /usr/local/freesurfer/subjects/Sub01/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1095495.0, rms=3.329 rms = 3.68, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1073989.8, rms=3.174 (4.646%) 062: dt: 0.2500, sse=1060324.8, rms=3.092 (2.598%) rms = 3.08, time step reduction 2 of 3 to 0.125... 063: dt: 0.2500, sse=1056746.6, rms=3.077 (0.478%) 064: dt: 0.1250, sse=1040895.6, rms=2.956 (3.942%) rms = 2.93, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=1036681.9, rms=2.928 (0.923%) positioning took 0.5 minutes writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/lh.area.pial vertex spacing 1.05 +- 0.45 (0.10-->8.15) (max @ vno 80200 --> 80185) face area 0.43 +- 0.33 (0.00-->5.01) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 118136 vertices processed 25000 of 118136 vertices processed 50000 of 118136 vertices processed 75000 of 118136 vertices processed 100000 of 118136 vertices processed 0 of 118136 vertices processed 25000 of 118136 vertices processed 50000 of 118136 vertices processed 75000 of 118136 vertices processed 100000 of 118136 vertices processed thickness calculation complete, 549:974 truncations. 24298 vertices at 0 distance 75378 vertices at 1 distance 75394 vertices at 2 distance 33647 vertices at 3 distance 10729 vertices at 4 distance 3170 vertices at 5 distance 981 vertices at 6 distance 340 vertices at 7 distance 154 vertices at 8 distance 94 vertices at 9 distance 58 vertices at 10 distance 47 vertices at 11 distance 39 vertices at 12 distance 39 vertices at 13 distance 32 vertices at 14 distance 15 vertices at 15 distance 12 vertices at 16 distance 12 vertices at 17 distance 10 vertices at 18 distance 16 vertices at 19 distance 23 vertices at 20 distance writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/lh.thickness positioning took 10.2 minutes #-------------------------------------------- #@# Make White Surf rh Sat May 20 20:17:45 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -mgz -T1 brain.finalsurfs Sub01 rh using white.preaparc as white matter name... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /usr/local/freesurfer/subjects/Sub01/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/Sub01/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/Sub01/mri/../mri/aseg.presurf.mgz... reading volume /usr/local/freesurfer/subjects/Sub01/mri/wm.mgz... 17673 bright wm thresholded. 1364 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/Sub01/surf/rh.orig... computing class statistics... border white: 222774 voxels (1.33%) border gray 251817 voxels (1.50%) WM (97.0): 96.9 +- 9.6 [70.0 --> 110.0] GM (65.0) : 65.2 +- 10.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.2 (was 70) setting MAX_BORDER_WHITE to 113.6 (was 105) setting MIN_BORDER_WHITE to 60.0 (was 85) setting MAX_CSF to 38.3 (was 40) setting MAX_GRAY to 94.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 49.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 27.5 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->4.28) (max @ vno 105402 --> 119254) face area 0.28 +- 0.12 (0.00-->5.45) mean absolute distance = 0.64 +- 0.77 3630 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104+-7.8, GM=60+-8.7 mean inside = 92.3, mean outside = 69.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=74.5, 34 (34) missing vertices, mean dist 0.3 [0.5 (%34.4)->0.7 (%65.6))] %72 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.09-->5.49) (max @ vno 105402 --> 119254) face area 0.28 +- 0.13 (0.00-->6.27) mean absolute distance = 0.31 +- 0.52 2788 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3907435.5, rms=12.281 001: dt: 0.5000, sse=2161425.2, rms=8.633 (29.708%) 002: dt: 0.5000, sse=1438393.5, rms=6.543 (24.204%) 003: dt: 0.5000, sse=1088252.8, rms=5.249 (19.774%) 004: dt: 0.5000, sse=940924.1, rms=4.590 (12.563%) 005: dt: 0.5000, sse=876071.8, rms=4.263 (7.128%) 006: dt: 0.5000, sse=855029.1, rms=4.148 (2.704%) 007: dt: 0.5000, sse=841759.8, rms=4.073 (1.805%) rms = 4.05, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=838603.6, rms=4.052 (0.516%) 009: dt: 0.2500, sse=622969.3, rms=2.542 (37.270%) 010: dt: 0.2500, sse=576734.9, rms=2.090 (17.754%) 011: dt: 0.2500, sse=565862.7, rms=1.965 (6.012%) 012: dt: 0.2500, sse=558960.2, rms=1.882 (4.229%) rms = 1.84, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=555855.8, rms=1.840 (2.210%) 014: dt: 0.1250, sse=540810.2, rms=1.642 (10.773%) rms = 1.62, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=539137.4, rms=1.618 (1.473%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=78.3, 29 (6) missing vertices, mean dist -0.2 [0.3 (%76.3)->0.2 (%23.7))] %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= X1, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.10-->5.54) (max @ vno 105402 --> 119254) face area 0.35 +- 0.16 (0.00-->8.29) mean absolute distance = 0.22 +- 0.37 2406 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1279218.4, rms=5.453 016: dt: 0.5000, sse=924037.9, rms=3.759 (31.072%) rms = 4.04, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=770845.0, rms=2.710 (27.915%) 018: dt: 0.2500, sse=701373.6, rms=2.064 (23.827%) 019: dt: 0.2500, sse=672128.7, rms=1.722 (16.556%) 020: dt: 0.2500, sse=664964.6, rms=1.619 (5.998%) 021: dt: 0.2500, sse=658624.1, rms=1.539 (4.964%) rms = 1.51, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=658020.1, rms=1.509 (1.946%) 023: dt: 0.1250, sse=648861.3, rms=1.378 (8.651%) rms = 1.36, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=647692.2, rms=1.363 (1.112%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.8, 31 (3) missing vertices, mean dist -0.1 [0.2 (%70.8)->0.2 (%29.2))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= X1, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.07-->5.49) (max @ vno 105402 --> 119254) face area 0.34 +- 0.16 (0.00-->7.88) mean absolute distance = 0.19 +- 0.30 2176 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=839662.9, rms=3.356 rms = 3.48, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=705897.5, rms=2.311 (31.137%) 026: dt: 0.2500, sse=637411.3, rms=1.489 (35.559%) 027: dt: 0.2500, sse=627275.6, rms=1.345 (9.669%) rms = 1.30, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=623747.9, rms=1.296 (3.681%) 029: dt: 0.1250, sse=617677.2, rms=1.197 (7.649%) rms = 1.19, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=618672.6, rms=1.193 (0.273%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=81.5, 45 (3) missing vertices, mean dist -0.0 [0.2 (%55.6)->0.2 (%44.4))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= X1, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /usr/local/freesurfer/subjects/Sub01/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=635093.0, rms=1.567 rms = 2.14, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=602919.2, rms=1.045 (33.291%) 032: dt: 0.2500, sse=596603.2, rms=0.882 (15.638%) rms = 0.89, time step reduction 2 of 3 to 0.125... rms = 0.88, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=595744.9, rms=0.877 (0.533%) positioning took 0.3 minutes generating cortex label... 8 non-cortical segments detected only using segment with 6973 vertices erasing segment 1 (vno[0] = 48310) erasing segment 2 (vno[0] = 84732) erasing segment 3 (vno[0] = 84899) erasing segment 4 (vno[0] = 85863) erasing segment 5 (vno[0] = 86804) erasing segment 6 (vno[0] = 94238) erasing segment 7 (vno[0] = 99798) writing cortex label to /usr/local/freesurfer/subjects/Sub01/label/rh.cortex.label... writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/rh.curv writing smoothed area to rh.area writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/rh.area vertex spacing 0.90 +- 0.25 (0.04-->5.51) (max @ vno 105402 --> 119254) face area 0.34 +- 0.16 (0.00-->7.86) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group smoothing surface for 5 iterations... mean border=47.3, 57 (57) missing vertices, mean dist 1.8 [0.2 (%0.0)->2.6 (%100.0))] %12 local maxima, %52 large gradients and %31 min vals, 330 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=26398372.0, rms=33.777 001: dt: 0.0500, sse=23090802.0, rms=31.546 (6.605%) 002: dt: 0.0500, sse=20550192.0, rms=29.719 (5.792%) 003: dt: 0.0500, sse=18582602.0, rms=28.222 (5.036%) 004: dt: 0.0500, sse=17019540.0, rms=26.974 (4.422%) 005: dt: 0.0500, sse=15736022.0, rms=25.904 (3.966%) 006: dt: 0.0500, sse=14653095.0, rms=24.966 (3.623%) 007: dt: 0.0500, sse=13720388.0, rms=24.128 (3.355%) 008: dt: 0.0500, sse=12904517.0, rms=23.371 (3.139%) 009: dt: 0.0500, sse=12180810.0, rms=22.678 (2.965%) 010: dt: 0.0500, sse=11532293.0, rms=22.038 (2.820%) positioning took 0.7 minutes mean border=47.1, 43 (17) missing vertices, mean dist 1.5 [0.1 (%0.2)->2.1 (%99.8))] %14 local maxima, %52 large gradients and %29 min vals, 292 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=12316312.0, rms=22.774 011: dt: 0.0500, sse=11723101.0, rms=22.192 (2.554%) 012: dt: 0.0500, sse=11185353.0, rms=21.651 (2.437%) 013: dt: 0.0500, sse=10694495.0, rms=21.146 (2.336%) 014: dt: 0.0500, sse=10245862.0, rms=20.672 (2.238%) 015: dt: 0.0500, sse=9835072.0, rms=20.229 (2.144%) 016: dt: 0.0500, sse=9457711.0, rms=19.813 (2.056%) 017: dt: 0.0500, sse=9107882.0, rms=19.420 (1.986%) 018: dt: 0.0500, sse=8783490.0, rms=19.048 (1.917%) 019: dt: 0.0500, sse=8481931.0, rms=18.695 (1.852%) 020: dt: 0.0500, sse=8200460.0, rms=18.359 (1.795%) positioning took 0.7 minutes mean border=46.9, 57 (12) missing vertices, mean dist 1.2 [0.1 (%3.9)->1.8 (%96.1))] %15 local maxima, %52 large gradients and %29 min vals, 280 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=8277230.0, rms=18.446 021: dt: 0.0500, sse=8006744.0, rms=18.119 (1.772%) 022: dt: 0.0500, sse=7754499.5, rms=17.809 (1.712%) 023: dt: 0.0500, sse=7515908.0, rms=17.510 (1.676%) 024: dt: 0.0500, sse=7292802.5, rms=17.226 (1.621%) 025: dt: 0.0500, sse=7083465.5, rms=16.956 (1.572%) 026: dt: 0.0500, sse=6886530.5, rms=16.697 (1.526%) 027: dt: 0.0500, sse=6699643.0, rms=16.447 (1.494%) 028: dt: 0.0500, sse=6520985.0, rms=16.205 (1.472%) 029: dt: 0.0500, sse=6350140.0, rms=15.970 (1.451%) 030: dt: 0.0500, sse=6186575.5, rms=15.742 (1.430%) positioning took 0.7 minutes mean border=46.9, 93 (10) missing vertices, mean dist 1.0 [0.1 (%14.1)->1.7 (%85.9))] %15 local maxima, %52 large gradients and %28 min vals, 231 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=6269682.0, rms=15.844 031: dt: 0.5000, sse=5127860.5, rms=14.161 (10.623%) 032: dt: 0.5000, sse=4326705.5, rms=12.841 (9.317%) 033: dt: 0.5000, sse=3699238.8, rms=11.706 (8.841%) 034: dt: 0.5000, sse=3193173.8, rms=10.696 (8.628%) 035: dt: 0.5000, sse=2754381.8, rms=9.740 (8.935%) 036: dt: 0.5000, sse=2367965.8, rms=8.810 (9.550%) 037: dt: 0.5000, sse=2022077.0, rms=7.890 (10.438%) 038: dt: 0.5000, sse=1743439.9, rms=7.061 (10.512%) 039: dt: 0.5000, sse=1532220.8, rms=6.365 (9.864%) 040: dt: 0.5000, sse=1397723.4, rms=5.874 (7.710%) 041: dt: 0.5000, sse=1297742.6, rms=5.486 (6.600%) 042: dt: 0.5000, sse=1243880.4, rms=5.259 (4.132%) 043: dt: 0.5000, sse=1199758.8, rms=5.072 (3.569%) 044: dt: 0.5000, sse=1179206.2, rms=4.978 (1.846%) 045: dt: 0.5000, sse=1158601.4, rms=4.887 (1.841%) rms = 4.87, time step reduction 1 of 3 to 0.250... 046: dt: 0.5000, sse=1154445.1, rms=4.865 (0.432%) 047: dt: 0.2500, sse=1038447.1, rms=4.249 (12.661%) 048: dt: 0.2500, sse=1006287.9, rms=4.077 (4.066%) rms = 4.08, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=1006734.2, rms=4.076 (0.020%) 050: dt: 0.1250, sse=986161.9, rms=3.956 (2.940%) rms = 3.94, time step reduction 3 of 3 to 0.062... 051: dt: 0.1250, sse=983624.9, rms=3.941 (0.378%) positioning took 1.7 minutes mean border=45.9, 1478 (7) missing vertices, mean dist 0.1 [0.2 (%50.6)->0.5 (%49.4))] %27 local maxima, %40 large gradients and %27 min vals, 78 gradients ignored tol=1.0e-04, sigma=1.0, host= X1, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1260335.1, rms=4.281 052: dt: 0.5000, sse=1227867.0, rms=4.125 (3.641%) rms = 4.12, time step reduction 1 of 3 to 0.250... 053: dt: 0.5000, sse=1219679.4, rms=4.122 (0.077%) 054: dt: 0.2500, sse=1099904.8, rms=3.342 (18.929%) 055: dt: 0.2500, sse=1070267.1, rms=3.141 (5.991%) rms = 3.12, time step reduction 2 of 3 to 0.125... 056: dt: 0.2500, sse=1067748.2, rms=3.122 (0.631%) 057: dt: 0.1250, sse=1040890.4, rms=2.914 (6.658%) rms = 2.88, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1036046.1, rms=2.878 (1.211%) positioning took 0.6 minutes mean border=45.0, 1494 (6) missing vertices, mean dist 0.1 [0.1 (%50.1)->0.3 (%49.9))] %43 local maxima, %25 large gradients and %26 min vals, 108 gradients ignored tol=1.0e-04, sigma=0.5, host= X1, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1095903.2, rms=3.301 rms = 3.72, time step reduction 1 of 3 to 0.250... 059: dt: 0.2500, sse=1057159.4, rms=3.021 (8.463%) 060: dt: 0.2500, sse=1043928.9, rms=2.925 (3.175%) rms = 2.95, time step reduction 2 of 3 to 0.125... rms = 2.89, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=1039152.4, rms=2.886 (1.343%) positioning took 0.3 minutes mean border=44.3, 2877 (6) missing vertices, mean dist 0.1 [0.1 (%49.3)->0.3 (%50.7))] %48 local maxima, %19 large gradients and %25 min vals, 115 gradients ignored tol=1.0e-04, sigma=0.2, host= X1, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /usr/local/freesurfer/subjects/Sub01/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1063255.2, rms=3.074 rms = 3.54, time step reduction 1 of 3 to 0.250... 062: dt: 0.2500, sse=1040745.4, rms=2.900 (5.662%) 063: dt: 0.2500, sse=1030769.9, rms=2.837 (2.162%) rms = 2.86, time step reduction 2 of 3 to 0.125... rms = 2.80, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=1026285.9, rms=2.799 (1.356%) positioning took 0.3 minutes writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/rh.area.pial vertex spacing 1.04 +- 0.45 (0.03-->9.44) (max @ vno 79640 --> 78609) face area 0.43 +- 0.33 (0.00-->8.89) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 119358 vertices processed 25000 of 119358 vertices processed 50000 of 119358 vertices processed 75000 of 119358 vertices processed 100000 of 119358 vertices processed 0 of 119358 vertices processed 25000 of 119358 vertices processed 50000 of 119358 vertices processed 75000 of 119358 vertices processed 100000 of 119358 vertices processed thickness calculation complete, 548:1091 truncations. 25143 vertices at 0 distance 78286 vertices at 1 distance 75079 vertices at 2 distance 33745 vertices at 3 distance 10407 vertices at 4 distance 2791 vertices at 5 distance 876 vertices at 6 distance 288 vertices at 7 distance 115 vertices at 8 distance 59 vertices at 9 distance 39 vertices at 10 distance 46 vertices at 11 distance 38 vertices at 12 distance 24 vertices at 13 distance 33 vertices at 14 distance 23 vertices at 15 distance 15 vertices at 16 distance 9 vertices at 17 distance 20 vertices at 18 distance 15 vertices at 19 distance 13 vertices at 20 distance writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/rh.thickness positioning took 10.0 minutes #-------------------------------------------- #@# Smooth2 lh Sat May 20 20:27:43 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth2 rh Sat May 20 20:27:46 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Sat May 20 20:27:50 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_inflate -rusage /usr/local/freesurfer/subjects/Sub01/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 43.4 mm, total surface area = 72564 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.179 (target=0.015) step 005: RMS=0.125 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 0.5 minutes mris_inflate utimesec 29.776000 mris_inflate stimesec 0.028000 mris_inflate ru_maxrss 156476 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 19157 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 344 mris_inflate ru_oublock 9240 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 3 mris_inflate ru_nivcsw 57 #-------------------------------------------- #@# Inflation2 rh Sat May 20 20:28:20 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_inflate -rusage /usr/local/freesurfer/subjects/Sub01/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 43.2 mm, total surface area = 72808 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.179 (target=0.015) step 005: RMS=0.124 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.076 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.053 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 0.5 minutes mris_inflate utimesec 30.076000 mris_inflate stimesec 0.044000 mris_inflate ru_maxrss 158248 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 19051 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 112 mris_inflate ru_oublock 9336 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2 mris_inflate ru_nivcsw 34 #-------------------------------------------- #@# Curv .H and .K lh Sat May 20 20:28:50 EDT 2017 /usr/local/freesurfer/subjects/Sub01/surf mris_curvature -w lh.white.preaparc total integrated curvature = 7.791*4pi (97.908) --> -7 handles ICI = 140.6, FI = 1539.7, variation=23903.960 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 163 vertices thresholded to be in k1 ~ [-0.18 0.88], k2 ~ [-0.09 0.04] total integrated curvature = 0.581*4pi (7.298) --> 0 handles ICI = 1.4, FI = 8.2, variation=141.158 91 vertices thresholded to be in [-0.03 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 113 vertices thresholded to be in [-0.12 0.25] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.022 done. #-------------------------------------------- #@# Curv .H and .K rh Sat May 20 20:29:37 EDT 2017 /usr/local/freesurfer/subjects/Sub01/surf mris_curvature -w rh.white.preaparc total integrated curvature = -1.021*4pi (-12.828) --> 2 handles ICI = 138.6, FI = 1538.5, variation=23970.827 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 191 vertices thresholded to be in k1 ~ [-0.19 0.38], k2 ~ [-0.10 0.06] total integrated curvature = 0.580*4pi (7.282) --> 0 handles ICI = 1.4, FI = 7.9, variation=138.045 109 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 135 vertices thresholded to be in [-0.12 0.19] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.022 done. #----------------------------------------- #@# Curvature Stats lh Sat May 20 20:30:24 EDT 2017 /usr/local/freesurfer/subjects/Sub01/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm Sub01 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ Sub01/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 200 ] Gb_filter = 0 WARN: S lookup min: -0.503639 WARN: S explicit min: 0.000000 vertex = 970 #----------------------------------------- #@# Curvature Stats rh Sat May 20 20:30:27 EDT 2017 /usr/local/freesurfer/subjects/Sub01/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm Sub01 rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ Sub01/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 209 ] Gb_filter = 0 WARN: S lookup min: -0.400908 WARN: S explicit min: 0.000000 vertex = 909 Started at Sat May 20 17:02:04 EDT 2017 Ended at Sat May 20 20:30:29 EDT 2017 #@#%# recon-all-run-time-hours 3.474 recon-all -s Sub01 finished without error at Sat May 20 20:30:29 EDT 2017 New invocation of recon-all Thu Jun 8 21:04:59 EDT 2017 /usr/local/freesurfer/subjects/Sub01 /usr/local/freesurfer/bin/recon-all -autorecon3 -s Sub01 subjid Sub01 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 X1 4.4.0-78-generic #99-Ubuntu SMP Thu Apr 27 15:29:09 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63057 maxlocks unlimited maxsignal 63057 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 16284624 1213048 10751116 385560 4320460 14262832 Swap: 16642044 0 16642044 ######################################## 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: 2017/06/09-01:04:59-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-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: 2017/06/09-01:04:59-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-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: 2017/06/09-01:04:59-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/09-01:04:59-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:04:59-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:04:59-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/09-01:04:59-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/09-01:04:59-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/09-01:04:59-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/09-01:04:59-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/09-01:04:59-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/09-01:04:59-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:04:59-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:04:59-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/09-01:04:59-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:04:59-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-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: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-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: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/06/09-01:05:00-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: amazinger Machine: X1 Platform: Linux PlatformVersion: 4.4.0-78-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 ####################################### #-------------------------------------------- #@# Sphere lh Thu Jun 8 21:05:00 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_sphere -rusage /usr/local/freesurfer/subjects/Sub01/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.341... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= X1, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.85 pass 1: epoch 2 of 3 starting distance error %19.80 unfolding complete - removing small folds... starting distance error %19.74 removing remaining folds... final distance error %19.76 MRISunfold() return, current seed 1234 -01: dt=0.0000, 118 negative triangles 171: dt=0.9900, 118 negative triangles 172: dt=0.9900, 45 negative triangles 173: dt=0.9900, 31 negative triangles 174: dt=0.9900, 14 negative triangles 175: dt=0.9900, 14 negative triangles 176: dt=0.9900, 8 negative triangles 177: dt=0.9900, 6 negative triangles 178: dt=0.9900, 4 negative triangles 179: dt=0.9900, 2 negative triangles 180: dt=0.9900, 2 negative triangles 181: dt=0.9900, 3 negative triangles 182: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.42 hours mris_sphere utimesec 1512.308000 mris_sphere stimesec 0.164000 mris_sphere ru_maxrss 214072 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 33400 mris_sphere ru_majflt 7 mris_sphere ru_nswap 0 mris_sphere ru_inblock 12656 mris_sphere ru_oublock 8312 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 15 mris_sphere ru_nivcsw 1257 FSRUNTIME@ mris_sphere 0.4202 hours 1 threads #-------------------------------------------- #@# Sphere rh Thu Jun 8 21:30:13 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_sphere -rusage /usr/local/freesurfer/subjects/Sub01/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.339... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= X1, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.48 pass 1: epoch 2 of 3 starting distance error %19.47 unfolding complete - removing small folds... starting distance error %19.42 removing remaining folds... final distance error %19.44 MRISunfold() return, current seed 1234 -01: dt=0.0000, 85 negative triangles 189: dt=0.9900, 85 negative triangles 190: dt=0.9900, 30 negative triangles 191: dt=0.9900, 16 negative triangles 192: dt=0.9900, 18 negative triangles 193: dt=0.9900, 13 negative triangles 194: dt=0.9900, 15 negative triangles 195: dt=0.9900, 7 negative triangles 196: dt=0.9900, 8 negative triangles 197: dt=0.9900, 9 negative triangles 198: dt=0.9900, 3 negative triangles 199: dt=0.9900, 7 negative triangles 200: dt=0.9900, 4 negative triangles 201: dt=0.9900, 3 negative triangles 202: dt=0.9900, 5 negative triangles 203: dt=0.9900, 2 negative triangles 204: dt=0.9900, 1 negative triangles 205: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.45 hours mris_sphere utimesec 1608.388000 mris_sphere stimesec 0.196000 mris_sphere ru_maxrss 215772 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 33371 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 11696 mris_sphere ru_oublock 8400 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 4 mris_sphere ru_nivcsw 1270 FSRUNTIME@ mris_sphere 0.4469 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Thu Jun 8 21:57:02 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_register -curv -rusage /usr/local/freesurfer/subjects/Sub01/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /usr/local/freesurfer/subjects/Sub01/scripts cmdline mris_register -curv -rusage /usr/local/freesurfer/subjects/Sub01/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host= X1, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host= X1, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = 0.000, std = 5.460 curvature mean = 0.034, std = 0.819 curvature mean = 0.017, std = 0.870 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 282261.5, tmin=0.7996 d=32.00 min @ (8.00, 8.00, -8.00) sse = 182381.5, tmin=1.6084 d=16.00 min @ (-4.00, 0.00, 0.00) sse = 168462.2, tmin=2.4271 d=8.00 min @ (0.00, -2.00, 2.00) sse = 159012.6, tmin=3.2437 d=4.00 min @ (0.00, 1.00, -1.00) sse = 158814.5, tmin=4.0670 d=2.00 min @ (0.00, -0.50, 0.50) sse = 157686.5, tmin=4.8917 d=1.00 min @ (0.25, 0.00, 0.00) sse = 157608.9, tmin=5.7203 tol=1.0e+00, sigma=0.5, host= X1, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 6.56 min curvature mean = -0.007, std = 0.833 curvature mean = 0.006, std = 0.950 curvature mean = -0.010, std = 0.844 curvature mean = 0.002, std = 0.980 curvature mean = -0.011, std = 0.847 curvature mean = 0.001, std = 0.993 2 Reading smoothwm curvature mean = -0.027, std = 0.291 curvature mean = 0.039, std = 0.249 curvature mean = 0.062, std = 0.357 curvature mean = 0.035, std = 0.309 curvature mean = 0.035, std = 0.553 curvature mean = 0.034, std = 0.336 curvature mean = 0.019, std = 0.689 curvature mean = 0.034, std = 0.347 curvature mean = 0.007, std = 0.792 MRISregister() return, current seed 0 -01: dt=0.0000, 17 negative triangles 101: dt=0.9900, 17 negative triangles expanding nbhd size to 1 102: dt=0.9900, 23 negative triangles 103: dt=0.9900, 16 negative triangles 104: dt=0.9900, 17 negative triangles 105: dt=0.9900, 12 negative triangles 106: dt=0.9900, 14 negative triangles 107: dt=0.9900, 12 negative triangles 108: dt=0.9900, 11 negative triangles 109: dt=0.9900, 11 negative triangles 110: dt=0.9900, 9 negative triangles 111: dt=0.9900, 8 negative triangles 112: dt=0.9900, 5 negative triangles 113: dt=0.9900, 10 negative triangles 114: dt=0.9900, 6 negative triangles 115: dt=0.9900, 3 negative triangles 116: dt=0.9900, 1 negative triangles 117: dt=0.9900, 2 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.53 hours mris_register utimesec 1922.516000 mris_register stimesec 0.288000 mris_register ru_maxrss 212960 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 25373 mris_register ru_majflt 9 mris_register ru_nswap 0 mris_register ru_inblock 8136 mris_register ru_oublock 8320 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 37 mris_register ru_nivcsw 5081 FSRUNTIME@ mris_register 0.5342 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Thu Jun 8 22:29:05 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_register -curv -rusage /usr/local/freesurfer/subjects/Sub01/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /usr/local/freesurfer/subjects/Sub01/scripts cmdline mris_register -curv -rusage /usr/local/freesurfer/subjects/Sub01/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host= X1, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host= X1, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = 0.000, std = 5.575 curvature mean = 0.029, std = 0.814 curvature mean = 0.017, std = 0.874 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 282115.7, tmin=0.8248 d=32.00 min @ (-8.00, -8.00, 0.00) sse = 212291.8, tmin=1.6803 d=16.00 min @ (4.00, 0.00, -4.00) sse = 196655.5, tmin=2.5161 d=8.00 min @ (-2.00, 0.00, 2.00) sse = 191661.9, tmin=3.3642 d=4.00 min @ (1.00, 1.00, -1.00) sse = 190075.6, tmin=4.2193 d=2.00 min @ (0.00, -0.50, 0.50) sse = 189514.1, tmin=5.0878 d=1.00 min @ (-0.25, 0.00, 0.00) sse = 189478.1, tmin=5.9494 d=0.50 min @ (0.00, 0.12, -0.12) sse = 189452.6, tmin=6.8234 tol=1.0e+00, sigma=0.5, host= X1, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 6.82 min curvature mean = 0.005, std = 0.832 curvature mean = 0.006, std = 0.954 curvature mean = 0.002, std = 0.844 curvature mean = 0.002, std = 0.982 curvature mean = 0.001, std = 0.847 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.025, std = 0.294 curvature mean = 0.036, std = 0.245 curvature mean = 0.057, std = 0.359 curvature mean = 0.030, std = 0.305 curvature mean = 0.031, std = 0.548 curvature mean = 0.029, std = 0.332 curvature mean = 0.017, std = 0.681 curvature mean = 0.029, std = 0.344 curvature mean = 0.006, std = 0.780 MRISregister() return, current seed 0 -01: dt=0.0000, 11 negative triangles 108: dt=0.9900, 11 negative triangles expanding nbhd size to 1 109: dt=0.9900, 17 negative triangles 110: dt=0.9900, 7 negative triangles 111: dt=0.9900, 7 negative triangles 112: dt=0.9900, 7 negative triangles 113: dt=0.9900, 7 negative triangles 114: dt=0.9900, 7 negative triangles 115: dt=0.9900, 7 negative triangles 116: dt=0.9900, 6 negative triangles 117: dt=0.9900, 4 negative triangles 118: dt=0.9900, 4 negative triangles 119: dt=0.9900, 3 negative triangles 120: dt=0.9900, 3 negative triangles 121: dt=0.9900, 2 negative triangles 122: dt=0.9900, 3 negative triangles 123: dt=0.9900, 2 negative triangles 124: dt=0.9900, 2 negative triangles 125: dt=0.9900, 2 negative triangles 126: dt=0.9900, 2 negative triangles 127: dt=0.9900, 1 negative triangles 128: dt=0.9900, 1 negative triangles 129: dt=0.9900, 1 negative triangles 130: dt=0.9900, 1 negative triangles 131: dt=0.9900, 2 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.65 hours mris_register utimesec 2343.888000 mris_register stimesec 0.364000 mris_register ru_maxrss 211752 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 25617 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 6520 mris_register ru_oublock 8400 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 25 mris_register ru_nivcsw 2931 FSRUNTIME@ mris_register 0.6512 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Thu Jun 8 23:08:09 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Thu Jun 8 23:08:11 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Thu Jun 8 23:08:12 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh Thu Jun 8 23:08:13 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Thu Jun 8 23:08:15 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Sub01 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1794 labels changed using aseg relabeling using gibbs priors... 000: 2691 changed, 118136 examined... 001: 583 changed, 11503 examined... 002: 149 changed, 3281 examined... 003: 55 changed, 876 examined... 004: 24 changed, 318 examined... 005: 10 changed, 159 examined... 006: 2 changed, 49 examined... 007: 0 changed, 13 examined... 247 labels changed using aseg 000: 121 total segments, 74 labels (211 vertices) changed 001: 47 total segments, 2 labels (7 vertices) changed 002: 45 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1175 vertices marked for relabeling... 1175 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 11 seconds. #----------------------------------------- #@# Cortical Parc rh Thu Jun 8 23:08:26 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Sub01 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1373 labels changed using aseg relabeling using gibbs priors... 000: 2388 changed, 119358 examined... 001: 558 changed, 10612 examined... 002: 114 changed, 3170 examined... 003: 40 changed, 683 examined... 004: 13 changed, 250 examined... 005: 0 changed, 80 examined... 167 labels changed using aseg 000: 91 total segments, 53 labels (340 vertices) changed 001: 42 total segments, 4 labels (12 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 8 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1330 vertices marked for relabeling... 1330 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 11 seconds. #-------------------------------------------- #@# Make Pial Surf lh Thu Jun 8 23:08:37 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs Sub01 lh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /usr/local/freesurfer/subjects/Sub01/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/Sub01/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/Sub01/mri/../mri/aseg.presurf.mgz... reading volume /usr/local/freesurfer/subjects/Sub01/mri/wm.mgz... 17673 bright wm thresholded. 1364 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/Sub01/surf/lh.orig... computing class statistics... border white: 222774 voxels (1.33%) border gray 251817 voxels (1.50%) WM (97.0): 96.9 +- 9.6 [70.0 --> 110.0] GM (65.0) : 65.2 +- 10.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 47.2 (was 70) setting MAX_BORDER_WHITE to 112.6 (was 105) setting MIN_BORDER_WHITE to 58.0 (was 85) setting MAX_CSF to 36.3 (was 40) setting MAX_GRAY to 93.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 47.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 25.5 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-7.8, GM=58+-9.6 mean inside = 91.8, mean outside = 68.9 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.25 (0.03-->4.80) (max @ vno 91217 --> 117852) face area 0.34 +- 0.16 (0.00-->4.16) mean absolute distance = 0.56 +- 0.75 3010 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 13 points - only 0.00% unknown deleting segment 1 with 10 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown deleting segment 6 with 174 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown deleting segment 8 with 9 points - only 0.00% unknown deleting segment 9 with 21 points - only 0.00% unknown deleting segment 10 with 9 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 11 with 4 points - only 0.00% unknown deleting segment 12 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown mean border=72.8, 50 (50) missing vertices, mean dist 0.4 [0.7 (%11.9)->0.5 (%88.1))] %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.94 +- 0.26 (0.08-->4.80) (max @ vno 117852 --> 91217) face area 0.34 +- 0.16 (0.00-->3.57) mean absolute distance = 0.33 +- 0.51 2908 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2594488.5, rms=9.489 001: dt: 0.5000, sse=1281302.8, rms=5.626 (40.713%) 002: dt: 0.5000, sse=990044.2, rms=4.336 (22.921%) 003: dt: 0.5000, sse=959438.2, rms=4.186 (3.467%) 004: dt: 0.5000, sse=905513.7, rms=3.896 (6.913%) rms = 4.06, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=728349.3, rms=2.654 (31.876%) 006: dt: 0.2500, sse=673887.3, rms=2.124 (19.984%) 007: dt: 0.2500, sse=658433.2, rms=1.904 (10.365%) 008: dt: 0.2500, sse=649960.4, rms=1.850 (2.840%) 009: dt: 0.2500, sse=646032.9, rms=1.797 (2.849%) rms = 1.77, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=644454.5, rms=1.769 (1.553%) 011: dt: 0.1250, sse=635830.2, rms=1.649 (6.763%) rms = 1.63, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=634578.4, rms=1.633 (1.015%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 18 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 4 with 72 points - only 0.00% unknown deleting segment 5 with 6 points - only 0.00% unknown deleting segment 6 with 10 points - only 0.00% unknown deleting segment 8 with 25 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 11 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown mean border=77.1, 57 (10) missing vertices, mean dist -0.2 [0.4 (%78.6)->0.2 (%21.4))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= X1, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.07-->4.98) (max @ vno 117852 --> 91217) face area 0.36 +- 0.17 (0.00-->4.17) mean absolute distance = 0.22 +- 0.36 2621 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1343290.1, rms=5.679 013: dt: 0.5000, sse=954048.6, rms=3.851 (32.190%) rms = 4.09, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=796265.8, rms=2.804 (27.177%) 015: dt: 0.2500, sse=720017.1, rms=2.104 (24.959%) 016: dt: 0.2500, sse=689182.6, rms=1.751 (16.790%) 017: dt: 0.2500, sse=681087.5, rms=1.617 (7.634%) 018: dt: 0.2500, sse=673469.9, rms=1.527 (5.614%) rms = 1.49, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=669773.4, rms=1.490 (2.383%) 020: dt: 0.1250, sse=660399.3, rms=1.332 (10.592%) rms = 1.32, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=659270.2, rms=1.317 (1.172%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 14 points - only 0.00% unknown deleting segment 1 with 7 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 4 with 97 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown deleting segment 6 with 10 points - only 0.00% unknown deleting segment 7 with 23 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown deleting segment 9 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown mean border=79.6, 51 (5) missing vertices, mean dist -0.1 [0.2 (%71.5)->0.2 (%28.5))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= X1, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.08-->5.07) (max @ vno 117852 --> 91217) face area 0.35 +- 0.17 (0.00-->4.17) mean absolute distance = 0.19 +- 0.31 2269 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=842618.8, rms=3.354 rms = 3.54, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=706009.2, rms=2.265 (32.477%) 023: dt: 0.2500, sse=639549.4, rms=1.434 (36.677%) 024: dt: 0.2500, sse=631001.3, rms=1.319 (8.015%) rms = 1.29, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=629076.4, rms=1.290 (2.226%) 026: dt: 0.1250, sse=624422.2, rms=1.176 (8.807%) rms = 1.17, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=622099.0, rms=1.172 (0.347%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown deleting segment 1 with 7 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown deleting segment 5 with 103 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown deleting segment 7 with 10 points - only 0.00% unknown deleting segment 8 with 8 points - only 0.00% unknown deleting segment 9 with 23 points - only 0.00% unknown deleting segment 10 with 14 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown mean border=80.4, 62 (4) missing vertices, mean dist -0.0 [0.2 (%55.6)->0.2 (%44.4))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= X1, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /usr/local/freesurfer/subjects/Sub01/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=639204.5, rms=1.587 rms = 2.21, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=607496.2, rms=1.053 (33.654%) 029: dt: 0.2500, sse=607034.4, rms=0.885 (15.987%) rms = 0.90, time step reduction 2 of 3 to 0.125... rms = 0.88, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=601639.5, rms=0.878 (0.750%) positioning took 0.3 minutes generating cortex label... 5 non-cortical segments detected only using segment with 7211 vertices erasing segment 1 (vno[0] = 74974) erasing segment 2 (vno[0] = 82241) erasing segment 3 (vno[0] = 84197) erasing segment 4 (vno[0] = 99066) writing cortex label to /usr/local/freesurfer/subjects/Sub01/label/lh.cortex.label... writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/lh.curv writing smoothed area to lh.area writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/lh.area vertex spacing 0.90 +- 0.26 (0.03-->5.16) (max @ vno 91217 --> 117852) face area 0.34 +- 0.17 (0.00-->4.05) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=45.7, 56 (56) missing vertices, mean dist 1.7 [0.0 (%0.0)->2.7 (%100.0))] %11 local maxima, %49 large gradients and %35 min vals, 287 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=28491852.0, rms=35.265 001: dt: 0.0500, sse=24858372.0, rms=32.890 (6.735%) 002: dt: 0.0500, sse=22251398.0, rms=31.075 (5.521%) 003: dt: 0.0500, sse=20265828.0, rms=29.617 (4.691%) 004: dt: 0.0500, sse=18673908.0, rms=28.394 (4.129%) 005: dt: 0.0500, sse=17349548.0, rms=27.335 (3.730%) 006: dt: 0.0500, sse=16213786.0, rms=26.393 (3.446%) 007: dt: 0.0500, sse=15222016.0, rms=25.542 (3.225%) 008: dt: 0.0500, sse=14341389.0, rms=24.762 (3.055%) 009: dt: 0.0500, sse=13551604.0, rms=24.040 (2.913%) 010: dt: 0.0500, sse=12836796.0, rms=23.368 (2.796%) positioning took 0.8 minutes mean border=45.6, 58 (36) missing vertices, mean dist 1.4 [0.1 (%0.0)->2.2 (%100.0))] %11 local maxima, %49 large gradients and %35 min vals, 280 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=13380938.0, rms=23.883 011: dt: 0.0500, sse=12726977.0, rms=23.265 (2.589%) 012: dt: 0.0500, sse=12128009.0, rms=22.684 (2.498%) 013: dt: 0.0500, sse=11577316.0, rms=22.136 (2.415%) 014: dt: 0.0500, sse=11069530.0, rms=21.619 (2.338%) 015: dt: 0.0500, sse=10601028.0, rms=21.130 (2.261%) 016: dt: 0.0500, sse=10168023.0, rms=20.668 (2.187%) 017: dt: 0.0500, sse=9766750.0, rms=20.230 (2.118%) 018: dt: 0.0500, sse=9395125.0, rms=19.816 (2.047%) 019: dt: 0.0500, sse=9050190.0, rms=19.424 (1.980%) 020: dt: 0.0500, sse=8729924.0, rms=19.052 (1.913%) positioning took 0.7 minutes mean border=45.5, 73 (30) missing vertices, mean dist 1.2 [0.1 (%0.7)->1.9 (%99.3))] %12 local maxima, %49 large gradients and %34 min vals, 249 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=8807092.0, rms=19.148 021: dt: 0.0500, sse=8504166.0, rms=18.791 (1.862%) 022: dt: 0.0500, sse=8222594.0, rms=18.454 (1.797%) 023: dt: 0.0500, sse=7959222.5, rms=18.132 (1.743%) 024: dt: 0.0500, sse=7713667.0, rms=17.827 (1.683%) 025: dt: 0.0500, sse=7484744.5, rms=17.537 (1.624%) 026: dt: 0.0500, sse=7270875.0, rms=17.262 (1.567%) 027: dt: 0.0500, sse=7069138.0, rms=16.999 (1.526%) 028: dt: 0.0500, sse=6877953.0, rms=16.745 (1.492%) 029: dt: 0.0500, sse=6696832.5, rms=16.501 (1.457%) 030: dt: 0.0500, sse=6524621.0, rms=16.266 (1.427%) positioning took 0.8 minutes mean border=45.4, 96 (25) missing vertices, mean dist 1.0 [0.1 (%7.8)->1.7 (%92.2))] %12 local maxima, %49 large gradients and %34 min vals, 239 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=6597966.0, rms=16.366 031: dt: 0.5000, sse=5414587.5, rms=14.658 (10.436%) 032: dt: 0.5000, sse=4602014.0, rms=13.352 (8.908%) 033: dt: 0.5000, sse=3954120.8, rms=12.212 (8.538%) 034: dt: 0.5000, sse=3425830.2, rms=11.191 (8.361%) 035: dt: 0.5000, sse=2957698.0, rms=10.204 (8.820%) 036: dt: 0.5000, sse=2534904.2, rms=9.220 (9.642%) 037: dt: 0.5000, sse=2153193.8, rms=8.237 (10.662%) 038: dt: 0.5000, sse=1839394.1, rms=7.329 (11.027%) 039: dt: 0.5000, sse=1598777.6, rms=6.552 (10.606%) 040: dt: 0.5000, sse=1435629.2, rms=5.964 (8.967%) 041: dt: 0.5000, sse=1326101.4, rms=5.539 (7.129%) 042: dt: 0.5000, sse=1262047.2, rms=5.270 (4.861%) 043: dt: 0.5000, sse=1221742.8, rms=5.097 (3.280%) 044: dt: 0.5000, sse=1203281.2, rms=5.012 (1.673%) 045: dt: 0.5000, sse=1188310.6, rms=4.946 (1.312%) rms = 4.93, time step reduction 1 of 3 to 0.250... 046: dt: 0.5000, sse=1184427.6, rms=4.925 (0.417%) 047: dt: 0.2500, sse=1082684.6, rms=4.385 (10.970%) 048: dt: 0.2500, sse=1055262.6, rms=4.241 (3.285%) rms = 4.24, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=1055597.6, rms=4.240 (0.023%) 050: dt: 0.1250, sse=1039143.2, rms=4.145 (2.229%) rms = 4.13, time step reduction 3 of 3 to 0.062... 051: dt: 0.1250, sse=1036947.4, rms=4.133 (0.294%) positioning took 2.3 minutes mean border=44.6, 1607 (10) missing vertices, mean dist 0.1 [0.2 (%52.5)->0.5 (%47.5))] %23 local maxima, %39 large gradients and %31 min vals, 100 gradients ignored tol=1.0e-04, sigma=1.0, host= X1, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1285420.4, rms=4.400 052: dt: 0.5000, sse=1255238.6, rms=4.259 (3.220%) rms = 4.27, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1159666.9, rms=3.690 (13.341%) 054: dt: 0.2500, sse=1129743.9, rms=3.500 (5.152%) 055: dt: 0.2500, sse=1119869.2, rms=3.439 (1.741%) rms = 3.41, time step reduction 2 of 3 to 0.125... 056: dt: 0.2500, sse=1115094.8, rms=3.410 (0.852%) 057: dt: 0.1250, sse=1095016.5, rms=3.267 (4.202%) rms = 3.24, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1090662.9, rms=3.239 (0.850%) positioning took 0.8 minutes mean border=44.0, 1652 (4) missing vertices, mean dist 0.1 [0.1 (%52.3)->0.4 (%47.7))] %38 local maxima, %26 large gradients and %30 min vals, 120 gradients ignored tol=1.0e-04, sigma=0.5, host= X1, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1133429.4, rms=3.516 rms = 3.87, time step reduction 1 of 3 to 0.250... 059: dt: 0.2500, sse=1104407.5, rms=3.320 (5.580%) 060: dt: 0.2500, sse=1093343.2, rms=3.250 (2.118%) rms = 3.25, time step reduction 2 of 3 to 0.125... 061: dt: 0.2500, sse=1091778.8, rms=3.248 (0.032%) 062: dt: 0.1250, sse=1076790.2, rms=3.137 (3.428%) rms = 3.11, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1072432.2, rms=3.109 (0.887%) positioning took 0.6 minutes mean border=43.2, 3347 (4) missing vertices, mean dist 0.1 [0.1 (%50.1)->0.3 (%49.9))] %43 local maxima, %20 large gradients and %29 min vals, 135 gradients ignored tol=1.0e-04, sigma=0.2, host= X1, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /usr/local/freesurfer/subjects/Sub01/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1093925.2, rms=3.257 rms = 3.59, time step reduction 1 of 3 to 0.250... 064: dt: 0.2500, sse=1076979.6, rms=3.132 (3.820%) 065: dt: 0.2500, sse=1066996.1, rms=3.073 (1.887%) rms = 3.07, time step reduction 2 of 3 to 0.125... rms = 3.05, time step reduction 3 of 3 to 0.062... 066: dt: 0.1250, sse=1063480.1, rms=3.045 (0.919%) positioning took 0.5 minutes writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/lh.area.pial vertex spacing 1.05 +- 0.46 (0.05-->7.62) (max @ vno 80280 --> 79270) face area 0.43 +- 0.33 (0.00-->7.55) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 118136 vertices processed 25000 of 118136 vertices processed 50000 of 118136 vertices processed 75000 of 118136 vertices processed 100000 of 118136 vertices processed 0 of 118136 vertices processed 25000 of 118136 vertices processed 50000 of 118136 vertices processed 75000 of 118136 vertices processed 100000 of 118136 vertices processed thickness calculation complete, 422:912 truncations. 27611 vertices at 0 distance 84346 vertices at 1 distance 71475 vertices at 2 distance 28778 vertices at 3 distance 8517 vertices at 4 distance 2324 vertices at 5 distance 751 vertices at 6 distance 288 vertices at 7 distance 142 vertices at 8 distance 93 vertices at 9 distance 62 vertices at 10 distance 32 vertices at 11 distance 26 vertices at 12 distance 29 vertices at 13 distance 26 vertices at 14 distance 20 vertices at 15 distance 13 vertices at 16 distance 12 vertices at 17 distance 12 vertices at 18 distance 8 vertices at 19 distance 23 vertices at 20 distance writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/lh.thickness positioning took 11.9 minutes #-------------------------------------------- #@# Make Pial Surf rh Thu Jun 8 23:20:32 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs Sub01 rh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /usr/local/freesurfer/subjects/Sub01/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/Sub01/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/Sub01/mri/../mri/aseg.presurf.mgz... reading volume /usr/local/freesurfer/subjects/Sub01/mri/wm.mgz... 17673 bright wm thresholded. 1364 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/Sub01/surf/rh.orig... computing class statistics... border white: 222774 voxels (1.33%) border gray 251817 voxels (1.50%) WM (97.0): 96.9 +- 9.6 [70.0 --> 110.0] GM (65.0) : 65.2 +- 10.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.2 (was 70) setting MAX_BORDER_WHITE to 113.6 (was 105) setting MIN_BORDER_WHITE to 60.0 (was 85) setting MAX_CSF to 38.3 (was 40) setting MAX_GRAY to 94.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 49.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 27.5 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104+-7.8, GM=60+-8.7 mean inside = 92.3, mean outside = 69.7 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.90 +- 0.25 (0.04-->5.51) (max @ vno 105402 --> 119254) face area 0.33 +- 0.16 (0.00-->7.83) mean absolute distance = 0.55 +- 0.76 2766 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 4 with 13 points - only 0.00% unknown deleting segment 6 with 221 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown deleting segment 9 with 8 points - only 0.00% unknown deleting segment 10 with 17 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown deleting segment 12 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 13 with 3 points - only 0.00% unknown deleting segment 14 with 7 points - only 0.00% unknown mean border=74.0, 40 (40) missing vertices, mean dist 0.4 [0.8 (%11.9)->0.5 (%88.1))] %68 local maxima, %27 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.93 +- 0.26 (0.09-->5.68) (max @ vno 105402 --> 119254) face area 0.33 +- 0.16 (0.00-->7.81) mean absolute distance = 0.33 +- 0.54 2920 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2529059.8, rms=9.272 001: dt: 0.5000, sse=1260324.2, rms=5.497 (40.719%) 002: dt: 0.5000, sse=978164.8, rms=4.242 (22.830%) 003: dt: 0.5000, sse=949633.6, rms=4.090 (3.579%) 004: dt: 0.5000, sse=898421.2, rms=3.818 (6.642%) rms = 3.98, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=724315.2, rms=2.580 (32.424%) 006: dt: 0.2500, sse=670144.4, rms=2.044 (20.784%) 007: dt: 0.2500, sse=650139.6, rms=1.808 (11.531%) 008: dt: 0.2500, sse=646713.5, rms=1.755 (2.939%) 009: dt: 0.2500, sse=642113.0, rms=1.698 (3.275%) rms = 1.67, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=640391.7, rms=1.668 (1.754%) 011: dt: 0.1250, sse=633236.1, rms=1.566 (6.112%) rms = 1.55, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=632214.1, rms=1.550 (1.037%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 7 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 4 with 14 points - only 0.00% unknown deleting segment 5 with 147 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 10 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown mean border=78.1, 26 (7) missing vertices, mean dist -0.2 [0.4 (%77.3)->0.2 (%22.7))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= X1, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.25 (0.11-->5.67) (max @ vno 105402 --> 119254) face area 0.36 +- 0.17 (0.00-->8.75) mean absolute distance = 0.22 +- 0.37 2412 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1319784.0, rms=5.550 013: dt: 0.5000, sse=939075.9, rms=3.744 (32.540%) rms = 3.97, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=787996.1, rms=2.713 (27.537%) 015: dt: 0.2500, sse=715892.6, rms=2.023 (25.431%) 016: dt: 0.2500, sse=685198.8, rms=1.671 (17.391%) 017: dt: 0.2500, sse=676527.2, rms=1.559 (6.746%) 018: dt: 0.2500, sse=673960.3, rms=1.478 (5.198%) rms = 1.45, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=669039.8, rms=1.446 (2.162%) 020: dt: 0.1250, sse=660832.8, rms=1.316 (8.982%) rms = 1.30, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=661849.6, rms=1.298 (1.387%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 7 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown deleting segment 2 with 14 points - only 0.00% unknown deleting segment 3 with 191 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown deleting segment 6 with 9 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown mean border=80.6, 26 (3) missing vertices, mean dist -0.1 [0.2 (%71.5)->0.2 (%28.5))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= X1, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.07-->5.61) (max @ vno 105402 --> 119254) face area 0.34 +- 0.17 (0.00-->8.28) mean absolute distance = 0.19 +- 0.30 2169 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=851727.4, rms=3.364 rms = 3.47, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=714136.2, rms=2.296 (31.760%) 023: dt: 0.2500, sse=647039.4, rms=1.438 (37.362%) 024: dt: 0.2500, sse=634519.5, rms=1.289 (10.367%) rms = 1.24, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=654296.5, rms=1.244 (3.472%) 026: dt: 0.1250, sse=624986.0, rms=1.140 (8.379%) rms = 1.14, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=623980.4, rms=1.136 (0.357%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 7 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown deleting segment 2 with 14 points - only 0.00% unknown deleting segment 3 with 197 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 8 points - only 0.00% unknown deleting segment 6 with 11 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown mean border=81.4, 34 (3) missing vertices, mean dist -0.0 [0.2 (%55.7)->0.2 (%44.3))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= X1, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /usr/local/freesurfer/subjects/Sub01/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=640576.2, rms=1.545 rms = 2.14, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=610339.8, rms=1.021 (33.921%) 029: dt: 0.2500, sse=604542.9, rms=0.863 (15.421%) rms = 0.87, time step reduction 2 of 3 to 0.125... rms = 0.86, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=603014.1, rms=0.857 (0.721%) positioning took 0.3 minutes generating cortex label... 9 non-cortical segments detected only using segment with 6969 vertices erasing segment 1 (vno[0] = 43364) erasing segment 2 (vno[0] = 82478) erasing segment 3 (vno[0] = 84731) erasing segment 4 (vno[0] = 84899) erasing segment 5 (vno[0] = 85863) erasing segment 6 (vno[0] = 86804) erasing segment 7 (vno[0] = 94238) erasing segment 8 (vno[0] = 99798) writing cortex label to /usr/local/freesurfer/subjects/Sub01/label/rh.cortex.label... writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/rh.curv writing smoothed area to rh.area writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/rh.area vertex spacing 0.90 +- 0.26 (0.04-->5.60) (max @ vno 105402 --> 119254) face area 0.34 +- 0.17 (0.00-->8.21) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 3 with 13 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=47.4, 65 (65) missing vertices, mean dist 1.8 [2.0 (%0.0)->2.7 (%100.0))] %12 local maxima, %52 large gradients and %31 min vals, 316 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=27788640.0, rms=34.623 001: dt: 0.0500, sse=24250334.0, rms=32.293 (6.728%) 002: dt: 0.0500, sse=21716036.0, rms=30.516 (5.505%) 003: dt: 0.0500, sse=19785026.0, rms=29.088 (4.678%) 004: dt: 0.0500, sse=18232924.0, rms=27.888 (4.127%) 005: dt: 0.0500, sse=16937090.0, rms=26.845 (3.741%) 006: dt: 0.0500, sse=15828672.0, rms=25.919 (3.449%) 007: dt: 0.0500, sse=14860116.0, rms=25.082 (3.229%) 008: dt: 0.0500, sse=14000330.0, rms=24.315 (3.059%) 009: dt: 0.0500, sse=13228017.0, rms=23.604 (2.922%) 010: dt: 0.0500, sse=12528311.0, rms=22.942 (2.808%) positioning took 0.8 minutes mean border=47.2, 55 (31) missing vertices, mean dist 1.5 [0.1 (%0.0)->2.2 (%100.0))] %13 local maxima, %51 large gradients and %30 min vals, 291 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=13094401.0, rms=23.480 011: dt: 0.0500, sse=12452464.0, rms=22.869 (2.600%) 012: dt: 0.0500, sse=11863927.0, rms=22.295 (2.512%) 013: dt: 0.0500, sse=11321973.0, rms=21.752 (2.433%) 014: dt: 0.0500, sse=10822179.0, rms=21.240 (2.356%) 015: dt: 0.0500, sse=10360271.0, rms=20.755 (2.284%) 016: dt: 0.0500, sse=9933189.0, rms=20.296 (2.211%) 017: dt: 0.0500, sse=9537754.0, rms=19.861 (2.140%) 018: dt: 0.0500, sse=9171020.0, rms=19.450 (2.073%) 019: dt: 0.0500, sse=8830889.0, rms=19.060 (2.004%) 020: dt: 0.0500, sse=8515590.0, rms=18.691 (1.934%) positioning took 0.9 minutes mean border=47.1, 61 (19) missing vertices, mean dist 1.2 [0.1 (%0.7)->1.8 (%99.3))] %14 local maxima, %51 large gradients and %30 min vals, 301 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=8605594.0, rms=18.802 021: dt: 0.0500, sse=8306447.5, rms=18.448 (1.886%) 022: dt: 0.0500, sse=8028506.0, rms=18.112 (1.820%) 023: dt: 0.0500, sse=7768646.5, rms=17.792 (1.765%) 024: dt: 0.0500, sse=7527089.5, rms=17.490 (1.700%) 025: dt: 0.0500, sse=7302254.0, rms=17.203 (1.638%) 026: dt: 0.0500, sse=7092226.5, rms=16.931 (1.581%) 027: dt: 0.0500, sse=6894478.5, rms=16.671 (1.537%) 028: dt: 0.0500, sse=6706196.0, rms=16.419 (1.510%) 029: dt: 0.0500, sse=6527062.0, rms=16.176 (1.482%) 030: dt: 0.0500, sse=6356430.0, rms=15.941 (1.454%) positioning took 0.8 minutes mean border=47.0, 76 (16) missing vertices, mean dist 1.0 [0.1 (%8.5)->1.7 (%91.5))] %14 local maxima, %51 large gradients and %30 min vals, 295 gradients ignored tol=1.0e-04, sigma=2.0, host= X1, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=6432356.0, rms=16.045 031: dt: 0.5000, sse=5241629.0, rms=14.309 (10.820%) 032: dt: 0.5000, sse=4411390.5, rms=12.955 (9.464%) 033: dt: 0.5000, sse=3757908.8, rms=11.781 (9.058%) 034: dt: 0.5000, sse=3225356.0, rms=10.723 (8.983%) 035: dt: 0.5000, sse=2772257.5, rms=9.736 (9.202%) 036: dt: 0.5000, sse=2377633.8, rms=8.783 (9.788%) 037: dt: 0.5000, sse=2033135.8, rms=7.863 (10.473%) 038: dt: 0.5000, sse=1757014.5, rms=7.037 (10.512%) 039: dt: 0.5000, sse=1552587.2, rms=6.360 (9.615%) 040: dt: 0.5000, sse=1418371.1, rms=5.870 (7.713%) 041: dt: 0.5000, sse=1325169.8, rms=5.509 (6.146%) 042: dt: 0.5000, sse=1270512.4, rms=5.280 (4.162%) 043: dt: 0.5000, sse=1231760.8, rms=5.118 (3.067%) 044: dt: 0.5000, sse=1208397.8, rms=5.012 (2.076%) 045: dt: 0.5000, sse=1193060.8, rms=4.946 (1.310%) rms = 4.91, time step reduction 1 of 3 to 0.250... 046: dt: 0.5000, sse=1185428.2, rms=4.908 (0.762%) 047: dt: 0.2500, sse=1071587.4, rms=4.312 (12.156%) 048: dt: 0.2500, sse=1040407.9, rms=4.147 (3.818%) rms = 4.15, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=1040664.7, rms=4.145 (0.036%) 050: dt: 0.1250, sse=1019808.7, rms=4.026 (2.885%) rms = 4.01, time step reduction 3 of 3 to 0.062... 051: dt: 0.1250, sse=1017018.8, rms=4.010 (0.386%) positioning took 2.0 minutes mean border=45.9, 1492 (7) missing vertices, mean dist 0.1 [0.2 (%50.4)->0.5 (%49.6))] %27 local maxima, %40 large gradients and %27 min vals, 106 gradients ignored tol=1.0e-04, sigma=1.0, host= X1, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1279564.5, rms=4.363 052: dt: 0.5000, sse=1234727.1, rms=4.139 (5.127%) rms = 4.12, time step reduction 1 of 3 to 0.250... 053: dt: 0.5000, sse=1223269.0, rms=4.121 (0.434%) 054: dt: 0.2500, sse=1102013.2, rms=3.329 (19.219%) 055: dt: 0.2500, sse=1071982.8, rms=3.125 (6.137%) rms = 3.10, time step reduction 2 of 3 to 0.125... 056: dt: 0.2500, sse=1069261.8, rms=3.103 (0.711%) 057: dt: 0.1250, sse=1042298.9, rms=2.893 (6.767%) rms = 2.86, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1037449.7, rms=2.858 (1.216%) positioning took 0.7 minutes mean border=45.0, 1579 (7) missing vertices, mean dist 0.1 [0.1 (%49.8)->0.3 (%50.2))] %43 local maxima, %25 large gradients and %26 min vals, 100 gradients ignored tol=1.0e-04, sigma=0.5, host= X1, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1100815.4, rms=3.298 rms = 3.71, time step reduction 1 of 3 to 0.250... 059: dt: 0.2500, sse=1061675.2, rms=3.016 (8.560%) 060: dt: 0.2500, sse=1047628.6, rms=2.913 (3.417%) rms = 2.93, time step reduction 2 of 3 to 0.125... rms = 2.87, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=1042799.1, rms=2.873 (1.360%) positioning took 0.4 minutes mean border=44.3, 2939 (6) missing vertices, mean dist 0.1 [0.1 (%49.4)->0.3 (%50.6))] %48 local maxima, %19 large gradients and %26 min vals, 120 gradients ignored tol=1.0e-04, sigma=0.2, host= X1, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /usr/local/freesurfer/subjects/Sub01/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1066295.2, rms=3.057 rms = 3.52, time step reduction 1 of 3 to 0.250... 062: dt: 0.2500, sse=1043775.9, rms=2.881 (5.757%) 063: dt: 0.2500, sse=1033952.2, rms=2.817 (2.211%) rms = 2.85, time step reduction 2 of 3 to 0.125... rms = 2.78, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=1029615.9, rms=2.780 (1.320%) positioning took 0.4 minutes writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/rh.area.pial vertex spacing 1.04 +- 0.45 (0.10-->8.33) (max @ vno 79627 --> 78576) face area 0.43 +- 0.33 (0.00-->10.26) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 119358 vertices processed 25000 of 119358 vertices processed 50000 of 119358 vertices processed 75000 of 119358 vertices processed 100000 of 119358 vertices processed 0 of 119358 vertices processed 25000 of 119358 vertices processed 50000 of 119358 vertices processed 75000 of 119358 vertices processed 100000 of 119358 vertices processed thickness calculation complete, 383:837 truncations. 28712 vertices at 0 distance 86477 vertices at 1 distance 71806 vertices at 2 distance 28143 vertices at 3 distance 8401 vertices at 4 distance 2332 vertices at 5 distance 661 vertices at 6 distance 238 vertices at 7 distance 89 vertices at 8 distance 45 vertices at 9 distance 34 vertices at 10 distance 29 vertices at 11 distance 35 vertices at 12 distance 23 vertices at 13 distance 16 vertices at 14 distance 13 vertices at 15 distance 12 vertices at 16 distance 15 vertices at 17 distance 18 vertices at 18 distance 11 vertices at 19 distance 12 vertices at 20 distance writing curvature file /usr/local/freesurfer/subjects/Sub01/surf/rh.thickness positioning took 11.8 minutes #-------------------------------------------- #@# Surf Volume lh Thu Jun 8 23:32:19 EDT 2017 /usr/local/freesurfer/subjects/Sub01/surf /usr/local/freesurfer/subjects/Sub01/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume Sub01 lh /usr/local/freesurfer/subjects/Sub01/surf/lh.volume masking with /usr/local/freesurfer/subjects/Sub01/label/lh.cortex.label Total face volume 230655 Total vertex volume 226253 (mask=0) #@# Sub01 lh 226253 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Thu Jun 8 23:32:21 EDT 2017 /usr/local/freesurfer/subjects/Sub01/surf /usr/local/freesurfer/subjects/Sub01/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume Sub01 rh /usr/local/freesurfer/subjects/Sub01/surf/rh.volume masking with /usr/local/freesurfer/subjects/Sub01/label/rh.cortex.label Total face volume 228402 Total vertex volume 224914 (mask=0) #@# Sub01 rh 224914 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Thu Jun 8 23:32:23 EDT 2017 /usr/local/freesurfer/subjects/Sub01/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon Sub01 SUBJECTS_DIR is /usr/local/freesurfer/subjects loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 165 writing volume /usr/local/freesurfer/subjects/Sub01/mri/ribbon.mgz mris_volmask took 7.01 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Thu Jun 8 23:39:24 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab Sub01 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /usr/local/freesurfer/subjects/Sub01/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/Sub01/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 230655 Total vertex volume 226253 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1273038 mm^3 (det: 1.530280 ) lhCtxGM: 225974.072 225810.000 diff= 164.1 pctdiff= 0.073 rhCtxGM: 224547.442 224320.000 diff= 227.4 pctdiff= 0.101 lhCtxWM: 190676.012 191659.000 diff= -983.0 pctdiff=-0.516 rhCtxWM: 193077.650 193632.000 diff= -554.3 pctdiff=-0.287 SubCortGMVol 55462.000 SupraTentVol 905178.177 (902446.000) diff=2732.177 pctdiff=0.302 SupraTentVolNotVent 893681.177 (890949.000) diff=2732.177 pctdiff=0.306 BrainSegVol 1028936.000 (1027351.000) diff=1585.000 pctdiff=0.154 BrainSegVolNotVent 1015175.000 (1013869.177) diff=1305.823 pctdiff=0.129 BrainSegVolNotVent 1015175.000 CerebellumVol 124066.000 VentChorVol 11497.000 3rd4th5thCSF 2264.000 CSFVol 679.000, OptChiasmVol 160.000 MaskVol 1348494.000 1426 1006 2540 2.516 0.479 0.093 0.014 7 0.8 bankssts 903 584 1862 2.781 0.729 0.131 0.025 14 0.9 caudalanteriorcingulate 2863 1948 6085 2.672 0.552 0.118 0.023 29 2.6 caudalmiddlefrontal 1979 1332 2901 1.949 0.465 0.154 0.048 34 3.8 cuneus 523 376 1852 3.398 0.948 0.112 0.021 4 0.5 entorhinal 4163 2860 9347 2.727 0.648 0.139 0.032 67 5.5 fusiform 6254 4293 12491 2.472 0.590 0.128 0.023 81 5.8 inferiorparietal 4533 3142 10648 2.830 0.731 0.124 0.029 55 5.9 inferiortemporal 1442 918 2389 2.219 0.880 0.120 0.025 21 1.2 isthmuscingulate 6411 4520 11747 2.279 0.632 0.154 0.036 109 10.1 lateraloccipital 3233 2357 7724 2.693 0.702 0.143 0.038 50 5.3 lateralorbitofrontal 3391 2392 6606 2.343 0.672 0.153 0.039 57 5.4 lingual 2309 1606 4741 2.481 0.639 0.129 0.035 34 3.3 medialorbitofrontal 4487 3101 11744 2.973 0.708 0.124 0.024 57 4.5 middletemporal 894 598 2039 2.763 0.690 0.092 0.017 6 0.6 parahippocampal 2408 1429 3455 2.262 0.660 0.116 0.040 28 4.4 paracentral 2031 1380 4399 2.703 0.558 0.137 0.031 26 2.6 parsopercularis 936 643 2660 2.993 0.579 0.149 0.037 19 1.5 parsorbitalis 1688 1175 3463 2.541 0.693 0.128 0.028 22 1.9 parstriangularis 1518 1045 2105 2.050 0.594 0.140 0.037 22 2.3 pericalcarine 6067 4135 10809 2.276 0.727 0.123 0.025 64 6.0 postcentral 1733 1135 3109 2.391 0.712 0.126 0.024 23 1.6 posteriorcingulate 6473 4157 12921 2.781 0.582 0.106 0.021 52 5.1 precentral 4566 3157 7948 2.224 0.578 0.120 0.026 52 4.8 precuneus 1137 787 2857 3.038 0.775 0.145 0.037 25 1.7 rostralanteriorcingulate 7578 5143 15059 2.477 0.622 0.127 0.029 102 9.1 rostralmiddlefrontal 9173 6236 20284 2.817 0.643 0.126 0.032 106 11.6 superiorfrontal 6460 4346 11239 2.245 0.517 0.128 0.026 77 6.7 superiorparietal 4926 3347 11276 2.836 0.671 0.096 0.017 41 3.4 superiortemporal 4493 3134 9328 2.630 0.652 0.131 0.030 64 5.4 supramarginal 386 262 1187 2.968 0.627 0.154 0.047 8 0.6 frontalpole 569 413 2419 3.986 0.621 0.146 0.034 10 0.8 temporalpole 538 355 911 2.551 0.470 0.139 0.025 6 0.5 transversetemporal 2745 1859 6038 3.232 0.809 0.115 0.028 25 2.8 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab Sub01 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /usr/local/freesurfer/subjects/Sub01/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/Sub01/surf/lh.pial... reading input pial surface /usr/local/freesurfer/subjects/Sub01/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 230655 Total vertex volume 226253 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1273038 mm^3 (det: 1.530280 ) lhCtxGM: 225974.072 225810.000 diff= 164.1 pctdiff= 0.073 rhCtxGM: 224547.442 224320.000 diff= 227.4 pctdiff= 0.101 lhCtxWM: 190676.012 191659.000 diff= -983.0 pctdiff=-0.516 rhCtxWM: 193077.650 193632.000 diff= -554.3 pctdiff=-0.287 SubCortGMVol 55462.000 SupraTentVol 905178.177 (902446.000) diff=2732.177 pctdiff=0.302 SupraTentVolNotVent 893681.177 (890949.000) diff=2732.177 pctdiff=0.306 BrainSegVol 1028936.000 (1027351.000) diff=1585.000 pctdiff=0.154 BrainSegVolNotVent 1015175.000 (1013869.177) diff=1305.823 pctdiff=0.129 BrainSegVolNotVent 1015175.000 CerebellumVol 124066.000 VentChorVol 11497.000 3rd4th5thCSF 2264.000 CSFVol 679.000, OptChiasmVol 160.000 MaskVol 1348494.000 1426 986 2540 2.516 0.479 0.130 0.032 16 2.0 bankssts 903 781 1862 2.781 0.729 0.162 0.040 25 1.4 caudalanteriorcingulate 2863 2489 6085 2.672 0.552 0.137 0.028 30 3.6 caudalmiddlefrontal 1979 1659 2901 1.949 0.465 0.149 0.034 26 3.0 cuneus 523 664 1852 3.398 0.948 0.165 0.033 4 0.8 entorhinal 4163 3900 9347 2.727 0.648 0.165 0.041 82 7.6 fusiform 6254 5590 12491 2.472 0.590 0.155 0.032 78 8.9 inferiorparietal 4533 4194 10648 2.830 0.731 0.153 0.033 58 7.2 inferiortemporal 1442 1179 2389 2.219 0.880 0.147 0.037 25 2.1 isthmuscingulate 6411 5759 11747 2.279 0.632 0.159 0.033 99 10.1 lateraloccipital 3233 3104 7724 2.693 0.702 0.181 0.042 58 6.6 lateralorbitofrontal 3391 3252 6606 2.343 0.672 0.181 0.046 75 7.3 lingual 2309 2138 4741 2.481 0.639 0.156 0.038 32 3.7 medialorbitofrontal 4487 4623 11744 2.973 0.708 0.158 0.031 50 6.5 middletemporal 894 907 2039 2.763 0.690 0.162 0.040 8 1.8 parahippocampal 2408 1648 3455 2.262 0.660 0.108 0.027 26 2.6 paracentral 2031 1816 4399 2.703 0.558 0.164 0.038 26 3.7 parsopercularis 936 1117 2660 2.993 0.579 0.194 0.041 12 1.6 parsorbitalis 1688 1486 3463 2.541 0.693 0.155 0.028 20 2.0 parstriangularis 1518 1048 2105 2.050 0.594 0.152 0.045 28 3.1 pericalcarine 6067 5357 10809 2.276 0.727 0.147 0.030 75 8.2 postcentral 1733 1397 3109 2.391 0.712 0.151 0.035 37 2.6 posteriorcingulate 6473 4906 12921 2.781 0.582 0.114 0.025 67 6.9 precentral 4566 3763 7948 2.224 0.578 0.147 0.032 57 6.6 precuneus 1137 1146 2857 3.038 0.775 0.162 0.036 12 1.8 rostralanteriorcingulate 7578 6593 15059 2.477 0.622 0.155 0.035 104 12.3 rostralmiddlefrontal 9173 7808 20284 2.817 0.643 0.144 0.034 123 13.6 superiorfrontal 6460 5455 11239 2.245 0.517 0.155 0.032 101 9.1 superiorparietal 4926 4355 11276 2.836 0.671 0.128 0.026 39 5.7 superiortemporal 4493 3886 9328 2.630 0.652 0.149 0.032 64 6.9 supramarginal 386 510 1187 2.968 0.627 0.217 0.042 4 0.8 frontalpole 569 780 2419 3.986 0.621 0.178 0.030 5 0.7 temporalpole 538 387 911 2.551 0.470 0.110 0.027 3 0.6 transversetemporal 2745 1706 6038 3.232 0.809 0.121 0.031 39 3.9 insula #----------------------------------------- #@# Parcellation Stats rh Thu Jun 8 23:40:14 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab Sub01 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /usr/local/freesurfer/subjects/Sub01/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/Sub01/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 228402 Total vertex volume 224914 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1273038 mm^3 (det: 1.530280 ) lhCtxGM: 225974.072 225810.000 diff= 164.1 pctdiff= 0.073 rhCtxGM: 224547.442 224320.000 diff= 227.4 pctdiff= 0.101 lhCtxWM: 190676.012 191659.000 diff= -983.0 pctdiff=-0.516 rhCtxWM: 193077.650 193632.000 diff= -554.3 pctdiff=-0.287 SubCortGMVol 55462.000 SupraTentVol 905178.177 (902446.000) diff=2732.177 pctdiff=0.302 SupraTentVolNotVent 893681.177 (890949.000) diff=2732.177 pctdiff=0.306 BrainSegVol 1028936.000 (1027351.000) diff=1585.000 pctdiff=0.154 BrainSegVolNotVent 1015175.000 (1013869.177) diff=1305.823 pctdiff=0.129 BrainSegVolNotVent 1015175.000 CerebellumVol 124066.000 VentChorVol 11497.000 3rd4th5thCSF 2264.000 CSFVol 679.000, OptChiasmVol 160.000 MaskVol 1348494.000 1313 925 2248 2.524 0.414 0.109 0.017 10 0.9 bankssts 932 637 1988 2.472 0.882 0.144 0.027 20 1.0 caudalanteriorcingulate 2607 1720 5270 2.572 0.652 0.103 0.021 21 2.0 caudalmiddlefrontal 1976 1328 3007 2.027 0.473 0.142 0.037 27 3.2 cuneus 460 343 1890 3.538 0.743 0.131 0.035 7 0.6 entorhinal 3662 2558 7988 2.675 0.598 0.134 0.024 49 3.5 fusiform 7141 4884 14174 2.417 0.622 0.128 0.026 98 7.6 inferiorparietal 4241 2980 9090 2.538 0.722 0.135 0.035 65 6.1 inferiortemporal 1399 924 2694 2.344 0.930 0.124 0.028 22 1.3 isthmuscingulate 6683 4491 12160 2.337 0.581 0.143 0.031 104 8.4 lateraloccipital 3620 2466 7497 2.748 0.888 0.130 0.032 44 5.1 lateralorbitofrontal 3654 2577 6409 2.274 0.702 0.154 0.040 63 5.9 lingual 2641 1818 5594 2.507 0.691 0.130 0.037 40 3.6 medialorbitofrontal 4722 3349 12174 2.843 0.745 0.133 0.029 76 5.5 middletemporal 803 534 1926 2.947 0.870 0.103 0.015 7 0.4 parahippocampal 2331 1392 3486 2.411 0.587 0.110 0.032 21 3.1 paracentral 1519 1024 2934 2.601 0.467 0.118 0.027 16 1.5 parsopercularis 975 721 2509 2.618 0.683 0.150 0.033 16 1.2 parsorbitalis 1867 1319 4190 2.543 0.606 0.141 0.033 28 2.5 parstriangularis 1676 1166 2065 1.879 0.576 0.147 0.037 26 2.3 pericalcarine 5768 3648 9395 2.196 0.705 0.111 0.026 61 5.9 postcentral 1856 1201 3678 2.612 0.836 0.138 0.029 28 2.0 posteriorcingulate 6977 4469 13283 2.675 0.534 0.110 0.026 63 7.2 precentral 5168 3487 9288 2.426 0.587 0.129 0.026 62 5.6 precuneus 692 458 1454 2.676 0.638 0.116 0.031 12 0.7 rostralanteriorcingulate 7431 5083 14608 2.400 0.640 0.135 0.031 101 9.2 rostralmiddlefrontal 8744 5908 20377 2.868 0.659 0.124 0.030 97 10.2 superiorfrontal 7034 4612 12135 2.266 0.540 0.121 0.023 79 6.6 superiorparietal 5003 3385 10586 2.679 0.616 0.101 0.018 43 3.8 superiortemporal 4312 3045 8808 2.549 0.596 0.130 0.028 61 4.7 supramarginal 506 356 1729 3.583 0.448 0.182 0.055 13 1.1 frontalpole 591 451 2991 4.250 0.527 0.152 0.035 9 0.9 temporalpole 464 288 721 2.215 0.364 0.122 0.018 6 0.3 transversetemporal 3104 2102 6551 3.125 0.862 0.123 0.030 34 3.7 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab Sub01 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /usr/local/freesurfer/subjects/Sub01/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/Sub01/surf/rh.pial... reading input pial surface /usr/local/freesurfer/subjects/Sub01/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 228402 Total vertex volume 224914 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1273038 mm^3 (det: 1.530280 ) lhCtxGM: 225974.072 225810.000 diff= 164.1 pctdiff= 0.073 rhCtxGM: 224547.442 224320.000 diff= 227.4 pctdiff= 0.101 lhCtxWM: 190676.012 191659.000 diff= -983.0 pctdiff=-0.516 rhCtxWM: 193077.650 193632.000 diff= -554.3 pctdiff=-0.287 SubCortGMVol 55462.000 SupraTentVol 905178.177 (902446.000) diff=2732.177 pctdiff=0.302 SupraTentVolNotVent 893681.177 (890949.000) diff=2732.177 pctdiff=0.306 BrainSegVol 1028936.000 (1027351.000) diff=1585.000 pctdiff=0.154 BrainSegVolNotVent 1015175.000 (1013869.177) diff=1305.823 pctdiff=0.129 BrainSegVolNotVent 1015175.000 CerebellumVol 124066.000 VentChorVol 11497.000 3rd4th5thCSF 2264.000 CSFVol 679.000, OptChiasmVol 160.000 MaskVol 1348494.000 1313 856 2248 2.524 0.414 0.122 0.030 14 1.9 bankssts 932 879 1988 2.472 0.882 0.162 0.035 25 1.4 caudalanteriorcingulate 2607 2187 5270 2.572 0.652 0.121 0.026 24 3.0 caudalmiddlefrontal 1976 1658 3007 2.027 0.473 0.141 0.031 24 2.7 cuneus 460 721 1890 3.538 0.743 0.229 0.043 5 1.0 entorhinal 3662 3283 7988 2.675 0.598 0.156 0.034 58 5.7 fusiform 7141 6471 14174 2.417 0.622 0.154 0.031 88 10.7 inferiorparietal 4241 3835 9090 2.538 0.722 0.163 0.039 72 8.0 inferiortemporal 1399 1261 2694 2.344 0.930 0.170 0.041 38 2.4 isthmuscingulate 6683 5830 12160 2.337 0.581 0.156 0.035 105 11.0 lateraloccipital 3620 2983 7497 2.748 0.888 0.144 0.036 58 5.7 lateralorbitofrontal 3654 3187 6409 2.274 0.702 0.159 0.039 55 6.4 lingual 2641 2467 5594 2.507 0.691 0.165 0.037 40 4.6 medialorbitofrontal 4722 4999 12174 2.843 0.745 0.169 0.035 54 7.7 middletemporal 803 754 1926 2.947 0.870 0.150 0.036 10 1.3 parahippocampal 2331 1516 3486 2.411 0.587 0.106 0.023 24 2.3 paracentral 1519 1207 2934 2.601 0.467 0.146 0.035 20 2.4 parsopercularis 975 1149 2509 2.618 0.683 0.196 0.039 12 1.7 parsorbitalis 1867 1861 4190 2.543 0.606 0.180 0.042 26 3.7 parstriangularis 1676 1117 2065 1.879 0.576 0.144 0.038 38 3.1 pericalcarine 5768 4795 9395 2.196 0.705 0.130 0.026 51 6.6 postcentral 1856 1481 3678 2.612 0.836 0.146 0.034 27 2.9 posteriorcingulate 6977 5155 13283 2.675 0.534 0.112 0.023 73 7.2 precentral 5168 4117 9288 2.426 0.587 0.149 0.036 84 8.3 precuneus 692 643 1454 2.676 0.638 0.167 0.045 19 1.0 rostralanteriorcingulate 7431 6782 14608 2.400 0.640 0.167 0.035 110 12.5 rostralmiddlefrontal 8744 7812 20377 2.868 0.659 0.149 0.034 112 13.2 superiorfrontal 7034 5828 12135 2.266 0.540 0.140 0.030 82 9.0 superiorparietal 5003 4375 10586 2.679 0.616 0.129 0.024 44 5.2 superiortemporal 4312 3695 8808 2.549 0.596 0.154 0.033 61 6.4 supramarginal 506 595 1729 3.583 0.448 0.200 0.040 9 1.0 frontalpole 591 904 2991 4.250 0.527 0.210 0.036 6 1.1 temporalpole 464 362 721 2.215 0.364 0.116 0.025 3 0.5 transversetemporal 3104 1939 6551 3.125 0.862 0.128 0.036 55 4.8 insula #----------------------------------------- #@# Cortical Parc 2 lh Thu Jun 8 23:41:00 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Sub01 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 2.9 using min determinant for regularization = 0.086 0 singular and 762 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 13 labels changed using aseg relabeling using gibbs priors... 000: 8202 changed, 118136 examined... 001: 1906 changed, 31720 examined... 002: 564 changed, 10083 examined... 003: 242 changed, 3231 examined... 004: 115 changed, 1383 examined... 005: 55 changed, 653 examined... 006: 28 changed, 313 examined... 007: 12 changed, 144 examined... 008: 6 changed, 73 examined... 009: 1 changed, 40 examined... 010: 0 changed, 5 examined... 0 labels changed using aseg 000: 236 total segments, 148 labels (1704 vertices) changed 001: 92 total segments, 5 labels (69 vertices) changed 002: 87 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 35 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 758 vertices marked for relabeling... 758 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 12 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Thu Jun 8 23:41:13 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Sub01 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 719 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 36 labels changed using aseg relabeling using gibbs priors... 000: 7727 changed, 119358 examined... 001: 1745 changed, 30521 examined... 002: 463 changed, 9344 examined... 003: 173 changed, 2666 examined... 004: 95 changed, 1047 examined... 005: 52 changed, 528 examined... 006: 27 changed, 299 examined... 007: 16 changed, 151 examined... 008: 4 changed, 95 examined... 009: 3 changed, 20 examined... 010: 2 changed, 20 examined... 011: 3 changed, 11 examined... 012: 0 changed, 11 examined... 29 labels changed using aseg 000: 208 total segments, 128 labels (1776 vertices) changed 001: 85 total segments, 5 labels (28 vertices) changed 002: 80 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 31 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1014 vertices marked for relabeling... 1014 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 12 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Thu Jun 8 23:41:25 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab Sub01 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /usr/local/freesurfer/subjects/Sub01/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/Sub01/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 230655 Total vertex volume 226253 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1273038 mm^3 (det: 1.530280 ) lhCtxGM: 225974.072 225810.000 diff= 164.1 pctdiff= 0.073 rhCtxGM: 224547.442 224320.000 diff= 227.4 pctdiff= 0.101 lhCtxWM: 190676.012 191659.000 diff= -983.0 pctdiff=-0.516 rhCtxWM: 193077.650 193632.000 diff= -554.3 pctdiff=-0.287 SubCortGMVol 55462.000 SupraTentVol 905178.177 (902446.000) diff=2732.177 pctdiff=0.302 SupraTentVolNotVent 893681.177 (890949.000) diff=2732.177 pctdiff=0.306 BrainSegVol 1028936.000 (1027351.000) diff=1585.000 pctdiff=0.154 BrainSegVolNotVent 1015175.000 (1013869.177) diff=1305.823 pctdiff=0.129 BrainSegVolNotVent 1015175.000 CerebellumVol 124066.000 VentChorVol 11497.000 3rd4th5thCSF 2264.000 CSFVol 679.000, OptChiasmVol 160.000 MaskVol 1348494.000 1465 1006 2773 2.292 0.633 0.128 0.029 19 1.7 G&S_frontomargin 1537 1075 3916 2.680 0.671 0.131 0.027 23 1.6 G&S_occipital_inf 1598 895 2214 2.197 0.657 0.117 0.045 21 3.2 G&S_paracentral 1301 854 2886 2.854 0.552 0.132 0.029 16 1.5 G&S_subcentral 648 488 1809 2.880 0.636 0.159 0.035 11 1.1 G&S_transv_frontopol 1986 1379 4092 2.752 0.721 0.139 0.032 33 2.6 G&S_cingul-Ant 1172 819 2492 2.784 0.476 0.114 0.023 9 1.0 G&S_cingul-Mid-Ant 1271 862 2366 2.638 0.575 0.105 0.022 8 1.1 G&S_cingul-Mid-Post 515 346 1371 2.864 0.656 0.159 0.037 10 0.8 G_cingul-Post-dorsal 322 206 674 2.773 0.763 0.160 0.039 7 0.4 G_cingul-Post-ventral 1832 1243 2924 1.972 0.503 0.164 0.051 36 3.8 G_cuneus 1294 838 3290 2.909 0.537 0.135 0.033 19 1.7 G_front_inf-Opercular 394 264 1117 2.900 0.541 0.141 0.027 8 0.5 G_front_inf-Orbital 889 595 2335 2.939 0.548 0.151 0.038 19 1.3 G_front_inf-Triangul 4080 2647 9455 2.700 0.604 0.130 0.029 64 4.8 G_front_middle 6673 4408 16464 2.956 0.650 0.138 0.040 101 10.6 G_front_sup 517 337 1313 3.678 0.703 0.140 0.035 7 0.8 G_Ins_lg&S_cent_ins 656 438 2245 3.893 0.702 0.114 0.034 9 0.7 G_insular_short 1916 1289 4483 2.594 0.584 0.147 0.035 36 2.6 G_occipital_middle 1356 922 2289 2.032 0.524 0.141 0.030 19 1.5 G_occipital_sup 1734 1199 4258 2.726 0.659 0.150 0.034 34 2.5 G_oc-temp_lat-fusifor 2337 1659 5187 2.460 0.715 0.172 0.048 49 4.6 G_oc-temp_med-Lingual 1162 776 3321 3.063 0.848 0.101 0.023 9 1.0 G_oc-temp_med-Parahip 2086 1481 6445 2.978 0.700 0.158 0.047 44 4.3 G_orbital 2723 1855 6686 2.693 0.631 0.151 0.031 56 3.4 G_pariet_inf-Angular 2222 1532 5920 2.969 0.571 0.146 0.037 38 3.3 G_pariet_inf-Supramar 2231 1507 4901 2.450 0.579 0.140 0.031 36 2.7 G_parietal_sup 2385 1581 5189 2.546 0.662 0.138 0.034 35 2.8 G_postcentral 2481 1522 6251 3.052 0.564 0.110 0.022 25 2.1 G_precentral 2384 1642 5123 2.389 0.620 0.139 0.035 40 3.3 G_precuneus 906 622 2271 2.557 0.701 0.150 0.052 20 1.9 G_rectus 182 128 404 2.897 0.659 0.080 0.032 1 0.1 G_subcallosal 384 251 766 2.607 0.569 0.139 0.029 5 0.4 G_temp_sup-G_T_transv 1831 1191 5857 3.300 0.591 0.131 0.026 32 2.0 G_temp_sup-Lateral 639 440 1558 3.201 0.559 0.062 0.010 1 0.2 G_temp_sup-Plan_polar 604 457 1323 2.668 0.519 0.070 0.013 2 0.2 G_temp_sup-Plan_tempo 2607 1788 6957 2.909 0.710 0.135 0.037 44 4.4 G_temporal_inf 2590 1750 8158 3.195 0.626 0.139 0.030 45 3.2 G_temporal_middle 285 193 349 1.965 0.422 0.103 0.021 1 0.2 Lat_Fis-ant-Horizont 275 210 451 2.348 0.473 0.101 0.018 1 0.2 Lat_Fis-ant-Vertical 873 582 1102 2.291 0.653 0.101 0.016 4 0.6 Lat_Fis-post 1866 1374 3216 2.052 0.593 0.184 0.052 45 4.7 Pole_occipital 1418 1021 5381 3.672 0.730 0.142 0.031 22 1.8 Pole_temporal 1790 1244 2504 2.063 0.588 0.123 0.031 21 2.3 S_calcarine 2891 2028 3610 1.966 0.661 0.104 0.017 16 2.1 S_central 1243 840 1806 2.049 0.456 0.099 0.016 11 0.8 S_cingul-Marginalis 417 305 717 2.594 0.477 0.084 0.012 1 0.2 S_circular_insula_ant 1213 829 1843 2.625 0.480 0.080 0.012 4 0.6 S_circular_insula_inf 1456 987 2181 2.694 0.563 0.111 0.019 8 1.3 S_circular_insula_sup 761 530 1329 2.540 0.565 0.107 0.019 6 0.5 S_collat_transv_ant 412 285 638 2.385 0.521 0.149 0.031 5 0.6 S_collat_transv_post 1781 1242 2789 2.334 0.452 0.111 0.021 14 1.6 S_front_inf 1259 917 2309 2.357 0.552 0.136 0.033 18 1.8 S_front_middle 2577 1771 4714 2.522 0.615 0.109 0.024 17 2.5 S_front_sup 400 274 449 1.855 0.343 0.117 0.016 2 0.3 S_interm_prim-Jensen 2361 1608 3393 2.202 0.422 0.120 0.023 23 2.3 S_intrapariet&P_trans 703 508 1011 2.118 0.559 0.138 0.022 7 0.7 S_oc_middle&Lunatus 1353 896 1680 2.028 0.366 0.113 0.019 11 1.0 S_oc_sup&transversal 726 506 973 2.219 0.502 0.126 0.026 6 0.7 S_occipital_ant 629 434 1042 2.800 0.509 0.129 0.022 6 0.6 S_oc-temp_lat 1757 1217 2804 2.468 0.513 0.123 0.027 17 1.8 S_oc-temp_med&Lingual 210 158 406 2.319 0.684 0.126 0.026 1 0.2 S_orbital_lateral 595 429 911 2.345 0.680 0.110 0.018 5 0.4 S_orbital_med-olfact 1207 879 2479 2.568 0.696 0.144 0.038 18 1.8 S_orbital-H_Shaped 1705 1177 2403 2.083 0.392 0.104 0.018 12 1.3 S_parieto_occipital 1402 824 1217 1.855 0.807 0.121 0.019 23 0.9 S_pericallosal 2627 1791 3643 2.216 0.473 0.108 0.019 20 2.1 S_postcentral 1284 895 2073 2.529 0.452 0.105 0.018 7 0.9 S_precentral-inf-part 1341 920 2157 2.522 0.413 0.101 0.017 8 0.9 S_precentral-sup-part 681 472 1032 2.404 0.514 0.114 0.018 6 0.5 S_suborbital 835 575 1129 2.064 0.549 0.109 0.016 5 0.6 S_subparietal 1645 1138 2428 2.502 0.667 0.108 0.018 9 1.3 S_temporal_inf 5118 3655 8507 2.408 0.483 0.095 0.015 25 3.0 S_temporal_sup 271 196 493 2.853 0.456 0.114 0.013 2 0.2 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Thu Jun 8 23:41:48 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab Sub01 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /usr/local/freesurfer/subjects/Sub01/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/Sub01/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 228402 Total vertex volume 224914 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1273038 mm^3 (det: 1.530280 ) lhCtxGM: 225974.072 225810.000 diff= 164.1 pctdiff= 0.073 rhCtxGM: 224547.442 224320.000 diff= 227.4 pctdiff= 0.101 lhCtxWM: 190676.012 191659.000 diff= -983.0 pctdiff=-0.516 rhCtxWM: 193077.650 193632.000 diff= -554.3 pctdiff=-0.287 SubCortGMVol 55462.000 SupraTentVol 905178.177 (902446.000) diff=2732.177 pctdiff=0.302 SupraTentVolNotVent 893681.177 (890949.000) diff=2732.177 pctdiff=0.306 BrainSegVol 1028936.000 (1027351.000) diff=1585.000 pctdiff=0.154 BrainSegVolNotVent 1015175.000 (1013869.177) diff=1305.823 pctdiff=0.129 BrainSegVolNotVent 1015175.000 CerebellumVol 124066.000 VentChorVol 11497.000 3rd4th5thCSF 2264.000 CSFVol 679.000, OptChiasmVol 160.000 MaskVol 1348494.000 885 617 1898 2.485 0.892 0.142 0.035 13 1.3 G&S_frontomargin 1201 805 2662 2.651 0.544 0.140 0.026 17 1.3 G&S_occipital_inf 1514 791 2296 2.377 0.551 0.108 0.034 15 2.0 G&S_paracentral 1264 883 2828 2.739 0.476 0.139 0.028 19 1.4 G&S_subcentral 1014 730 2999 3.086 0.783 0.167 0.046 22 2.1 G&S_transv_frontopol 2524 1728 5182 2.616 0.577 0.126 0.031 34 2.8 G&S_cingul-Ant 1359 946 2808 2.784 0.514 0.118 0.024 16 1.3 G&S_cingul-Mid-Ant 1344 917 2670 2.668 0.594 0.124 0.026 14 1.3 G&S_cingul-Mid-Post 586 374 1823 3.312 0.640 0.164 0.047 12 1.1 G_cingul-Post-dorsal 283 194 714 2.589 0.761 0.147 0.028 7 0.3 G_cingul-Post-ventral 1849 1203 2763 1.987 0.494 0.138 0.039 26 3.0 G_cuneus 959 654 2524 2.803 0.411 0.135 0.030 15 1.1 G_front_inf-Opercular 502 335 1390 2.700 0.589 0.156 0.035 11 0.6 G_front_inf-Orbital 710 512 1935 2.745 0.623 0.161 0.043 14 1.3 G_front_inf-Triangul 3621 2403 9492 2.779 0.641 0.135 0.032 58 4.4 G_front_middle 5902 3812 15517 3.074 0.633 0.132 0.038 83 8.9 G_front_sup 520 371 1396 3.419 0.605 0.137 0.034 7 0.5 G_Ins_lg&S_cent_ins 907 591 2460 3.726 0.884 0.145 0.044 16 1.7 G_insular_short 2150 1425 5066 2.672 0.616 0.148 0.036 43 3.1 G_occipital_middle 1220 803 2360 2.367 0.470 0.132 0.026 17 1.3 G_occipital_sup 1770 1149 4184 2.722 0.632 0.142 0.027 34 1.9 G_oc-temp_lat-fusifor 2283 1598 4562 2.331 0.749 0.167 0.049 47 4.2 G_oc-temp_med-Lingual 866 592 3148 3.448 0.808 0.121 0.025 10 0.7 G_oc-temp_med-Parahip 2439 1656 6463 2.872 0.879 0.144 0.042 45 4.1 G_orbital 2782 1854 7024 2.706 0.630 0.145 0.032 59 3.5 G_pariet_inf-Angular 1928 1338 4823 2.814 0.543 0.142 0.035 34 2.7 G_pariet_inf-Supramar 2533 1631 5531 2.489 0.610 0.133 0.028 40 2.9 G_parietal_sup 2150 1272 4225 2.467 0.723 0.124 0.036 32 3.0 G_postcentral 2642 1573 6433 2.920 0.509 0.114 0.035 33 3.5 G_precentral 2277 1497 5093 2.576 0.577 0.141 0.033 37 3.0 G_precuneus 803 558 2085 2.542 0.786 0.147 0.058 17 1.8 G_rectus 139 98 312 2.920 0.678 0.096 0.025 1 0.1 G_subcallosal 360 215 692 2.461 0.367 0.136 0.020 6 0.2 G_temp_sup-G_T_transv 1786 1182 4995 3.046 0.644 0.139 0.030 28 2.3 G_temp_sup-Lateral 591 402 1577 3.344 0.642 0.081 0.015 2 0.3 G_temp_sup-Plan_polar 774 566 1517 2.399 0.434 0.127 0.024 12 0.8 G_temp_sup-Plan_tempo 2175 1538 6044 2.746 0.771 0.154 0.051 54 4.2 G_temporal_inf 2799 1946 8456 3.066 0.709 0.144 0.036 59 3.8 G_temporal_middle 324 229 404 2.200 0.550 0.107 0.014 2 0.2 Lat_Fis-ant-Horizont 248 179 399 2.424 0.476 0.095 0.018 1 0.1 Lat_Fis-ant-Vertical 1211 833 1702 2.354 0.536 0.104 0.019 7 0.9 Lat_Fis-post 2993 2057 5183 2.171 0.602 0.165 0.041 58 5.3 Pole_occipital 1653 1245 6424 3.421 0.874 0.144 0.030 23 2.1 Pole_temporal 1796 1246 2273 2.137 0.747 0.123 0.024 20 1.8 S_calcarine 2894 1964 3445 1.962 0.634 0.094 0.016 13 1.9 S_central 1343 914 1929 2.280 0.480 0.098 0.016 7 0.8 S_cingul-Marginalis 490 342 784 2.888 0.781 0.112 0.017 3 0.4 S_circular_insula_ant 1149 757 1529 2.347 0.472 0.070 0.009 3 0.4 S_circular_insula_inf 1247 849 1913 2.571 0.507 0.101 0.017 5 1.0 S_circular_insula_sup 863 630 1302 2.208 0.506 0.101 0.013 5 0.5 S_collat_transv_ant 263 182 365 2.512 0.552 0.114 0.020 2 0.2 S_collat_transv_post 1611 1102 2387 2.128 0.460 0.110 0.022 12 1.3 S_front_inf 2055 1418 2862 2.192 0.442 0.124 0.025 18 2.1 S_front_middle 2064 1437 3243 2.293 0.526 0.107 0.018 13 1.6 S_front_sup 239 175 343 2.303 0.366 0.127 0.024 2 0.2 S_interm_prim-Jensen 2868 1916 3653 2.035 0.420 0.104 0.016 20 1.9 S_intrapariet&P_trans 680 500 838 1.830 0.300 0.119 0.022 4 0.6 S_oc_middle&Lunatus 1223 843 1621 2.120 0.297 0.125 0.023 12 1.1 S_oc_sup&transversal 568 422 871 2.211 0.389 0.106 0.014 3 0.4 S_occipital_ant 982 703 1572 2.428 0.436 0.117 0.024 7 1.0 S_oc-temp_lat 1912 1344 3048 2.457 0.518 0.119 0.019 14 1.6 S_oc-temp_med&Lingual 381 262 560 2.014 0.500 0.132 0.023 4 0.4 S_orbital_lateral 775 568 1102 2.230 0.628 0.119 0.019 7 0.7 S_orbital_med-olfact 1348 952 2768 2.729 0.828 0.131 0.030 13 1.8 S_orbital-H_Shaped 2078 1419 2926 2.211 0.490 0.127 0.022 22 1.9 S_parieto_occipital 1397 838 1050 1.579 0.585 0.126 0.021 26 0.8 S_pericallosal 2211 1485 2726 2.025 0.388 0.108 0.020 16 1.8 S_postcentral 1449 967 2121 2.448 0.463 0.110 0.021 10 1.2 S_precentral-inf-part 1353 930 1991 2.507 0.408 0.101 0.017 7 1.0 S_precentral-sup-part 349 238 548 2.538 0.546 0.104 0.010 2 0.2 S_suborbital 1074 739 1793 2.469 0.528 0.125 0.027 8 1.3 S_subparietal 1200 838 1481 2.076 0.427 0.120 0.019 9 1.1 S_temporal_inf 5925 4189 9444 2.347 0.488 0.104 0.017 42 4.3 S_temporal_sup 245 180 364 2.202 0.310 0.085 0.010 1 0.1 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Thu Jun 8 23:42:12 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Sub01 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1314 labels changed using aseg relabeling using gibbs priors... 000: 1701 changed, 118136 examined... 001: 394 changed, 8049 examined... 002: 103 changed, 2282 examined... 003: 28 changed, 572 examined... 004: 10 changed, 170 examined... 005: 4 changed, 60 examined... 006: 1 changed, 26 examined... 007: 2 changed, 7 examined... 008: 3 changed, 11 examined... 009: 8 changed, 20 examined... 010: 3 changed, 25 examined... 011: 1 changed, 13 examined... 012: 1 changed, 8 examined... 013: 0 changed, 4 examined... 69 labels changed using aseg 000: 55 total segments, 22 labels (182 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 10 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 627 vertices marked for relabeling... 627 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 10 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Thu Jun 8 23:42:22 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 Sub01 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1606 labels changed using aseg relabeling using gibbs priors... 000: 1779 changed, 119358 examined... 001: 408 changed, 8314 examined... 002: 99 changed, 2385 examined... 003: 42 changed, 606 examined... 004: 19 changed, 234 examined... 005: 11 changed, 106 examined... 006: 6 changed, 51 examined... 007: 4 changed, 37 examined... 008: 3 changed, 24 examined... 009: 1 changed, 11 examined... 010: 0 changed, 7 examined... 135 labels changed using aseg 000: 52 total segments, 19 labels (172 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 5 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 775 vertices marked for relabeling... 775 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 10 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Thu Jun 8 23:42:31 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab Sub01 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /usr/local/freesurfer/subjects/Sub01/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/Sub01/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 230655 Total vertex volume 226253 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1273038 mm^3 (det: 1.530280 ) lhCtxGM: 225974.072 225810.000 diff= 164.1 pctdiff= 0.073 rhCtxGM: 224547.442 224320.000 diff= 227.4 pctdiff= 0.101 lhCtxWM: 190676.012 191659.000 diff= -983.0 pctdiff=-0.516 rhCtxWM: 193077.650 193632.000 diff= -554.3 pctdiff=-0.287 SubCortGMVol 55462.000 SupraTentVol 905178.177 (902446.000) diff=2732.177 pctdiff=0.302 SupraTentVolNotVent 893681.177 (890949.000) diff=2732.177 pctdiff=0.306 BrainSegVol 1028936.000 (1027351.000) diff=1585.000 pctdiff=0.154 BrainSegVolNotVent 1015175.000 (1013869.177) diff=1305.823 pctdiff=0.129 BrainSegVolNotVent 1015175.000 CerebellumVol 124066.000 VentChorVol 11497.000 3rd4th5thCSF 2264.000 CSFVol 679.000, OptChiasmVol 160.000 MaskVol 1348494.000 1476 974 2800 2.706 0.614 0.125 0.025 18 1.4 caudalanteriorcingulate 3018 2058 6447 2.677 0.555 0.116 0.023 30 2.7 caudalmiddlefrontal 2584 1771 4025 2.002 0.463 0.143 0.041 40 4.2 cuneus 486 357 1738 3.366 0.977 0.120 0.027 4 0.5 entorhinal 3716 2560 7814 2.655 0.613 0.139 0.032 57 4.8 fusiform 6379 4394 12723 2.462 0.592 0.128 0.024 86 6.1 inferiorparietal 4643 3190 11600 2.915 0.741 0.128 0.030 63 6.4 inferiortemporal 1446 928 2404 2.245 0.854 0.123 0.027 21 1.3 isthmuscingulate 6554 4594 12120 2.276 0.640 0.152 0.036 111 10.2 lateraloccipital 3562 2570 8417 2.637 0.788 0.146 0.040 60 6.0 lateralorbitofrontal 3400 2403 6591 2.334 0.678 0.154 0.039 58 5.5 lingual 1957 1347 4227 2.525 0.661 0.131 0.040 34 3.2 medialorbitofrontal 5929 4126 14218 2.857 0.692 0.120 0.023 67 5.5 middletemporal 938 629 2138 2.761 0.692 0.091 0.016 6 0.6 parahippocampal 2794 1691 4065 2.279 0.650 0.119 0.039 32 5.1 paracentral 1908 1303 4116 2.709 0.559 0.136 0.031 23 2.5 parsopercularis 931 639 2085 2.627 0.617 0.115 0.022 11 0.8 parsorbitalis 1912 1322 3809 2.515 0.695 0.130 0.029 26 2.1 parstriangularis 1476 1018 2050 2.054 0.590 0.140 0.037 22 2.3 pericalcarine 6744 4601 11913 2.298 0.717 0.124 0.025 71 6.7 postcentral 1912 1246 3252 2.342 0.714 0.123 0.024 25 1.9 posteriorcingulate 6535 4183 12917 2.775 0.579 0.106 0.021 53 5.3 precentral 4518 3124 8069 2.238 0.587 0.124 0.027 55 5.0 precuneus 1494 1031 3358 2.924 0.744 0.146 0.036 30 2.0 rostralanteriorcingulate 5341 3590 11024 2.547 0.628 0.127 0.029 73 6.6 rostralmiddlefrontal 10231 7007 23605 2.805 0.656 0.129 0.033 128 13.3 superiorfrontal 5087 3401 8778 2.260 0.518 0.124 0.025 58 4.9 superiorparietal 6380 4386 15232 2.908 0.759 0.100 0.018 55 4.6 superiortemporal 3998 2775 8392 2.648 0.661 0.132 0.030 54 5.0 supramarginal 566 372 940 2.534 0.467 0.135 0.025 6 0.5 transversetemporal 2362 1613 5387 3.241 0.745 0.112 0.024 21 2.1 insula #----------------------------------------- #@# Parcellation Stats 3 rh Thu Jun 8 23:42:54 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab Sub01 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /usr/local/freesurfer/subjects/Sub01/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/Sub01/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 228402 Total vertex volume 224914 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1273038 mm^3 (det: 1.530280 ) lhCtxGM: 225974.072 225810.000 diff= 164.1 pctdiff= 0.073 rhCtxGM: 224547.442 224320.000 diff= 227.4 pctdiff= 0.101 lhCtxWM: 190676.012 191659.000 diff= -983.0 pctdiff=-0.516 rhCtxWM: 193077.650 193632.000 diff= -554.3 pctdiff=-0.287 SubCortGMVol 55462.000 SupraTentVol 905178.177 (902446.000) diff=2732.177 pctdiff=0.302 SupraTentVolNotVent 893681.177 (890949.000) diff=2732.177 pctdiff=0.306 BrainSegVol 1028936.000 (1027351.000) diff=1585.000 pctdiff=0.154 BrainSegVolNotVent 1015175.000 (1013869.177) diff=1305.823 pctdiff=0.129 BrainSegVolNotVent 1015175.000 CerebellumVol 124066.000 VentChorVol 11497.000 3rd4th5thCSF 2264.000 CSFVol 679.000, OptChiasmVol 160.000 MaskVol 1348494.000 1051 722 2183 2.443 0.889 0.142 0.027 22 1.1 caudalanteriorcingulate 2719 1800 5375 2.559 0.644 0.104 0.020 22 2.1 caudalmiddlefrontal 2450 1643 3678 2.029 0.471 0.140 0.035 33 3.7 cuneus 432 325 1751 3.485 0.752 0.127 0.032 6 0.5 entorhinal 3445 2368 7067 2.611 0.567 0.132 0.024 46 3.3 fusiform 7187 4912 14239 2.415 0.623 0.129 0.026 100 7.8 inferiorparietal 4562 3226 10431 2.619 0.756 0.137 0.034 70 6.4 inferiortemporal 1373 913 2654 2.336 0.927 0.123 0.029 21 1.3 isthmuscingulate 6539 4420 11841 2.320 0.571 0.145 0.032 102 8.4 lateraloccipital 4259 2906 9261 2.773 0.913 0.136 0.037 60 6.9 lateralorbitofrontal 3617 2542 6320 2.279 0.711 0.153 0.040 62 5.8 lingual 1759 1236 4089 2.589 0.757 0.129 0.037 27 2.4 medialorbitofrontal 5737 4053 13824 2.770 0.720 0.127 0.027 84 6.1 middletemporal 825 551 1943 2.937 0.858 0.104 0.015 7 0.4 parahippocampal 2449 1459 3725 2.427 0.584 0.111 0.032 23 3.4 paracentral 1827 1226 3457 2.571 0.478 0.122 0.028 19 1.9 parsopercularis 958 668 2063 2.469 0.594 0.141 0.028 15 0.9 parsorbitalis 1727 1230 3692 2.453 0.646 0.136 0.032 25 2.2 parstriangularis 1650 1157 2098 1.908 0.585 0.148 0.037 26 2.3 pericalcarine 6289 3995 10153 2.195 0.694 0.112 0.026 65 6.4 postcentral 1988 1275 3941 2.635 0.804 0.136 0.029 28 2.1 posteriorcingulate 6708 4296 12976 2.677 0.542 0.110 0.026 63 6.9 precentral 5275 3555 9686 2.439 0.589 0.128 0.026 64 5.7 precuneus 863 571 1671 2.606 0.642 0.119 0.029 13 0.9 rostralanteriorcingulate 5423 3720 10842 2.435 0.626 0.133 0.028 69 6.2 rostralmiddlefrontal 11377 7708 26012 2.806 0.682 0.128 0.032 141 14.2 superiorfrontal 5874 3851 10251 2.273 0.551 0.120 0.023 67 5.6 superiorparietal 6439 4425 15147 2.833 0.763 0.108 0.020 60 5.4 superiortemporal 4033 2841 8212 2.560 0.585 0.129 0.028 57 4.5 supramarginal 470 292 737 2.232 0.349 0.124 0.018 6 0.3 transversetemporal 2567 1769 5594 3.116 0.830 0.123 0.026 27 2.7 insula #----------------------------------------- #@# WM/GM Contrast lh Thu Jun 8 23:43:17 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts pctsurfcon --s Sub01 --lh-only Log file is /usr/local/freesurfer/subjects/Sub01/scripts/pctsurfcon.log Thu Jun 8 23:43:17 EDT 2017 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/Sub01/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux X1 4.4.0-78-generic #99-Ubuntu SMP Thu Apr 27 15:29:09 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /usr/local/freesurfer/subjects/Sub01/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /usr/local/freesurfer/subjects/Sub01/surf/tmp.pctsurfcon.3714/lh.wm.mgh --regheader Sub01 --cortex srcvol = /usr/local/freesurfer/subjects/Sub01/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /usr/local/freesurfer/subjects/Sub01/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99991 0.01250 -0.00396 -0.00006; -0.00401 -0.00409 0.99998 0.00000; -0.01248 -0.99991 -0.00414 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /usr/local/freesurfer/subjects/Sub01/label/lh.cortex.label Reading surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 65117 Masking with /usr/local/freesurfer/subjects/Sub01/label/lh.cortex.label Writing to /usr/local/freesurfer/subjects/Sub01/surf/tmp.pctsurfcon.3714/lh.wm.mgh Dim: 118136 1 1 mri_vol2surf --mov /usr/local/freesurfer/subjects/Sub01/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /usr/local/freesurfer/subjects/Sub01/surf/tmp.pctsurfcon.3714/lh.gm.mgh --projfrac 0.3 --regheader Sub01 --cortex srcvol = /usr/local/freesurfer/subjects/Sub01/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /usr/local/freesurfer/subjects/Sub01/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99991 0.01250 -0.00396 -0.00006; -0.00401 -0.00409 0.99998 0.00000; -0.01248 -0.99991 -0.00414 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /usr/local/freesurfer/subjects/Sub01/label/lh.cortex.label Reading surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/Sub01/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 78810 Masking with /usr/local/freesurfer/subjects/Sub01/label/lh.cortex.label Writing to /usr/local/freesurfer/subjects/Sub01/surf/tmp.pctsurfcon.3714/lh.gm.mgh Dim: 118136 1 1 mri_concat /usr/local/freesurfer/subjects/Sub01/surf/tmp.pctsurfcon.3714/lh.wm.mgh /usr/local/freesurfer/subjects/Sub01/surf/tmp.pctsurfcon.3714/lh.gm.mgh --paired-diff-norm --mul 100 --o /usr/local/freesurfer/subjects/Sub01/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /usr/local/freesurfer/subjects/Sub01/surf/lh.w-g.pct.mgh mri_segstats --in /usr/local/freesurfer/subjects/Sub01/surf/lh.w-g.pct.mgh --annot Sub01 lh aparc --sum /usr/local/freesurfer/subjects/Sub01/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /usr/local/freesurfer/subjects/Sub01/surf/lh.w-g.pct.mgh --annot Sub01 lh aparc --sum /usr/local/freesurfer/subjects/Sub01/stats/lh.w-g.pct.stats --snr sysname Linux hostname X1 machine x86_64 user amazinger UseRobust 0 Constructing seg from annotation Reading annotation /usr/local/freesurfer/subjects/Sub01/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /usr/local/freesurfer/subjects/Sub01/surf/lh.w-g.pct.mgh Vertex Area is 0.679326 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# WM/GM Contrast rh Thu Jun 8 23:43:21 EDT 2017 /usr/local/freesurfer/subjects/Sub01/scripts pctsurfcon --s Sub01 --rh-only Log file is /usr/local/freesurfer/subjects/Sub01/scripts/pctsurfcon.log Thu Jun 8 23:43:21 EDT 2017 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/Sub01/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux X1 4.4.0-78-generic #99-Ubuntu SMP Thu Apr 27 15:29:09 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /usr/local/freesurfer/subjects/Sub01/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /usr/local/freesurfer/subjects/Sub01/surf/tmp.pctsurfcon.3768/rh.wm.mgh --regheader Sub01 --cortex srcvol = /usr/local/freesurfer/subjects/Sub01/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /usr/local/freesurfer/subjects/Sub01/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99991 0.01250 -0.00396 -0.00006; -0.00401 -0.00409 0.99998 0.00000; -0.01248 -0.99991 -0.00414 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /usr/local/freesurfer/subjects/Sub01/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 65808 Masking with /usr/local/freesurfer/subjects/Sub01/label/rh.cortex.label Writing to /usr/local/freesurfer/subjects/Sub01/surf/tmp.pctsurfcon.3768/rh.wm.mgh Dim: 119358 1 1 mri_vol2surf --mov /usr/local/freesurfer/subjects/Sub01/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /usr/local/freesurfer/subjects/Sub01/surf/tmp.pctsurfcon.3768/rh.gm.mgh --projfrac 0.3 --regheader Sub01 --cortex srcvol = /usr/local/freesurfer/subjects/Sub01/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /usr/local/freesurfer/subjects/Sub01/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99991 0.01250 -0.00396 -0.00006; -0.00401 -0.00409 0.99998 0.00000; -0.01248 -0.99991 -0.00414 -0.00002; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /usr/local/freesurfer/subjects/Sub01/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/Sub01/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 79107 Masking with /usr/local/freesurfer/subjects/Sub01/label/rh.cortex.label Writing to /usr/local/freesurfer/subjects/Sub01/surf/tmp.pctsurfcon.3768/rh.gm.mgh Dim: 119358 1 1 mri_concat /usr/local/freesurfer/subjects/Sub01/surf/tmp.pctsurfcon.3768/rh.wm.mgh /usr/local/freesurfer/subjects/Sub01/surf/tmp.pctsurfcon.3768/rh.gm.mgh --paired-diff-norm --mul 100 --o /usr/local/freesurfer/subjects/Sub01/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /usr/local/freesurfer/subjects/Sub01/surf/rh.w-g.pct.mgh mri_segstats --in /usr/local/freesurfer/subjects/Sub01/surf/rh.w-g.pct.mgh --annot Sub01 rh aparc --sum /usr/local/freesurfer/subjects/Sub01/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /usr/local/freesurfer/subjects/Sub01/surf/rh.w-g.pct.mgh --annot Sub01 rh aparc --sum /usr/local/freesurfer/subjects/Sub01/stats/rh.w-g.pct.stats --snr sysname Linux hostname X1 machine x86_64 user amazinger UseRobust 0 Constructing seg from annotation Reading annotation /usr/local/freesurfer/subjects/Sub01/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /usr/local/freesurfer/subjects/Sub01/surf/rh.w-g.pct.mgh Vertex Area is 0.674024 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# Relabel Hypointensities Thu Jun 8 23:43:25 EDT 2017 /usr/local/freesurfer/subjects/Sub01/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 958 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 634 voxels changed to hypointensity... 1657 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Thu Jun 8 23:43:39 EDT 2017 /usr/local/freesurfer/subjects/Sub01 mri_aparc2aseg --s Sub01 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /usr/local/freesurfer/subjects subject Sub01 outvol /usr/local/freesurfer/subjects/Sub01/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/Sub01/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/Sub01/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/Sub01/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/Sub01/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /usr/local/freesurfer/subjects/Sub01/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /usr/local/freesurfer/subjects/Sub01/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 5.65 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 103 rescaling Left_Cerebral_Cortex from 61 --> 52 rescaling Left_Lateral_Ventricle from 13 --> 8 rescaling Left_Inf_Lat_Vent from 34 --> 29 rescaling Left_Cerebellum_White_Matter from 86 --> 84 rescaling Left_Cerebellum_Cortex from 60 --> 49 rescaling Left_Thalamus from 94 --> 90 rescaling Left_Thalamus_Proper from 84 --> 85 rescaling Left_Caudate from 75 --> 61 rescaling Left_Putamen from 80 --> 79 rescaling Left_Pallidum from 98 --> 91 rescaling Third_Ventricle from 25 --> 14 rescaling Fourth_Ventricle from 22 --> 8 rescaling Brain_Stem from 81 --> 80 rescaling Left_Hippocampus from 57 --> 52 rescaling Left_Amygdala from 56 --> 54 rescaling CSF from 32 --> 19 rescaling Left_Accumbens_area from 62 --> 55 rescaling Left_VentralDC from 87 --> 88 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 54 rescaling Right_Lateral_Ventricle from 13 --> 8 rescaling Right_Inf_Lat_Vent from 25 --> 24 rescaling Right_Cerebellum_White_Matter from 87 --> 89 rescaling Right_Cerebellum_Cortex from 59 --> 52 rescaling Right_Thalamus_Proper from 85 --> 79 rescaling Right_Caudate from 62 --> 61 rescaling Right_Putamen from 80 --> 76 rescaling Right_Pallidum from 97 --> 89 rescaling Right_Hippocampus from 53 --> 57 rescaling Right_Amygdala from 55 --> 58 rescaling Right_Accumbens_area from 65 --> 59 rescaling Right_VentralDC from 86 --> 86 rescaling Fifth_Ventricle from 40 --> 17 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 44 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 449060 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 124 changed. pass 2: 7 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /usr/local/freesurfer/subjects/Sub01/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Thu Jun 8 23:47:11 EDT 2017 /usr/local/freesurfer/subjects/Sub01 mri_aparc2aseg --s Sub01 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /usr/local/freesurfer/subjects subject Sub01 outvol /usr/local/freesurfer/subjects/Sub01/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/Sub01/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/Sub01/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/Sub01/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/Sub01/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /usr/local/freesurfer/subjects/Sub01/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /usr/local/freesurfer/subjects/Sub01/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 5.65 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 103 rescaling Left_Cerebral_Cortex from 61 --> 52 rescaling Left_Lateral_Ventricle from 13 --> 8 rescaling Left_Inf_Lat_Vent from 34 --> 29 rescaling Left_Cerebellum_White_Matter from 86 --> 84 rescaling Left_Cerebellum_Cortex from 60 --> 49 rescaling Left_Thalamus from 94 --> 90 rescaling Left_Thalamus_Proper from 84 --> 85 rescaling Left_Caudate from 75 --> 61 rescaling Left_Putamen from 80 --> 79 rescaling Left_Pallidum from 98 --> 91 rescaling Third_Ventricle from 25 --> 14 rescaling Fourth_Ventricle from 22 --> 8 rescaling Brain_Stem from 81 --> 80 rescaling Left_Hippocampus from 57 --> 52 rescaling Left_Amygdala from 56 --> 54 rescaling CSF from 32 --> 19 rescaling Left_Accumbens_area from 62 --> 55 rescaling Left_VentralDC from 87 --> 88 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 54 rescaling Right_Lateral_Ventricle from 13 --> 8 rescaling Right_Inf_Lat_Vent from 25 --> 24 rescaling Right_Cerebellum_White_Matter from 87 --> 89 rescaling Right_Cerebellum_Cortex from 59 --> 52 rescaling Right_Thalamus_Proper from 85 --> 79 rescaling Right_Caudate from 62 --> 61 rescaling Right_Putamen from 80 --> 76 rescaling Right_Pallidum from 97 --> 89 rescaling Right_Hippocampus from 53 --> 57 rescaling Right_Amygdala from 55 --> 58 rescaling Right_Accumbens_area from 65 --> 59 rescaling Right_VentralDC from 86 --> 86 rescaling Fifth_Ventricle from 40 --> 17 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 44 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 449115 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 124 changed. pass 2: 7 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /usr/local/freesurfer/subjects/Sub01/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Thu Jun 8 23:50:40 EDT 2017 /usr/local/freesurfer/subjects/Sub01 mri_aparc2aseg --s Sub01 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /usr/local/freesurfer/subjects subject Sub01 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/Sub01/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/Sub01/label/lh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/Sub01/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/Sub01/label/rh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /usr/local/freesurfer/subjects/Sub01/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /usr/local/freesurfer/subjects/Sub01/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 5.65 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 103 rescaling Left_Cerebral_Cortex from 61 --> 52 rescaling Left_Lateral_Ventricle from 13 --> 8 rescaling Left_Inf_Lat_Vent from 34 --> 29 rescaling Left_Cerebellum_White_Matter from 86 --> 84 rescaling Left_Cerebellum_Cortex from 60 --> 49 rescaling Left_Thalamus from 94 --> 90 rescaling Left_Thalamus_Proper from 84 --> 85 rescaling Left_Caudate from 75 --> 61 rescaling Left_Putamen from 80 --> 79 rescaling Left_Pallidum from 98 --> 91 rescaling Third_Ventricle from 25 --> 14 rescaling Fourth_Ventricle from 22 --> 8 rescaling Brain_Stem from 81 --> 80 rescaling Left_Hippocampus from 57 --> 52 rescaling Left_Amygdala from 56 --> 54 rescaling CSF from 32 --> 19 rescaling Left_Accumbens_area from 62 --> 55 rescaling Left_VentralDC from 87 --> 88 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 54 rescaling Right_Lateral_Ventricle from 13 --> 8 rescaling Right_Inf_Lat_Vent from 25 --> 24 rescaling Right_Cerebellum_White_Matter from 87 --> 89 rescaling Right_Cerebellum_Cortex from 59 --> 52 rescaling Right_Thalamus_Proper from 85 --> 79 rescaling Right_Caudate from 62 --> 61 rescaling Right_Putamen from 80 --> 76 rescaling Right_Pallidum from 97 --> 89 rescaling Right_Hippocampus from 53 --> 57 rescaling Right_Amygdala from 55 --> 58 rescaling Right_Accumbens_area from 65 --> 59 rescaling Right_VentralDC from 86 --> 86 rescaling Fifth_Ventricle from 40 --> 17 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 44 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 449115 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 124 changed. pass 2: 7 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Thu Jun 8 23:54:08 EDT 2017 /usr/local/freesurfer/subjects/Sub01/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Thu Jun 8 23:54:08 EDT 2017 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/Sub01/mri /usr/local/freesurfer/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux X1 4.4.0-78-generic #99-Ubuntu SMP Thu Apr 27 15:29:09 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /usr/local/freesurfer/subjects/Sub01/mri cmdline mri_binarize.bin --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 sysname Linux hostname X1 machine x86_64 user amazinger input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done Started at Thu Jun 8 23:54:08 EDT 2017 Ended at Thu Jun 8 23:54:13 EDT 2017 Apas2aseg-Run-Time-Sec 5 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Thu Jun 8 23:54:13 EDT 2017 /usr/local/freesurfer/subjects/Sub01 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject Sub01 $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject Sub01 sysname Linux hostname X1 machine x86_64 user amazinger UseRobust 0 atlas_icv (eTIV) = 1273038 mm^3 (det: 1.530280 ) Computing euler number orig.nofix lheno = -50, rheno = -54 orig.nofix lhholes = 26, rhholes = 28 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 225974.072 225810.000 diff= 164.1 pctdiff= 0.073 rhCtxGM: 224547.442 224320.000 diff= 227.4 pctdiff= 0.101 lhCtxWM: 190676.012 191659.000 diff= -983.0 pctdiff=-0.516 rhCtxWM: 193077.650 193632.000 diff= -554.3 pctdiff=-0.287 SubCortGMVol 55462.000 SupraTentVol 905178.177 (902446.000) diff=2732.177 pctdiff=0.302 SupraTentVolNotVent 893681.177 (890949.000) diff=2732.177 pctdiff=0.306 BrainSegVol 1028936.000 (1027351.000) diff=1585.000 pctdiff=0.154 BrainSegVolNotVent 1015175.000 (1013869.177) diff=1305.823 pctdiff=0.129 BrainSegVolNotVent 1015175.000 CerebellumVol 124066.000 VentChorVol 11497.000 3rd4th5thCSF 2264.000 CSFVol 679.000, OptChiasmVol 160.000 MaskVol 1348494.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Thu Jun 8 23:57:16 EDT 2017 /usr/local/freesurfer/subjects/Sub01 mri_aparc2aseg --s Sub01 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /usr/local/freesurfer/subjects subject Sub01 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /usr/local/freesurfer/subjects/Sub01/mri/aparc+aseg.mgz Reading lh white surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/Sub01/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/Sub01/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/Sub01/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/Sub01/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /usr/local/freesurfer/subjects/Sub01/mri/ribbon.mgz Loading filled from /usr/local/freesurfer/subjects/Sub01/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 7900 vertices from left hemi Ripped 7486 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /usr/local/freesurfer/subjects/Sub01/mri/aseg.mgz Loading Ctx Seg File /usr/local/freesurfer/subjects/Sub01/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 832615 Used brute-force search on 487 voxels Fixing Parahip LH WM Found 11 clusters 0 k 1.000000 1 k 1.000000 2 k 3.000000 3 k 1.000000 4 k 2.000000 5 k 1.000000 6 k 3.000000 7 k 2.000000 8 k 2.000000 9 k 1230.000000 10 k 2.000000 Fixing Parahip RH WM Found 7 clusters 0 k 1.000000 1 k 2.000000 2 k 1.000000 3 k 8.000000 4 k 1.000000 5 k 1.000000 6 k 1150.000000 Writing output aseg to mri/wmparc.mgz mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject Sub01 --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject Sub01 --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname X1 machine x86_64 user amazinger UseRobust 0 atlas_icv (eTIV) = 1273038 mm^3 (det: 1.530280 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 225974.072 225810.000 diff= 164.1 pctdiff= 0.073 rhCtxGM: 224547.442 224320.000 diff= 227.4 pctdiff= 0.101 lhCtxWM: 190676.012 191659.000 diff= -983.0 pctdiff=-0.516 rhCtxWM: 193077.650 193632.000 diff= -554.3 pctdiff=-0.287 SubCortGMVol 55462.000 SupraTentVol 905178.177 (902446.000) diff=2732.177 pctdiff=0.302 SupraTentVolNotVent 893681.177 (890949.000) diff=2732.177 pctdiff=0.306 BrainSegVol 1028936.000 (1027351.000) diff=1585.000 pctdiff=0.154 BrainSegVolNotVent 1015175.000 (1013869.177) diff=1305.823 pctdiff=0.129 BrainSegVolNotVent 1015175.000 CerebellumVol 124066.000 VentChorVol 11497.000 3rd4th5thCSF 2264.000 CSFVol 679.000, OptChiasmVol 160.000 MaskVol 1348494.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done /usr/local/freesurfer/subjects/Sub01/label #-------------------------------------------- #@# BA_exvivo Labels lh Fri Jun 9 00:05:15 EDT 2017 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject Sub01 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 255 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4384 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.label --trgsubject Sub01 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 322 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8231 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.label --trgsubject Sub01 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 113 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4190 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.label --trgsubject Sub01 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 245 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6228 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.label --trgsubject Sub01 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 282 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6066 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.label --trgsubject Sub01 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 108 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4178 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.label --trgsubject Sub01 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 844 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14433 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.label --trgsubject Sub01 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 197 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4378 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.label --trgsubject Sub01 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 307 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3729 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.label --trgsubject Sub01 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 725 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5366 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.label --trgsubject Sub01 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 1761 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 9875 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.label --trgsubject Sub01 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 333 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2351 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject Sub01 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 64 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1354 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject Sub01 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 45 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1244 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject Sub01 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.BA1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 80 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1094 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject Sub01 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.BA2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 170 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2262 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject Sub01 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.BA3a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 43 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1547 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject Sub01 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.BA3b_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 88 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2084 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject Sub01 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.BA4a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 150 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2469 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject Sub01 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.BA4p_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 34 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1583 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject Sub01 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.BA6_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 367 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7402 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject Sub01 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.BA44_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 60 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 1972 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject Sub01 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.BA45_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 145 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1296 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject Sub01 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.V1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 435 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 3840 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject Sub01 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.V2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 894 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4228 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject Sub01 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.MT_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 54 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 567 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject Sub01 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 18 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 488 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject Sub01 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./lh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 118136 Number of reverse mapping hits = 17 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 467 mri_label2label: Done mris_label2annot --s Sub01 --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /usr/local/freesurfer/subjects/Sub01/label cmdline mris_label2annot --s Sub01 --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname X1 machine x86_64 user amazinger subject Sub01 hemi lh SUBJECTS_DIR /usr/local/freesurfer/subjects ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /usr/local/freesurfer/subjects/Sub01/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 82361 unhit vertices Writing annot to /usr/local/freesurfer/subjects/Sub01/label/lh.BA_exvivo.annot mris_label2annot --s Sub01 --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /usr/local/freesurfer/subjects/Sub01/label cmdline mris_label2annot --s Sub01 --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname X1 machine x86_64 user amazinger subject Sub01 hemi lh SUBJECTS_DIR /usr/local/freesurfer/subjects ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /usr/local/freesurfer/subjects/Sub01/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 96883 unhit vertices Writing annot to /usr/local/freesurfer/subjects/Sub01/label/lh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab Sub01 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /usr/local/freesurfer/subjects/Sub01/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/Sub01/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 230655 Total vertex volume 226253 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1273038 mm^3 (det: 1.530280 ) lhCtxGM: 225974.072 225810.000 diff= 164.1 pctdiff= 0.073 rhCtxGM: 224547.442 224320.000 diff= 227.4 pctdiff= 0.101 lhCtxWM: 190676.012 191659.000 diff= -983.0 pctdiff=-0.516 rhCtxWM: 193077.650 193632.000 diff= -554.3 pctdiff=-0.287 SubCortGMVol 55462.000 SupraTentVol 905178.177 (902446.000) diff=2732.177 pctdiff=0.302 SupraTentVolNotVent 893681.177 (890949.000) diff=2732.177 pctdiff=0.306 BrainSegVol 1028936.000 (1027351.000) diff=1585.000 pctdiff=0.154 BrainSegVolNotVent 1015175.000 (1013869.177) diff=1305.823 pctdiff=0.129 BrainSegVolNotVent 1015175.000 CerebellumVol 124066.000 VentChorVol 11497.000 3rd4th5thCSF 2264.000 CSFVol 679.000, OptChiasmVol 160.000 MaskVol 1348494.000 1050 730 2377 2.547 0.604 0.141 0.035 15 1.3 BA1_exvivo 3519 2390 6327 2.434 0.609 0.117 0.023 37 3.2 BA2_exvivo 1044 680 965 1.785 0.450 0.121 0.024 8 1.1 BA3a_exvivo 2238 1507 3362 2.000 0.719 0.119 0.024 22 2.1 BA3b_exvivo 1638 948 2864 2.706 0.650 0.110 0.033 16 2.5 BA4a_exvivo 1104 764 2091 2.703 0.502 0.100 0.020 6 0.8 BA4p_exvivo 8484 5656 19261 2.847 0.618 0.123 0.030 95 9.9 BA6_exvivo 1925 1272 3890 2.664 0.529 0.123 0.029 21 2.2 BA44_exvivo 2428 1689 5093 2.573 0.659 0.127 0.028 31 2.7 BA45_exvivo 2552 1833 4242 2.042 0.644 0.154 0.043 48 4.5 V1_exvivo 6814 4750 11822 2.179 0.630 0.162 0.043 124 12.7 V2_exvivo 1919 1314 3991 2.492 0.623 0.138 0.028 27 2.2 MT_exvivo 491 335 1784 3.543 0.755 0.103 0.026 5 0.5 perirhinal_exvivo 569 405 1397 3.083 0.880 0.102 0.018 3 0.4 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab Sub01 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /usr/local/freesurfer/subjects/Sub01/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/Sub01/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/Sub01/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 230655 Total vertex volume 226253 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1273038 mm^3 (det: 1.530280 ) lhCtxGM: 225974.072 225810.000 diff= 164.1 pctdiff= 0.073 rhCtxGM: 224547.442 224320.000 diff= 227.4 pctdiff= 0.101 lhCtxWM: 190676.012 191659.000 diff= -983.0 pctdiff=-0.516 rhCtxWM: 193077.650 193632.000 diff= -554.3 pctdiff=-0.287 SubCortGMVol 55462.000 SupraTentVol 905178.177 (902446.000) diff=2732.177 pctdiff=0.302 SupraTentVolNotVent 893681.177 (890949.000) diff=2732.177 pctdiff=0.306 BrainSegVol 1028936.000 (1027351.000) diff=1585.000 pctdiff=0.154 BrainSegVolNotVent 1015175.000 (1013869.177) diff=1305.823 pctdiff=0.129 BrainSegVolNotVent 1015175.000 CerebellumVol 124066.000 VentChorVol 11497.000 3rd4th5thCSF 2264.000 CSFVol 679.000, OptChiasmVol 160.000 MaskVol 1348494.000 731 469 1581 2.607 0.600 0.144 0.038 10 1.1 BA1_exvivo 1653 1114 3289 2.541 0.618 0.125 0.023 19 1.4 BA2_exvivo 882 569 765 1.755 0.447 0.120 0.022 6 0.8 BA3a_exvivo 1385 997 1742 1.633 0.443 0.110 0.021 11 1.0 BA3b_exvivo 1536 900 2742 2.741 0.622 0.102 0.028 12 2.0 BA4a_exvivo 931 651 1700 2.681 0.459 0.100 0.019 5 0.7 BA4p_exvivo 4695 3132 10323 2.818 0.627 0.125 0.031 49 6.0 BA6_exvivo 1218 795 2615 2.688 0.558 0.127 0.032 15 1.6 BA44_exvivo 1013 681 2450 2.809 0.638 0.134 0.030 15 1.2 BA45_exvivo 2730 1970 4808 2.092 0.689 0.154 0.043 48 4.9 V1_exvivo 3474 2438 5490 2.036 0.544 0.178 0.052 73 7.9 V2_exvivo 461 333 681 1.979 0.417 0.130 0.023 4 0.4 MT_exvivo 243 177 1068 3.716 0.669 0.080 0.013 1 0.1 perirhinal_exvivo 301 222 747 2.925 0.806 0.086 0.014 1 0.2 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Fri Jun 9 00:08:23 EDT 2017 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.label --trgsubject Sub01 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 285 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4247 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.label --trgsubject Sub01 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 306 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6993 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.label --trgsubject Sub01 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 98 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4078 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.label --trgsubject Sub01 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 266 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4788 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.label --trgsubject Sub01 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 347 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6094 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.label --trgsubject Sub01 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 216 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4689 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.label --trgsubject Sub01 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 615 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12871 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.label --trgsubject Sub01 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 393 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7305 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.label --trgsubject Sub01 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 491 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 5846 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.label --trgsubject Sub01 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 893 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5620 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.label --trgsubject Sub01 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 1577 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 9593 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.label --trgsubject Sub01 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 292 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2224 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject Sub01 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 46 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1084 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject Sub01 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 13 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 765 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject Sub01 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 127 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 1003 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject Sub01 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 79 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2767 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject Sub01 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 38 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1736 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject Sub01 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 82 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2265 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject Sub01 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 95 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1483 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject Sub01 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 64 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1553 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject Sub01 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 307 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7266 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject Sub01 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1059 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject Sub01 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 83 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1261 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject Sub01 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 521 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 3753 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject Sub01 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 776 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4213 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject Sub01 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 50 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 318 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject Sub01 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 22 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 716 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject Sub01 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = Sub01 trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/Sub01/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 119358 Number of reverse mapping hits = 4 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 295 mri_label2label: Done mris_label2annot --s Sub01 --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /usr/local/freesurfer/subjects/Sub01/label cmdline mris_label2annot --s Sub01 --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname X1 machine x86_64 user amazinger subject Sub01 hemi rh SUBJECTS_DIR /usr/local/freesurfer/subjects ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /usr/local/freesurfer/subjects/Sub01/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 83963 unhit vertices Writing annot to /usr/local/freesurfer/subjects/Sub01/label/rh.BA_exvivo.annot mris_label2annot --s Sub01 --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /usr/local/freesurfer/subjects/Sub01/label cmdline mris_label2annot --s Sub01 --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname X1 machine x86_64 user amazinger subject Sub01 hemi rh SUBJECTS_DIR /usr/local/freesurfer/subjects ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /usr/local/freesurfer/subjects/Sub01/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 99413 unhit vertices Writing annot to /usr/local/freesurfer/subjects/Sub01/label/rh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab Sub01 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /usr/local/freesurfer/subjects/Sub01/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/Sub01/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 228402 Total vertex volume 224914 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1273038 mm^3 (det: 1.530280 ) lhCtxGM: 225974.072 225810.000 diff= 164.1 pctdiff= 0.073 rhCtxGM: 224547.442 224320.000 diff= 227.4 pctdiff= 0.101 lhCtxWM: 190676.012 191659.000 diff= -983.0 pctdiff=-0.516 rhCtxWM: 193077.650 193632.000 diff= -554.3 pctdiff=-0.287 SubCortGMVol 55462.000 SupraTentVol 905178.177 (902446.000) diff=2732.177 pctdiff=0.302 SupraTentVolNotVent 893681.177 (890949.000) diff=2732.177 pctdiff=0.306 BrainSegVol 1028936.000 (1027351.000) diff=1585.000 pctdiff=0.154 BrainSegVolNotVent 1015175.000 (1013869.177) diff=1305.823 pctdiff=0.129 BrainSegVolNotVent 1015175.000 CerebellumVol 124066.000 VentChorVol 11497.000 3rd4th5thCSF 2264.000 CSFVol 679.000, OptChiasmVol 160.000 MaskVol 1348494.000 994 516 1970 2.657 0.681 0.122 0.044 15 1.6 BA1_exvivo 2871 1892 4658 2.234 0.553 0.113 0.024 29 2.8 BA2_exvivo 1040 705 986 1.759 0.429 0.125 0.026 9 1.1 BA3a_exvivo 1884 1198 2500 1.775 0.563 0.098 0.020 15 1.5 BA3b_exvivo 1523 902 2857 2.663 0.529 0.109 0.040 15 2.6 BA4a_exvivo 1230 774 2013 2.594 0.452 0.086 0.017 6 0.8 BA4p_exvivo 7194 4648 15631 2.835 0.573 0.113 0.030 73 8.2 BA6_exvivo 2954 2001 5853 2.623 0.452 0.120 0.024 33 2.7 BA44_exvivo 3559 2476 7496 2.438 0.633 0.140 0.032 52 4.4 BA45_exvivo 3003 2139 4627 1.976 0.627 0.160 0.047 58 6.1 V1_exvivo 6566 4459 10593 2.195 0.611 0.148 0.035 100 9.0 V2_exvivo 1818 1245 3177 2.300 0.564 0.124 0.026 22 1.8 MT_exvivo 482 340 1985 3.697 0.639 0.113 0.027 5 0.4 perirhinal_exvivo 277 215 958 3.309 0.798 0.123 0.017 2 0.2 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab Sub01 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /usr/local/freesurfer/subjects/Sub01/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/Sub01/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/Sub01/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 228402 Total vertex volume 224914 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1273038 mm^3 (det: 1.530280 ) lhCtxGM: 225974.072 225810.000 diff= 164.1 pctdiff= 0.073 rhCtxGM: 224547.442 224320.000 diff= 227.4 pctdiff= 0.101 lhCtxWM: 190676.012 191659.000 diff= -983.0 pctdiff=-0.516 rhCtxWM: 193077.650 193632.000 diff= -554.3 pctdiff=-0.287 SubCortGMVol 55462.000 SupraTentVol 905178.177 (902446.000) diff=2732.177 pctdiff=0.302 SupraTentVolNotVent 893681.177 (890949.000) diff=2732.177 pctdiff=0.306 BrainSegVol 1028936.000 (1027351.000) diff=1585.000 pctdiff=0.154 BrainSegVolNotVent 1015175.000 (1013869.177) diff=1305.823 pctdiff=0.129 BrainSegVolNotVent 1015175.000 CerebellumVol 124066.000 VentChorVol 11497.000 3rd4th5thCSF 2264.000 CSFVol 679.000, OptChiasmVol 160.000 MaskVol 1348494.000 696 369 1305 2.512 0.671 0.128 0.045 10 1.2 BA1_exvivo 1689 1099 3040 2.413 0.653 0.108 0.024 18 1.6 BA2_exvivo 941 625 799 1.763 0.396 0.125 0.024 7 0.9 BA3a_exvivo 1466 988 1650 1.556 0.399 0.088 0.016 7 1.0 BA3b_exvivo 930 512 1643 2.763 0.660 0.121 0.046 12 1.7 BA4a_exvivo 993 661 1735 2.681 0.453 0.083 0.015 3 0.6 BA4p_exvivo 4582 3004 9976 2.820 0.535 0.114 0.030 43 4.9 BA6_exvivo 709 485 1593 2.726 0.432 0.126 0.024 10 0.7 BA44_exvivo 856 620 2157 2.677 0.594 0.158 0.041 14 1.5 BA45_exvivo 2838 1999 4203 1.949 0.606 0.158 0.047 54 5.7 V1_exvivo 3495 2416 5649 2.121 0.613 0.159 0.042 61 5.7 V2_exvivo 278 176 646 2.641 0.459 0.128 0.025 4 0.2 MT_exvivo 281 201 1188 3.834 0.531 0.085 0.017 1 0.2 perirhinal_exvivo 191 142 653 3.401 0.708 0.126 0.021 2 0.2 entorhinal_exvivo Started at Thu Jun 8 21:04:59 EDT 2017 Ended at Fri Jun 9 00:11:33 EDT 2017 #@#%# recon-all-run-time-hours 3.109 recon-all -s Sub01 finished without error at Fri Jun 9 00:11:33 EDT 2017