Thu Sep 7 11:44:40 CEST 2017 /home/gc/study/recon-all/400614dclass /usr/local/freesurfer/bin/recon-all -all -cw256 -3T -multistrip -clean-bm -i /home/MRIdata/PUD/31148_MRI_sMRI_400614.nii -s /home/gc/study/recon-all/400614dclass subjid 400614dclass setenv SUBJECTS_DIR /home/gc/study/recon-all 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 lugh.fisica.uniud.it 2.6.32-642.4.2.el6.x86_64 #1 SMP Tue Aug 23 11:15:56 CDT 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 4096 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 12188716 4561256 7627460 3516 494428 3261584 -/+ buffers/cache: 805244 11383472 Swap: 6160380 62108 6098272 ######################################## 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: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/07-09:44:40-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: gc Machine: lugh.fisica.uniud.it Platform: Linux PlatformVersion: 2.6.32-642.4.2.el6.x86_64 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 ####################################### mv -f /home/gc/study/recon-all/400614dclass/mri/optimal_preflood_height /home/gc/study/recon-all/400614dclass/trash mv: cannot stat `/home/gc/study/recon-all/400614dclass/mri/optimal_preflood_height': No such file or directory mv -f /home/gc/study/recon-all/400614dclass/mri/optimal_skullstrip_invol /home/gc/study/recon-all/400614dclass/trash mv: cannot stat `/home/gc/study/recon-all/400614dclass/mri/optimal_skullstrip_invol': No such file or directory mv -f /home/gc/study/recon-all/400614dclass/mri/brainmask.mgz /home/gc/study/recon-all/400614dclass/trash mv: cannot stat `/home/gc/study/recon-all/400614dclass/mri/brainmask.mgz': No such file or directory -cw256 option is now persistent (remove with -clean-cw256) /home/gc/study/recon-all/400614dclass mri_convert /home/MRIdata/PUD/31148_MRI_sMRI_400614.nii /home/gc/study/recon-all/400614dclass/mri/orig/001.mgz mri_convert.bin /home/MRIdata/PUD/31148_MRI_sMRI_400614.nii /home/gc/study/recon-all/400614dclass/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/MRIdata/PUD/31148_MRI_sMRI_400614.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0266636, -0.998354, 0.0507764) j_ras = (-0.0789969, -0.05274, -0.995479) k_ras = (0.996518, 0.0225319, -0.0802731) writing to /home/gc/study/recon-all/400614dclass/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Sep 7 11:44:45 CEST 2017 Found 1 runs /home/gc/study/recon-all/400614dclass/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 /home/gc/study/recon-all/400614dclass/mri/orig/001.mgz /home/gc/study/recon-all/400614dclass/mri/rawavg.mgz /home/gc/study/recon-all/400614dclass mri_convert /home/gc/study/recon-all/400614dclass/mri/rawavg.mgz /home/gc/study/recon-all/400614dclass/mri/orig.mgz --conform --cw256 mri_convert.bin /home/gc/study/recon-all/400614dclass/mri/rawavg.mgz /home/gc/study/recon-all/400614dclass/mri/orig.mgz --conform --cw256 $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/gc/study/recon-all/400614dclass/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0266636, -0.998354, 0.0507764) j_ras = (-0.0789969, -0.05274, -0.995479) k_ras = (0.996518, 0.0225319, -0.0802731) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/gc/study/recon-all/400614dclass/mri/orig.mgz... mri_add_xform_to_header -c /home/gc/study/recon-all/400614dclass/mri/transforms/talairach.xfm /home/gc/study/recon-all/400614dclass/mri/orig.mgz /home/gc/study/recon-all/400614dclass/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Sep 7 11:44:55 CEST 2017 /home/gc/study/recon-all/400614dclass/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/gc/study/recon-all/400614dclass/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 lugh.fisica.uniud.it 2.6.32-642.4.2.el6.x86_64 #1 SMP Tue Aug 23 11:15:56 CDT 2016 x86_64 x86_64 x86_64 GNU/Linux Thu Sep 7 11:44:55 CEST 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.17965 /home/gc/study/recon-all/400614dclass/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17965/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.17965/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.86265e-09, -7.45058e-09) j_ras = (-1.49012e-08, -2.67755e-09, -1) k_ras = (-1.86265e-09, 1, -3.14321e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.17965/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Sep 7 11:44:57 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.17965/nu0.mnc ./tmp.mri_nu_correct.mni.17965/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.17965/0/ -iterations 1000 -distance 50 [gc@lugh.fisica.uniud.it:/home/gc/study/recon-all/400614dclass/mri/] [2017-09-07 11:44:57] 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.17965/0/ ./tmp.mri_nu_correct.mni.17965/nu0.mnc ./tmp.mri_nu_correct.mni.17965/nu1.imp 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2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.17965/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.86265e-09, -7.45058e-09) j_ras = (-1.49012e-08, -2.67755e-09, -1) k_ras = (-1.86265e-09, 1, -3.14321e-09) 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... Thu Sep 7 11:46:26 CEST 2017 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig talairach_avi log file is transforms/talairach_avi.log... Started at Thu Sep 7 11:46:26 CEST 2017 Ended at Thu Sep 7 11:46:59 CEST 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Sep 7 11:47:01 CEST 2017 /home/gc/study/recon-all/400614dclass/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7600, pval=0.6675 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /home/gc/study/recon-all/400614dclass/mri/transforms/talairach_avi.log tal_QC_AZS /home/gc/study/recon-all/400614dclass/mri/transforms/talairach_avi.log TalAviQA: 0.00000 z-score: -222 WARNING: Talairach QA check failed! z-score of -222 is <= threshold of -9 Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach INFO: Trying MINC mritotal to perform Talairach align... #-------------------------------------------- #@# Talairach Thu Sep 7 11:47:01 CEST 2017 /home/gc/study/recon-all/400614dclass/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/gc/study/recon-all/400614dclass/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 lugh.fisica.uniud.it 2.6.32-642.4.2.el6.x86_64 #1 SMP Tue Aug 23 11:15:56 CDT 2016 x86_64 x86_64 x86_64 GNU/Linux Thu Sep 7 11:47:02 CEST 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.19212 /home/gc/study/recon-all/400614dclass/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.19212/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.19212/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.86265e-09, -7.45058e-09) j_ras = (-1.49012e-08, -2.67755e-09, -1) k_ras = (-1.86265e-09, 1, -3.14321e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.19212/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Sep 7 11:47:04 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.19212/nu0.mnc ./tmp.mri_nu_correct.mni.19212/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.19212/0/ -iterations 1000 -distance 50 [gc@lugh.fisica.uniud.it:/home/gc/study/recon-all/400614dclass/mri/] [2017-09-07 11:47:04] 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.19212/0/ ./tmp.mri_nu_correct.mni.19212/nu0.mnc ./tmp.mri_nu_correct.mni.19212/nu1.imp 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2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.19212/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.86265e-09, -7.45058e-09) j_ras = (-1.49012e-08, -2.67755e-09, -1) k_ras = (-1.86265e-09, 1, -3.14321e-09) 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... Thu Sep 7 11:48:31 CEST 2017 mri_nu_correct.mni done talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /home/gc/study/recon-all/400614dclass/mri /usr/local/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.8 2016/02/16 17:17:20 zkaufman Exp $ Linux lugh.fisica.uniud.it 2.6.32-642.4.2.el6.x86_64 #1 SMP Tue Aug 23 11:15:56 CDT 2016 x86_64 x86_64 x86_64 GNU/Linux Thu Sep 7 11:48:31 CEST 2017 tmpdir is transforms/tmp.talairach.20301 /home/gc/study/recon-all/400614dclass/mri mri_convert orig_nu.mgz transforms/tmp.talairach.20301/src.mnc mri_convert.bin orig_nu.mgz transforms/tmp.talairach.20301/src.mnc $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig_nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.86265e-09, -7.45058e-09) j_ras = (-1.49012e-08, -2.67755e-09, -1) k_ras = (-1.86265e-09, 1, -3.14321e-09) writing to transforms/tmp.talairach.20301/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.20301/src.mnc transforms/talairach.auto.xfm Transforming slices:................................................................................................................................Done Copying chunks:......................................................................................................................................................Done. Copying chunks:..........................................................................................................Done. Transforming slices:......................................................................................................................................................Done Copying chunks:....................................................................................................................Done. Copying chunks:....................................................................................................................Done. Source volume size: 74 by 106 by 106 Source voxel size = 2.000 2.000 2.000 Source min/max real range = -0.000 175.790 Source min/max voxel= -0.000 177.883 Target volume size: 58 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.970 123.710 Target min/max voxel = -0.000 123.710 AFTER init_params() Transform matrix = 1.0000 0.0000 0.0000 -3.2078 0.0000 1.0000 0.0000 -30.0524 0.0000 0.0000 1.0000 6.1757 Transform center = 3.536 12.461 3.279 Transform rotations = 0.000 0.000 0.000 Transform trans = -3.208 -30.052 6.176 Transform scale = 1.000 1.000 1.000 Transform shear = 0.000 0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -85.095 -125.510 -47.250 Lattice count = 43 55 29 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = -0.000 191.369 Source min/max voxel= -0.000 191.369 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= -0.000 144.070 Target min/max voxel = -0.000 144.070 AFTER init_params() Transform matrix = 1.0901 -0.0086 -0.0822 -1.6365 0.0332 1.0412 0.3318 -30.9779 0.0757 -0.3334 1.0384 -6.2706 Transform center = 3.536 12.461 3.279 Transform rotations = -0.311 -0.069 0.030 Transform trans = -1.694 -29.260 -10.031 Transform scale = 1.093 1.093 1.093 Transform shear = 0.000 -0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -85.095 -125.510 -57.250 Lattice count = 43 55 34 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.072 20.330 Source min/max voxel= 0.072 20.940 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 1.0949 -0.0038 -0.0740 -2.1860 0.0224 1.0616 0.2769 -30.9156 0.0706 -0.2778 1.0593 -10.9903 Transform center = 3.536 12.461 3.279 Transform rotations = -0.256 -0.064 0.020 Transform trans = -2.141 -29.161 -14.008 Transform scale = 1.097 1.097 1.097 Transform shear = 0.000 -0.000 -0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.072 20.330 Source min/max voxel= 0.072 20.940 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 1.1071 -0.0240 -0.0921 -1.9311 0.0427 1.0865 0.2290 -28.3119 0.0851 -0.2317 1.0835 -13.0522 Transform center = 3.536 12.461 3.279 Transform rotations = -0.211 -0.077 0.039 Transform trans = -2.154 -26.332 -15.365 Transform scale = 1.111 1.111 1.111 Transform shear = 0.000 0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.072 20.330 Source min/max voxel= 0.072 20.940 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 1.1029 -0.0238 -0.0858 -1.9183 0.0385 1.0061 0.2159 -27.1940 0.0857 -0.2548 1.1720 -14.0491 Transform center = 3.536 12.461 3.279 Transform rotations = -0.214 -0.071 0.037 Transform trans = -2.132 -26.274 -16.358 Transform scale = 1.106 1.030 1.202 Transform shear = -0.000 -0.000 -0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.072 20.330 Source min/max voxel= 0.072 20.940 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 1.1051 -0.0156 -0.0873 -1.9525 0.0315 1.0063 0.2185 -27.2854 0.0891 -0.2575 1.1732 -14.2249 Transform center = 3.536 12.461 3.279 Transform rotations = -0.216 -0.074 0.031 Transform trans = -2.062 -26.379 -16.551 Transform scale = 1.109 1.030 1.204 Transform shear = 0.000 0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Thu Sep 7 11:48:42 CEST 2017 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Sep 7 11:48:44 CEST 2017 /home/gc/study/recon-all/400614dclass/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7943, pval=0.8469 >= threshold=0.0050) #-------------------------------------------- #@# Nu Intensity Correction Thu Sep 7 11:48:44 CEST 2017 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 /home/gc/study/recon-all/400614dclass/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux lugh.fisica.uniud.it 2.6.32-642.4.2.el6.x86_64 #1 SMP Tue Aug 23 11:15:56 CDT 2016 x86_64 x86_64 x86_64 GNU/Linux Thu Sep 7 11:48:44 CEST 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.20447 /home/gc/study/recon-all/400614dclass/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20447/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.20447/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.86265e-09, -7.45058e-09) j_ras = (-1.49012e-08, -2.67755e-09, -1) k_ras = (-1.86265e-09, 1, -3.14321e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.20447/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Sep 7 11:48:46 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.20447/nu0.mnc ./tmp.mri_nu_correct.mni.20447/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.20447/0/ -iterations 1000 -distance 50 [gc@lugh.fisica.uniud.it:/home/gc/study/recon-all/400614dclass/mri/] [2017-09-07 11:48:46] 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.20447/0/ ./tmp.mri_nu_correct.mni.20447/nu0.mnc ./tmp.mri_nu_correct.mni.20447/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 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cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.20447/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.20447/ones.mgz sysname Linux hostname lugh.fisica.uniud.it machine x86_64 user gc input ./tmp.mri_nu_correct.mni.20447/nu1.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.20447/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.20447/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.20447/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20447/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.20447/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.20447/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20447/input.mean.dat sysname Linux hostname lugh.fisica.uniud.it machine x86_64 user gc UseRobust 0 Loading ./tmp.mri_nu_correct.mni.20447/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.20447/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.20447/ones.mgz --i ./tmp.mri_nu_correct.mni.20447/nu1.mnc --sum ./tmp.mri_nu_correct.mni.20447/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20447/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.20447/ones.mgz --i ./tmp.mri_nu_correct.mni.20447/nu1.mnc --sum ./tmp.mri_nu_correct.mni.20447/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20447/output.mean.dat sysname Linux hostname lugh.fisica.uniud.it machine x86_64 user gc UseRobust 0 Loading ./tmp.mri_nu_correct.mni.20447/ones.mgz Loading ./tmp.mri_nu_correct.mni.20447/nu1.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.20447/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.20447/nu1.mnc ./tmp.mri_nu_correct.mni.20447/nu1.mnc mul .78721245312251693599 Saving result to './tmp.mri_nu_correct.mni.20447/nu1.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.20447/nu1.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.20447/nu1.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.20447/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.86265e-09, -7.45058e-09) j_ras = (-1.49012e-08, -2.67755e-09, -1) k_ras = (-1.86265e-09, 1, -3.14321e-09) 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 9 seconds. mapping ( 7, 166) to ( 3, 110) Thu Sep 7 11:50:45 CEST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /home/gc/study/recon-all/400614dclass/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Sep 7 11:50:45 CEST 2017 /home/gc/study/recon-all/400614dclass/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 1.10350 -0.02180 -0.08530 -1.96982; 0.03706 1.01000 0.22133 -27.35934; 0.08500 -0.25856 1.16567 -14.19462; 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 = 15 Starting OpenSpline(): npoints = 15 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 86 (86), valley at 52 (52) csf peak at 44, setting threshold to 72 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 83 (83), valley at 49 (49) csf peak at 42, setting threshold to 69 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 45 seconds. #-------------------------------------------- #@# Skull Stripping Thu Sep 7 11:53:31 CEST 2017 /home/gc/study/recon-all/400614dclass/mri mri_em_register -rusage /home/gc/study/recon-all/400614dclass/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=30.1 skull bounding box = (51, 24, 13) --> (205, 210, 219) using (102, 86, 116) as brain centroid... mean wm in atlas = 108, using box (83,63,91) --> (120, 108,141) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 107 +- 3.9 after smoothing, mri peak at 107, scaling input intensities by 1.009 scaling channel 0 by 1.00935 initial log_p = -4.510 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.484514 @ (-9.091, 9.091, -9.091) max log p = -4.386978 @ (13.636, 4.545, 4.545) max log p = -4.369251 @ (-2.273, -2.273, -2.273) max log p = -4.355327 @ (-3.409, -1.136, 1.136) max log p = -4.341358 @ (0.568, -1.705, -1.705) max log p = -4.341358 @ (0.000, 0.000, 0.000) Found translation: (-0.6, 8.5, -7.4): log p = -4.341 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.209, old_max_log_p =-4.341 (thresh=-4.3) 1.06375 0.00000 0.00000 -8.56520; 0.00000 1.13509 0.16902 -14.65745; 0.00000 -0.11161 0.99651 9.90158; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.209, old_max_log_p =-4.209 (thresh=-4.2) 1.06375 0.00000 0.00000 -8.56520; 0.00000 1.13509 0.16902 -14.65745; 0.00000 -0.11161 0.99651 9.90158; 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=-4.172, old_max_log_p =-4.209 (thresh=-4.2) 1.08370 0.00000 0.00000 -11.06720; 0.00000 1.13814 0.13632 -13.14113; 0.00000 -0.07442 1.00151 6.57659; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.172, old_max_log_p =-4.172 (thresh=-4.2) 1.08370 0.00000 0.00000 -11.06720; 0.00000 1.13814 0.13632 -13.14113; 0.00000 -0.07442 1.00151 6.57659; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.169, old_max_log_p =-4.172 (thresh=-4.2) 1.08370 0.00000 0.00000 -11.06720; 0.00000 1.13947 0.13648 -13.79147; 0.00000 -0.07468 1.00503 6.20947; 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 1.08370 0.00000 0.00000 -11.06720; 0.00000 1.13947 0.13648 -13.79147; 0.00000 -0.07468 1.00503 6.20947; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.08370 0.00000 0.00000 -11.06720; 0.00000 1.13947 0.13648 -13.79147; 0.00000 -0.07468 1.00503 6.20947; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.08370 0.00000 0.00000 -11.06720; 0.00000 1.13947 0.13648 -13.79147; 0.00000 -0.07468 1.00503 6.20947; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.169 (old=-4.510) transform before final EM align: 1.08370 0.00000 0.00000 -11.06720; 0.00000 1.13947 0.13648 -13.79147; 0.00000 -0.07468 1.00503 6.20947; 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 1.08370 0.00000 0.00000 -11.06720; 0.00000 1.13947 0.13648 -13.79147; 0.00000 -0.07468 1.00503 6.20947; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.08370 0.00000 0.00000 -11.06720; 0.00000 1.13947 0.13648 -13.79147; 0.00000 -0.07468 1.00503 6.20947; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = 4.5 tol 0.000000 final transform: 1.08370 0.00000 0.00000 -11.06720; 0.00000 1.13947 0.13648 -13.79147; 0.00000 -0.07468 1.00503 6.20947; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 860.373203 mri_em_register stimesec 0.700893 mri_em_register ru_maxrss 609776 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157313 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 19 mri_em_register ru_nivcsw 87330 registration took 14 minutes and 23 seconds. mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 5 orig.mgz brainmask_orig_PFH5.auto.mgz mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 10 orig.mgz brainmask_orig_PFH10.auto.mgz mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 20 orig.mgz brainmask_orig_PFH20.auto.mgz mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 30 orig.mgz brainmask_orig_PFH30.auto.mgz mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 5 orig_nu.mgz brainmask_orig_nu_PFH5.auto.mgz mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 10 orig_nu.mgz brainmask_orig_nu_PFH10.auto.mgz mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 20 orig_nu.mgz brainmask_orig_nu_PFH20.auto.mgz mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 30 orig_nu.mgz brainmask_orig_nu_PFH30.auto.mgz mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 5 T1.mgz brainmask_T1_PFH5.auto.mgz mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 10 T1.mgz brainmask_T1_PFH10.auto.mgz mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 20 T1.mgz brainmask_T1_PFH20.auto.mgz mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 30 T1.mgz brainmask_T1_PFH30.auto.mgz mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 5 orig.mgz brainmask_orig_PFH5.auto.mgz Mode: Use the information of atlas (default parms, --help for details) Mode: Preflooding height manually specified ********************************************************* The input file is orig.mgz The output file is brainmask_orig_PFH5.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=122 z=109 r=74 first estimation of the main basin volume: 1761830 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=108, y=112, z=107, Imax=255 CSF=23, WM_intensity=215, WM_VARIANCE=7 WM_MIN=188, WM_HALF_MIN=198, WM_HALF_MAX=224, WM_MAX=232 preflooding height equal to 5 percent done. Analyze... main basin size=8364389755 voxels, voxel volume =1.000 = 8364389755 mmm3 = 8364389.888 cm3 done. PostAnalyze...Basin Prior 332 basins merged thanks to atlas ambiguous basin, merged: at least 19 ambiguous voxels; size: 5922 voxels ambiguous basin, merged: at least 19 ambiguous voxels; size: 6348 voxels ***** 2 basin(s) merged in 2 iteration(s) ***** 12270 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=106, r=10567 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=24 , nb = 44774 RIGHT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=33 , nb = -1036768289 LEFT_CER CSF_MIN=0, CSF_intensity=6, CSF_MAX=33 , nb = 1052306189 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=26 , nb = 1081751587 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=23 , nb = 1076968642 OTHER CSF_MIN=1, CSF_intensity=56, CSF_MAX=91 , nb = 1072774702 Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 24, 23, 18, 135 after analyzing : 23, 37, 44, 61 RIGHT_CER before analyzing : 33, 54, 107, 164 after analyzing : 33, 89, 107, 107 LEFT_CER before analyzing : 33, 52, 94, 151 after analyzing : 33, 80, 94, 97 RIGHT_BRAIN before analyzing : 26, 25, 20, 138 after analyzing : 25, 37, 44, 62 LEFT_BRAIN before analyzing : 23, 22, 21, 127 after analyzing : 22, 36, 44, 58 OTHER before analyzing : 91, 66, 50, 73 after analyzing : 63, 66, 66, 67 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...64 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.010 curvature mean = 70.438, std = 7.901 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.32, sigma = 1.92 after rotation: sse = 1.32, sigma = 1.92 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 1.32, its var is 1.46 before Erosion-Dilatation 0.00% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...33 iterations mri_strip_skull: done peeling brain Brain Size = 1692752 voxels, voxel volume = 1.000 mm3 = 1692752 mmm3 = 1692.752 cm3 ****************************** Saving brainmask_orig_PFH5.auto.mgz done mri_watershed utimesec 42.511537 mri_watershed stimesec 0.405938 mri_watershed ru_maxrss 814292 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 209207 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 3392 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 1 mri_watershed ru_nivcsw 7328 mri_watershed done mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 10 orig.mgz brainmask_orig_PFH10.auto.mgz Mode: Use the information of atlas (default parms, --help for details) Mode: Preflooding height manually specified ********************************************************* The input file is orig.mgz The output file is brainmask_orig_PFH10.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=122 z=109 r=74 first estimation of the main basin volume: 1761830 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=108, y=112, z=107, Imax=255 CSF=23, WM_intensity=215, WM_VARIANCE=7 WM_MIN=188, WM_HALF_MIN=198, WM_HALF_MAX=224, WM_MAX=232 preflooding height equal to 10 percent done. Analyze... main basin size=8558596442 voxels, voxel volume =1.000 = 8558596442 mmm3 = 8558596.608 cm3 done. PostAnalyze...Basin Prior 41 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=126,y=104, z=106, r=10660 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=25 , nb = 44937 RIGHT_CER CSF_MIN=0, CSF_intensity=8, CSF_MAX=34 , nb = -1036636466 LEFT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=41 , nb = -1087391717 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=26 , nb = 1082366119 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=23 , nb = 1072257418 OTHER CSF_MIN=0, CSF_intensity=10, CSF_MAX=18 , nb = 1078532981 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 25, 40, 90, 142 after analyzing : 25, 73, 90, 90 RIGHT_CER before analyzing : 34, 63, 113, 157 after analyzing : 34, 96, 113, 111 LEFT_CER before analyzing : 41, 68, 107, 153 after analyzing : 41, 94, 107, 108 RIGHT_BRAIN before analyzing : 26, 45, 95, 137 after analyzing : 26, 78, 95, 92 LEFT_BRAIN before analyzing : 23, 38, 90, 135 after analyzing : 23, 72, 90, 87 OTHER before analyzing : 18, 24, 42, 64 after analyzing : 18, 37, 44, 43 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...64 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.010 curvature mean = 69.486, std = 7.463 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.41, sigma = 2.13 after rotation: sse = 1.41, sigma = 2.13 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 1.42, its var is 1.66 before Erosion-Dilatation 0.00% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...45 iterations mri_strip_skull: done peeling brain Brain Size = 1693388 voxels, voxel volume = 1.000 mm3 = 1693388 mmm3 = 1693.388 cm3 ****************************** Saving brainmask_orig_PFH10.auto.mgz done mri_watershed utimesec 44.685206 mri_watershed stimesec 0.487925 mri_watershed ru_maxrss 818296 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 210356 mri_watershed ru_majflt 143 mri_watershed ru_nswap 0 mri_watershed ru_inblock 8944 mri_watershed ru_oublock 3392 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 146 mri_watershed ru_nivcsw 7684 mri_watershed done mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 20 orig.mgz brainmask_orig_PFH20.auto.mgz Mode: Use the information of atlas (default parms, --help for details) Mode: Preflooding height manually specified ********************************************************* The input file is orig.mgz The output file is brainmask_orig_PFH20.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=122 z=109 r=74 first estimation of the main basin volume: 1761830 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=108, y=112, z=107, Imax=255 CSF=23, WM_intensity=215, WM_VARIANCE=7 WM_MIN=188, WM_HALF_MIN=198, WM_HALF_MAX=224, WM_MAX=232 preflooding height equal to 20 percent done. Analyze... main basin size=8444769578 voxels, voxel volume =1.000 = 8444769578 mmm3 = 8444769.792 cm3 done. PostAnalyze...Basin Prior 4 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=126,y=103, z=106, r=10657 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=26 , nb = 45045 RIGHT_CER CSF_MIN=0, CSF_intensity=7, CSF_MAX=33 , nb = -1036434898 LEFT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=51 , nb = -1105980936 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=27 , nb = 1081878571 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=24 , nb = 1073849436 OTHER CSF_MIN=0, CSF_intensity=10, CSF_MAX=18 , nb = 1076580441 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 26, 45, 93, 135 after analyzing : 26, 77, 93, 91 RIGHT_CER before analyzing : 33, 60, 110, 158 after analyzing : 33, 93, 110, 109 LEFT_CER before analyzing : 51, 76, 105, 153 after analyzing : 51, 95, 105, 109 RIGHT_BRAIN before analyzing : 27, 49, 97, 136 after analyzing : 27, 81, 97, 94 LEFT_BRAIN before analyzing : 24, 41, 92, 134 after analyzing : 24, 75, 92, 89 OTHER before analyzing : 18, 24, 42, 64 after analyzing : 18, 37, 44, 43 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...64 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.010 curvature mean = 69.526, std = 7.285 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.59, sigma = 2.36 after rotation: sse = 1.59, sigma = 2.36 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 1.59, its var is 1.84 before Erosion-Dilatation 0.00% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...46 iterations mri_strip_skull: done peeling brain Brain Size = 1703774 voxels, voxel volume = 1.000 mm3 = 1703774 mmm3 = 1703.774 cm3 ****************************** Saving brainmask_orig_PFH20.auto.mgz done mri_watershed utimesec 44.955165 mri_watershed stimesec 0.437933 mri_watershed ru_maxrss 827396 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 209207 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 3416 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 0 mri_watershed ru_nivcsw 11135 mri_watershed done mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 30 orig.mgz brainmask_orig_PFH30.auto.mgz Mode: Use the information of atlas (default parms, --help for details) Mode: Preflooding height manually specified ********************************************************* The input file is orig.mgz The output file is brainmask_orig_PFH30.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=122 z=109 r=74 first estimation of the main basin volume: 1761830 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=108, y=112, z=107, Imax=255 CSF=23, WM_intensity=215, WM_VARIANCE=7 WM_MIN=188, WM_HALF_MIN=198, WM_HALF_MAX=224, WM_MAX=232 preflooding height equal to 30 percent done. Analyze... main basin size=8413129521 voxels, voxel volume =1.000 = 8413129521 mmm3 = 8413129.728 cm3 done. PostAnalyze...Basin Prior 0 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=126,y=104, z=108, r=11058 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=26 , nb = 44811 RIGHT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=27 , nb = -1036049783 LEFT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=55 , nb = 1075692157 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=27 , nb = 1083758224 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=23 , nb = 1077538128 OTHER CSF_MIN=0, CSF_intensity=9, CSF_MAX=30 , nb = 1072168612 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 26, 43, 91, 139 after analyzing : 26, 75, 91, 91 RIGHT_CER before analyzing : 27, 41, 96, 162 after analyzing : 27, 77, 96, 98 LEFT_CER before analyzing : 55, 82, 108, 151 after analyzing : 55, 99, 108, 112 RIGHT_BRAIN before analyzing : 27, 46, 94, 139 after analyzing : 27, 78, 94, 93 LEFT_BRAIN before analyzing : 23, 39, 92, 135 after analyzing : 23, 74, 92, 89 OTHER before analyzing : 30, 33, 38, 64 after analyzing : 30, 40, 44, 46 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...64 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.010 curvature mean = 70.225, std = 7.344 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.25, sigma = 4.31 after rotation: sse = 2.25, sigma = 4.31 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.29, its var is 3.55 before Erosion-Dilatation 0.45% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...45 iterations mri_strip_skull: done peeling brain Brain Size = 1733544 voxels, voxel volume = 1.000 mm3 = 1733544 mmm3 = 1733.544 cm3 ****************************** Saving brainmask_orig_PFH30.auto.mgz done mri_watershed utimesec 45.277116 mri_watershed stimesec 0.433934 mri_watershed ru_maxrss 820720 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 210016 mri_watershed ru_majflt 90 mri_watershed ru_nswap 0 mri_watershed ru_inblock 5728 mri_watershed ru_oublock 3480 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 90 mri_watershed ru_nivcsw 7794 mri_watershed done mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 5 orig_nu.mgz brainmask_orig_nu_PFH5.auto.mgz Mode: Use the information of atlas (default parms, --help for details) Mode: Preflooding height manually specified ********************************************************* The input file is orig_nu.mgz The output file is brainmask_orig_nu_PFH5.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=121 z=109 r=75 first estimation of the main basin volume: 1817039 voxels Looking for seedpoints 2 found in the cerebellum 17 found in the rest of the brain global maximum in x=139, y=93, z=86, Imax=255 CSF=21, WM_intensity=177, WM_VARIANCE=5 WM_MIN=167, WM_HALF_MIN=174, WM_HALF_MAX=181, WM_MAX=185 preflooding height equal to 5 percent done. Analyze... main basin size=8812694274 voxels, voxel volume =1.000 = 8812694274 mmm3 = 8812694.528 cm3 done. PostAnalyze...Basin Prior 409 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=106, r=10464 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ (2) Problem with the least square interpolation for CSF_MAX GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=36 , nb = 43713 RIGHT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=36 , nb = -1036907840 LEFT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=43 , nb = -1096831554 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=36 , nb = 1079492642 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=34 , nb = 1071827244 OTHER CSF_MIN=17, CSF_intensity=50, CSF_MAX=64 , nb = 1078252973 Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 36, 30, 6, 135 after analyzing : 30, 36, 39, 60 RIGHT_CER before analyzing : 36, 30, 0, 150 after analyzing : 30, 36, 39, 64 LEFT_CER before analyzing : 43, 36, 29, 64 after analyzing : 36, 38, 39, 44 RIGHT_BRAIN before analyzing : 36, 31, 12, 135 after analyzing : 31, 36, 39, 60 LEFT_BRAIN before analyzing : 34, 29, 7, 136 after analyzing : 29, 35, 39, 60 OTHER before analyzing : 64, 56, 49, 64 after analyzing : 54, 56, 56, 58 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...62 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.010 curvature mean = 70.701, std = 7.847 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.24, sigma = 2.05 after rotation: sse = 1.24, sigma = 2.05 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 1.25, its var is 1.65 before Erosion-Dilatation 0.00% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...26 iterations mri_strip_skull: done peeling brain Brain Size = 1678711 voxels, voxel volume = 1.000 mm3 = 1678711 mmm3 = 1678.711 cm3 ****************************** Saving brainmask_orig_nu_PFH5.auto.mgz done mri_watershed utimesec 39.122052 mri_watershed stimesec 0.448931 mri_watershed ru_maxrss 819848 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 209831 mri_watershed ru_majflt 69 mri_watershed ru_nswap 0 mri_watershed ru_inblock 4416 mri_watershed ru_oublock 3232 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 72 mri_watershed ru_nivcsw 6710 mri_watershed done mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 10 orig_nu.mgz brainmask_orig_nu_PFH10.auto.mgz Mode: Use the information of atlas (default parms, --help for details) Mode: Preflooding height manually specified ********************************************************* The input file is orig_nu.mgz The output file is brainmask_orig_nu_PFH10.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=121 z=109 r=75 first estimation of the main basin volume: 1817039 voxels Looking for seedpoints 2 found in the cerebellum 17 found in the rest of the brain global maximum in x=139, y=93, z=86, Imax=255 CSF=21, WM_intensity=177, WM_VARIANCE=5 WM_MIN=167, WM_HALF_MIN=174, WM_HALF_MAX=181, WM_MAX=185 preflooding height equal to 10 percent done. Analyze... main basin size=9127200140 voxels, voxel volume =1.000 = 9127200140 mmm3 = 9127199.744 cm3 done. PostAnalyze...Basin Prior 51 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=106, r=10465 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=35 , nb = 43947 RIGHT_CER CSF_MIN=1, CSF_intensity=9, CSF_MAX=36 , nb = -1036742942 LEFT_CER CSF_MIN=0, CSF_intensity=13, CSF_MAX=42 , nb = -1094227677 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=35 , nb = 1081593431 LEFT_BRAIN CSF_MIN=0, CSF_intensity=12, CSF_MAX=32 , nb = 1076357300 OTHER CSF_MIN=2, CSF_intensity=57, CSF_MAX=90 , nb = 1074072472 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 35, 64, 102, 135 after analyzing : 35, 89, 102, 100 RIGHT_CER before analyzing : 36, 64, 108, 150 after analyzing : 36, 93, 108, 107 LEFT_CER before analyzing : 42, 61, 98, 151 after analyzing : 42, 85, 98, 101 RIGHT_BRAIN before analyzing : 35, 66, 104, 135 after analyzing : 35, 91, 104, 102 LEFT_BRAIN before analyzing : 32, 58, 103, 136 after analyzing : 32, 88, 103, 100 OTHER before analyzing : 90, 61, 49, 64 after analyzing : 59, 61, 61, 61 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...62 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 69.161, std = 7.818 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.27, sigma = 1.97 after rotation: sse = 1.27, sigma = 1.97 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 1.27, its var is 1.53 before Erosion-Dilatation 0.00% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...45 iterations mri_strip_skull: done peeling brain Brain Size = 1679698 voxels, voxel volume = 1.000 mm3 = 1679698 mmm3 = 1679.698 cm3 ****************************** Saving brainmask_orig_nu_PFH10.auto.mgz done mri_watershed utimesec 45.542076 mri_watershed stimesec 0.459930 mri_watershed ru_maxrss 820120 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 210089 mri_watershed ru_majflt 77 mri_watershed ru_nswap 0 mri_watershed ru_inblock 4824 mri_watershed ru_oublock 3240 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 78 mri_watershed ru_nivcsw 7748 mri_watershed done mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 20 orig_nu.mgz brainmask_orig_nu_PFH20.auto.mgz Mode: Use the information of atlas (default parms, --help for details) Mode: Preflooding height manually specified ********************************************************* The input file is orig_nu.mgz The output file is brainmask_orig_nu_PFH20.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=121 z=109 r=75 first estimation of the main basin volume: 1817039 voxels Looking for seedpoints 2 found in the cerebellum 17 found in the rest of the brain global maximum in x=139, y=93, z=86, Imax=255 CSF=21, WM_intensity=177, WM_VARIANCE=5 WM_MIN=167, WM_HALF_MIN=174, WM_HALF_MAX=181, WM_MAX=185 preflooding height equal to 20 percent done. Analyze... main basin size=9029277114 voxels, voxel volume =1.000 = 9029277114 mmm3 = 9029276.672 cm3 done. PostAnalyze...Basin Prior 2 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=126,y=104, z=105, r=10565 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=36 , nb = 44073 RIGHT_CER CSF_MIN=1, CSF_intensity=9, CSF_MAX=33 , nb = -1035662389 LEFT_CER CSF_MIN=1, CSF_intensity=9, CSF_MAX=52 , nb = 1074298910 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=9, CSF_MAX=36 , nb = 1083749514 LEFT_BRAIN CSF_MIN=0, CSF_intensity=14, CSF_MAX=33 , nb = 1080987118 OTHER CSF_MIN=12, CSF_intensity=45, CSF_MAX=153 , nb = 1064252532 Problem with the least square interpolation in GM_MIN calculation. (2) Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 36, 68, 105, 135 after analyzing : 36, 92, 105, 102 RIGHT_CER before analyzing : 33, 53, 99, 152 after analyzing : 33, 83, 99, 100 LEFT_CER before analyzing : 52, 71, 96, 152 after analyzing : 52, 87, 96, 103 RIGHT_BRAIN before analyzing : 36, 69, 106, 135 after analyzing : 36, 93, 106, 103 LEFT_BRAIN before analyzing : 33, 58, 103, 137 after analyzing : 33, 88, 103, 100 OTHER before analyzing : 153, 12, 0, 9 after analyzing : 12, 30, 39, 32 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...65 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.010 curvature mean = 69.419, std = 7.224 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.64, sigma = 2.46 after rotation: sse = 1.64, sigma = 2.46 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 1.64, its var is 1.88 before Erosion-Dilatation 0.00% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...46 iterations mri_strip_skull: done peeling brain Brain Size = 1700486 voxels, voxel volume = 1.000 mm3 = 1700486 mmm3 = 1700.486 cm3 ****************************** Saving brainmask_orig_nu_PFH20.auto.mgz done mri_watershed utimesec 46.479933 mri_watershed stimesec 0.456930 mri_watershed ru_maxrss 820784 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 210081 mri_watershed ru_majflt 76 mri_watershed ru_nswap 0 mri_watershed ru_inblock 4832 mri_watershed ru_oublock 3296 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 85 mri_watershed ru_nivcsw 9171 mri_watershed done mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 30 orig_nu.mgz brainmask_orig_nu_PFH30.auto.mgz Mode: Use the information of atlas (default parms, --help for details) Mode: Preflooding height manually specified ********************************************************* The input file is orig_nu.mgz The output file is brainmask_orig_nu_PFH30.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=121 z=109 r=75 first estimation of the main basin volume: 1817039 voxels Looking for seedpoints 2 found in the cerebellum 17 found in the rest of the brain global maximum in x=139, y=93, z=86, Imax=255 CSF=21, WM_intensity=177, WM_VARIANCE=5 WM_MIN=167, WM_HALF_MIN=174, WM_HALF_MAX=181, WM_MAX=185 preflooding height equal to 30 percent done. Analyze... main basin size=9365828745 voxels, voxel volume =1.000 = 9365828745 mmm3 = 9365828.608 cm3 done. PostAnalyze...Basin Prior 0 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=126,y=104, z=106, r=10460 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=38 , nb = 44594 RIGHT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=32 , nb = -1035476470 LEFT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=57 , nb = 1072115819 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=14, CSF_MAX=38 , nb = 1082913302 LEFT_BRAIN CSF_MIN=0, CSF_intensity=14, CSF_MAX=33 , nb = 1078436408 OTHER CSF_MIN=0, CSF_intensity=6, CSF_MAX=115 , nb = 1070424415 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 38, 70, 105, 135 after analyzing : 38, 93, 105, 103 RIGHT_CER before analyzing : 32, 45, 84, 150 after analyzing : 32, 71, 84, 90 LEFT_CER before analyzing : 57, 83, 108, 152 after analyzing : 57, 99, 108, 112 RIGHT_BRAIN before analyzing : 38, 69, 107, 135 after analyzing : 38, 94, 107, 104 LEFT_BRAIN before analyzing : 33, 59, 104, 135 after analyzing : 33, 89, 104, 100 OTHER before analyzing : 115, 51, 35, 64 after analyzing : 35, 51, 51, 54 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...67 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.010 curvature mean = 69.542, std = 7.225 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.74, sigma = 2.74 after rotation: sse = 1.74, sigma = 2.74 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 1.79, its var is 2.38 before Erosion-Dilatation 0.06% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...47 iterations mri_strip_skull: done peeling brain Brain Size = 1713557 voxels, voxel volume = 1.000 mm3 = 1713557 mmm3 = 1713.557 cm3 ****************************** Saving brainmask_orig_nu_PFH30.auto.mgz done mri_watershed utimesec 46.774889 mri_watershed stimesec 0.456930 mri_watershed ru_maxrss 817272 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 210028 mri_watershed ru_majflt 111 mri_watershed ru_nswap 0 mri_watershed ru_inblock 13168 mri_watershed ru_oublock 3304 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 143 mri_watershed ru_nivcsw 19083 mri_watershed done mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 5 T1.mgz brainmask_T1_PFH5.auto.mgz Mode: Use the information of atlas (default parms, --help for details) Mode: Preflooding height manually specified ********************************************************* The input file is T1.mgz The output file is brainmask_T1_PFH5.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=121 z=109 r=75 first estimation of the main basin volume: 1799996 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=152, y=92, z=73, Imax=255 CSF=12, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 5 percent done. Analyze... main basin size=8576555683 voxels, voxel volume =1.000 = 8576555683 mmm3 = 8576555.520 cm3 done. PostAnalyze...Basin Prior 83 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=105, z=106, r=10467 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=5, CSF_MAX=19 , nb = 43893 RIGHT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=19 , nb = -1036781800 LEFT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=47 , nb = -1112952814 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=20 , nb = 1080323947 LEFT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=17 , nb = 1075442876 OTHER CSF_MIN=0, CSF_intensity=32, CSF_MAX=39 , nb = 1074860032 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 19, 35, 59, 79 after analyzing : 19, 51, 59, 58 RIGHT_CER before analyzing : 19, 31, 59, 93 after analyzing : 19, 49, 59, 60 LEFT_CER before analyzing : 47, 54, 60, 92 after analyzing : 47, 58, 60, 66 RIGHT_BRAIN before analyzing : 20, 38, 60, 78 after analyzing : 20, 52, 60, 58 LEFT_BRAIN before analyzing : 17, 31, 58, 79 after analyzing : 17, 49, 58, 56 OTHER before analyzing : 39, 47, 72, 92 after analyzing : 39, 63, 72, 70 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...72 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 68.669, std = 8.385 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.22, sigma = 1.97 after rotation: sse = 1.22, sigma = 1.97 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 1.22, its var is 1.53 before Erosion-Dilatation 0.00% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...51 iterations mri_strip_skull: done peeling brain Brain Size = 1670276 voxels, voxel volume = 1.000 mm3 = 1670276 mmm3 = 1670.276 cm3 ****************************** Saving brainmask_T1_PFH5.auto.mgz done mri_watershed utimesec 45.563073 mri_watershed stimesec 0.510922 mri_watershed ru_maxrss 807520 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 209320 mri_watershed ru_majflt 186 mri_watershed ru_nswap 0 mri_watershed ru_inblock 11792 mri_watershed ru_oublock 2624 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 190 mri_watershed ru_nivcsw 7946 mri_watershed done mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 10 T1.mgz brainmask_T1_PFH10.auto.mgz Mode: Use the information of atlas (default parms, --help for details) Mode: Preflooding height manually specified ********************************************************* The input file is T1.mgz The output file is brainmask_T1_PFH10.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=121 z=109 r=75 first estimation of the main basin volume: 1799996 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=152, y=92, z=73, Imax=255 CSF=12, 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=8322834795 voxels, voxel volume =1.000 = 8322834795 mmm3 = 8322834.944 cm3 done. PostAnalyze...Basin Prior 16 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=126,y=105, z=106, r=10463 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=5, CSF_MAX=18 , nb = 44271 RIGHT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=20 , nb = -1036513012 LEFT_CER CSF_MIN=0, CSF_intensity=5, CSF_MAX=44 , nb = -1092530524 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=18 , nb = 1082155113 LEFT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=17 , nb = 1074058434 OTHER CSF_MIN=0, CSF_intensity=32, CSF_MAX=39 , nb = 1076400782 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 18, 35, 60, 79 after analyzing : 18, 51, 60, 58 RIGHT_CER before analyzing : 20, 32, 59, 94 after analyzing : 20, 50, 59, 61 LEFT_CER before analyzing : 44, 52, 60, 92 after analyzing : 44, 57, 60, 65 RIGHT_BRAIN before analyzing : 18, 33, 58, 79 after analyzing : 18, 49, 58, 56 LEFT_BRAIN before analyzing : 17, 33, 60, 79 after analyzing : 17, 51, 60, 58 OTHER before analyzing : 39, 44, 64, 91 after analyzing : 39, 57, 64, 65 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...64 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 68.836, std = 8.296 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.23, sigma = 2.05 after rotation: sse = 1.23, sigma = 2.05 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 1.23, its var is 1.58 before Erosion-Dilatation 0.00% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...47 iterations mri_strip_skull: done peeling brain Brain Size = 1671074 voxels, voxel volume = 1.000 mm3 = 1671074 mmm3 = 1671.074 cm3 ****************************** Saving brainmask_T1_PFH10.auto.mgz done mri_watershed utimesec 45.456089 mri_watershed stimesec 0.462929 mri_watershed ru_maxrss 813316 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 207983 mri_watershed ru_majflt 35 mri_watershed ru_nswap 0 mri_watershed ru_inblock 2200 mri_watershed ru_oublock 2632 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 39 mri_watershed ru_nivcsw 7978 mri_watershed done mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 20 T1.mgz brainmask_T1_PFH20.auto.mgz Mode: Use the information of atlas (default parms, --help for details) Mode: Preflooding height manually specified ********************************************************* The input file is T1.mgz The output file is brainmask_T1_PFH20.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=121 z=109 r=75 first estimation of the main basin volume: 1799996 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=152, y=92, z=73, Imax=255 CSF=12, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 20 percent done. Analyze... main basin size=8639340539 voxels, voxel volume =1.000 = 8639340539 mmm3 = 8639340.544 cm3 done. PostAnalyze...Basin Prior 8 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=126,y=104, z=106, r=10554 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=5, CSF_MAX=20 , nb = 44649 RIGHT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=18 , nb = -1035519858 LEFT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=40 , nb = 1074874145 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=20 , nb = 1083091094 LEFT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=18 , nb = 1076685588 OTHER CSF_MIN=0, CSF_intensity=18, CSF_MAX=53 , nb = 1071912990 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 20, 37, 60, 79 after analyzing : 20, 52, 60, 58 RIGHT_CER before analyzing : 18, 29, 58, 94 after analyzing : 18, 48, 58, 59 LEFT_CER before analyzing : 40, 49, 59, 92 after analyzing : 40, 55, 59, 64 RIGHT_BRAIN before analyzing : 20, 38, 60, 78 after analyzing : 20, 52, 60, 58 LEFT_BRAIN before analyzing : 18, 33, 58, 79 after analyzing : 18, 49, 58, 56 OTHER before analyzing : 53, 65, 73, 92 after analyzing : 53, 70, 73, 75 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...74 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.012 curvature mean = 68.556, std = 8.470 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.29, sigma = 2.08 after rotation: sse = 1.29, sigma = 2.08 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 1.29, its var is 1.62 before Erosion-Dilatation 0.00% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...47 iterations mri_strip_skull: done peeling brain Brain Size = 1692872 voxels, voxel volume = 1.000 mm3 = 1692872 mmm3 = 1692.872 cm3 ****************************** Saving brainmask_T1_PFH20.auto.mgz done mri_watershed utimesec 45.858028 mri_watershed stimesec 0.404938 mri_watershed ru_maxrss 814392 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 208474 mri_watershed ru_majflt 105 mri_watershed ru_nswap 0 mri_watershed ru_inblock 6632 mri_watershed ru_oublock 2680 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 109 mri_watershed ru_nivcsw 6183 mri_watershed done mri_watershed -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mri_watershed.dat -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta -h 30 T1.mgz brainmask_T1_PFH30.auto.mgz Mode: Use the information of atlas (default parms, --help for details) Mode: Preflooding height manually specified ********************************************************* The input file is T1.mgz The output file is brainmask_T1_PFH30.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=121 z=109 r=75 first estimation of the main basin volume: 1799996 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=152, y=92, z=73, Imax=255 CSF=12, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 30 percent done. Analyze... main basin size=8649275142 voxels, voxel volume =1.000 = 8649275142 mmm3 = 8649275.392 cm3 done. PostAnalyze...Basin Prior 8 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=10455 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=5, CSF_MAX=20 , nb = 44558 RIGHT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=22 , nb = -1036238953 LEFT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=38 , nb = 1077729860 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=20 , nb = 1077939970 LEFT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=18 , nb = 1071343104 OTHER CSF_MIN=0, CSF_intensity=15, CSF_MAX=51 , nb = 1077844008 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 20, 36, 59, 79 after analyzing : 20, 51, 59, 58 RIGHT_CER before analyzing : 22, 34, 58, 94 after analyzing : 22, 50, 58, 61 LEFT_CER before analyzing : 38, 51, 63, 92 after analyzing : 38, 59, 63, 67 RIGHT_BRAIN before analyzing : 20, 37, 60, 79 after analyzing : 20, 52, 60, 58 LEFT_BRAIN before analyzing : 18, 33, 58, 79 after analyzing : 18, 49, 58, 56 OTHER before analyzing : 51, 59, 66, 92 after analyzing : 51, 63, 66, 70 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...81 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.012 curvature mean = 68.966, std = 8.785 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.67, sigma = 2.78 after rotation: sse = 1.67, sigma = 2.78 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 1.67, its var is 2.22 before Erosion-Dilatation 0.07% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...51 iterations mri_strip_skull: done peeling brain Brain Size = 1718700 voxels, voxel volume = 1.000 mm3 = 1718700 mmm3 = 1718.700 cm3 ****************************** Saving brainmask_T1_PFH30.auto.mgz done mri_watershed utimesec 47.584766 mri_watershed stimesec 0.458930 mri_watershed ru_maxrss 811544 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 208815 mri_watershed ru_majflt 172 mri_watershed ru_nswap 0 mri_watershed ru_inblock 12632 mri_watershed ru_oublock 2712 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 175 mri_watershed ru_nivcsw 12610 mri_watershed done mri_mask T1.mgz brainmask_orig_PFH5.auto.mgz brainmask_orig_PFH5.auto.mgz mri_mask T1.mgz brainmask_orig_PFH10.auto.mgz brainmask_orig_PFH10.auto.mgz mri_mask T1.mgz brainmask_orig_PFH20.auto.mgz brainmask_orig_PFH20.auto.mgz mri_mask T1.mgz brainmask_orig_PFH30.auto.mgz brainmask_orig_PFH30.auto.mgz mri_mask T1.mgz brainmask_orig_PFH5.auto.mgz brainmask_orig_PFH5.auto.mgz DoAbs = 0 Writing masked volume to brainmask_orig_PFH5.auto.mgz...done. mri_mask T1.mgz brainmask_orig_PFH10.auto.mgz brainmask_orig_PFH10.auto.mgz DoAbs = 0 Writing masked volume to brainmask_orig_PFH10.auto.mgz...done. mri_mask T1.mgz brainmask_orig_PFH20.auto.mgz brainmask_orig_PFH20.auto.mgz DoAbs = 0 Writing masked volume to brainmask_orig_PFH20.auto.mgz...done. mri_mask T1.mgz brainmask_orig_PFH30.auto.mgz brainmask_orig_PFH30.auto.mgz DoAbs = 0 Writing masked volume to brainmask_orig_PFH30.auto.mgz...done. mri_log_likelihood -orig T1.mgz brainmask_orig_PFH5.auto.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach_with_skull.lta valid intensity range = [26, 116] 3897 zero brain voxels -46038 brainmask_orig_PFH5.auto.mgz log_likelihood= -46038 mri_log_likelihood -orig T1.mgz brainmask_orig_PFH10.auto.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach_with_skull.lta valid intensity range = [26, 116] 3976 zero brain voxels -46103 brainmask_orig_PFH10.auto.mgz log_likelihood= -46103 mri_log_likelihood -orig T1.mgz brainmask_orig_PFH20.auto.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach_with_skull.lta valid intensity range = [26, 116] 3923 zero brain voxels -46190 brainmask_orig_PFH20.auto.mgz log_likelihood= -46190 mri_log_likelihood -orig T1.mgz brainmask_orig_PFH30.auto.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach_with_skull.lta valid intensity range = [26, 116] 3433 zero brain voxels -46862 brainmask_orig_PFH30.auto.mgz log_likelihood= -46862 mri_log_likelihood -orig T1.mgz brainmask_orig_nu_PFH5.auto.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach_with_skull.lta valid intensity range = [26, 116] 4133 zero brain voxels -110622 brainmask_orig_nu_PFH5.auto.mgz log_likelihood= -110622 mri_log_likelihood -orig T1.mgz brainmask_orig_nu_PFH10.auto.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach_with_skull.lta valid intensity range = [26, 116] 4394 zero brain voxels -110543 brainmask_orig_nu_PFH10.auto.mgz log_likelihood= -110543 mri_log_likelihood -orig T1.mgz brainmask_orig_nu_PFH20.auto.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach_with_skull.lta valid intensity range = [26, 116] 3835 zero brain voxels -111329 brainmask_orig_nu_PFH20.auto.mgz log_likelihood= -111329 mri_log_likelihood -orig T1.mgz brainmask_orig_nu_PFH30.auto.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach_with_skull.lta valid intensity range = [26, 116] 3566 zero brain voxels -111780 brainmask_orig_nu_PFH30.auto.mgz log_likelihood= -111780 mri_log_likelihood -orig T1.mgz brainmask_T1_PFH5.auto.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach_with_skull.lta valid intensity range = [26, 116] 4539 zero brain voxels -46045 brainmask_T1_PFH5.auto.mgz log_likelihood= -46045 mri_log_likelihood -orig T1.mgz brainmask_T1_PFH10.auto.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach_with_skull.lta valid intensity range = [26, 116] 4540 zero brain voxels -46077 brainmask_T1_PFH10.auto.mgz log_likelihood= -46077 mri_log_likelihood -orig T1.mgz brainmask_T1_PFH20.auto.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach_with_skull.lta valid intensity range = [26, 116] 4068 zero brain voxels -46229 brainmask_T1_PFH20.auto.mgz log_likelihood= -46229 mri_log_likelihood -orig T1.mgz brainmask_T1_PFH30.auto.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach_with_skull.lta valid intensity range = [26, 116] 3268 zero brain voxels -46877 brainmask_T1_PFH30.auto.mgz log_likelihood= -46877 Optimal input vol: orig, pre-flood height= 5, results in log_likelihood= -46038 cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Sep 7 12:10:21 CEST 2017 /home/gc/study/recon-all/400614dclass/mri mri_em_register -rusage /home/gc/study/recon-all/400614dclass/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=18.0 skull bounding box = (63, 43, 30) --> (191, 176, 199) using (106, 87, 115) as brain centroid... mean wm in atlas = 107, using box (90,71,94) --> (121, 103,135) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 107 +- 3.3 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.277 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.167400 @ (-9.091, 9.091, -9.091) max log p = -3.911179 @ (13.636, 4.545, 4.545) max log p = -3.867040 @ (-6.818, 6.818, 2.273) max log p = -3.825970 @ (3.409, -5.682, -3.409) max log p = -3.825970 @ (0.000, 0.000, 0.000) max log p = -3.825970 @ (0.000, 0.000, 0.000) Found translation: (1.1, 14.8, -5.7): log p = -3.826 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.759, old_max_log_p =-3.826 (thresh=-3.8) 1.07500 0.00000 0.00000 -8.28371; 0.00000 1.07500 0.00000 6.93393; 0.00000 0.00000 0.92500 2.65264; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.759, old_max_log_p =-3.759 (thresh=-3.8) 1.07500 0.00000 0.00000 -8.28371; 0.00000 1.07500 0.00000 6.93393; 0.00000 0.00000 0.92500 2.65264; 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=-3.646, old_max_log_p =-3.759 (thresh=-3.8) 1.05249 -0.06492 -0.01607 0.97403; 0.06293 1.05211 0.18193 -18.56639; -0.00520 -0.21881 0.95892 26.20923; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.646, old_max_log_p =-3.646 (thresh=-3.6) 1.05249 -0.06492 -0.01607 0.97403; 0.06293 1.05211 0.18193 -18.56639; -0.00520 -0.21881 0.95892 26.20923; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.631, old_max_log_p =-3.646 (thresh=-3.6) 1.04879 -0.06469 -0.01601 0.94708; 0.06301 1.05334 0.18215 -19.19632; -0.00521 -0.21906 0.96005 25.64894; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.622, old_max_log_p =-3.631 (thresh=-3.6) 1.05123 -0.08400 -0.01131 2.62782; 0.08006 1.04904 0.18963 -21.26666; -0.01435 -0.22791 0.96200 27.07178; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.622, old_max_log_p =-3.622 (thresh=-3.6) 1.05123 -0.08400 -0.01131 2.62782; 0.08006 1.04904 0.18963 -21.26666; -0.01435 -0.22791 0.96200 27.07178; 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 1.05123 -0.08400 -0.01131 2.62782; 0.08006 1.04904 0.18963 -21.26666; -0.01435 -0.22791 0.96200 27.07178; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.05123 -0.08400 -0.01131 2.62782; 0.08006 1.04904 0.18963 -21.26666; -0.01435 -0.22791 0.96200 27.07178; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.05123 -0.08400 -0.01131 2.62782; 0.08006 1.04904 0.18963 -21.26666; -0.01435 -0.22791 0.96200 27.07178; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.622 (old=-4.277) transform before final EM align: 1.05123 -0.08400 -0.01131 2.62782; 0.08006 1.04904 0.18963 -21.26666; -0.01435 -0.22791 0.96200 27.07178; 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 1.05123 -0.08400 -0.01131 2.62782; 0.08006 1.04904 0.18963 -21.26666; -0.01435 -0.22791 0.96200 27.07178; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.05123 -0.08400 -0.01131 2.62782; 0.08006 1.04904 0.18963 -21.26666; -0.01435 -0.22791 0.96200 27.07178; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.0 tol 0.000000 final transform: 1.05123 -0.08400 -0.01131 2.62782; 0.08006 1.04904 0.18963 -21.26666; -0.01435 -0.22791 0.96200 27.07178; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1026.311976 mri_em_register stimesec 0.922859 mri_em_register ru_maxrss 599000 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 158565 mri_em_register ru_majflt 3 mri_em_register ru_nswap 0 mri_em_register ru_inblock 544 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 28 mri_em_register ru_nivcsw 104147 registration took 17 minutes and 10 seconds. #-------------------------------------- #@# CA Normalize Thu Sep 7 12:27:31 CEST 2017 /home/gc/study/recon-all/400614dclass/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=17.0 skull bounding box = (63, 43, 29) --> (192, 176, 199) using (106, 87, 114) as brain centroid... mean wm in atlas = 107, using box (90,71,93) --> (121, 103,134) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 107 +- 3.3 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 using 246344 sample points... INFO: compute sample coordinates transform 1.05123 -0.08400 -0.01131 2.62782; 0.08006 1.04904 0.18963 -21.26666; -0.01435 -0.22791 0.96200 27.07178; 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 (126, 41, 30) --> (191, 148, 199) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 1 of 5765 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 45, 29) --> (128, 152, 199) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 14 of 6357 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 127, 60) --> (178, 164, 115) Left_Cerebellum_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 188 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (89, 127, 57) --> (130, 167, 116) Right_Cerebellum_White_Matter: limiting intensities to 100.0 --> 132.0 0 of 67 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 115, 96) --> (148, 181, 126) Brain_Stem: limiting intensities to 96.0 --> 132.0 0 of 273 (0.0%) samples deleted using 12650 total control points for intensity normalization... bias field = 0.973 +- 0.062 158 of 12635 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 41, 30) --> (191, 148, 199) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 1 of 6118 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 45, 29) --> (128, 152, 199) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 11 of 6634 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 127, 60) --> (178, 164, 115) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 14 of 287 (4.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (89, 127, 57) --> (130, 167, 116) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 10 of 131 (7.6%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 115, 96) --> (148, 181, 126) Brain_Stem: limiting intensities to 88.0 --> 132.0 1 of 366 (0.3%) samples deleted using 13536 total control points for intensity normalization... bias field = 1.055 +- 0.060 110 of 13426 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 41, 30) --> (191, 148, 199) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 129.0 15 of 6135 (0.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (65, 45, 29) --> (128, 152, 199) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 129.0 23 of 6679 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (130, 127, 60) --> (178, 164, 115) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 129.0 75 of 328 (22.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (89, 127, 57) --> (130, 167, 116) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 129.0 33 of 165 (20.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (113, 115, 96) --> (148, 181, 126) Brain_Stem: limiting intensities to 88.0 --> 129.0 21 of 410 (5.1%) samples deleted using 13717 total control points for intensity normalization... bias field = 1.049 +- 0.051 93 of 13359 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 34 seconds. #-------------------------------------- #@# CA Reg Thu Sep 7 12:30:06 CEST 2017 /home/gc/study/recon-all/400614dclass/mri mri_ca_register -rusage /home/gc/study/recon-all/400614dclass/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) = 1.11 (predicted orig area = 7.2) 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=0.875, neg=0, invalid=762 0001: dt=227.752500, rms=0.783 (10.568%), neg=0, invalid=762 0002: dt=189.580756, rms=0.763 (2.559%), neg=0, invalid=762 0003: dt=232.679089, rms=0.751 (1.566%), neg=0, invalid=762 0004: dt=129.472000, rms=0.747 (0.554%), neg=0, invalid=762 0005: dt=517.888000, rms=0.740 (0.945%), neg=0, invalid=762 0006: dt=110.976000, rms=0.738 (0.219%), neg=0, invalid=762 0007: dt=110.976000, rms=0.737 (0.143%), neg=0, invalid=762 0008: dt=110.976000, rms=0.735 (0.228%), neg=0, invalid=762 0009: dt=110.976000, rms=0.733 (0.263%), neg=0, invalid=762 0010: dt=110.976000, rms=0.731 (0.266%), neg=0, invalid=762 0011: dt=110.976000, rms=0.730 (0.249%), neg=0, invalid=762 0012: dt=110.976000, rms=0.728 (0.222%), neg=0, invalid=762 0013: dt=110.976000, rms=0.727 (0.193%), neg=0, invalid=762 0014: dt=110.976000, rms=0.725 (0.175%), neg=0, invalid=762 0015: dt=110.976000, rms=0.724 (0.170%), neg=0, invalid=762 0016: dt=110.976000, rms=0.723 (0.167%), neg=0, invalid=762 0017: dt=110.976000, rms=0.722 (0.171%), neg=0, invalid=762 0018: dt=110.976000, rms=0.720 (0.173%), neg=0, invalid=762 0019: dt=110.976000, rms=0.719 (0.164%), neg=0, invalid=762 0020: dt=110.976000, rms=0.718 (0.161%), neg=0, invalid=762 0021: dt=110.976000, rms=0.717 (0.131%), neg=0, invalid=762 0022: dt=110.976000, rms=0.716 (0.111%), neg=0, invalid=762 0023: dt=110.976000, rms=0.715 (0.116%), neg=0, invalid=762 0024: dt=110.976000, rms=0.714 (0.129%), neg=0, invalid=762 0025: dt=110.976000, rms=0.714 (0.129%), neg=0, invalid=762 0026: dt=110.976000, rms=0.713 (0.101%), neg=0, invalid=762 0027: dt=110.976000, rms=0.712 (0.079%), neg=0, invalid=762 0028: dt=1479.680000, rms=0.711 (0.190%), neg=0, invalid=762 0029: dt=129.472000, rms=0.710 (0.114%), neg=0, invalid=762 0030: dt=129.472000, rms=0.710 (0.021%), neg=0, invalid=762 0031: dt=129.472000, rms=0.710 (0.021%), neg=0, invalid=762 0032: dt=129.472000, rms=0.710 (0.018%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.710, neg=0, invalid=762 0033: dt=129.472000, rms=0.706 (0.572%), neg=0, invalid=762 0034: dt=517.888000, rms=0.704 (0.271%), neg=0, invalid=762 0035: dt=129.472000, rms=0.704 (0.078%), neg=0, invalid=762 0036: dt=129.472000, rms=0.704 (0.029%), neg=0, invalid=762 0037: dt=129.472000, rms=0.703 (0.049%), neg=0, invalid=762 0038: dt=129.472000, rms=0.703 (0.065%), neg=0, invalid=762 0039: dt=129.472000, rms=0.702 (0.087%), neg=0, invalid=762 0040: dt=129.472000, rms=0.701 (0.101%), neg=0, invalid=762 0041: dt=129.472000, rms=0.701 (0.100%), neg=0, invalid=762 0042: dt=129.472000, rms=0.700 (0.094%), neg=0, invalid=762 0043: dt=443.904000, rms=0.700 (0.027%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.709, neg=0, invalid=762 0044: dt=36.288000, rms=0.707 (0.248%), neg=0, invalid=762 0045: dt=165.362162, rms=0.703 (0.646%), neg=0, invalid=762 0046: dt=201.099526, rms=0.688 (2.103%), neg=0, invalid=762 0047: dt=24.025559, rms=0.685 (0.438%), neg=0, invalid=762 0048: dt=9.072000, rms=0.685 (0.010%), neg=0, invalid=762 0049: dt=9.072000, rms=0.685 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.685, neg=0, invalid=762 0050: dt=156.710280, rms=0.680 (0.791%), neg=0, invalid=762 0051: dt=36.288000, rms=0.678 (0.303%), neg=0, invalid=762 0052: dt=414.720000, rms=0.674 (0.595%), neg=0, invalid=762 0053: dt=67.572816, rms=0.670 (0.587%), neg=0, invalid=762 0054: dt=36.288000, rms=0.669 (0.087%), neg=0, invalid=762 0055: dt=36.288000, rms=0.669 (0.061%), neg=0, invalid=762 0056: dt=36.288000, rms=0.668 (0.119%), neg=0, invalid=762 0057: dt=36.288000, rms=0.667 (0.168%), neg=0, invalid=762 0058: dt=36.288000, rms=0.666 (0.199%), neg=0, invalid=762 0059: dt=36.288000, rms=0.664 (0.228%), neg=0, invalid=762 0060: dt=36.288000, rms=0.662 (0.240%), neg=0, invalid=762 0061: dt=36.288000, rms=0.661 (0.234%), neg=0, invalid=762 0062: dt=36.288000, rms=0.659 (0.234%), neg=0, invalid=762 0063: dt=36.288000, rms=0.658 (0.231%), neg=0, invalid=762 0064: dt=36.288000, rms=0.656 (0.219%), neg=0, invalid=762 0065: dt=36.288000, rms=0.655 (0.221%), neg=0, invalid=762 0066: dt=36.288000, rms=0.653 (0.217%), neg=0, invalid=762 0067: dt=36.288000, rms=0.652 (0.219%), neg=0, invalid=762 0068: dt=36.288000, rms=0.651 (0.196%), neg=0, invalid=762 0069: dt=36.288000, rms=0.650 (0.177%), neg=0, invalid=762 0070: dt=36.288000, rms=0.649 (0.160%), neg=0, invalid=762 0071: dt=36.288000, rms=0.647 (0.166%), neg=0, invalid=762 0072: dt=36.288000, rms=0.646 (0.167%), neg=0, invalid=762 0073: dt=36.288000, rms=0.645 (0.150%), neg=0, invalid=762 0074: dt=36.288000, rms=0.645 (0.134%), neg=0, invalid=762 0075: dt=36.288000, rms=0.644 (0.122%), neg=0, invalid=762 0076: dt=36.288000, rms=0.643 (0.109%), neg=0, invalid=762 0077: dt=103.680000, rms=0.643 (0.020%), neg=0, invalid=762 0078: dt=103.680000, rms=0.643 (0.011%), neg=0, invalid=762 0079: dt=103.680000, rms=0.643 (0.026%), neg=0, invalid=762 0080: dt=103.680000, rms=0.642 (0.061%), neg=0, invalid=762 0081: dt=103.680000, rms=0.642 (0.054%), neg=0, invalid=762 0082: dt=103.680000, rms=0.642 (0.058%), neg=0, invalid=762 0083: dt=103.680000, rms=0.641 (0.059%), neg=0, invalid=762 0084: dt=103.680000, rms=0.641 (0.100%), neg=0, invalid=762 0085: dt=103.680000, rms=0.640 (0.105%), neg=0, invalid=762 0086: dt=103.680000, rms=0.639 (0.093%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.667, neg=0, invalid=762 0087: dt=2.800000, rms=0.666 (0.112%), neg=0, invalid=762 0088: dt=2.800000, rms=0.666 (0.019%), neg=0, invalid=762 0089: dt=2.800000, rms=0.666 (0.004%), neg=0, invalid=762 0090: dt=2.800000, rms=0.666 (-0.024%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.667, neg=0, invalid=762 0091: dt=1.600000, rms=0.666 (0.097%), neg=0, invalid=762 0092: dt=0.400000, rms=0.666 (0.003%), neg=0, invalid=762 0093: dt=0.400000, rms=0.666 (-0.008%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.741, neg=0, invalid=762 0094: dt=6.395522, rms=0.719 (2.909%), neg=0, invalid=762 0095: dt=7.122677, rms=0.716 (0.482%), neg=0, invalid=762 0096: dt=4.600000, rms=0.715 (0.057%), neg=0, invalid=762 0097: dt=4.600000, rms=0.715 (0.041%), neg=0, invalid=762 0098: dt=4.600000, rms=0.715 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.716, neg=0, invalid=762 0099: dt=0.000000, rms=0.715 (0.072%), neg=0, invalid=762 0100: dt=0.000000, rms=0.715 (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=0.769, neg=0, invalid=762 0101: dt=0.000000, rms=0.768 (0.063%), neg=0, invalid=762 0102: dt=0.000000, rms=0.768 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.769, neg=0, invalid=762 0103: dt=0.028000, rms=0.768 (0.063%), neg=0, invalid=762 0104: dt=0.020000, rms=0.768 (0.000%), neg=0, invalid=762 0105: dt=0.020000, rms=0.768 (-0.000%), 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=0.679, neg=0, invalid=762 0106: dt=0.725515, rms=0.664 (2.119%), neg=0, invalid=762 0107: dt=0.064000, rms=0.664 (0.076%), neg=0, invalid=762 0108: dt=0.064000, rms=0.664 (-0.054%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.664, neg=0, invalid=762 0109: dt=0.028000, rms=0.664 (0.095%), neg=0, invalid=762 0110: dt=0.001250, rms=0.664 (-0.000%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.11044 (33) Left_Lateral_Ventricle (4): linear fit = 1.91 x + 0.0 (1458 voxels, overlap=0.099) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (1458 voxels, peak = 38), gca=30.0 gca peak = 0.15565 (16) mri peak = 0.09000 (33) Right_Lateral_Ventricle (43): linear fit = 2.13 x + 0.0 (1037 voxels, overlap=0.030) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1037 voxels, peak = 34), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.11181 (99) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (1105 voxels, overlap=0.997) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (1105 voxels, peak = 99), gca=99.4 gca peak = 0.20183 (93) mri peak = 0.07466 (96) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (949 voxels, overlap=1.007) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (949 voxels, peak = 95), gca=95.3 gca peak = 0.21683 (55) mri peak = 0.11156 (76) Right_Hippocampus (53): linear fit = 1.34 x + 0.0 (1249 voxels, overlap=0.015) Right_Hippocampus (53): linear fit = 1.34 x + 0.0 (1249 voxels, peak = 73), gca=73.4 gca peak = 0.30730 (58) mri peak = 0.09873 (75) Left_Hippocampus (17): linear fit = 1.26 x + 0.0 (1254 voxels, overlap=0.019) Left_Hippocampus (17): linear fit = 1.26 x + 0.0 (1254 voxels, peak = 73), gca=73.4 gca peak = 0.11430 (101) mri peak = 0.12523 (102) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (77580 voxels, overlap=0.745) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (77580 voxels, peak = 101), gca=101.0 gca peak = 0.12076 (102) mri peak = 0.10995 (103) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (78800 voxels, overlap=0.719) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (78800 voxels, peak = 104), gca=103.5 gca peak = 0.14995 (59) mri peak = 0.03612 (83) Left_Cerebral_Cortex (3): linear fit = 1.41 x + 0.0 (32762 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.41 x + 0.0 (32762 voxels, peak = 83), gca=83.5 gca peak = 0.15082 (58) mri peak = 0.03885 (78) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (35049 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (35049 voxels, peak = 78), gca=78.0 gca peak = 0.14161 (67) mri peak = 0.13428 (82) Right_Caudate (50): linear fit = 1.25 x + 0.0 (937 voxels, overlap=0.011) Right_Caudate (50): linear fit = 1.25 x + 0.0 (937 voxels, peak = 83), gca=83.4 gca peak = 0.15243 (71) mri peak = 0.11533 (88) Left_Caudate (11): linear fit = 1.21 x + 0.0 (1142 voxels, overlap=0.012) Left_Caudate (11): linear fit = 1.21 x + 0.0 (1142 voxels, peak = 86), gca=85.6 gca peak = 0.13336 (57) mri peak = 0.05635 (78) Left_Cerebellum_Cortex (8): linear fit = 1.40 x + 0.0 (26798 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.40 x + 0.0 (26798 voxels, peak = 80), gca=80.1 gca peak = 0.13252 (56) mri peak = 0.05758 (79) Right_Cerebellum_Cortex (47): linear fit = 1.39 x + 0.0 (27075 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.39 x + 0.0 (27075 voxels, peak = 78), gca=78.1 gca peak = 0.18181 (84) mri peak = 0.06173 (89) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (10108 voxels, overlap=0.958) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (10108 voxels, peak = 89), gca=88.6 gca peak = 0.20573 (83) mri peak = 0.06139 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (8396 voxels, overlap=0.924) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (8396 voxels, peak = 90), gca=90.1 gca peak = 0.21969 (57) mri peak = 0.12944 (80) Left_Amygdala (18): linear fit = 1.38 x + 0.0 (522 voxels, overlap=0.065) Left_Amygdala (18): linear fit = 1.38 x + 0.0 (522 voxels, peak = 79), gca=78.9 gca peak = 0.39313 (56) mri peak = 0.09433 (82) Right_Amygdala (54): linear fit = 1.38 x + 0.0 (624 voxels, overlap=0.046) Right_Amygdala (54): linear fit = 1.38 x + 0.0 (624 voxels, peak = 78), gca=77.6 gca peak = 0.14181 (85) mri peak = 0.09687 (96) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (6092 voxels, overlap=0.339) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (6092 voxels, peak = 95), gca=94.8 gca peak = 0.11978 (83) mri peak = 0.08438 (96) Right_Thalamus_Proper (49): linear fit = 1.15 x + 0.0 (4987 voxels, overlap=0.101) Right_Thalamus_Proper (49): linear fit = 1.15 x + 0.0 (4987 voxels, peak = 96), gca=95.9 gca peak = 0.13399 (79) mri peak = 0.09662 (90) Left_Putamen (12): linear fit = 1.14 x + 0.0 (2754 voxels, overlap=0.159) Left_Putamen (12): linear fit = 1.14 x + 0.0 (2754 voxels, peak = 90), gca=90.5 gca peak = 0.14159 (79) mri peak = 0.11080 (90) Right_Putamen (51): linear fit = 1.15 x + 0.0 (2860 voxels, overlap=0.009) Right_Putamen (51): linear fit = 1.15 x + 0.0 (2860 voxels, peak = 91), gca=91.2 gca peak = 0.10025 (80) mri peak = 0.08755 (92) Brain_Stem (16): linear fit = 1.15 x + 0.0 (11959 voxels, overlap=0.029) Brain_Stem (16): linear fit = 1.15 x + 0.0 (11959 voxels, peak = 92), gca=92.4 gca peak = 0.13281 (86) mri peak = 0.08361 (99) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (1397 voxels, overlap=0.075) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (1397 voxels, peak = 98), gca=98.5 gca peak = 0.12801 (89) mri peak = 0.07864 (99) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (1727 voxels, overlap=0.165) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (1727 voxels, peak = 101), gca=101.0 gca peak = 0.20494 (23) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15061 (21) mri peak = 0.22781 (33) Fourth_Ventricle (15): linear fit = 1.53 x + 0.0 (684 voxels, overlap=0.022) Fourth_Ventricle (15): linear fit = 1.53 x + 0.0 (684 voxels, peak = 32), gca=32.2 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.36 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.50 x + 0.0 Right_Putamen too bright - rescaling by 1.009 (from 1.155) to 92.0 (was 91.2) Right_Pallidum too bright - rescaling by 0.998 (from 1.035) to 99.2 (was 99.4) 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=0.660, neg=0, invalid=762 0111: dt=103.125812, rms=0.624 (5.412%), neg=0, invalid=762 0112: dt=221.952000, rms=0.616 (1.190%), neg=0, invalid=762 0113: dt=295.936000, rms=0.613 (0.617%), neg=0, invalid=762 0114: dt=129.472000, rms=0.611 (0.263%), neg=0, invalid=762 0115: dt=369.920000, rms=0.610 (0.179%), neg=0, invalid=762 0116: dt=110.976000, rms=0.609 (0.176%), neg=0, invalid=762 0117: dt=221.952000, rms=0.608 (0.122%), neg=0, invalid=762 0118: dt=92.480000, rms=0.608 (0.067%), neg=0, invalid=762 0119: dt=1183.744000, rms=0.606 (0.311%), neg=0, invalid=762 0120: dt=73.984000, rms=0.605 (0.148%), neg=0, invalid=762 0121: dt=129.472000, rms=0.605 (0.015%), neg=0, invalid=762 0122: dt=129.472000, rms=0.605 (0.047%), neg=0, invalid=762 0123: dt=129.472000, rms=0.604 (0.063%), neg=0, invalid=762 0124: dt=129.472000, rms=0.604 (0.073%), neg=0, invalid=762 0125: dt=129.472000, rms=0.603 (0.085%), neg=0, invalid=762 0126: dt=129.472000, rms=0.603 (0.110%), neg=0, invalid=762 0127: dt=129.472000, rms=0.602 (0.116%), neg=0, invalid=762 0128: dt=129.472000, rms=0.601 (0.107%), neg=0, invalid=762 0129: dt=129.472000, rms=0.601 (0.097%), neg=0, invalid=762 0130: dt=129.472000, rms=0.600 (0.098%), neg=0, invalid=762 0131: dt=129.472000, rms=0.599 (0.106%), neg=0, invalid=762 0132: dt=129.472000, rms=0.599 (0.093%), neg=0, invalid=762 0133: dt=129.472000, rms=0.598 (0.080%), neg=0, invalid=762 0134: dt=129.472000, rms=0.598 (0.075%), neg=0, invalid=762 0135: dt=129.472000, rms=0.597 (0.081%), neg=0, invalid=762 0136: dt=129.472000, rms=0.597 (0.088%), neg=0, invalid=762 0137: dt=129.472000, rms=0.596 (0.080%), neg=0, invalid=762 0138: dt=129.472000, rms=0.596 (0.077%), neg=0, invalid=762 0139: dt=129.472000, rms=0.595 (0.074%), neg=0, invalid=762 0140: dt=129.472000, rms=0.595 (0.080%), neg=0, invalid=762 0141: dt=129.472000, rms=0.595 (0.075%), neg=0, invalid=762 0142: dt=129.472000, rms=0.594 (0.066%), neg=0, invalid=762 0143: dt=129.472000, rms=0.594 (0.060%), neg=0, invalid=762 0144: dt=129.472000, rms=0.593 (0.064%), neg=0, invalid=762 0145: dt=129.472000, rms=0.593 (0.055%), neg=0, invalid=762 0146: dt=129.472000, rms=0.593 (0.036%), neg=0, invalid=762 0147: dt=129.472000, rms=0.593 (0.042%), neg=0, invalid=762 0148: dt=129.472000, rms=0.592 (0.050%), neg=0, invalid=762 0149: dt=129.472000, rms=0.592 (0.046%), neg=0, invalid=762 0150: dt=129.472000, rms=0.592 (0.040%), neg=0, invalid=762 0151: dt=129.472000, rms=0.592 (0.033%), neg=0, invalid=762 0152: dt=129.472000, rms=0.591 (0.038%), neg=0, invalid=762 0153: dt=129.472000, rms=0.591 (0.043%), neg=0, invalid=762 0154: dt=129.472000, rms=0.591 (0.030%), neg=0, invalid=762 0155: dt=129.472000, rms=0.591 (0.030%), neg=0, invalid=762 0156: dt=129.472000, rms=0.591 (0.031%), neg=0, invalid=762 0157: dt=129.472000, rms=0.590 (0.032%), neg=0, invalid=762 0158: dt=129.472000, rms=0.590 (0.028%), neg=0, invalid=762 0159: dt=129.472000, rms=0.590 (0.029%), neg=0, invalid=762 0160: dt=129.472000, rms=0.590 (0.029%), neg=0, invalid=762 0161: dt=129.472000, rms=0.590 (0.028%), neg=0, invalid=762 0162: dt=129.472000, rms=0.590 (0.024%), neg=0, invalid=762 0163: dt=129.472000, rms=0.589 (0.025%), neg=0, invalid=762 0164: dt=129.472000, rms=0.589 (0.028%), neg=0, invalid=762 0165: dt=129.472000, rms=0.589 (0.031%), neg=0, invalid=762 0166: dt=129.472000, rms=0.589 (0.019%), neg=0, invalid=762 0167: dt=129.472000, rms=0.589 (0.022%), neg=0, invalid=762 0168: dt=129.472000, rms=0.589 (0.021%), neg=0, invalid=762 0169: dt=1183.744000, rms=0.588 (0.045%), neg=0, invalid=762 0170: dt=27.744000, rms=0.588 (0.001%), neg=0, invalid=762 0171: dt=27.744000, rms=0.588 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.589, neg=0, invalid=762 0172: dt=295.936000, rms=0.587 (0.204%), neg=0, invalid=762 0173: dt=129.472000, rms=0.587 (0.065%), neg=0, invalid=762 0174: dt=221.952000, rms=0.587 (0.038%), neg=0, invalid=762 0175: dt=221.952000, rms=0.587 (0.016%), neg=0, invalid=762 0176: dt=221.952000, rms=0.586 (0.076%), neg=0, invalid=762 0177: dt=221.952000, rms=0.586 (0.048%), neg=0, invalid=762 0178: dt=221.952000, rms=0.586 (0.054%), neg=0, invalid=762 0179: dt=221.952000, rms=0.585 (0.061%), neg=0, invalid=762 0180: dt=221.952000, rms=0.585 (0.047%), neg=0, invalid=762 0181: dt=221.952000, rms=0.585 (0.049%), neg=0, invalid=762 0182: dt=221.952000, rms=0.585 (0.043%), neg=0, invalid=762 0183: dt=221.952000, rms=0.584 (0.056%), neg=0, invalid=762 0184: dt=221.952000, rms=0.584 (0.040%), neg=0, invalid=762 0185: dt=221.952000, rms=0.584 (0.024%), neg=0, invalid=762 0186: dt=221.952000, rms=0.583 (0.054%), neg=0, invalid=762 0187: dt=221.952000, rms=0.583 (0.038%), neg=0, invalid=762 0188: dt=221.952000, rms=0.583 (0.021%), neg=0, invalid=762 0189: dt=221.952000, rms=0.583 (0.031%), neg=0, invalid=762 0190: dt=221.952000, rms=0.583 (0.040%), neg=0, invalid=762 0191: dt=221.952000, rms=0.583 (0.025%), neg=0, invalid=762 0192: dt=221.952000, rms=0.582 (0.029%), neg=0, invalid=762 0193: dt=221.952000, rms=0.582 (0.028%), neg=0, invalid=762 0194: dt=221.952000, rms=0.582 (0.028%), neg=0, invalid=762 0195: dt=221.952000, rms=0.582 (0.020%), neg=0, invalid=762 0196: dt=221.952000, rms=0.582 (0.026%), neg=0, invalid=762 0197: dt=221.952000, rms=0.582 (0.028%), neg=0, invalid=762 0198: dt=221.952000, rms=0.582 (0.018%), neg=0, invalid=762 0199: dt=221.952000, rms=0.581 (0.019%), neg=0, invalid=762 0200: dt=221.952000, rms=0.581 (0.015%), neg=0, invalid=762 0201: dt=129.472000, rms=0.581 (0.011%), neg=0, invalid=762 0202: dt=129.472000, rms=0.581 (0.002%), neg=0, invalid=762 0203: dt=129.472000, rms=0.581 (0.004%), neg=0, invalid=762 0204: dt=129.472000, rms=0.581 (0.006%), neg=0, invalid=762 0205: dt=129.472000, rms=0.581 (0.006%), neg=0, invalid=762 0206: dt=129.472000, rms=0.581 (0.006%), neg=0, invalid=762 0207: dt=129.472000, rms=0.581 (0.005%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.582, neg=0, invalid=762 0208: dt=36.288000, rms=0.582 (0.102%), neg=0, invalid=762 0209: dt=103.680000, rms=0.581 (0.156%), neg=0, invalid=762 0210: dt=497.664000, rms=0.574 (1.120%), neg=0, invalid=762 0211: dt=36.288000, rms=0.573 (0.216%), neg=0, invalid=762 0212: dt=82.944000, rms=0.573 (0.097%), neg=0, invalid=762 0213: dt=331.776000, rms=0.568 (0.826%), neg=0, invalid=762 0214: dt=31.104000, rms=0.567 (0.174%), neg=0, invalid=762 0215: dt=15.552000, rms=0.567 (0.007%), neg=0, invalid=762 0216: dt=15.552000, rms=0.567 (0.002%), neg=0, invalid=762 0217: dt=15.552000, rms=0.567 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.567, neg=0, invalid=762 0218: dt=145.152000, rms=0.563 (0.679%), neg=0, invalid=762 0219: dt=75.443709, rms=0.562 (0.153%), neg=0, invalid=762 0220: dt=82.944000, rms=0.562 (0.131%), neg=0, invalid=762 0221: dt=36.288000, rms=0.561 (0.124%), neg=0, invalid=762 0222: dt=580.608000, rms=0.557 (0.636%), neg=0, invalid=762 0223: dt=83.862069, rms=0.556 (0.201%), neg=0, invalid=762 0224: dt=36.288000, rms=0.556 (0.045%), neg=0, invalid=762 0225: dt=36.288000, rms=0.556 (0.033%), neg=0, invalid=762 0226: dt=36.288000, rms=0.555 (0.056%), neg=0, invalid=762 0227: dt=36.288000, rms=0.555 (0.079%), neg=0, invalid=762 0228: dt=36.288000, rms=0.554 (0.099%), neg=0, invalid=762 0229: dt=36.288000, rms=0.554 (0.113%), neg=0, invalid=762 0230: dt=36.288000, rms=0.553 (0.129%), neg=0, invalid=762 0231: dt=36.288000, rms=0.552 (0.128%), neg=0, invalid=762 0232: dt=36.288000, rms=0.552 (0.140%), neg=0, invalid=762 0233: dt=36.288000, rms=0.551 (0.134%), neg=0, invalid=762 0234: dt=36.288000, rms=0.550 (0.152%), neg=0, invalid=762 0235: dt=36.288000, rms=0.549 (0.145%), neg=0, invalid=762 0236: dt=36.288000, rms=0.548 (0.135%), neg=0, invalid=762 0237: dt=36.288000, rms=0.548 (0.140%), neg=0, invalid=762 0238: dt=36.288000, rms=0.547 (0.125%), neg=0, invalid=762 0239: dt=36.288000, rms=0.546 (0.124%), neg=0, invalid=762 0240: dt=36.288000, rms=0.546 (0.114%), neg=0, invalid=762 0241: dt=36.288000, rms=0.545 (0.111%), neg=0, invalid=762 0242: dt=36.288000, rms=0.545 (0.110%), neg=0, invalid=762 0243: dt=36.288000, rms=0.544 (0.101%), neg=0, invalid=762 0244: dt=36.288000, rms=0.543 (0.099%), neg=0, invalid=762 0245: dt=36.288000, rms=0.543 (0.089%), neg=0, invalid=762 0246: dt=36.288000, rms=0.542 (0.085%), neg=0, invalid=762 0247: dt=36.288000, rms=0.542 (0.079%), neg=0, invalid=762 0248: dt=36.288000, rms=0.542 (0.083%), neg=0, invalid=762 0249: dt=36.288000, rms=0.541 (0.074%), neg=0, invalid=762 0250: dt=36.288000, rms=0.541 (0.078%), neg=0, invalid=762 0251: dt=36.288000, rms=0.540 (0.065%), neg=0, invalid=762 0252: dt=36.288000, rms=0.540 (0.069%), neg=0, invalid=762 0253: dt=36.288000, rms=0.540 (0.066%), neg=0, invalid=762 0254: dt=36.288000, rms=0.539 (0.065%), neg=0, invalid=762 0255: dt=36.288000, rms=0.539 (0.061%), neg=0, invalid=762 0256: dt=36.288000, rms=0.539 (0.068%), neg=0, invalid=762 0257: dt=36.288000, rms=0.538 (0.057%), neg=0, invalid=762 0258: dt=36.288000, rms=0.538 (0.054%), neg=0, invalid=762 0259: dt=36.288000, rms=0.538 (0.053%), neg=0, invalid=762 0260: dt=36.288000, rms=0.537 (0.049%), neg=0, invalid=762 0261: dt=36.288000, rms=0.537 (0.057%), neg=0, invalid=762 0262: dt=36.288000, rms=0.537 (0.057%), neg=0, invalid=762 0263: dt=36.288000, rms=0.537 (0.052%), neg=0, invalid=762 0264: dt=36.288000, rms=0.536 (0.049%), neg=0, invalid=762 0265: dt=36.288000, rms=0.536 (0.045%), neg=0, invalid=762 0266: dt=36.288000, rms=0.536 (0.043%), neg=0, invalid=762 0267: dt=36.288000, rms=0.536 (0.042%), neg=0, invalid=762 0268: dt=36.288000, rms=0.535 (0.042%), neg=0, invalid=762 0269: dt=36.288000, rms=0.535 (0.041%), neg=0, invalid=762 0270: dt=36.288000, rms=0.535 (0.045%), neg=0, invalid=762 0271: dt=36.288000, rms=0.535 (0.038%), neg=0, invalid=762 0272: dt=36.288000, rms=0.535 (0.043%), neg=0, invalid=762 0273: dt=36.288000, rms=0.534 (0.036%), neg=0, invalid=762 0274: dt=36.288000, rms=0.534 (0.036%), neg=0, invalid=762 0275: dt=36.288000, rms=0.534 (0.034%), neg=0, invalid=762 0276: dt=36.288000, rms=0.534 (0.040%), neg=0, invalid=762 0277: dt=36.288000, rms=0.534 (0.041%), neg=0, invalid=762 0278: dt=36.288000, rms=0.533 (0.037%), neg=0, invalid=762 0279: dt=36.288000, rms=0.533 (0.033%), neg=0, invalid=762 0280: dt=36.288000, rms=0.533 (0.032%), neg=0, invalid=762 0281: dt=36.288000, rms=0.533 (0.031%), neg=0, invalid=762 0282: dt=36.288000, rms=0.533 (0.040%), neg=0, invalid=762 0283: dt=36.288000, rms=0.532 (0.041%), neg=0, invalid=762 0284: dt=36.288000, rms=0.532 (0.033%), neg=0, invalid=762 0285: dt=36.288000, rms=0.532 (0.033%), neg=0, invalid=762 0286: dt=36.288000, rms=0.532 (0.030%), neg=0, invalid=762 0287: dt=36.288000, rms=0.532 (0.027%), neg=0, invalid=762 0288: dt=36.288000, rms=0.532 (0.031%), neg=0, invalid=762 0289: dt=36.288000, rms=0.531 (0.034%), neg=0, invalid=762 0290: dt=36.288000, rms=0.531 (0.030%), neg=0, invalid=762 0291: dt=36.288000, rms=0.531 (0.028%), neg=0, invalid=762 0292: dt=36.288000, rms=0.531 (0.027%), neg=0, invalid=762 0293: dt=36.288000, rms=0.531 (0.025%), neg=0, invalid=762 0294: dt=36.288000, rms=0.531 (0.025%), neg=0, invalid=762 0295: dt=36.288000, rms=0.531 (0.027%), neg=0, invalid=762 0296: dt=36.288000, rms=0.530 (0.030%), neg=0, invalid=762 0297: dt=36.288000, rms=0.530 (0.028%), neg=0, invalid=762 0298: dt=36.288000, rms=0.530 (0.024%), neg=0, invalid=762 0299: dt=36.288000, rms=0.530 (0.025%), neg=0, invalid=762 0300: dt=36.288000, rms=0.530 (0.024%), neg=0, invalid=762 0301: dt=103.680000, rms=0.530 (0.009%), neg=0, invalid=762 0302: dt=103.680000, rms=0.530 (0.003%), neg=0, invalid=762 0303: dt=103.680000, rms=0.530 (0.019%), neg=0, invalid=762 0304: dt=103.680000, rms=0.530 (0.015%), neg=0, invalid=762 0305: dt=103.680000, rms=0.529 (0.019%), neg=0, invalid=762 0306: dt=103.680000, rms=0.529 (0.022%), neg=0, invalid=762 0307: dt=103.680000, rms=0.529 (0.033%), neg=0, invalid=762 0308: dt=103.680000, rms=0.529 (0.029%), neg=0, invalid=762 0309: dt=103.680000, rms=0.529 (0.020%), neg=0, invalid=762 0310: dt=103.680000, rms=0.529 (0.044%), neg=0, invalid=762 0311: dt=103.680000, rms=0.529 (0.035%), neg=0, invalid=762 0312: dt=103.680000, rms=0.528 (0.033%), neg=0, invalid=762 0313: dt=103.680000, rms=0.528 (0.042%), neg=0, invalid=762 0314: dt=103.680000, rms=0.528 (0.050%), neg=0, invalid=762 0315: dt=103.680000, rms=0.528 (0.034%), neg=0, invalid=762 0316: dt=103.680000, rms=0.527 (0.038%), neg=0, invalid=762 0317: dt=103.680000, rms=0.527 (0.048%), neg=0, invalid=762 0318: dt=103.680000, rms=0.527 (0.036%), neg=0, invalid=762 0319: dt=103.680000, rms=0.527 (0.047%), neg=0, invalid=762 0320: dt=103.680000, rms=0.527 (0.046%), neg=0, invalid=762 0321: dt=103.680000, rms=0.526 (0.046%), neg=0, invalid=762 0322: dt=103.680000, rms=0.526 (0.035%), neg=0, invalid=762 0323: dt=103.680000, rms=0.526 (0.051%), neg=0, invalid=762 0324: dt=103.680000, rms=0.526 (0.040%), neg=0, invalid=762 0325: dt=103.680000, rms=0.525 (0.040%), neg=0, invalid=762 0326: dt=103.680000, rms=0.525 (0.051%), neg=0, invalid=762 0327: dt=103.680000, rms=0.525 (0.039%), neg=0, invalid=762 0328: dt=103.680000, rms=0.525 (0.030%), neg=0, invalid=762 0329: dt=103.680000, rms=0.525 (0.046%), neg=0, invalid=762 0330: dt=103.680000, rms=0.524 (0.042%), neg=0, invalid=762 0331: dt=103.680000, rms=0.524 (0.027%), neg=0, invalid=762 0332: dt=103.680000, rms=0.524 (0.039%), neg=0, invalid=762 0333: dt=103.680000, rms=0.524 (0.034%), neg=0, invalid=762 0334: dt=103.680000, rms=0.524 (0.032%), neg=0, invalid=762 0335: dt=103.680000, rms=0.524 (0.022%), neg=0, invalid=762 0336: dt=103.680000, rms=0.523 (0.038%), neg=0, invalid=762 0337: dt=103.680000, rms=0.523 (0.027%), neg=0, invalid=762 0338: dt=103.680000, rms=0.523 (0.037%), neg=0, invalid=762 0339: dt=103.680000, rms=0.523 (0.029%), neg=0, invalid=762 0340: dt=103.680000, rms=0.523 (0.023%), neg=0, invalid=762 0341: dt=103.680000, rms=0.523 (0.032%), neg=0, invalid=762 0342: dt=103.680000, rms=0.522 (0.029%), neg=0, invalid=762 0343: dt=103.680000, rms=0.522 (0.021%), neg=0, invalid=762 0344: dt=103.680000, rms=0.522 (0.022%), neg=0, invalid=762 0345: dt=103.680000, rms=0.522 (0.037%), neg=0, invalid=762 0346: dt=103.680000, rms=0.522 (0.012%), neg=0, invalid=762 0347: dt=103.680000, rms=0.522 (0.023%), neg=0, invalid=762 0348: dt=103.680000, rms=0.522 (0.024%), neg=0, invalid=762 0349: dt=103.680000, rms=0.522 (0.026%), neg=0, invalid=762 0350: dt=103.680000, rms=0.522 (0.010%), neg=0, invalid=762 0351: dt=103.680000, rms=0.521 (0.028%), neg=0, invalid=762 0352: dt=103.680000, rms=0.521 (0.013%), neg=0, invalid=762 0353: dt=103.680000, rms=0.521 (0.024%), neg=0, invalid=762 0354: dt=103.680000, rms=0.521 (0.017%), neg=0, invalid=762 0355: dt=82.944000, rms=0.521 (0.010%), neg=0, invalid=762 0356: dt=82.944000, rms=0.521 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.529, neg=0, invalid=762 0357: dt=8.000000, rms=0.529 (0.064%), neg=0, invalid=762 0358: dt=6.400000, rms=0.529 (0.011%), neg=0, invalid=762 0359: dt=6.400000, rms=0.529 (0.007%), neg=0, invalid=762 0360: dt=6.400000, rms=0.529 (-0.011%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.529, neg=0, invalid=762 0361: dt=67.555556, rms=0.526 (0.494%), neg=0, invalid=762 0362: dt=21.218329, rms=0.525 (0.255%), neg=0, invalid=762 0363: dt=44.800000, rms=0.523 (0.263%), neg=0, invalid=762 0364: dt=25.600000, rms=0.523 (0.152%), neg=0, invalid=762 0365: dt=44.800000, rms=0.522 (0.211%), neg=0, invalid=762 0366: dt=19.200000, rms=0.521 (0.157%), neg=0, invalid=762 0367: dt=102.400000, rms=0.519 (0.304%), neg=0, invalid=762 0368: dt=11.200000, rms=0.518 (0.206%), neg=0, invalid=762 0369: dt=38.400000, rms=0.517 (0.120%), neg=0, invalid=762 0370: dt=25.600000, rms=0.517 (0.134%), neg=0, invalid=762 0371: dt=32.000000, rms=0.516 (0.101%), neg=0, invalid=762 0372: dt=32.000000, rms=0.516 (0.112%), neg=0, invalid=762 0373: dt=25.600000, rms=0.515 (0.102%), neg=0, invalid=762 0374: dt=32.000000, rms=0.515 (0.092%), neg=0, invalid=762 0375: dt=25.600000, rms=0.514 (0.093%), neg=0, invalid=762 0376: dt=38.400000, rms=0.514 (0.086%), neg=0, invalid=762 0377: dt=25.600000, rms=0.513 (0.098%), neg=0, invalid=762 0378: dt=32.000000, rms=0.513 (0.070%), neg=0, invalid=762 0379: dt=25.600000, rms=0.512 (0.092%), neg=0, invalid=762 0380: dt=32.000000, rms=0.512 (0.065%), neg=0, invalid=762 0381: dt=25.600000, rms=0.512 (0.088%), neg=0, invalid=762 0382: dt=38.400000, rms=0.511 (0.058%), neg=0, invalid=762 0383: dt=25.600000, rms=0.511 (0.092%), neg=0, invalid=762 0384: dt=25.600000, rms=0.511 (0.049%), neg=0, invalid=762 0385: dt=25.600000, rms=0.510 (0.070%), neg=0, invalid=762 0386: dt=25.600000, rms=0.510 (0.101%), neg=0, invalid=762 0387: dt=25.600000, rms=0.509 (0.145%), neg=0, invalid=762 0388: dt=25.600000, rms=0.508 (0.166%), neg=0, invalid=762 0389: dt=25.600000, rms=0.507 (0.204%), neg=0, invalid=762 0390: dt=25.600000, rms=0.506 (0.194%), neg=0, invalid=762 0391: dt=25.600000, rms=0.505 (0.209%), neg=0, invalid=762 0392: dt=25.600000, rms=0.504 (0.211%), neg=0, invalid=762 0393: dt=25.600000, rms=0.503 (0.218%), neg=0, invalid=762 0394: dt=25.600000, rms=0.502 (0.187%), neg=0, invalid=762 0395: dt=25.600000, rms=0.501 (0.183%), neg=0, invalid=762 0396: dt=25.600000, rms=0.501 (0.020%), neg=0, invalid=762 0397: dt=25.600000, rms=0.501 (0.016%), neg=0, invalid=762 0398: dt=44.800000, rms=0.501 (0.012%), neg=0, invalid=762 0399: dt=44.800000, rms=0.501 (0.021%), neg=0, invalid=762 0400: dt=44.800000, rms=0.501 (0.021%), neg=0, invalid=762 0401: dt=44.800000, rms=0.500 (0.061%), neg=0, invalid=762 0402: dt=44.800000, rms=0.500 (0.050%), neg=0, invalid=762 0403: dt=44.800000, rms=0.500 (0.073%), neg=0, invalid=762 0404: dt=44.800000, rms=0.500 (0.020%), neg=0, invalid=762 0405: dt=44.800000, rms=0.500 (-0.050%), neg=0, invalid=762 0406: dt=11.200000, rms=0.500 (0.010%), neg=0, invalid=762 0407: dt=32.000000, rms=0.499 (0.015%), neg=0, invalid=762 0408: dt=11.200000, rms=0.499 (0.011%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.515, neg=0, invalid=762 0409: dt=0.000000, rms=0.514 (0.042%), neg=0, invalid=762 0410: dt=0.000000, rms=0.514 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.515, neg=0, invalid=762 0411: dt=0.000000, rms=0.514 (0.042%), neg=0, invalid=762 0412: dt=0.000000, rms=0.514 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.545, neg=0, invalid=762 0413: dt=1.536000, rms=0.542 (0.625%), neg=0, invalid=762 0414: dt=0.448000, rms=0.542 (0.018%), neg=0, invalid=762 0415: dt=0.448000, rms=0.542 (-0.012%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.542, neg=0, invalid=762 0416: dt=1.280000, rms=0.541 (0.209%), neg=0, invalid=762 0417: dt=0.448000, rms=0.541 (0.011%), neg=0, invalid=762 0418: dt=0.448000, rms=0.541 (-0.001%), 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=0.510, neg=0, invalid=762 0419: dt=0.448000, rms=0.498 (2.406%), neg=0, invalid=762 0420: dt=0.448000, rms=0.496 (0.499%), neg=0, invalid=762 0421: dt=0.448000, rms=0.494 (0.299%), neg=0, invalid=762 0422: dt=0.558824, rms=0.493 (0.207%), neg=0, invalid=762 0423: dt=0.448000, rms=0.492 (0.120%), neg=0, invalid=762 0424: dt=0.448000, rms=0.492 (0.077%), neg=0, invalid=762 0425: dt=0.448000, rms=0.492 (0.069%), neg=0, invalid=762 0426: dt=0.448000, rms=0.492 (0.042%), neg=0, invalid=762 0427: dt=0.448000, rms=0.491 (0.046%), neg=0, invalid=762 0428: dt=0.448000, rms=0.491 (0.069%), neg=0, invalid=762 0429: dt=0.448000, rms=0.491 (0.072%), neg=0, invalid=762 0430: dt=0.448000, rms=0.490 (0.081%), neg=0, invalid=762 0431: dt=0.448000, rms=0.490 (0.004%), neg=0, invalid=762 0432: dt=0.448000, rms=0.490 (-0.009%), neg=0, invalid=762 0433: dt=0.080000, rms=0.490 (0.000%), neg=0, invalid=762 0434: dt=0.192000, rms=0.490 (0.001%), neg=0, invalid=762 0435: dt=0.448000, rms=0.490 (0.007%), neg=0, invalid=762 0436: dt=0.000000, rms=0.490 (0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.490, neg=0, invalid=762 0437: dt=0.448000, rms=0.487 (0.778%), neg=0, invalid=762 0438: dt=0.448000, rms=0.486 (0.133%), neg=0, invalid=762 0439: dt=0.448000, rms=0.486 (0.042%), neg=0, invalid=762 0440: dt=0.448000, rms=0.486 (0.025%), neg=0, invalid=762 0441: dt=0.448000, rms=0.486 (0.028%), neg=0, invalid=762 0442: dt=0.448000, rms=0.485 (0.003%), neg=0, invalid=762 0443: dt=0.448000, rms=0.485 (0.014%), neg=0, invalid=762 0444: dt=0.448000, rms=0.485 (0.020%), neg=0, invalid=762 0445: dt=0.448000, rms=0.485 (0.019%), neg=0, invalid=762 0446: dt=0.256000, rms=0.485 (0.004%), neg=0, invalid=762 0447: dt=0.256000, rms=0.485 (0.008%), neg=0, invalid=762 0448: dt=0.256000, rms=0.485 (0.007%), neg=0, invalid=762 0449: dt=0.256000, rms=0.485 (0.010%), neg=0, invalid=762 0450: dt=0.256000, rms=0.485 (0.005%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.483, neg=0, invalid=762 0451: dt=0.000000, rms=0.483 (0.053%), neg=0, invalid=762 0452: dt=0.000000, rms=0.483 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.483, neg=0, invalid=762 0453: dt=221.952000, rms=0.483 (0.128%), neg=0, invalid=762 0454: dt=92.480000, rms=0.483 (0.020%), neg=0, invalid=762 0455: dt=92.480000, rms=0.483 (0.003%), neg=0, invalid=762 0456: dt=92.480000, rms=0.483 (0.006%), neg=0, invalid=762 0457: dt=92.480000, rms=0.482 (0.018%), neg=0, invalid=762 0458: dt=92.480000, rms=0.482 (0.015%), neg=0, invalid=762 0459: dt=92.480000, rms=0.482 (0.016%), neg=0, invalid=762 0460: dt=92.480000, rms=0.482 (0.009%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.483, neg=0, invalid=762 0461: dt=0.000000, rms=0.482 (0.052%), neg=0, invalid=762 0462: dt=0.000000, rms=0.482 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.483, neg=0, invalid=762 0463: dt=145.152000, rms=0.481 (0.331%), neg=0, invalid=762 0464: dt=62.208000, rms=0.480 (0.095%), neg=0, invalid=762 0465: dt=62.208000, rms=0.480 (0.075%), neg=0, invalid=762 0466: dt=62.208000, rms=0.479 (0.150%), neg=0, invalid=762 0467: dt=62.208000, rms=0.479 (0.140%), neg=0, invalid=762 0468: dt=62.208000, rms=0.478 (0.151%), neg=0, invalid=762 0469: dt=62.208000, rms=0.477 (0.144%), neg=0, invalid=762 0470: dt=62.208000, rms=0.477 (0.149%), neg=0, invalid=762 0471: dt=62.208000, rms=0.476 (0.096%), neg=0, invalid=762 0472: dt=62.208000, rms=0.476 (0.104%), neg=0, invalid=762 0473: dt=62.208000, rms=0.475 (0.093%), neg=0, invalid=762 0474: dt=36.288000, rms=0.475 (0.018%), neg=0, invalid=762 0475: dt=36.288000, rms=0.475 (0.007%), neg=0, invalid=762 0476: dt=36.288000, rms=0.475 (0.016%), neg=0, invalid=762 0477: dt=36.288000, rms=0.475 (0.024%), neg=0, invalid=762 0478: dt=36.288000, rms=0.475 (0.023%), neg=0, invalid=762 0479: dt=36.288000, rms=0.475 (0.025%), neg=0, invalid=762 0480: dt=36.288000, rms=0.475 (0.023%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.475, neg=0, invalid=762 0481: dt=11.200000, rms=0.475 (0.117%), neg=0, invalid=762 0482: dt=11.200000, rms=0.475 (0.038%), neg=0, invalid=762 0483: dt=11.200000, rms=0.474 (0.041%), neg=0, invalid=762 0484: dt=11.200000, rms=0.474 (0.014%), neg=0, invalid=762 0485: dt=11.200000, rms=0.474 (-0.036%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.475, neg=0, invalid=762 0486: dt=53.000000, rms=0.469 (1.089%), neg=0, invalid=762 0487: dt=20.675799, rms=0.468 (0.296%), neg=0, invalid=762 0488: dt=44.800000, rms=0.467 (0.236%), neg=0, invalid=762 0489: dt=44.800000, rms=0.467 (-0.046%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.469, neg=0, invalid=762 0490: dt=8.863636, rms=0.467 (0.437%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 9 iterations, nbhd size=1, neg = 0 0491: dt=23.384615, rms=0.465 (0.436%), neg=0, invalid=762 0492: dt=5.818182, rms=0.465 (0.056%), neg=0, invalid=762 0493: dt=5.818182, rms=0.465 (0.103%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0494: dt=5.818182, rms=0.464 (0.110%), neg=0, invalid=762 0495: dt=5.818182, rms=0.464 (0.089%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0496: dt=5.818182, rms=0.463 (0.060%), neg=0, invalid=762 0497: dt=4.032000, rms=0.463 (0.011%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.464, neg=0, invalid=762 0498: dt=18.502058, rms=0.459 (1.084%), neg=0, invalid=762 0499: dt=8.301887, rms=0.458 (0.192%), neg=0, invalid=762 0500: dt=8.301887, rms=0.457 (0.075%), neg=0, invalid=762 0501: dt=8.301887, rms=0.457 (0.095%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 4 iterations, nbhd size=0, neg = 0 0502: dt=8.301887, rms=0.457 (0.103%), neg=0, invalid=762 0503: dt=8.301887, rms=0.456 (0.109%), neg=0, invalid=762 0504: dt=8.301887, rms=0.455 (0.125%), neg=0, invalid=762 0505: dt=8.301887, rms=0.455 (0.149%), neg=0, invalid=762 0506: dt=8.301887, rms=0.454 (0.161%), neg=0, invalid=762 0507: dt=8.301887, rms=0.453 (0.138%), neg=0, invalid=762 0508: dt=8.301887, rms=0.453 (0.121%), neg=0, invalid=762 0509: dt=8.301887, rms=0.452 (0.111%), neg=0, invalid=762 0510: dt=11.520000, rms=0.452 (0.027%), neg=0, invalid=762 0511: dt=11.520000, rms=0.452 (-0.038%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.458, neg=0, invalid=762 0512: dt=0.000000, rms=0.458 (0.048%), neg=0, invalid=762 0513: dt=0.000000, rms=0.458 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.458, neg=0, invalid=762 0514: dt=0.000000, rms=0.458 (0.048%), neg=0, invalid=762 0515: dt=0.000000, rms=0.458 (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=0.449, neg=0, invalid=762 iter 0, gcam->neg = 431 after 13 iterations, nbhd size=1, neg = 0 0516: dt=1.854231, rms=0.430 (4.237%), neg=0, invalid=762 0517: dt=0.028000, rms=0.430 (0.018%), neg=0, invalid=762 0518: dt=0.028000, rms=0.430 (-0.006%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.430, neg=0, invalid=762 0519: dt=0.080000, rms=0.430 (0.111%), neg=0, invalid=762 0520: dt=0.007000, rms=0.430 (-0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.419, neg=0, invalid=762 0521: dt=0.000000, rms=0.419 (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 0522: dt=3.468000, rms=0.419 (0.000%), neg=0, invalid=762 0523: dt=0.090313, rms=0.419 (0.000%), neg=0, invalid=762 0524: dt=0.090313, rms=0.419 (0.000%), neg=0, invalid=762 0525: dt=0.090313, rms=0.419 (-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=0.419, neg=0, invalid=762 0526: dt=0.000000, rms=0.419 (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 0527: dt=36.288000, rms=0.419 (0.020%), neg=0, invalid=762 0528: dt=82.944000, rms=0.419 (0.016%), neg=0, invalid=762 0529: dt=82.944000, rms=0.419 (0.037%), neg=0, invalid=762 0530: dt=82.944000, rms=0.419 (0.045%), neg=0, invalid=762 0531: dt=82.944000, rms=0.418 (0.027%), neg=0, invalid=762 0532: dt=82.944000, rms=0.418 (0.020%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.419, neg=0, invalid=762 0533: dt=2.800000, rms=0.419 (0.009%), neg=0, invalid=762 0534: dt=2.000000, rms=0.419 (0.002%), neg=0, invalid=762 0535: dt=2.000000, rms=0.419 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.419, neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0536: dt=119.970480, rms=0.415 (0.847%), neg=0, invalid=762 0537: dt=11.200000, rms=0.415 (0.141%), neg=0, invalid=762 0538: dt=11.200000, rms=0.415 (0.037%), neg=0, invalid=762 0539: dt=11.200000, rms=0.415 (0.010%), neg=0, invalid=762 0540: dt=11.200000, rms=0.415 (-0.020%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.417, neg=0, invalid=762 0541: dt=3.466667, rms=0.417 (0.043%), neg=0, invalid=762 0542: dt=0.864000, rms=0.417 (0.002%), neg=0, invalid=762 0543: dt=0.864000, rms=0.417 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.417, neg=0, invalid=762 iter 0, gcam->neg = 6 after 10 iterations, nbhd size=1, neg = 0 0544: dt=27.809524, rms=0.414 (0.679%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0545: dt=9.882353, rms=0.413 (0.215%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0546: dt=9.882353, rms=0.413 (0.037%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0547: dt=9.882353, rms=0.412 (0.062%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0548: dt=9.882353, rms=0.412 (0.119%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0549: dt=9.882353, rms=0.411 (0.118%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 0550: dt=9.882353, rms=0.411 (0.106%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0551: dt=16.128000, rms=0.411 (0.018%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.416, neg=0, invalid=762 0552: dt=0.000050, rms=0.416 (0.000%), neg=0, invalid=762 0553: dt=0.000000, rms=0.416 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.416, neg=0, invalid=762 0554: dt=0.000000, rms=0.416 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.408, neg=0, invalid=762 iter 0, gcam->neg = 333 after 15 iterations, nbhd size=1, neg = 0 0555: dt=1.159257, rms=0.401 (1.569%), neg=0, invalid=762 0556: dt=0.000023, rms=0.401 (0.000%), neg=0, invalid=762 0557: dt=0.000023, rms=0.401 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.401, neg=0, invalid=762 0558: dt=0.112000, rms=0.401 (0.078%), neg=0, invalid=762 0559: dt=0.112000, rms=0.401 (0.038%), neg=0, invalid=762 0560: dt=0.112000, rms=0.401 (0.028%), neg=0, invalid=762 0561: dt=0.112000, rms=0.401 (-0.002%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 3 hours, 11 minutes and 20 seconds. mri_ca_register utimesec 11453.373822 mri_ca_register stimesec 7.946791 mri_ca_register ru_maxrss 1338552 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 5561463 mri_ca_register ru_majflt 45 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 8872 mri_ca_register ru_oublock 63304 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 90 mri_ca_register ru_nivcsw 1163973 FSRUNTIME@ mri_ca_register 3.1890 hours 1 threads #-------------------------------------- #@# SubCort Seg Thu Sep 7 15:41:27 CEST 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 lugh.fisica.uniud.it machine x86_64 setenv SUBJECTS_DIR /home/gc/study/recon-all cd /home/gc/study/recon-all/400614dclass/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 7.19 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 = 0.16140 (33) Left_Lateral_Ventricle (4): linear fit = 1.74 x + 0.0 (597 voxels, overlap=0.038) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (597 voxels, peak = 35), gca=30.0 gca peak = 0.17677 (13) mri peak = 0.21683 (31) Right_Lateral_Ventricle (43): linear fit = 2.31 x + 0.0 (308 voxels, overlap=0.042) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (308 voxels, peak = 30), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.15393 (100) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (966 voxels, overlap=0.955) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (966 voxels, peak = 99), gca=99.3 gca peak = 0.16930 (96) mri peak = 0.15771 (99) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (855 voxels, overlap=0.626) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (855 voxels, peak = 100), gca=100.3 gca peak = 0.24553 (55) mri peak = 0.12645 (76) Right_Hippocampus (53): linear fit = 1.36 x + 0.0 (1124 voxels, overlap=0.019) Right_Hippocampus (53): linear fit = 1.36 x + 0.0 (1124 voxels, peak = 75), gca=74.5 gca peak = 0.30264 (59) mri peak = 0.15584 (75) Left_Hippocampus (17): linear fit = 1.27 x + 0.0 (1007 voxels, overlap=0.016) Left_Hippocampus (17): linear fit = 1.27 x + 0.0 (1007 voxels, peak = 75), gca=75.2 gca peak = 0.07580 (103) mri peak = 0.13911 (102) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45389 voxels, overlap=0.659) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45389 voxels, peak = 102), gca=102.5 gca peak = 0.07714 (104) mri peak = 0.12524 (103) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37863 voxels, overlap=0.642) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37863 voxels, peak = 103), gca=103.5 gca peak = 0.09712 (58) mri peak = 0.04207 (77) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (37454 voxels, overlap=0.002) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (37454 voxels, peak = 78), gca=78.0 gca peak = 0.11620 (58) mri peak = 0.04272 (79) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (30939 voxels, overlap=0.001) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (30939 voxels, peak = 78), gca=78.0 gca peak = 0.30970 (66) mri peak = 0.14461 (85) Right_Caudate (50): linear fit = 1.26 x + 0.0 (812 voxels, overlap=0.018) Right_Caudate (50): linear fit = 1.26 x + 0.0 (812 voxels, peak = 83), gca=83.5 gca peak = 0.15280 (69) mri peak = 0.15105 (88) Left_Caudate (11): linear fit = 1.17 x + 0.0 (854 voxels, overlap=0.019) Left_Caudate (11): linear fit = 1.17 x + 0.0 (854 voxels, peak = 81), gca=81.1 gca peak = 0.13902 (56) mri peak = 0.07411 (77) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (33906 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (33906 voxels, peak = 77), gca=77.0 gca peak = 0.14777 (55) mri peak = 0.07555 (78) Right_Cerebellum_Cortex (47): linear fit = 1.38 x + 0.0 (35245 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.38 x + 0.0 (35245 voxels, peak = 76), gca=75.6 gca peak = 0.16765 (84) mri peak = 0.11912 (89) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (6402 voxels, overlap=0.530) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (6402 voxels, peak = 89), gca=89.5 gca peak = 0.18739 (84) mri peak = 0.16019 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (6586 voxels, overlap=0.138) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (6586 voxels, peak = 91), gca=91.1 gca peak = 0.29869 (57) mri peak = 0.14957 (79) Left_Amygdala (18): linear fit = 1.35 x + 0.0 (575 voxels, overlap=0.049) Left_Amygdala (18): linear fit = 1.35 x + 0.0 (575 voxels, peak = 77), gca=76.7 gca peak = 0.33601 (57) mri peak = 0.13680 (79) Right_Amygdala (54): linear fit = 1.38 x + 0.0 (573 voxels, overlap=0.039) Right_Amygdala (54): linear fit = 1.38 x + 0.0 (573 voxels, peak = 79), gca=78.9 gca peak = 0.11131 (90) mri peak = 0.10150 (96) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (5005 voxels, overlap=0.528) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (5005 voxels, peak = 97), gca=96.8 gca peak = 0.11793 (83) mri peak = 0.09635 (95) Right_Thalamus_Proper (49): linear fit = 1.15 x + 0.0 (4577 voxels, overlap=0.097) Right_Thalamus_Proper (49): linear fit = 1.15 x + 0.0 (4577 voxels, peak = 96), gca=95.9 gca peak = 0.08324 (81) mri peak = 0.12582 (89) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1979 voxels, overlap=0.154) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1979 voxels, peak = 90), gca=90.3 gca peak = 0.10360 (77) mri peak = 0.11997 (91) Right_Putamen (51): linear fit = 1.16 x + 0.0 (2307 voxels, overlap=0.043) Right_Putamen (51): linear fit = 1.16 x + 0.0 (2307 voxels, peak = 90), gca=89.7 gca peak = 0.08424 (78) mri peak = 0.07297 (89) Brain_Stem (16): linear fit = 1.12 x + 0.0 (13510 voxels, overlap=0.414) Brain_Stem (16): linear fit = 1.12 x + 0.0 (13510 voxels, peak = 88), gca=87.8 gca peak = 0.12631 (89) mri peak = 0.09075 (99) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1711 voxels, overlap=0.012) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1711 voxels, peak = 100), gca=100.1 gca peak = 0.14500 (87) mri peak = 0.08560 (99) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1767 voxels, overlap=0.331) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1767 voxels, peak = 96), gca=96.1 gca peak = 0.14975 (24) mri peak = 0.08175 (33) gca peak = 0.19357 (14) mri peak = 0.14834 (32) Fourth_Ventricle (15): linear fit = 2.14 x + 0.0 (755 voxels, overlap=0.078) Fourth_Ventricle (15): linear fit = 2.14 x + 0.0 (755 voxels, peak = 30), gca=30.0 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.34 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.50 x + 0.0 Left_Pallidum too bright - rescaling by 0.996 (from 1.045) to 99.9 (was 100.3) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.12544 (31) mri peak = 0.16140 (33) Left_Lateral_Ventricle (4): linear fit = 1.14 x + 0.0 (597 voxels, overlap=0.488) Left_Lateral_Ventricle (4): linear fit = 1.14 x + 0.0 (597 voxels, peak = 35), gca=35.5 gca peak = 0.13981 (19) mri peak = 0.21683 (31) Right_Lateral_Ventricle (43): linear fit = 1.60 x + 0.0 (308 voxels, overlap=0.262) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (308 voxels, peak = 30), gca=28.5 gca peak = 0.28910 (100) mri peak = 0.15393 (100) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (966 voxels, overlap=1.002) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (966 voxels, peak = 100), gca=100.5 gca peak = 0.15324 (99) mri peak = 0.15771 (99) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (855 voxels, overlap=0.996) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (855 voxels, peak = 99), gca=99.0 gca peak = 0.21449 (75) mri peak = 0.12645 (76) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1124 voxels, overlap=0.976) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1124 voxels, peak = 75), gca=75.0 gca peak = 0.23896 (72) mri peak = 0.15584 (75) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1007 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1007 voxels, peak = 71), gca=70.9 gca peak = 0.07866 (102) mri peak = 0.13911 (102) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45389 voxels, overlap=0.652) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45389 voxels, peak = 101), gca=101.5 gca peak = 0.08042 (104) mri peak = 0.12524 (103) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37863 voxels, overlap=0.631) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37863 voxels, peak = 103), gca=103.5 gca peak = 0.07334 (78) mri peak = 0.04207 (77) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (37454 voxels, overlap=0.965) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (37454 voxels, peak = 77), gca=76.8 gca peak = 0.08773 (78) mri peak = 0.04272 (79) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (30939 voxels, overlap=0.968) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (30939 voxels, peak = 77), gca=76.8 gca peak = 0.21463 (83) mri peak = 0.14461 (85) Right_Caudate (50): linear fit = 1.00 x + 0.0 (812 voxels, overlap=0.999) Right_Caudate (50): linear fit = 1.00 x + 0.0 (812 voxels, peak = 83), gca=83.0 gca peak = 0.14944 (91) mri peak = 0.15105 (88) Left_Caudate (11): linear fit = 0.99 x + 0.0 (854 voxels, overlap=0.918) Left_Caudate (11): linear fit = 0.99 x + 0.0 (854 voxels, peak = 90), gca=89.6 gca peak = 0.10524 (76) mri peak = 0.07411 (77) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (33906 voxels, overlap=0.938) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (33906 voxels, peak = 76), gca=76.0 gca peak = 0.11458 (75) mri peak = 0.07555 (78) Right_Cerebellum_Cortex (47): linear fit = 1.01 x + 0.0 (35245 voxels, overlap=0.925) Right_Cerebellum_Cortex (47): linear fit = 1.01 x + 0.0 (35245 voxels, peak = 76), gca=76.1 gca peak = 0.15948 (90) mri peak = 0.11912 (89) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6402 voxels, overlap=0.904) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6402 voxels, peak = 91), gca=91.3 gca peak = 0.14713 (91) mri peak = 0.16019 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6586 voxels, overlap=0.849) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6586 voxels, peak = 91), gca=91.0 gca peak = 0.29162 (78) mri peak = 0.14957 (79) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (575 voxels, overlap=1.007) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (575 voxels, peak = 79), gca=79.2 gca peak = 0.25614 (79) mri peak = 0.13680 (79) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (573 voxels, overlap=0.993) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (573 voxels, peak = 80), gca=80.2 gca peak = 0.10059 (96) mri peak = 0.10150 (96) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5005 voxels, overlap=0.873) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5005 voxels, peak = 96), gca=96.0 gca peak = 0.10103 (93) mri peak = 0.09635 (95) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (4577 voxels, overlap=0.858) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (4577 voxels, peak = 92), gca=91.6 gca peak = 0.08274 (92) mri peak = 0.12582 (89) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1979 voxels, overlap=0.711) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1979 voxels, peak = 94), gca=94.3 gca peak = 0.08099 (88) mri peak = 0.11997 (91) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2307 voxels, overlap=0.703) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2307 voxels, peak = 89), gca=89.3 gca peak = 0.08007 (88) mri peak = 0.07297 (89) Brain_Stem (16): linear fit = 1.00 x + 0.0 (13510 voxels, overlap=0.797) Brain_Stem (16): linear fit = 1.00 x + 0.0 (13510 voxels, peak = 88), gca=87.6 gca peak = 0.10547 (101) mri peak = 0.09075 (99) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1711 voxels, overlap=0.789) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1711 voxels, peak = 102), gca=101.5 gca peak = 0.15057 (96) mri peak = 0.08560 (99) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1767 voxels, overlap=0.892) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1767 voxels, peak = 96), gca=96.0 gca peak = 0.12656 (38) mri peak = 0.08175 (33) gca peak = 0.16542 (24) mri peak = 0.14834 (32) Fourth_Ventricle (15): linear fit = 1.43 x + 0.0 (755 voxels, overlap=0.180) Fourth_Ventricle (15): linear fit = 1.43 x + 0.0 (755 voxels, peak = 34), gca=34.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.13499 (41) gca peak Left_Thalamus = 0.36646 (102) gca peak Third_Ventricle = 0.12656 (38) gca peak CSF = 0.15446 (55) gca peak Left_Accumbens_area = 0.63017 (73) gca peak Left_undetermined = 0.95280 (34) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12303 (35) gca peak Right_Inf_Lat_Vent = 0.19032 (31) gca peak Right_Accumbens_area = 0.29880 (82) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14504 (37) gca peak Fifth_Ventricle = 0.51780 (46) gca peak WM_hypointensities = 0.07860 (76) gca peak non_WM_hypointensities = 0.11534 (54) gca peak Optic_Chiasm = 0.61319 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.36 x + 0.0 Left_Putamen too bright - rescaling by 0.978 (from 1.025) to 92.2 (was 94.3) Left_Pallidum too bright - rescaling by 1.004 (from 1.000) to 99.4 (was 99.0) Right_Pallidum too bright - rescaling by 0.989 (from 1.005) to 99.4 (was 100.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 64722 voxels changed in iteration 0 of unlikely voxel relabeling 410 voxels changed in iteration 1 of unlikely voxel relabeling 70 voxels changed in iteration 2 of unlikely voxel relabeling 13 voxels changed in iteration 3 of unlikely voxel relabeling 7 voxels changed in iteration 4 of unlikely voxel relabeling 92956 gm and wm labels changed (%31 to gray, %69 to white out of all changed labels) 544 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 70213 changed. image ll: -2.112, PF=0.500 pass 2: 18882 changed. image ll: -2.111, PF=0.500 pass 3: 5747 changed. pass 4: 2108 changed. 79651 voxels changed in iteration 0 of unlikely voxel relabeling 434 voxels changed in iteration 1 of unlikely voxel relabeling 128 voxels changed in iteration 2 of unlikely voxel relabeling 51 voxels changed in iteration 3 of unlikely voxel relabeling 6 voxels changed in iteration 4 of unlikely voxel relabeling 5787 voxels changed in iteration 0 of unlikely voxel relabeling 81 voxels changed in iteration 1 of unlikely voxel relabeling 8 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 5426 voxels changed in iteration 0 of unlikely voxel relabeling 49 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4530 voxels changed in iteration 0 of unlikely voxel relabeling 20 voxels changed in iteration 1 of unlikely voxel relabeling 18 voxels changed in iteration 2 of unlikely voxel relabeling 12 voxels changed in iteration 3 of unlikely voxel relabeling 4 voxels changed in iteration 4 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 4801.249099 mri_ca_label stimesec 1.622753 mri_ca_label ru_maxrss 2115768 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 697129 mri_ca_label ru_majflt 9 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 1584 mri_ca_label ru_oublock 472 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 98 mri_ca_label ru_nivcsw 486719 auto-labeling took 80 minutes and 9 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/gc/study/recon-all/400614dclass/mri/transforms/cc_up.lta 400614dclass will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/gc/study/recon-all/400614dclass/mri/transforms/cc_up.lta reading aseg from /home/gc/study/recon-all/400614dclass/mri/aseg.auto_noCCseg.mgz reading norm from /home/gc/study/recon-all/400614dclass/mri/norm.mgz 37779 voxels in left wm, 41026 in right wm, xrange [121, 130] searching rotation angles z=[-2 12], y=[-6 8] searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.6 searching scale 1 Z rot 6.8 searching scale 1 Z rot 7.1 searching scale 1 Z rot 7.3 searching scale 1 Z rot 7.6 searching scale 1 Z rot 7.8 searching scale 1 Z rot 8.1 searching scale 1 Z rot 8.3 searching scale 1 Z rot 8.6 searching scale 1 Z rot 8.8 searching scale 1 Z rot 9.1 searching scale 1 Z rot 9.3 searching scale 1 Z rot 9.6 searching scale 1 Z rot 9.8 searching scale 1 Z rot 10.1 searching scale 1 Z rot 10.3 searching scale 1 Z rot 10.6 searching scale 1 Z rot 10.8 searching scale 1 Z rot 11.1 searching scale 1 Z rot 11.3 global minimum found at slice 125.3, rotations (0.62, 4.60) final transformation (x=125.3, yr=0.619, zr=4.595): 0.99673 -0.08012 0.01077 8.99282; 0.08011 0.99679 0.00087 30.15075; -0.01081 0.00000 0.99994 18.36038; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 130] in xformed coordinates best xformed slice 127 cc center is found at 127 88 111 eigenvectors: 0.01017 0.00390 0.99994; -0.01267 -0.99991 0.00403; 0.99987 -0.01271 -0.01012; writing aseg with callosum to /home/gc/study/recon-all/400614dclass/mri/aseg.auto.mgz... corpus callosum segmentation took 0.8 minutes #-------------------------------------- #@# Merge ASeg Thu Sep 7 17:02:26 CEST 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Sep 7 17:02:26 CEST 2017 /home/gc/study/recon-all/400614dclass/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... 945 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 86 (86), valley at 47 (47) csf peak at 43, setting threshold to 71 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 84 (84), valley at 48 (48) csf peak at 42, setting threshold to 70 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 4 minutes and 19 seconds. #-------------------------------------------- #@# Mask BFS Thu Sep 7 17:06:47 CEST 2017 /home/gc/study/recon-all/400614dclass/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1636882 voxels in mask (pct= 9.76) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Sep 7 17:06:50 CEST 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 (102.0): 102.1 +- 6.3 [79.0 --> 125.0] GM (78.0) : 77.0 +- 10.3 [30.0 --> 95.0] setting bottom of white matter range to 87.3 setting top of gray matter range to 97.6 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... 2854 sparsely connected voxels removed... thickening thin strands.... 20 segments, 2591 filled 141 bright non-wm voxels segmented. 2930 diagonally connected voxels added... white matter segmentation took 2.1 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.58 minutes reading wm segmentation from wm.seg.mgz... 23 voxels added to wm to prevent paths from MTL structures to cortex 3398 additional wm voxels added 0 additional wm voxels added SEG EDIT: 27599 voxels turned on, 80485 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+): 16 found - 16 modified | TOTAL: 16 pass 2 (xy+): 0 found - 16 modified | TOTAL: 16 pass 1 (xy-): 20 found - 20 modified | TOTAL: 36 pass 2 (xy-): 0 found - 20 modified | TOTAL: 36 pass 1 (yz+): 12 found - 12 modified | TOTAL: 48 pass 2 (yz+): 0 found - 12 modified | TOTAL: 48 pass 1 (yz-): 33 found - 33 modified | TOTAL: 81 pass 2 (yz-): 0 found - 33 modified | TOTAL: 81 pass 1 (xz+): 20 found - 20 modified | TOTAL: 101 pass 2 (xz+): 0 found - 20 modified | TOTAL: 101 pass 1 (xz-): 13 found - 13 modified | TOTAL: 114 pass 2 (xz-): 0 found - 13 modified | TOTAL: 114 Iteration Number : 1 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 8 found - 8 modified | TOTAL: 14 pass 2 (+++): 0 found - 8 modified | TOTAL: 14 pass 1 (+++): 4 found - 4 modified | TOTAL: 18 pass 2 (+++): 0 found - 4 modified | TOTAL: 18 pass 1 (+++): 4 found - 4 modified | TOTAL: 22 pass 2 (+++): 0 found - 4 modified | TOTAL: 22 Iteration Number : 1 pass 1 (++): 30 found - 30 modified | TOTAL: 30 pass 2 (++): 0 found - 30 modified | TOTAL: 30 pass 1 (+-): 41 found - 41 modified | TOTAL: 71 pass 2 (+-): 0 found - 41 modified | TOTAL: 71 pass 1 (--): 43 found - 43 modified | TOTAL: 114 pass 2 (--): 0 found - 43 modified | TOTAL: 114 pass 1 (-+): 44 found - 44 modified | TOTAL: 158 pass 2 (-+): 0 found - 44 modified | TOTAL: 158 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 3 found - 3 modified | TOTAL: 5 pass 2 (yz+): 0 found - 3 modified | TOTAL: 5 pass 1 (yz-): 1 found - 1 modified | TOTAL: 6 pass 2 (yz-): 0 found - 1 modified | TOTAL: 6 pass 1 (xz+): 1 found - 1 modified | TOTAL: 7 pass 2 (xz+): 0 found - 1 modified | TOTAL: 7 pass 1 (xz-): 0 found - 0 modified | TOTAL: 7 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 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 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 = 305 (out of 542869: 0.056183) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Sep 7 17:09:38 CEST 2017 /home/gc/study/recon-all/400614dclass/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 1.05123 -0.08400 -0.01131 2.62780; 0.08006 1.04904 0.18963 -21.26665; -0.01435 -0.22791 0.96200 27.07178; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.05123 -0.08400 -0.01131 2.62780; 0.08006 1.04904 0.18963 -21.26665; -0.01435 -0.22791 0.96200 27.07178; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 2296 (min = 350, max = 1400), aspect = 1.16 (min = 0.10, max = 0.75) need search nearby using seed (124, 122, 147), TAL = (4.0, 19.0, 6.0) talairach voxel to voxel transform 0.94551 0.07492 -0.00365 -0.79253; -0.07164 0.90843 -0.17991 24.37802; -0.00287 0.21634 0.99682 -22.37741; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (124, 122, 147) --> (4.0, 19.0, 6.0) done. writing output to filled.mgz... filling took 0.8 minutes talairach cc position changed to (4.00, 19.00, 6.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(22.00, 19.00, 6.00) SRC: (108.03, 101.17, 150.25) search lh wm seed point around talairach space (-14.00, 19.00, 6.00), SRC: (142.07, 98.59, 150.14) 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 Thu Sep 7 17:10:28 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 4 found - 4 modified | TOTAL: 5 pass 2 (yz+): 0 found - 4 modified | TOTAL: 5 pass 1 (yz-): 0 found - 0 modified | TOTAL: 5 pass 1 (xz+): 1 found - 1 modified | TOTAL: 6 pass 2 (xz+): 0 found - 1 modified | TOTAL: 6 pass 1 (xz-): 1 found - 1 modified | TOTAL: 7 pass 2 (xz-): 0 found - 1 modified | TOTAL: 7 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 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 = 8 (out of 260134: 0.003075) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 2872 vertices, 3036 faces slice 50: 9592 vertices, 9863 faces slice 60: 18348 vertices, 18645 faces slice 70: 28377 vertices, 28749 faces slice 80: 38234 vertices, 38592 faces slice 90: 48552 vertices, 48912 faces slice 100: 60445 vertices, 60866 faces slice 110: 72214 vertices, 72628 faces slice 120: 82974 vertices, 83388 faces slice 130: 93831 vertices, 94244 faces slice 140: 104805 vertices, 105179 faces slice 150: 113925 vertices, 114311 faces slice 160: 122009 vertices, 122343 faces slice 170: 129052 vertices, 129363 faces slice 180: 135123 vertices, 135384 faces slice 190: 139608 vertices, 139840 faces slice 200: 141385 vertices, 141485 faces slice 210: 141410 vertices, 141500 faces slice 220: 141410 vertices, 141500 faces slice 230: 141410 vertices, 141500 faces slice 240: 141410 vertices, 141500 faces slice 250: 141410 vertices, 141500 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... 141410 voxel in cpt #1: X=-90 [v=141410,e=424500,f=283000] located at (-25.253086, -18.864445, 31.733477) For the whole surface: X=-90 [v=141410,e=424500,f=283000] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Thu Sep 7 17:10:36 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 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 = 1 (out of 262064: 0.000382) 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 30: 18 vertices, 24 faces slice 40: 2469 vertices, 2642 faces slice 50: 9221 vertices, 9480 faces slice 60: 17530 vertices, 17828 faces slice 70: 27384 vertices, 27761 faces slice 80: 38262 vertices, 38614 faces slice 90: 49189 vertices, 49541 faces slice 100: 61240 vertices, 61642 faces slice 110: 72690 vertices, 73109 faces slice 120: 83529 vertices, 83898 faces slice 130: 93969 vertices, 94382 faces slice 140: 105000 vertices, 105407 faces slice 150: 113647 vertices, 114001 faces slice 160: 121684 vertices, 122016 faces slice 170: 128325 vertices, 128613 faces slice 180: 134417 vertices, 134690 faces slice 190: 138771 vertices, 139007 faces slice 200: 140708 vertices, 140802 faces slice 210: 140708 vertices, 140802 faces slice 220: 140708 vertices, 140802 faces slice 230: 140708 vertices, 140802 faces slice 240: 140708 vertices, 140802 faces slice 250: 140708 vertices, 140802 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... 140708 voxel in cpt #1: X=-94 [v=140708,e=422406,f=281604] located at (29.051661, -19.114912, 28.250008) For the whole surface: X=-94 [v=140708,e=422406,f=281604] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Sep 7 17:10:43 CEST 2017 /home/gc/study/recon-all/400614dclass/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 Thu Sep 7 17:10:49 CEST 2017 /home/gc/study/recon-all/400614dclass/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 Thu Sep 7 17:10:55 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 46.7 mm, total surface area = 74744 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.158 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.079 (target=0.015) step 020: RMS=0.070 (target=0.015) step 025: RMS=0.063 (target=0.015) step 030: RMS=0.057 (target=0.015) step 035: RMS=0.053 (target=0.015) step 040: RMS=0.051 (target=0.015) step 045: RMS=0.049 (target=0.015) step 050: RMS=0.048 (target=0.015) step 055: RMS=0.048 (target=0.015) step 060: RMS=0.047 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 39.358016 mris_inflate stimesec 0.052991 mris_inflate ru_maxrss 181552 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 23038 mris_inflate ru_majflt 9 mris_inflate ru_nswap 0 mris_inflate ru_inblock 1832 mris_inflate ru_oublock 9952 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 9 mris_inflate ru_nivcsw 4032 #-------------------------------------------- #@# Inflation1 rh Thu Sep 7 17:11:35 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 46.6 mm, total surface area = 74707 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.6 minutes step 000: RMS=0.158 (target=0.015) step 005: RMS=0.121 (target=0.015) step 010: RMS=0.092 (target=0.015) step 015: RMS=0.079 (target=0.015) step 020: RMS=0.068 (target=0.015) step 025: RMS=0.060 (target=0.015) step 030: RMS=0.056 (target=0.015) step 035: RMS=0.053 (target=0.015) step 040: RMS=0.050 (target=0.015) step 045: RMS=0.048 (target=0.015) step 050: RMS=0.046 (target=0.015) step 055: RMS=0.047 (target=0.015) step 060: RMS=0.046 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 38.706115 mris_inflate stimesec 0.064990 mris_inflate ru_maxrss 180604 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 23320 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9904 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 3944 #-------------------------------------------- #@# QSphere lh Thu Sep 7 17:12:13 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.97 +- 0.59 (0.00-->7.37) (max @ vno 57811 --> 58978) face area 0.02 +- 0.03 (-0.18-->0.61) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.293... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.601, avgs=0 005/300: dt: 0.9000, rms radial error=177.340, avgs=0 010/300: dt: 0.9000, rms radial error=176.782, avgs=0 015/300: dt: 0.9000, rms radial error=176.049, avgs=0 020/300: dt: 0.9000, rms radial error=175.215, avgs=0 025/300: dt: 0.9000, rms radial error=174.323, avgs=0 030/300: dt: 0.9000, rms radial error=173.398, avgs=0 035/300: dt: 0.9000, rms radial error=172.457, avgs=0 040/300: dt: 0.9000, rms radial error=171.507, avgs=0 045/300: dt: 0.9000, rms radial error=170.555, avgs=0 050/300: dt: 0.9000, rms radial error=169.603, avgs=0 055/300: dt: 0.9000, rms radial error=168.654, avgs=0 060/300: dt: 0.9000, rms radial error=167.709, avgs=0 065/300: dt: 0.9000, rms radial error=166.769, avgs=0 070/300: dt: 0.9000, rms radial error=165.833, avgs=0 075/300: dt: 0.9000, rms radial error=164.902, avgs=0 080/300: dt: 0.9000, rms radial error=163.976, avgs=0 085/300: dt: 0.9000, rms radial error=163.055, avgs=0 090/300: dt: 0.9000, rms radial error=162.139, avgs=0 095/300: dt: 0.9000, rms radial error=161.227, avgs=0 100/300: dt: 0.9000, rms radial error=160.321, avgs=0 105/300: dt: 0.9000, rms radial error=159.420, avgs=0 110/300: dt: 0.9000, rms radial error=158.523, avgs=0 115/300: dt: 0.9000, rms radial error=157.632, avgs=0 120/300: dt: 0.9000, rms radial error=156.745, avgs=0 125/300: dt: 0.9000, rms radial error=155.864, avgs=0 130/300: dt: 0.9000, rms radial error=154.987, avgs=0 135/300: dt: 0.9000, rms radial error=154.115, avgs=0 140/300: dt: 0.9000, rms radial error=153.247, avgs=0 145/300: dt: 0.9000, rms radial error=152.385, avgs=0 150/300: dt: 0.9000, rms radial error=151.527, avgs=0 155/300: dt: 0.9000, rms radial error=150.674, avgs=0 160/300: dt: 0.9000, rms radial error=149.825, avgs=0 165/300: dt: 0.9000, rms radial error=148.982, avgs=0 170/300: dt: 0.9000, rms radial error=148.143, avgs=0 175/300: dt: 0.9000, rms radial error=147.309, avgs=0 180/300: dt: 0.9000, rms radial error=146.479, avgs=0 185/300: dt: 0.9000, rms radial error=145.654, avgs=0 190/300: dt: 0.9000, rms radial error=144.833, avgs=0 195/300: dt: 0.9000, rms radial error=144.017, avgs=0 200/300: dt: 0.9000, rms radial error=143.206, avgs=0 205/300: dt: 0.9000, rms radial error=142.399, avgs=0 210/300: dt: 0.9000, rms radial error=141.597, avgs=0 215/300: dt: 0.9000, rms radial error=140.799, avgs=0 220/300: dt: 0.9000, rms radial error=140.006, avgs=0 225/300: dt: 0.9000, rms radial error=139.217, avgs=0 230/300: dt: 0.9000, rms radial error=138.433, avgs=0 235/300: dt: 0.9000, rms radial error=137.654, avgs=0 240/300: dt: 0.9000, rms radial error=136.880, avgs=0 245/300: dt: 0.9000, rms radial error=136.110, avgs=0 250/300: dt: 0.9000, rms radial error=135.345, avgs=0 255/300: dt: 0.9000, rms radial error=134.583, avgs=0 260/300: dt: 0.9000, rms radial error=133.826, avgs=0 265/300: dt: 0.9000, rms radial error=133.073, avgs=0 270/300: dt: 0.9000, rms radial error=132.325, avgs=0 275/300: dt: 0.9000, rms radial error=131.580, avgs=0 280/300: dt: 0.9000, rms radial error=130.840, avgs=0 285/300: dt: 0.9000, rms radial error=130.104, avgs=0 290/300: dt: 0.9000, rms radial error=129.372, avgs=0 295/300: dt: 0.9000, rms radial error=128.644, avgs=0 300/300: dt: 0.9000, rms radial error=127.920, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16869.90 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 2 (K=40.0), pass 1, starting sse = 2948.88 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00002 epoch 3 (K=160.0), pass 1, starting sse = 336.63 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00319 epoch 4 (K=640.0), pass 1, starting sse = 30.05 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/12 = 0.00804 final distance error %28.82 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 242.401149 mris_sphere stimesec 0.123981 mris_sphere ru_maxrss 181760 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 23589 mris_sphere ru_majflt 11 mris_sphere ru_nswap 0 mris_sphere ru_inblock 1856 mris_sphere ru_oublock 9952 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 11 mris_sphere ru_nivcsw 24811 FSRUNTIME@ mris_sphere 0.0675 hours 1 threads #-------------------------------------------- #@# QSphere rh Thu Sep 7 17:16:16 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.98 +- 0.59 (0.00-->8.41) (max @ vno 54694 --> 56056) face area 0.02 +- 0.03 (-0.24-->0.71) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.298... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.282, avgs=0 005/300: dt: 0.9000, rms radial error=177.022, avgs=0 010/300: dt: 0.9000, rms radial error=176.462, avgs=0 015/300: dt: 0.9000, rms radial error=175.725, avgs=0 020/300: dt: 0.9000, rms radial error=174.886, avgs=0 025/300: dt: 0.9000, rms radial error=173.988, avgs=0 030/300: dt: 0.9000, rms radial error=173.059, avgs=0 035/300: dt: 0.9000, rms radial error=172.117, avgs=0 040/300: dt: 0.9000, rms radial error=171.172, avgs=0 045/300: dt: 0.9000, rms radial error=170.225, avgs=0 050/300: dt: 0.9000, rms radial error=169.278, avgs=0 055/300: dt: 0.9000, rms radial error=168.335, avgs=0 060/300: dt: 0.9000, rms radial error=167.395, avgs=0 065/300: dt: 0.9000, rms radial error=166.460, avgs=0 070/300: dt: 0.9000, rms radial error=165.529, avgs=0 075/300: dt: 0.9000, rms radial error=164.603, avgs=0 080/300: dt: 0.9000, rms radial error=163.682, avgs=0 085/300: dt: 0.9000, rms radial error=162.767, avgs=0 090/300: dt: 0.9000, rms radial error=161.856, avgs=0 095/300: dt: 0.9000, rms radial error=160.950, avgs=0 100/300: dt: 0.9000, rms radial error=160.049, avgs=0 105/300: dt: 0.9000, rms radial error=159.153, avgs=0 110/300: dt: 0.9000, rms radial error=158.261, avgs=0 115/300: dt: 0.9000, rms radial error=157.375, avgs=0 120/300: dt: 0.9000, rms radial error=156.493, avgs=0 125/300: dt: 0.9000, rms radial error=155.616, avgs=0 130/300: dt: 0.9000, rms radial error=154.743, avgs=0 135/300: dt: 0.9000, rms radial error=153.876, avgs=0 140/300: dt: 0.9000, rms radial error=153.013, avgs=0 145/300: dt: 0.9000, rms radial error=152.154, avgs=0 150/300: dt: 0.9000, rms radial error=151.300, avgs=0 155/300: dt: 0.9000, rms radial error=150.452, avgs=0 160/300: dt: 0.9000, rms radial error=149.607, avgs=0 165/300: dt: 0.9000, rms radial error=148.768, avgs=0 170/300: dt: 0.9000, rms radial error=147.932, avgs=0 175/300: dt: 0.9000, rms radial error=147.102, avgs=0 180/300: dt: 0.9000, rms radial error=146.275, avgs=0 185/300: dt: 0.9000, rms radial error=145.454, avgs=0 190/300: dt: 0.9000, rms radial error=144.637, avgs=0 195/300: dt: 0.9000, rms radial error=143.824, avgs=0 200/300: dt: 0.9000, rms radial error=143.016, avgs=0 205/300: dt: 0.9000, rms radial error=142.212, avgs=0 210/300: dt: 0.9000, rms radial error=141.412, avgs=0 215/300: dt: 0.9000, rms radial error=140.617, avgs=0 220/300: dt: 0.9000, rms radial error=139.827, avgs=0 225/300: dt: 0.9000, rms radial error=139.040, avgs=0 230/300: dt: 0.9000, rms radial error=138.259, avgs=0 235/300: dt: 0.9000, rms radial error=137.481, avgs=0 240/300: dt: 0.9000, rms radial error=136.708, avgs=0 245/300: dt: 0.9000, rms radial error=135.939, avgs=0 250/300: dt: 0.9000, rms radial error=135.174, avgs=0 255/300: dt: 0.9000, rms radial error=134.414, avgs=0 260/300: dt: 0.9000, rms radial error=133.657, avgs=0 265/300: dt: 0.9000, rms radial error=132.905, avgs=0 270/300: dt: 0.9000, rms radial error=132.158, avgs=0 275/300: dt: 0.9000, rms radial error=131.414, avgs=0 280/300: dt: 0.9000, rms radial error=130.674, avgs=0 285/300: dt: 0.9000, rms radial error=129.939, avgs=0 290/300: dt: 0.9000, rms radial error=129.207, avgs=0 295/300: dt: 0.9000, rms radial error=128.480, avgs=0 300/300: dt: 0.9000, rms radial error=127.757, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16689.95 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 2 (K=40.0), pass 1, starting sse = 2880.51 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 3 (K=160.0), pass 1, starting sse = 330.32 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00613 epoch 4 (K=640.0), pass 1, starting sse = 28.62 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/14 = 0.00943 final distance error %27.62 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 254.836259 mris_sphere stimesec 0.154976 mris_sphere ru_maxrss 180804 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 22850 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9904 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 0 mris_sphere ru_nivcsw 25805 FSRUNTIME@ mris_sphere 0.0709 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Thu Sep 7 17:20:32 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Thu Sep 7 17:20:32 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Thu Sep 7 17:20:32 CEST 2017 mris_fix_topology -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 400614dclass 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=-90 (nv=141410, nf=283000, ne=424500, g=46) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 10042 ambiguous faces found in tessellation segmenting defects... 39 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 7 into 6 38 defects to be corrected 0 vertices coincident reading input surface /home/gc/study/recon-all/400614dclass/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.9243 (-4.4621) -vertex loglikelihood: -5.5317 (-2.7659) -normal dot loglikelihood: -3.6182 (-3.6182) -quad curv loglikelihood: -6.2816 (-3.1408) Total Loglikelihood : -24.3558 CORRECTING DEFECT 0 (vertices=101, convex hull=117, v0=2167) After retessellation of defect 0 (v0=2167), euler #=-34 (135545,404798,269219) : difference with theory (-35) = -1 CORRECTING DEFECT 1 (vertices=665, convex hull=178, v0=10905) After retessellation of defect 1 (v0=10905), euler #=-33 (135624,405136,269479) : difference with theory (-34) = -1 CORRECTING DEFECT 2 (vertices=825, convex hull=260, v0=49346) normal vector of length zero at vertex 136802 with 4 faces normal vector of length zero at vertex 136802 with 4 faces normal vector of length zero at vertex 136802 with 4 faces After retessellation of defect 2 (v0=49346), euler #=-32 (135837,405907,270038) : difference with theory (-33) = -1 CORRECTING DEFECT 3 (vertices=31, convex hull=35, v0=51801) After retessellation of defect 3 (v0=51801), euler #=-31 (135844,405938,270063) : difference with theory (-32) = -1 CORRECTING DEFECT 4 (vertices=54, convex hull=104, v0=53222) After retessellation of defect 4 (v0=53222), euler #=-30 (135881,406091,270180) : difference with theory (-31) = -1 CORRECTING DEFECT 5 (vertices=41, convex hull=70, v0=56911) After retessellation of defect 5 (v0=56911), euler #=-29 (135905,406193,270259) : difference with theory (-30) = -1 CORRECTING DEFECT 6 (vertices=58, convex hull=49, v0=68254) After retessellation of defect 6 (v0=68254), euler #=-27 (135918,406255,270310) : difference with theory (-29) = -2 CORRECTING DEFECT 7 (vertices=158, convex hull=125, v0=74407) After retessellation of defect 7 (v0=74407), euler #=-26 (135982,406503,270495) : difference with theory (-28) = -2 CORRECTING DEFECT 8 (vertices=1580, convex hull=748, v0=80469) XL defect detected... After retessellation of defect 8 (v0=80469), euler #=-27 (136057,407135,271051) : difference with theory (-27) = 0 CORRECTING DEFECT 9 (vertices=104, convex hull=172, v0=82935) After retessellation of defect 9 (v0=82935), euler #=-26 (136130,407437,271281) : difference with theory (-26) = 0 CORRECTING DEFECT 10 (vertices=17, convex hull=61, v0=84506) After retessellation of defect 10 (v0=84506), euler #=-25 (136140,407488,271323) : difference with theory (-25) = 0 CORRECTING DEFECT 11 (vertices=55, convex hull=86, v0=85696) After retessellation of defect 11 (v0=85696), euler #=-24 (136170,407614,271420) : difference with theory (-24) = 0 CORRECTING DEFECT 12 (vertices=125, convex hull=87, v0=88264) After retessellation of defect 12 (v0=88264), euler #=-23 (136195,407723,271505) : difference with theory (-23) = 0 CORRECTING DEFECT 13 (vertices=35, convex hull=77, v0=93429) After retessellation of defect 13 (v0=93429), euler #=-22 (136206,407787,271559) : difference with theory (-22) = 0 CORRECTING DEFECT 14 (vertices=473, convex hull=244, v0=100396) After retessellation of defect 14 (v0=100396), euler #=-21 (136321,408253,271911) : difference with theory (-21) = 0 CORRECTING DEFECT 15 (vertices=10, convex hull=14, v0=101346) After retessellation of defect 15 (v0=101346), euler #=-20 (136322,408262,271920) : difference with theory (-20) = 0 CORRECTING DEFECT 16 (vertices=25, convex hull=27, v0=102766) After retessellation of defect 16 (v0=102766), euler #=-19 (136324,408277,271934) : difference with theory (-19) = 0 CORRECTING DEFECT 17 (vertices=38, convex hull=93, v0=103875) After retessellation of defect 17 (v0=103875), euler #=-18 (136347,408387,272022) : difference with theory (-18) = 0 CORRECTING DEFECT 18 (vertices=48, convex hull=53, v0=105000) After retessellation of defect 18 (v0=105000), euler #=-17 (136356,408435,272062) : difference with theory (-17) = 0 CORRECTING DEFECT 19 (vertices=97, convex hull=109, v0=109285) After retessellation of defect 19 (v0=109285), euler #=-16 (136390,408583,272177) : difference with theory (-16) = 0 CORRECTING DEFECT 20 (vertices=28, convex hull=53, v0=109860) After retessellation of defect 20 (v0=109860), euler #=-15 (136404,408645,272226) : difference with theory (-15) = 0 CORRECTING DEFECT 21 (vertices=29, convex hull=75, v0=110074) After retessellation of defect 21 (v0=110074), euler #=-14 (136413,408701,272274) : difference with theory (-14) = 0 CORRECTING DEFECT 22 (vertices=18, convex hull=29, v0=111076) After retessellation of defect 22 (v0=111076), euler #=-13 (136415,408717,272289) : difference with theory (-13) = 0 CORRECTING DEFECT 23 (vertices=100, convex hull=106, v0=113846) After retessellation of defect 23 (v0=113846), euler #=-12 (136445,408848,272391) : difference with theory (-12) = 0 CORRECTING DEFECT 24 (vertices=16, convex hull=22, v0=114718) After retessellation of defect 24 (v0=114718), euler #=-11 (136447,408860,272402) : difference with theory (-11) = 0 CORRECTING DEFECT 25 (vertices=260, convex hull=212, v0=116328) After retessellation of defect 25 (v0=116328), euler #=-10 (136568,409342,272764) : difference with theory (-10) = 0 CORRECTING DEFECT 26 (vertices=218, convex hull=58, v0=118624) After retessellation of defect 26 (v0=118624), euler #=-9 (136583,409408,272816) : difference with theory (-9) = 0 CORRECTING DEFECT 27 (vertices=35, convex hull=74, v0=124802) After retessellation of defect 27 (v0=124802), euler #=-8 (136599,409488,272881) : difference with theory (-8) = 0 CORRECTING DEFECT 28 (vertices=55, convex hull=90, v0=126383) After retessellation of defect 28 (v0=126383), euler #=-7 (136625,409600,272968) : difference with theory (-7) = 0 CORRECTING DEFECT 29 (vertices=32, convex hull=56, v0=128252) After retessellation of defect 29 (v0=128252), euler #=-6 (136635,409650,273009) : difference with theory (-6) = 0 CORRECTING DEFECT 30 (vertices=19, convex hull=18, v0=128396) After retessellation of defect 30 (v0=128396), euler #=-5 (136636,409656,273015) : difference with theory (-5) = 0 CORRECTING DEFECT 31 (vertices=293, convex hull=216, v0=133422) After retessellation of defect 31 (v0=133422), euler #=-4 (136734,410058,273320) : difference with theory (-4) = 0 CORRECTING DEFECT 32 (vertices=79, convex hull=91, v0=137717) After retessellation of defect 32 (v0=137717), euler #=-3 (136769,410203,273431) : difference with theory (-3) = 0 CORRECTING DEFECT 33 (vertices=43, convex hull=90, v0=138612) After retessellation of defect 33 (v0=138612), euler #=-2 (136783,410280,273495) : difference with theory (-2) = 0 CORRECTING DEFECT 34 (vertices=53, convex hull=78, v0=139350) After retessellation of defect 34 (v0=139350), euler #=-1 (136812,410397,273584) : difference with theory (-1) = 0 CORRECTING DEFECT 35 (vertices=43, convex hull=29, v0=140210) After retessellation of defect 35 (v0=140210), euler #=0 (136816,410422,273606) : difference with theory (0) = 0 CORRECTING DEFECT 36 (vertices=22, convex hull=32, v0=140812) After retessellation of defect 36 (v0=140812), euler #=1 (136819,410441,273623) : difference with theory (1) = 0 CORRECTING DEFECT 37 (vertices=7, convex hull=30, v0=141091) After retessellation of defect 37 (v0=141091), euler #=2 (136820,410454,273636) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.26 (0.08-->13.60) (max @ vno 89732 --> 97089) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.26 (0.08-->13.60) (max @ vno 89732 --> 97089) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 121 mutations (35.4%), 221 crossovers (64.6%), 729 vertices were eliminated building final representation... 4590 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=136820, nf=273636, ne=410454, g=0) writing corrected surface to /home/gc/study/recon-all/400614dclass/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 40.2 minutes 0 defective edges removing intersecting faces 000: 592 intersecting 001: 23 intersecting mris_fix_topology utimesec 2406.113215 mris_fix_topology stimesec 0.164974 mris_fix_topology ru_maxrss 461748 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 58450 mris_fix_topology ru_majflt 12 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 1816 mris_fix_topology ru_oublock 14400 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 41 mris_fix_topology ru_nivcsw 244339 FSRUNTIME@ mris_fix_topology lh 0.6693 hours 1 threads #@# Fix Topology rh Thu Sep 7 18:00:41 CEST 2017 mris_fix_topology -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 400614dclass 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=-94 (nv=140708, nf=281604, ne=422406, g=48) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 9119 ambiguous faces found in tessellation segmenting defects... 37 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 9 into 7 -merging segment 21 into 18 -merging segment 33 into 32 34 defects to be corrected 0 vertices coincident reading input surface /home/gc/study/recon-all/400614dclass/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.9208 (-4.4604) -vertex loglikelihood: -5.5081 (-2.7540) -normal dot loglikelihood: -3.6054 (-3.6054) -quad curv loglikelihood: -6.1563 (-3.0782) Total Loglikelihood : -24.1906 CORRECTING DEFECT 0 (vertices=31, convex hull=57, v0=35773) After retessellation of defect 0 (v0=35773), euler #=-33 (135377,404341,268931) : difference with theory (-31) = 2 CORRECTING DEFECT 1 (vertices=698, convex hull=278, v0=48873) After retessellation of defect 1 (v0=48873), euler #=-32 (135513,404890,269345) : difference with theory (-30) = 2 CORRECTING DEFECT 2 (vertices=75, convex hull=68, v0=51210) After retessellation of defect 2 (v0=51210), euler #=-31 (135536,404986,269419) : difference with theory (-29) = 2 CORRECTING DEFECT 3 (vertices=30, convex hull=83, v0=52310) After retessellation of defect 3 (v0=52310), euler #=-30 (135546,405047,269471) : difference with theory (-28) = 2 CORRECTING DEFECT 4 (vertices=21, convex hull=29, v0=57118) After retessellation of defect 4 (v0=57118), euler #=-29 (135550,405069,269490) : difference with theory (-27) = 2 CORRECTING DEFECT 5 (vertices=59, convex hull=83, v0=63458) After retessellation of defect 5 (v0=63458), euler #=-28 (135591,405230,269611) : difference with theory (-26) = 2 CORRECTING DEFECT 6 (vertices=77, convex hull=115, v0=74989) After retessellation of defect 6 (v0=74989), euler #=-27 (135629,405396,269740) : difference with theory (-25) = 2 CORRECTING DEFECT 7 (vertices=1373, convex hull=665, v0=77019) XL defect detected... After retessellation of defect 7 (v0=77019), euler #=-26 (136039,407012,270947) : difference with theory (-24) = 2 CORRECTING DEFECT 8 (vertices=72, convex hull=103, v0=82522) After retessellation of defect 8 (v0=82522), euler #=-25 (136079,407178,271074) : difference with theory (-23) = 2 CORRECTING DEFECT 9 (vertices=65, convex hull=89, v0=90755) After retessellation of defect 9 (v0=90755), euler #=-24 (136114,407320,271182) : difference with theory (-22) = 2 CORRECTING DEFECT 10 (vertices=76, convex hull=99, v0=96139) After retessellation of defect 10 (v0=96139), euler #=-23 (136160,407499,271316) : difference with theory (-21) = 2 CORRECTING DEFECT 11 (vertices=65, convex hull=43, v0=98190) After retessellation of defect 11 (v0=98190), euler #=-22 (136170,407544,271352) : difference with theory (-20) = 2 CORRECTING DEFECT 12 (vertices=44, convex hull=37, v0=98443) After retessellation of defect 12 (v0=98443), euler #=-21 (136179,407588,271388) : difference with theory (-19) = 2 CORRECTING DEFECT 13 (vertices=41, convex hull=38, v0=98588) After retessellation of defect 13 (v0=98588), euler #=-20 (136183,407617,271414) : difference with theory (-18) = 2 CORRECTING DEFECT 14 (vertices=194, convex hull=139, v0=100537) After retessellation of defect 14 (v0=100537), euler #=-19 (136222,407797,271556) : difference with theory (-17) = 2 CORRECTING DEFECT 15 (vertices=75, convex hull=108, v0=101587) After retessellation of defect 15 (v0=101587), euler #=-18 (136264,407971,271689) : difference with theory (-16) = 2 CORRECTING DEFECT 16 (vertices=386, convex hull=122, v0=102802) After retessellation of defect 16 (v0=102802), euler #=-17 (136287,408095,271791) : difference with theory (-15) = 2 CORRECTING DEFECT 17 (vertices=339, convex hull=246, v0=103900) After retessellation of defect 17 (v0=103900), euler #=-15 (136398,408545,272132) : difference with theory (-14) = 1 CORRECTING DEFECT 18 (vertices=37, convex hull=33, v0=106629) After retessellation of defect 18 (v0=106629), euler #=-14 (136403,408571,272154) : difference with theory (-13) = 1 CORRECTING DEFECT 19 (vertices=251, convex hull=151, v0=106675) After retessellation of defect 19 (v0=106675), euler #=-13 (136478,408863,272372) : difference with theory (-12) = 1 CORRECTING DEFECT 20 (vertices=51, convex hull=75, v0=107400) After retessellation of defect 20 (v0=107400), euler #=-12 (136511,408992,272469) : difference with theory (-11) = 1 CORRECTING DEFECT 21 (vertices=28, convex hull=68, v0=110763) After retessellation of defect 21 (v0=110763), euler #=-11 (136530,409073,272532) : difference with theory (-10) = 1 CORRECTING DEFECT 22 (vertices=259, convex hull=170, v0=111958) After retessellation of defect 22 (v0=111958), euler #=-10 (136619,409420,272791) : difference with theory (-9) = 1 CORRECTING DEFECT 23 (vertices=208, convex hull=93, v0=112587) After retessellation of defect 23 (v0=112587), euler #=-9 (136670,409613,272934) : difference with theory (-8) = 1 CORRECTING DEFECT 24 (vertices=13, convex hull=28, v0=116853) After retessellation of defect 24 (v0=116853), euler #=-8 (136673,409632,272951) : difference with theory (-7) = 1 CORRECTING DEFECT 25 (vertices=283, convex hull=265, v0=118467) After retessellation of defect 25 (v0=118467), euler #=-7 (136731,409936,273198) : difference with theory (-6) = 1 CORRECTING DEFECT 26 (vertices=108, convex hull=126, v0=121600) After retessellation of defect 26 (v0=121600), euler #=-6 (136769,410114,273339) : difference with theory (-5) = 1 CORRECTING DEFECT 27 (vertices=98, convex hull=94, v0=123437) After retessellation of defect 27 (v0=123437), euler #=-5 (136806,410263,273452) : difference with theory (-4) = 1 CORRECTING DEFECT 28 (vertices=30, convex hull=45, v0=123683) After retessellation of defect 28 (v0=123683), euler #=-4 (136809,410288,273475) : difference with theory (-3) = 1 CORRECTING DEFECT 29 (vertices=22, convex hull=18, v0=130632) After retessellation of defect 29 (v0=130632), euler #=-3 (136813,410306,273490) : difference with theory (-2) = 1 CORRECTING DEFECT 30 (vertices=24, convex hull=26, v0=132730) After retessellation of defect 30 (v0=132730), euler #=-1 (136814,410326,273511) : difference with theory (-1) = 0 CORRECTING DEFECT 31 (vertices=15, convex hull=34, v0=134399) After retessellation of defect 31 (v0=134399), euler #=0 (136815,410342,273527) : difference with theory (0) = 0 CORRECTING DEFECT 32 (vertices=141, convex hull=125, v0=135151) After retessellation of defect 32 (v0=135151), euler #=1 (136862,410538,273677) : difference with theory (1) = 0 CORRECTING DEFECT 33 (vertices=51, convex hull=93, v0=136067) After retessellation of defect 33 (v0=136067), euler #=2 (136891,410667,273778) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.25 (0.09-->9.71) (max @ vno 137085 --> 137488) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.25 (0.09-->9.71) (max @ vno 137085 --> 137488) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 99 mutations (33.0%), 201 crossovers (67.0%), 341 vertices were eliminated building final representation... 3817 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=136891, nf=273778, ne=410667, g=0) writing corrected surface to /home/gc/study/recon-all/400614dclass/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 37.4 minutes 0 defective edges removing intersecting faces 000: 430 intersecting 001: 8 intersecting mris_fix_topology utimesec 2241.354262 mris_fix_topology stimesec 0.167974 mris_fix_topology ru_maxrss 445892 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 55987 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 14392 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 19 mris_fix_topology ru_nivcsw 228307 FSRUNTIME@ mris_fix_topology rh 0.6235 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 136820 - 410454 + 273636 = 2 --> 0 holes F =2V-4: 273636 = 273640-4 (0) 2E=3F: 820908 = 820908 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 136891 - 410667 + 273778 = 2 --> 0 holes F =2V-4: 273778 = 273782-4 (0) 2E=3F: 821334 = 821334 (0) total defect index = 0 /home/gc/study/recon-all/400614dclass/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 117 intersecting 001: 18 intersecting 002: 2 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /home/gc/study/recon-all/400614dclass/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 104 intersecting 001: 2 intersecting expanding nbhd size to 2 002: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Sep 7 18:38:20 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 400614dclass lh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /home/gc/study/recon-all/400614dclass/mri/filled.mgz... reading volume /home/gc/study/recon-all/400614dclass/mri/brain.finalsurfs.mgz... reading volume /home/gc/study/recon-all/400614dclass/mri/../mri/aseg.presurf.mgz... reading volume /home/gc/study/recon-all/400614dclass/mri/wm.mgz... 18256 bright wm thresholded. 269 bright non-wm voxels segmented. reading original surface position from /home/gc/study/recon-all/400614dclass/surf/lh.orig... computing class statistics... border white: 261544 voxels (1.56%) border gray 289857 voxels (1.73%) WM (101.0): 101.2 +- 6.0 [70.0 --> 110.0] GM (84.0) : 82.4 +- 9.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 70.8 (was 70) setting MAX_BORDER_WHITE to 111.0 (was 105) setting MIN_BORDER_WHITE to 80.0 (was 85) setting MAX_CSF to 61.6 (was 40) setting MAX_GRAY to 99.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 70.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 52.4 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.02-->5.58) (max @ vno 133851 --> 136688) face area 0.28 +- 0.13 (0.00-->5.51) mean absolute distance = 0.76 +- 0.93 4147 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-4.3, GM=80+-7.0 mean inside = 98.3, mean outside = 85.6 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=88.8, 74 (74) missing vertices, mean dist 0.3 [0.6 (%35.4)->0.8 (%64.6))] %63 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=lugh., nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.08-->6.14) (max @ vno 90703 --> 100654) face area 0.28 +- 0.13 (0.00-->3.91) mean absolute distance = 0.42 +- 0.67 5028 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1988283.8, rms=7.310 001: dt: 0.5000, sse=1252742.8, rms=5.138 (29.714%) 002: dt: 0.5000, sse=916762.5, rms=3.709 (27.807%) 003: dt: 0.5000, sse=761463.6, rms=2.824 (23.862%) 004: dt: 0.5000, sse=692326.1, rms=2.310 (18.194%) 005: dt: 0.5000, sse=663062.4, rms=2.049 (11.315%) 006: dt: 0.5000, sse=651436.4, rms=1.931 (5.770%) 007: dt: 0.5000, sse=646013.0, rms=1.870 (3.151%) rms = 1.85, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=644066.2, rms=1.845 (1.305%) 009: dt: 0.2500, sse=612413.5, rms=1.272 (31.080%) 010: dt: 0.2500, sse=601880.8, rms=1.200 (5.684%) rms = 1.18, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=600945.4, rms=1.180 (1.593%) rms = 1.17, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=599862.5, rms=1.169 (0.961%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=90.9, 47 (12) missing vertices, mean dist -0.3 [0.5 (%69.7)->0.3 (%30.3))] %73 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=lugh., nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.06-->6.03) (max @ vno 89732 --> 97089) face area 0.35 +- 0.17 (0.00-->5.31) mean absolute distance = 0.33 +- 0.45 4901 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1025979.5, rms=3.475 013: dt: 0.5000, sse=832559.0, rms=2.162 (37.775%) 014: dt: 0.5000, sse=775911.5, rms=1.672 (22.679%) 015: dt: 0.5000, sse=760026.3, rms=1.481 (11.407%) 016: dt: 0.5000, sse=764477.2, rms=1.416 (4.397%) rms = 1.45, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=740175.4, rms=1.189 (16.057%) 018: dt: 0.2500, sse=736741.0, rms=1.073 (9.752%) rms = 1.04, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=735872.9, rms=1.044 (2.667%) rms = 1.03, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=733833.1, rms=1.028 (1.489%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=92.9, 69 (5) missing vertices, mean dist -0.2 [0.4 (%72.8)->0.2 (%27.2))] %83 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=lugh., nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.05-->5.94) (max @ vno 90703 --> 100654) face area 0.34 +- 0.17 (0.00-->5.48) mean absolute distance = 0.25 +- 0.36 3902 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=880905.6, rms=2.792 021: dt: 0.5000, sse=739923.7, rms=1.504 (46.135%) 022: dt: 0.5000, sse=721805.1, rms=1.248 (17.035%) 023: dt: 0.5000, sse=719187.7, rms=1.192 (4.508%) rms = 1.24, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=706371.8, rms=1.009 (15.352%) 025: dt: 0.2500, sse=707569.4, rms=0.939 (6.867%) rms = 0.94, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=706464.0, rms=0.938 (0.189%) rms = 0.93, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=703353.8, rms=0.933 (0.513%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group mean border=93.7, 110 (2) missing vertices, mean dist -0.1 [0.3 (%59.9)->0.2 (%40.1))] %88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=lugh., nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /home/gc/study/recon-all/400614dclass/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=710199.9, rms=1.379 028: dt: 0.5000, sse=684691.2, rms=0.890 (35.445%) rms = 1.03, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=678414.4, rms=0.789 (11.291%) rms = 0.77, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=691750.9, rms=0.772 (2.260%) rms = 0.76, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=672479.4, rms=0.761 (1.309%) positioning took 0.5 minutes generating cortex label... 8 non-cortical segments detected only using segment with 6245 vertices erasing segment 1 (vno[0] = 69801) erasing segment 2 (vno[0] = 84341) erasing segment 3 (vno[0] = 96906) erasing segment 4 (vno[0] = 97940) erasing segment 5 (vno[0] = 100648) erasing segment 6 (vno[0] = 102100) erasing segment 7 (vno[0] = 122184) writing cortex label to /home/gc/study/recon-all/400614dclass/label/lh.cortex.label... writing curvature file /home/gc/study/recon-all/400614dclass/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/gc/study/recon-all/400614dclass/surf/lh.area vertex spacing 0.88 +- 0.25 (0.02-->5.97) (max @ vno 90703 --> 100654) face area 0.33 +- 0.16 (0.00-->5.36) refinement took 5.6 minutes #-------------------------------------------- #@# Make White Surf rh Thu Sep 7 18:43:58 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 400614dclass rh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /home/gc/study/recon-all/400614dclass/mri/filled.mgz... reading volume /home/gc/study/recon-all/400614dclass/mri/brain.finalsurfs.mgz... reading volume /home/gc/study/recon-all/400614dclass/mri/../mri/aseg.presurf.mgz... reading volume /home/gc/study/recon-all/400614dclass/mri/wm.mgz... 18256 bright wm thresholded. 269 bright non-wm voxels segmented. reading original surface position from /home/gc/study/recon-all/400614dclass/surf/rh.orig... computing class statistics... border white: 261544 voxels (1.56%) border gray 289857 voxels (1.73%) WM (101.0): 101.2 +- 6.0 [70.0 --> 110.0] GM (84.0) : 82.4 +- 9.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 70.8 (was 70) setting MAX_BORDER_WHITE to 110.0 (was 105) setting MIN_BORDER_WHITE to 80.0 (was 85) setting MAX_CSF to 61.6 (was 40) setting MAX_GRAY to 98.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 70.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 52.4 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.05-->7.79) (max @ vno 135758 --> 135945) face area 0.28 +- 0.13 (0.00-->5.74) mean absolute distance = 0.76 +- 0.93 3935 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104+-4.3, GM=80+-7.0 mean inside = 98.1, mean outside = 85.8 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 mean border=88.9, 70 (70) missing vertices, mean dist 0.3 [0.6 (%35.3)->0.8 (%64.7))] %64 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=lugh., 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 +- 0.26 (0.09-->9.18) (max @ vno 135758 --> 135945) face area 0.28 +- 0.14 (0.00-->8.91) mean absolute distance = 0.43 +- 0.72 4423 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1901225.2, rms=7.082 001: dt: 0.5000, sse=1214125.0, rms=4.997 (29.438%) 002: dt: 0.5000, sse=900690.6, rms=3.629 (27.382%) 003: dt: 0.5000, sse=756929.3, rms=2.786 (23.231%) 004: dt: 0.5000, sse=689755.8, rms=2.290 (17.795%) 005: dt: 0.5000, sse=660889.0, rms=2.028 (11.447%) 006: dt: 0.5000, sse=648410.4, rms=1.897 (6.461%) 007: dt: 0.5000, sse=641954.6, rms=1.827 (3.712%) rms = 1.79, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=638848.3, rms=1.792 (1.891%) 009: dt: 0.2500, sse=604282.4, rms=1.246 (30.494%) 010: dt: 0.2500, sse=600605.0, rms=1.177 (5.515%) rms = 1.16, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=599699.6, rms=1.160 (1.446%) rms = 1.15, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=598653.1, rms=1.148 (1.065%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=91.0, 63 (16) missing vertices, mean dist -0.3 [0.5 (%69.0)->0.3 (%31.0))] %72 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=lugh., nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.08-->9.40) (max @ vno 135758 --> 135945) face area 0.36 +- 0.18 (0.00-->12.73) mean absolute distance = 0.36 +- 0.50 4327 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1018869.0, rms=3.449 013: dt: 0.5000, sse=821082.2, rms=2.121 (38.498%) 014: dt: 0.5000, sse=772287.8, rms=1.648 (22.296%) 015: dt: 0.5000, sse=754422.3, rms=1.451 (11.976%) 016: dt: 0.5000, sse=746260.8, rms=1.363 (6.028%) rms = 1.38, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=736006.4, rms=1.155 (15.263%) 018: dt: 0.2500, sse=731504.6, rms=1.039 (10.015%) rms = 1.01, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=729255.1, rms=1.009 (2.932%) rms = 1.00, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=728342.9, rms=0.995 (1.361%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=93.0, 72 (10) missing vertices, mean dist -0.2 [0.4 (%71.6)->0.2 (%28.4))] %83 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=lugh., nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.05-->9.51) (max @ vno 135758 --> 135945) face area 0.34 +- 0.17 (0.00-->13.23) mean absolute distance = 0.28 +- 0.39 4035 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=880575.2, rms=2.796 021: dt: 0.5000, sse=737202.2, rms=1.503 (46.267%) 022: dt: 0.5000, sse=715949.5, rms=1.200 (20.157%) 023: dt: 0.5000, sse=714259.1, rms=1.128 (5.938%) rms = 1.17, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=702828.1, rms=0.964 (14.580%) 025: dt: 0.2500, sse=700836.5, rms=0.902 (6.384%) rms = 0.90, time step reduction 2 of 3 to 0.125... rms = 0.90, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=699648.5, rms=0.899 (0.415%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=93.8, 79 (8) missing vertices, mean dist -0.1 [0.3 (%59.7)->0.2 (%40.3))] %88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=lugh., nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /home/gc/study/recon-all/400614dclass/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=708935.8, rms=1.413 027: dt: 0.5000, sse=682199.4, rms=0.883 (37.545%) rms = 1.00, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=674551.6, rms=0.772 (12.518%) rms = 0.74, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=676205.8, rms=0.744 (3.591%) rms = 0.73, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=674226.2, rms=0.733 (1.579%) positioning took 0.5 minutes generating cortex label... 11 non-cortical segments detected only using segment with 6855 vertices erasing segment 0 (vno[0] = 34688) erasing segment 2 (vno[0] = 64172) erasing segment 3 (vno[0] = 67568) erasing segment 4 (vno[0] = 71085) erasing segment 5 (vno[0] = 83772) erasing segment 6 (vno[0] = 91480) erasing segment 7 (vno[0] = 98992) erasing segment 8 (vno[0] = 99012) erasing segment 9 (vno[0] = 101760) erasing segment 10 (vno[0] = 101793) writing cortex label to /home/gc/study/recon-all/400614dclass/label/rh.cortex.label... writing curvature file /home/gc/study/recon-all/400614dclass/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/gc/study/recon-all/400614dclass/surf/rh.area vertex spacing 0.88 +- 0.26 (0.05-->9.54) (max @ vno 135758 --> 135945) face area 0.33 +- 0.17 (0.00-->13.43) refinement took 5.6 minutes #-------------------------------------------- #@# Smooth2 lh Thu Sep 7 18:49:32 CEST 2017 /home/gc/study/recon-all/400614dclass/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 Thu Sep 7 18:49:38 CEST 2017 /home/gc/study/recon-all/400614dclass/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 Thu Sep 7 18:49:43 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_inflate -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 46.9 mm, total surface area = 81411 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.173 (target=0.015) step 005: RMS=0.124 (target=0.015) step 010: RMS=0.092 (target=0.015) step 015: RMS=0.074 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 0.6 minutes mris_inflate utimesec 36.526447 mris_inflate stimesec 0.056991 mris_inflate ru_maxrss 175900 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 22651 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 152 mris_inflate ru_oublock 10704 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 1 mris_inflate ru_nivcsw 3722 #-------------------------------------------- #@# Inflation2 rh Thu Sep 7 18:50:20 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_inflate -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 46.7 mm, total surface area = 81715 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.173 (target=0.015) step 005: RMS=0.124 (target=0.015) step 010: RMS=0.091 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.043 (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=0.026 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. inflation took 0.6 minutes mris_inflate utimesec 36.600435 mris_inflate stimesec 0.054991 mris_inflate ru_maxrss 175916 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 22657 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10704 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 3719 #-------------------------------------------- #@# Curv .H and .K lh Thu Sep 7 18:50:57 CEST 2017 /home/gc/study/recon-all/400614dclass/surf mris_curvature -w lh.white.preaparc total integrated curvature = 8.506*4pi (106.893) --> -8 handles ICI = 163.3, FI = 1599.1, variation=25462.965 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 170 vertices thresholded to be in k1 ~ [-0.16 0.86], k2 ~ [-0.13 0.06] total integrated curvature = 0.501*4pi (6.297) --> 0 handles ICI = 1.4, FI = 8.6, variation=147.298 128 vertices thresholded to be in [-0.05 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 121 vertices thresholded to be in [-0.13 0.19] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.021 done. #-------------------------------------------- #@# Curv .H and .K rh Thu Sep 7 18:52:34 CEST 2017 /home/gc/study/recon-all/400614dclass/surf mris_curvature -w rh.white.preaparc total integrated curvature = 5.853*4pi (73.548) --> -5 handles ICI = 167.3, FI = 1562.7, variation=25199.978 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 166 vertices thresholded to be in k1 ~ [-0.19 0.47], k2 ~ [-0.12 0.07] total integrated curvature = 0.548*4pi (6.880) --> 0 handles ICI = 1.3, FI = 9.0, variation=151.047 117 vertices thresholded to be in [-0.02 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 139 vertices thresholded to be in [-0.12 0.20] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.022 done. #----------------------------------------- #@# Curvature Stats lh Thu Sep 7 18:54:09 CEST 2017 /home/gc/study/recon-all/400614dclass/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 400614dclass 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 [ 400614dclass/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 [ 279 ] Gb_filter = 0 WARN: S lookup min: -0.076645 WARN: S explicit min: 0.000000 vertex = 588 #----------------------------------------- #@# Curvature Stats rh Thu Sep 7 18:54:13 CEST 2017 /home/gc/study/recon-all/400614dclass/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 400614dclass 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 [ 400614dclass/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 [ 249 ] Gb_filter = 0 WARN: S lookup min: -0.249954 WARN: S explicit min: 0.000000 vertex = 4 #-------------------------------------------- #@# Sphere lh Thu Sep 7 18:54:17 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_sphere -rusage /home/gc/study/recon-all/400614dclass/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 0.278... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=lugh., nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.03 pass 1: epoch 2 of 3 starting distance error %19.94 unfolding complete - removing small folds... starting distance error %19.89 removing remaining folds... final distance error %19.91 MRISunfold() return, current seed 1234 -01: dt=0.0000, 138 negative triangles 161: dt=0.9900, 138 negative triangles 162: dt=0.9900, 88 negative triangles 163: dt=0.9900, 66 negative triangles 164: dt=0.9900, 59 negative triangles 165: dt=0.9900, 58 negative triangles 166: dt=0.9900, 49 negative triangles 167: dt=0.9900, 38 negative triangles 168: dt=0.9900, 38 negative triangles 169: dt=0.9900, 35 negative triangles 170: dt=0.9900, 37 negative triangles 171: dt=0.9900, 41 negative triangles 172: dt=0.9900, 29 negative triangles 173: dt=0.9900, 27 negative triangles 174: dt=0.9900, 26 negative triangles 175: dt=0.9900, 22 negative triangles 176: dt=0.9900, 22 negative triangles 177: dt=0.9900, 17 negative triangles 178: dt=0.9900, 23 negative triangles 179: dt=0.9900, 20 negative triangles 180: dt=0.9900, 18 negative triangles 181: dt=0.9900, 18 negative triangles 182: dt=0.9900, 18 negative triangles 183: dt=0.9900, 11 negative triangles 184: dt=0.9900, 19 negative triangles 185: dt=0.9900, 11 negative triangles 186: dt=0.9900, 12 negative triangles 187: dt=0.9900, 7 negative triangles 188: dt=0.9900, 9 negative triangles 189: dt=0.9900, 13 negative triangles 190: dt=0.9900, 8 negative triangles 191: dt=0.9900, 4 negative triangles 192: dt=0.9900, 11 negative triangles 193: dt=0.9900, 5 negative triangles 194: dt=0.9900, 7 negative triangles 195: dt=0.9900, 4 negative triangles 196: dt=0.9900, 3 negative triangles 197: dt=0.9900, 5 negative triangles 198: dt=0.9900, 1 negative triangles 199: dt=0.9900, 4 negative triangles 200: dt=0.9900, 7 negative triangles 201: dt=0.9900, 2 negative triangles 202: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.76 hours mris_sphere utimesec 2726.778466 mris_sphere stimesec 0.273958 mris_sphere ru_maxrss 241780 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 39118 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9632 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 8 mris_sphere ru_nivcsw 276231 FSRUNTIME@ mris_sphere 0.7586 hours 1 threads #-------------------------------------------- #@# Sphere rh Thu Sep 7 19:39:47 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_sphere -rusage /home/gc/study/recon-all/400614dclass/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 0.281... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=lugh., 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 %19.66 pass 1: epoch 2 of 3 starting distance error %19.54 unfolding complete - removing small folds... starting distance error %19.47 removing remaining folds... final distance error %19.49 MRISunfold() return, current seed 1234 -01: dt=0.0000, 120 negative triangles 189: dt=0.9900, 120 negative triangles 190: dt=0.9900, 58 negative triangles 191: dt=0.9900, 39 negative triangles 192: dt=0.9900, 27 negative triangles 193: dt=0.9900, 26 negative triangles 194: dt=0.9900, 17 negative triangles 195: dt=0.9900, 19 negative triangles 196: dt=0.9900, 17 negative triangles 197: dt=0.9900, 12 negative triangles 198: dt=0.9900, 10 negative triangles 199: dt=0.9900, 6 negative triangles 200: dt=0.9900, 3 negative triangles 201: dt=0.9900, 7 negative triangles 202: dt=0.9900, 4 negative triangles 203: dt=0.9900, 6 negative triangles 204: dt=0.9900, 6 negative triangles 205: dt=0.9900, 2 negative triangles 206: dt=0.9900, 4 negative triangles 207: dt=0.9900, 2 negative triangles 208: dt=0.9900, 4 negative triangles 209: dt=0.9900, 1 negative triangles 210: dt=0.9900, 3 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.86 hours mris_sphere utimesec 3089.507323 mris_sphere stimesec 0.313952 mris_sphere ru_maxrss 242076 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 39180 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 9632 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 2 mris_sphere ru_nivcsw 313042 FSRUNTIME@ mris_sphere 0.8593 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Thu Sep 7 20:31:21 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_register -curv -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /home/gc/study/recon-all/400614dclass/scripts cmdline mris_register -curv -rusage /home/gc/study/recon-all/400614dclass/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=lugh., 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=lugh., 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 = 5.506 curvature mean = 0.010, std = 0.813 curvature mean = 0.025, std = 0.857 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (0.00, -8.00, 8.00) sse = 229751.1, tmin=2.3908 d=16.00 min @ (4.00, 4.00, 0.00) sse = 212466.8, tmin=3.6332 d=8.00 min @ (-2.00, 0.00, -2.00) sse = 204237.1, tmin=4.9025 d=4.00 min @ (1.00, -1.00, 0.00) sse = 202417.9, tmin=6.1814 d=2.00 min @ (-0.50, 0.50, 0.50) sse = 201595.6, tmin=7.4619 d=1.00 min @ (0.00, -0.25, -0.25) sse = 201491.7, tmin=8.7759 d=0.50 min @ (0.12, 0.12, 0.12) sse = 201450.2, tmin=10.0654 tol=1.0e+00, sigma=0.5, host=lugh., 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 10.07 min curvature mean = -0.028, std = 0.830 curvature mean = 0.009, std = 0.947 curvature mean = -0.033, std = 0.840 curvature mean = 0.003, std = 0.979 curvature mean = -0.036, std = 0.841 curvature mean = 0.001, std = 0.992 2 Reading smoothwm curvature mean = -0.034, std = 0.284 curvature mean = 0.031, std = 0.247 curvature mean = 0.076, std = 0.372 curvature mean = 0.027, std = 0.305 curvature mean = 0.036, std = 0.575 curvature mean = 0.026, std = 0.332 curvature mean = 0.018, std = 0.721 curvature mean = 0.026, std = 0.343 curvature mean = 0.007, std = 0.826 MRISregister() return, current seed 0 -01: dt=0.0000, 34 negative triangles 115: dt=0.9900, 34 negative triangles 116: dt=0.9900, 33 negative triangles 117: dt=0.9900, 40 negative triangles 118: dt=0.9900, 30 negative triangles 119: dt=0.9900, 33 negative triangles 120: dt=0.9900, 26 negative triangles 121: dt=0.9900, 30 negative triangles 122: dt=0.9900, 23 negative triangles 123: dt=0.9900, 28 negative triangles 124: dt=0.9900, 25 negative triangles 125: dt=0.9900, 21 negative triangles 126: dt=0.9900, 26 negative triangles 127: dt=0.9900, 23 negative triangles 128: dt=0.9900, 22 negative triangles 129: dt=0.9900, 22 negative triangles 130: dt=0.9900, 18 negative triangles 131: dt=0.9900, 20 negative triangles 132: dt=0.9900, 15 negative triangles 133: dt=0.9900, 15 negative triangles 134: dt=0.9900, 15 negative triangles 135: dt=0.9900, 19 negative triangles 136: dt=0.9900, 18 negative triangles 137: dt=0.9900, 12 negative triangles 138: dt=0.9900, 8 negative triangles 139: dt=0.9900, 11 negative triangles 140: dt=0.9900, 7 negative triangles 141: dt=0.9900, 7 negative triangles 142: dt=0.9900, 8 negative triangles 143: dt=0.9900, 7 negative triangles 144: dt=0.9900, 5 negative triangles 145: dt=0.9900, 5 negative triangles 146: dt=0.9900, 3 negative triangles 147: dt=0.9900, 3 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.79 hours mris_register utimesec 2853.909139 mris_register stimesec 0.317951 mris_register ru_maxrss 229160 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 28805 mris_register ru_majflt 14 mris_register ru_nswap 0 mris_register ru_inblock 7928 mris_register ru_oublock 9632 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 34 mris_register ru_nivcsw 288978 FSRUNTIME@ mris_register 0.7938 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Thu Sep 7 21:18:59 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_register -curv -rusage /home/gc/study/recon-all/400614dclass/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /home/gc/study/recon-all/400614dclass/scripts cmdline mris_register -curv -rusage /home/gc/study/recon-all/400614dclass/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=lugh., 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=lugh., 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 = 5.585 curvature mean = 0.026, std = 0.808 curvature mean = 0.023, std = 0.863 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 16.00) sse = 347971.1, tmin=1.2696 d=32.00 min @ (-8.00, -8.00, -8.00) sse = 276036.8, tmin=2.5821 d=16.00 min @ (0.00, 4.00, 4.00) sse = 231702.7, tmin=3.9116 d=4.00 min @ (-1.00, -1.00, 0.00) sse = 229331.7, tmin=6.5454 d=2.00 min @ (0.00, 0.00, -0.50) sse = 228762.5, tmin=7.8266 d=1.00 min @ (0.25, 0.00, 0.00) sse = 228679.6, tmin=9.1249 d=0.50 min @ (-0.12, -0.12, 0.00) sse = 228642.8, tmin=10.4223 tol=1.0e+00, sigma=0.5, host=lugh., 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 10.42 min curvature mean = -0.022, std = 0.822 curvature mean = 0.009, std = 0.948 curvature mean = -0.028, std = 0.829 curvature mean = 0.003, std = 0.980 curvature mean = -0.030, std = 0.830 curvature mean = 0.000, std = 0.992 2 Reading smoothwm curvature mean = -0.033, std = 0.275 curvature mean = 0.030, std = 0.240 curvature mean = 0.073, std = 0.382 curvature mean = 0.026, std = 0.298 curvature mean = 0.037, std = 0.585 curvature mean = 0.026, std = 0.323 curvature mean = 0.020, std = 0.731 curvature mean = 0.026, std = 0.333 curvature mean = 0.007, std = 0.836 MRISregister() return, current seed 0 -01: dt=0.0000, 29 negative triangles 112: dt=0.9900, 29 negative triangles expanding nbhd size to 1 113: dt=0.9900, 37 negative triangles 114: dt=0.9900, 28 negative triangles 115: dt=0.9900, 27 negative triangles 116: dt=0.9900, 27 negative triangles 117: dt=0.9900, 25 negative triangles 118: dt=0.9900, 18 negative triangles 119: dt=0.9900, 18 negative triangles 120: dt=0.9900, 15 negative triangles 121: dt=0.9900, 14 negative triangles 122: dt=0.9900, 8 negative triangles 123: dt=0.9900, 7 negative triangles 124: dt=0.9900, 6 negative triangles 125: dt=0.9900, 6 negative triangles 126: dt=0.9900, 9 negative triangles 127: dt=0.9900, 3 negative triangles 128: dt=0.9900, 2 negative triangles 129: dt=0.9900, 2 negative triangles 130: dt=0.9900, 2 negative triangles 131: dt=0.9900, 4 negative triangles 132: dt=0.9900, 1 negative triangles 133: dt=0.9900, 4 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.90 hours mris_register utimesec 3222.359126 mris_register stimesec 0.388940 mris_register ru_maxrss 231712 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 28949 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 5584 mris_register ru_oublock 9632 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 21 mris_register ru_nivcsw 326815 FSRUNTIME@ mris_register 0.8967 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Thu Sep 7 22:12:47 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Thu Sep 7 22:12:49 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Thu Sep 7 22:12:51 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh Thu Sep 7 22:12:53 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Thu Sep 7 22:12:55 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 400614dclass 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... 1219 labels changed using aseg relabeling using gibbs priors... 000: 2920 changed, 136820 examined... 001: 671 changed, 12569 examined... 002: 206 changed, 3694 examined... 003: 68 changed, 1188 examined... 004: 20 changed, 401 examined... 005: 10 changed, 105 examined... 006: 1 changed, 55 examined... 007: 0 changed, 7 examined... 299 labels changed using aseg 000: 100 total segments, 55 labels (286 vertices) changed 001: 41 total segments, 3 labels (8 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... 2108 vertices marked for relabeling... 2108 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 18 seconds. #----------------------------------------- #@# Cortical Parc rh Thu Sep 7 22:13:13 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 400614dclass 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... 985 labels changed using aseg relabeling using gibbs priors... 000: 2616 changed, 136891 examined... 001: 595 changed, 11501 examined... 002: 114 changed, 3322 examined... 003: 34 changed, 674 examined... 004: 10 changed, 221 examined... 005: 8 changed, 65 examined... 006: 4 changed, 47 examined... 007: 1 changed, 24 examined... 008: 0 changed, 7 examined... 125 labels changed using aseg 000: 80 total segments, 41 labels (188 vertices) changed 001: 40 total segments, 2 labels (2 vertices) changed 002: 38 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... 1534 vertices marked for relabeling... 1534 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 17 seconds. #-------------------------------------------- #@# Make Pial Surf lh Thu Sep 7 22:13:30 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 400614dclass lh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /home/gc/study/recon-all/400614dclass/mri/filled.mgz... reading volume /home/gc/study/recon-all/400614dclass/mri/brain.finalsurfs.mgz... reading volume /home/gc/study/recon-all/400614dclass/mri/../mri/aseg.presurf.mgz... reading volume /home/gc/study/recon-all/400614dclass/mri/wm.mgz... 18256 bright wm thresholded. 269 bright non-wm voxels segmented. reading original surface position from /home/gc/study/recon-all/400614dclass/surf/lh.orig... computing class statistics... border white: 261544 voxels (1.56%) border gray 289857 voxels (1.73%) WM (101.0): 101.2 +- 6.0 [70.0 --> 110.0] GM (84.0) : 82.4 +- 9.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 70.8 (was 70) setting MAX_BORDER_WHITE to 111.0 (was 105) setting MIN_BORDER_WHITE to 80.0 (was 85) setting MAX_CSF to 61.6 (was 40) setting MAX_GRAY to 99.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 70.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 52.4 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-4.3, GM=80+-7.0 mean inside = 98.3, mean outside = 85.6 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.88 +- 0.25 (0.02-->5.97) (max @ vno 90703 --> 100654) face area 0.32 +- 0.16 (0.00-->5.29) mean absolute distance = 0.73 +- 0.91 2927 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 20 points - only 0.00% unknown deleting segment 2 with 78 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 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 10 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 20 points - only 0.00% unknown deleting segment 9 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown mean border=88.7, 113 (113) missing vertices, mean dist 0.5 [0.9 (%14.6)->0.7 (%85.4))] %62 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=lugh., nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.09-->5.92) (max @ vno 135715 --> 135786) face area 0.32 +- 0.16 (0.00-->5.05) mean absolute distance = 0.41 +- 0.67 4195 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1750902.8, rms=6.462 001: dt: 0.5000, sse=1079079.8, rms=4.045 (37.409%) 002: dt: 0.5000, sse=831286.7, rms=2.669 (34.010%) 003: dt: 0.5000, sse=750380.8, rms=2.038 (23.645%) 004: dt: 0.5000, sse=722371.8, rms=1.761 (13.607%) 005: dt: 0.5000, sse=716149.4, rms=1.676 (4.786%) rms = 1.63, time step reduction 1 of 3 to 0.250... 006: dt: 0.5000, sse=716817.1, rms=1.635 (2.480%) 007: dt: 0.2500, sse=693642.2, rms=1.273 (22.124%) rms = 1.23, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=687637.2, rms=1.227 (3.596%) rms = 1.21, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=686152.2, rms=1.212 (1.222%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 16 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 2 with 67 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown deleting segment 5 with 8 points - only 0.00% unknown deleting segment 6 with 9 points - only 0.00% unknown deleting segment 7 with 8 points - only 0.00% unknown mean border=90.9, 72 (14) missing vertices, mean dist -0.3 [0.5 (%69.7)->0.2 (%30.3))] %72 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=lugh., nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.07-->5.94) (max @ vno 87695 --> 86682) face area 0.36 +- 0.17 (0.00-->5.54) mean absolute distance = 0.33 +- 0.45 4746 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1013688.9, rms=3.401 010: dt: 0.5000, sse=825988.2, rms=2.120 (37.667%) 011: dt: 0.5000, sse=776843.6, rms=1.633 (22.975%) 012: dt: 0.5000, sse=758650.9, rms=1.428 (12.552%) 013: dt: 0.5000, sse=754504.9, rms=1.365 (4.413%) rms = 1.41, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=745541.4, rms=1.143 (16.287%) 015: dt: 0.2500, sse=750742.2, rms=1.044 (8.620%) rms = 1.04, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=736583.9, rms=1.035 (0.865%) rms = 1.03, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=736181.0, rms=1.025 (0.968%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 16 points - only 0.00% unknown deleting segment 1 with 78 points - only 0.00% unknown deleting segment 3 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 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 6 points - only 0.00% unknown deleting segment 8 with 14 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 7 points - only 0.00% unknown deleting segment 11 with 7 points - only 0.00% unknown deleting segment 12 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 13 with 1 points - only 0.00% unknown mean border=93.0, 95 (8) missing vertices, mean dist -0.2 [0.4 (%72.9)->0.2 (%27.1))] %84 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=lugh., nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.06-->6.13) (max @ vno 87695 --> 86682) face area 0.34 +- 0.17 (0.00-->5.30) mean absolute distance = 0.25 +- 0.36 3733 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=878476.8, rms=2.771 018: dt: 0.5000, sse=742401.4, rms=1.479 (46.618%) 019: dt: 0.5000, sse=747993.1, rms=1.218 (17.653%) rms = 1.17, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=720761.9, rms=1.170 (3.907%) 021: dt: 0.2500, sse=708849.0, rms=0.926 (20.910%) rms = 0.91, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=704776.6, rms=0.905 (2.185%) rms = 0.90, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=700632.8, rms=0.899 (0.725%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 16 points - only 0.00% unknown deleting segment 1 with 68 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 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 9 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 21 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 7 points - only 0.00% unknown deleting segment 9 with 7 points - only 0.00% unknown deleting segment 10 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown mean border=93.7, 109 (5) missing vertices, mean dist -0.1 [0.3 (%59.9)->0.2 (%40.1))] %88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=lugh., nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /home/gc/study/recon-all/400614dclass/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=708275.1, rms=1.361 024: dt: 0.5000, sse=685830.5, rms=0.871 (35.990%) rms = 1.01, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=677239.6, rms=0.767 (11.938%) rms = 0.74, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=679097.9, rms=0.745 (2.921%) rms = 0.74, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=676780.8, rms=0.736 (1.214%) positioning took 0.5 minutes generating cortex label... 9 non-cortical segments detected only using segment with 6227 vertices erasing segment 1 (vno[0] = 58290) erasing segment 2 (vno[0] = 84341) erasing segment 3 (vno[0] = 96906) erasing segment 4 (vno[0] = 96988) erasing segment 5 (vno[0] = 100648) erasing segment 6 (vno[0] = 100663) erasing segment 7 (vno[0] = 102100) erasing segment 8 (vno[0] = 122184) writing cortex label to /home/gc/study/recon-all/400614dclass/label/lh.cortex.label... writing curvature file /home/gc/study/recon-all/400614dclass/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/gc/study/recon-all/400614dclass/surf/lh.area vertex spacing 0.88 +- 0.26 (0.02-->6.20) (max @ vno 86682 --> 87695) face area 0.33 +- 0.17 (0.00-->5.19) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 29 points - only 0.00% unknown deleting segment 1 with 17 points - only 0.00% unknown deleting segment 3 with 101 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown deleting segment 8 with 138 points - only 0.00% unknown deleting segment 9 with 19 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=69.3, 112 (112) missing vertices, mean dist 1.6 [0.0 (%0.0)->2.8 (%100.0))] %19 local maxima, %36 large gradients and %42 min vals, 208 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=lugh., 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=17634196.0, rms=25.392 001: dt: 0.0500, sse=16005240.0, rms=24.144 (4.914%) 002: dt: 0.0500, sse=14843675.0, rms=23.213 (3.855%) 003: dt: 0.0500, sse=13950864.0, rms=22.472 (3.195%) 004: dt: 0.0500, sse=13222422.0, rms=21.848 (2.777%) 005: dt: 0.0500, sse=12603067.0, rms=21.303 (2.494%) 006: dt: 0.0500, sse=12059895.0, rms=20.813 (2.299%) 007: dt: 0.0500, sse=11573064.0, rms=20.364 (2.157%) 008: dt: 0.0500, sse=11129688.0, rms=19.946 (2.052%) 009: dt: 0.0500, sse=10721384.0, rms=19.553 (1.969%) 010: dt: 0.0500, sse=10341822.0, rms=19.181 (1.904%) positioning took 1.1 minutes mean border=69.1, 101 (58) missing vertices, mean dist 1.3 [0.1 (%0.0)->2.3 (%100.0))] %19 local maxima, %36 large gradients and %41 min vals, 215 gradients ignored tol=1.0e-04, sigma=2.0, host=lugh., 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=10987473.0, rms=19.807 011: dt: 0.0500, sse=10630454.0, rms=19.462 (1.744%) 012: dt: 0.0500, sse=10294436.0, rms=19.131 (1.700%) 013: dt: 0.0500, sse=9977145.0, rms=18.813 (1.661%) 014: dt: 0.0500, sse=9677173.0, rms=18.507 (1.624%) 015: dt: 0.0500, sse=9392831.0, rms=18.213 (1.591%) 016: dt: 0.0500, sse=9123491.0, rms=17.930 (1.556%) 017: dt: 0.0500, sse=8867653.0, rms=17.656 (1.525%) 018: dt: 0.0500, sse=8624661.0, rms=17.392 (1.494%) 019: dt: 0.0500, sse=8393680.0, rms=17.138 (1.464%) 020: dt: 0.0500, sse=8173638.5, rms=16.892 (1.437%) positioning took 1.0 minutes mean border=69.0, 101 (42) missing vertices, mean dist 1.1 [0.1 (%0.5)->2.0 (%99.5))] %20 local maxima, %36 large gradients and %41 min vals, 215 gradients ignored tol=1.0e-04, sigma=2.0, host=lugh., 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=8267168.0, rms=17.000 021: dt: 0.0500, sse=8053170.5, rms=16.759 (1.420%) 022: dt: 0.0500, sse=7849497.0, rms=16.526 (1.391%) 023: dt: 0.0500, sse=7654811.0, rms=16.300 (1.367%) 024: dt: 0.0500, sse=7469579.5, rms=16.082 (1.338%) 025: dt: 0.0500, sse=7293035.5, rms=15.871 (1.310%) 026: dt: 0.0500, sse=7124595.5, rms=15.667 (1.284%) 027: dt: 0.0500, sse=6963142.0, rms=15.470 (1.263%) 028: dt: 0.0500, sse=6807045.0, rms=15.276 (1.253%) 029: dt: 0.0500, sse=6656145.5, rms=15.086 (1.243%) 030: dt: 0.0500, sse=6510029.5, rms=14.900 (1.234%) positioning took 1.0 minutes mean border=68.9, 133 (38) missing vertices, mean dist 0.9 [0.1 (%6.0)->1.7 (%94.0))] %20 local maxima, %36 large gradients and %41 min vals, 201 gradients ignored tol=1.0e-04, sigma=2.0, host=lugh., 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=6557104.0, rms=14.959 031: dt: 0.5000, sse=5468884.5, rms=13.498 (9.767%) 032: dt: 0.5000, sse=4597157.5, rms=12.198 (9.633%) 033: dt: 0.5000, sse=3828565.5, rms=10.925 (10.434%) 034: dt: 0.5000, sse=3143514.8, rms=9.647 (11.697%) 035: dt: 0.5000, sse=2559950.2, rms=8.408 (12.847%) 036: dt: 0.5000, sse=2092915.5, rms=7.262 (13.626%) 037: dt: 0.5000, sse=1731331.4, rms=6.236 (14.125%) 038: dt: 0.5000, sse=1495990.8, rms=5.460 (12.447%) 039: dt: 0.5000, sse=1340531.8, rms=4.887 (10.503%) 040: dt: 0.5000, sse=1260138.5, rms=4.555 (6.783%) 041: dt: 0.5000, sse=1202417.1, rms=4.307 (5.444%) 042: dt: 0.5000, sse=1180208.2, rms=4.202 (2.446%) 043: dt: 0.5000, sse=1156567.4, rms=4.097 (2.505%) rms = 4.07, time step reduction 1 of 3 to 0.250... 044: dt: 0.5000, sse=1151055.1, rms=4.065 (0.763%) 045: dt: 0.2500, sse=1047511.6, rms=3.485 (14.266%) 046: dt: 0.2500, sse=1020740.6, rms=3.333 (4.377%) rms = 3.32, time step reduction 2 of 3 to 0.125... 047: dt: 0.2500, sse=1018677.6, rms=3.317 (0.467%) 048: dt: 0.1250, sse=1003351.4, rms=3.221 (2.889%) rms = 3.21, time step reduction 3 of 3 to 0.062... 049: dt: 0.1250, sse=1000600.0, rms=3.205 (0.508%) positioning took 2.9 minutes mean border=67.9, 2008 (15) missing vertices, mean dist 0.1 [0.2 (%42.9)->0.5 (%57.1))] %32 local maxima, %26 large gradients and %37 min vals, 120 gradients ignored tol=1.0e-04, sigma=1.0, host=lugh., 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=1239990.2, rms=3.743 050: dt: 0.5000, sse=1195250.6, rms=3.524 (5.866%) 051: dt: 0.5000, sse=1167450.5, rms=3.401 (3.495%) rms = 3.55, time step reduction 1 of 3 to 0.250... 052: dt: 0.2500, sse=1076351.4, rms=2.788 (18.021%) 053: dt: 0.2500, sse=1049259.0, rms=2.577 (7.564%) rms = 2.55, time step reduction 2 of 3 to 0.125... 054: dt: 0.2500, sse=1045612.7, rms=2.548 (1.116%) 055: dt: 0.1250, sse=1029446.0, rms=2.413 (5.310%) rms = 2.40, time step reduction 3 of 3 to 0.062... 056: dt: 0.1250, sse=1027213.2, rms=2.396 (0.697%) positioning took 1.5 minutes mean border=67.3, 2329 (14) missing vertices, mean dist 0.1 [0.1 (%43.1)->0.3 (%56.9))] %41 local maxima, %18 large gradients and %36 min vals, 153 gradients ignored tol=1.0e-04, sigma=0.5, host=lugh., 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=1055674.6, rms=2.625 rms = 2.86, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=1034427.6, rms=2.458 (6.381%) 058: dt: 0.2500, sse=1027126.1, rms=2.401 (2.287%) rms = 2.39, time step reduction 2 of 3 to 0.125... 059: dt: 0.2500, sse=1025068.4, rms=2.392 (0.380%) rms = 2.35, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1020409.9, rms=2.350 (1.783%) positioning took 1.0 minutes mean border=67.0, 4685 (13) missing vertices, mean dist 0.0 [0.1 (%45.8)->0.2 (%54.2))] %44 local maxima, %14 large gradients and %35 min vals, 184 gradients ignored tol=1.0e-04, sigma=0.2, host=lugh., nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /home/gc/study/recon-all/400614dclass/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1026559.2, rms=2.403 rms = 2.60, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1017254.7, rms=2.325 (3.247%) rms = 2.29, time step reduction 2 of 3 to 0.125... 062: dt: 0.2500, sse=1011301.9, rms=2.290 (1.521%) rms = 2.26, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1007722.1, rms=2.256 (1.454%) positioning took 0.8 minutes writing curvature file /home/gc/study/recon-all/400614dclass/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/gc/study/recon-all/400614dclass/surf/lh.area.pial vertex spacing 0.98 +- 0.41 (0.07-->7.90) (max @ vno 55407 --> 135656) face area 0.38 +- 0.29 (0.00-->7.26) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 136820 vertices processed 25000 of 136820 vertices processed 50000 of 136820 vertices processed 75000 of 136820 vertices processed 100000 of 136820 vertices processed 125000 of 136820 vertices processed 0 of 136820 vertices processed 25000 of 136820 vertices processed 50000 of 136820 vertices processed 75000 of 136820 vertices processed 100000 of 136820 vertices processed 125000 of 136820 vertices processed thickness calculation complete, 277:509 truncations. 36277 vertices at 0 distance 101363 vertices at 1 distance 78300 vertices at 2 distance 31635 vertices at 3 distance 10608 vertices at 4 distance 3372 vertices at 5 distance 1165 vertices at 6 distance 444 vertices at 7 distance 164 vertices at 8 distance 67 vertices at 9 distance 45 vertices at 10 distance 38 vertices at 11 distance 30 vertices at 12 distance 17 vertices at 13 distance 30 vertices at 14 distance 27 vertices at 15 distance 29 vertices at 16 distance 18 vertices at 17 distance 6 vertices at 18 distance 5 vertices at 19 distance 8 vertices at 20 distance writing curvature file /home/gc/study/recon-all/400614dclass/surf/lh.thickness positioning took 17.2 minutes #-------------------------------------------- #@# Make Pial Surf rh Thu Sep 7 22:30:39 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 400614dclass rh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /home/gc/study/recon-all/400614dclass/mri/filled.mgz... reading volume /home/gc/study/recon-all/400614dclass/mri/brain.finalsurfs.mgz... reading volume /home/gc/study/recon-all/400614dclass/mri/../mri/aseg.presurf.mgz... reading volume /home/gc/study/recon-all/400614dclass/mri/wm.mgz... 18256 bright wm thresholded. 269 bright non-wm voxels segmented. reading original surface position from /home/gc/study/recon-all/400614dclass/surf/rh.orig... computing class statistics... border white: 261544 voxels (1.56%) border gray 289857 voxels (1.73%) WM (101.0): 101.2 +- 6.0 [70.0 --> 110.0] GM (84.0) : 82.4 +- 9.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 70.8 (was 70) setting MAX_BORDER_WHITE to 110.0 (was 105) setting MIN_BORDER_WHITE to 80.0 (was 85) setting MAX_CSF to 61.6 (was 40) setting MAX_GRAY to 98.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 70.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 52.4 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104+-4.3, GM=80+-7.0 mean inside = 98.1, mean outside = 85.8 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.88 +- 0.26 (0.05-->9.54) (max @ vno 135758 --> 135945) face area 0.33 +- 0.17 (0.00-->13.23) mean absolute distance = 0.73 +- 0.91 2958 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 37 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 12 points - only 0.00% unknown deleting segment 4 with 118 points - only 0.00% unknown deleting segment 5 with 18 points - only 0.00% unknown deleting segment 6 with 12 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 65 points - only 24.62% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown deleting segment 11 with 67 points - only 0.00% unknown deleting segment 12 with 45 points - only 0.00% unknown deleting segment 13 with 35 points - only 0.00% unknown deleting segment 14 with 50 points - only 0.00% unknown mean border=88.8, 97 (96) missing vertices, mean dist 0.5 [0.9 (%14.5)->0.7 (%85.5))] %63 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=lugh., 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 +- 0.26 (0.06-->9.66) (max @ vno 135758 --> 135945) face area 0.33 +- 0.17 (0.00-->11.75) mean absolute distance = 0.43 +- 0.73 4423 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1713203.1, rms=6.341 001: dt: 0.5000, sse=1077381.9, rms=4.041 (36.277%) 002: dt: 0.5000, sse=838354.9, rms=2.727 (32.505%) 003: dt: 0.5000, sse=756866.2, rms=2.092 (23.279%) 004: dt: 0.5000, sse=724512.6, rms=1.786 (14.634%) 005: dt: 0.5000, sse=713745.4, rms=1.664 (6.860%) 006: dt: 0.5000, sse=708534.3, rms=1.600 (3.848%) rms = 1.59, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=707284.2, rms=1.588 (0.753%) 008: dt: 0.2500, sse=685235.5, rms=1.190 (25.055%) rms = 1.14, time step reduction 2 of 3 to 0.125... 009: dt: 0.2500, sse=682271.8, rms=1.141 (4.082%) rms = 1.13, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=681724.9, rms=1.129 (1.058%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 29 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 13 points - only 0.00% unknown deleting segment 3 with 8 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown deleting segment 5 with 13 points - only 0.00% unknown deleting segment 6 with 39 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 9 with 6 points - only 0.00% unknown deleting segment 10 with 48 points - only 0.00% unknown deleting segment 11 with 43 points - only 0.00% unknown deleting segment 12 with 25 points - only 0.00% unknown deleting segment 13 with 45 points - only 0.00% unknown mean border=91.0, 45 (15) missing vertices, mean dist -0.3 [0.5 (%68.5)->0.2 (%31.5))] %72 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=lugh., nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.26 (0.08-->9.76) (max @ vno 135758 --> 135945) face area 0.36 +- 0.18 (0.00-->13.78) mean absolute distance = 0.36 +- 0.50 4462 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1005081.7, rms=3.333 011: dt: 0.5000, sse=841185.8, rms=2.061 (38.171%) 012: dt: 0.5000, sse=777543.9, rms=1.608 (21.951%) 013: dt: 0.5000, sse=760712.2, rms=1.404 (12.742%) 014: dt: 0.5000, sse=754861.7, rms=1.317 (6.197%) rms = 1.34, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=742656.0, rms=1.111 (15.636%) 016: dt: 0.2500, sse=747022.9, rms=1.002 (9.774%) rms = 0.98, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=736661.1, rms=0.978 (2.430%) rms = 0.97, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=737137.1, rms=0.966 (1.156%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 35 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 13 points - only 0.00% unknown deleting segment 3 with 84 points - only 0.00% unknown deleting segment 4 with 16 points - only 0.00% unknown deleting segment 5 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 7 points - only 0.00% unknown deleting segment 8 with 46 points - only 0.00% unknown deleting segment 9 with 43 points - only 0.00% unknown deleting segment 10 with 25 points - only 0.00% unknown deleting segment 11 with 39 points - only 0.00% unknown mean border=93.0, 54 (11) missing vertices, mean dist -0.2 [0.4 (%71.7)->0.2 (%28.3))] %83 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=lugh., nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.26 (0.08-->9.79) (max @ vno 135758 --> 135945) face area 0.34 +- 0.18 (0.00-->14.05) mean absolute distance = 0.28 +- 0.40 4016 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=887867.1, rms=2.796 019: dt: 0.5000, sse=747494.4, rms=1.507 (46.105%) 020: dt: 0.5000, sse=724265.4, rms=1.191 (20.998%) 021: dt: 0.5000, sse=720217.1, rms=1.118 (6.102%) rms = 1.15, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=710090.1, rms=0.950 (14.987%) 023: dt: 0.2500, sse=716255.6, rms=0.886 (6.826%) rms = 0.88, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=706337.2, rms=0.885 (0.111%) rms = 0.88, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=705176.8, rms=0.881 (0.459%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 33 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 15 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 86 points - only 0.00% unknown deleting segment 5 with 16 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown deleting segment 8 with 7 points - only 0.00% unknown deleting segment 9 with 44 points - only 0.00% unknown deleting segment 10 with 42 points - only 0.00% unknown deleting segment 11 with 25 points - only 0.00% unknown deleting segment 12 with 33 points - only 0.00% unknown mean border=93.8, 58 (10) missing vertices, mean dist -0.1 [0.3 (%59.9)->0.2 (%40.1))] %88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=lugh., nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /home/gc/study/recon-all/400614dclass/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=713643.7, rms=1.407 026: dt: 0.5000, sse=686304.1, rms=0.845 (39.946%) rms = 0.97, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=679280.3, rms=0.747 (11.559%) rms = 0.73, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=678845.2, rms=0.727 (2.704%) rms = 0.72, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=676734.5, rms=0.716 (1.497%) positioning took 0.5 minutes generating cortex label... 10 non-cortical segments detected only using segment with 6809 vertices erasing segment 0 (vno[0] = 35841) erasing segment 2 (vno[0] = 66558) erasing segment 3 (vno[0] = 83772) erasing segment 4 (vno[0] = 86750) erasing segment 5 (vno[0] = 99014) erasing segment 6 (vno[0] = 100021) erasing segment 7 (vno[0] = 101760) erasing segment 8 (vno[0] = 101793) erasing segment 9 (vno[0] = 135528) writing cortex label to /home/gc/study/recon-all/400614dclass/label/rh.cortex.label... writing curvature file /home/gc/study/recon-all/400614dclass/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/gc/study/recon-all/400614dclass/surf/rh.area vertex spacing 0.88 +- 0.27 (0.05-->9.77) (max @ vno 135758 --> 135945) face area 0.33 +- 0.18 (0.00-->13.95) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 26 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown deleting segment 2 with 37 points - only 0.00% unknown deleting segment 4 with 70 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown removing 4 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 9 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 15 points - only 0.00% unknown deleting segment 13 with 10 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=69.1, 85 (85) missing vertices, mean dist 1.6 [0.1 (%0.0)->2.9 (%100.0))] %18 local maxima, %36 large gradients and %42 min vals, 276 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=lugh., 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=17832628.0, rms=25.588 001: dt: 0.0500, sse=16247702.0, rms=24.381 (4.720%) 002: dt: 0.0500, sse=15121672.0, rms=23.485 (3.675%) 003: dt: 0.0500, sse=14254344.0, rms=22.770 (3.041%) 004: dt: 0.0500, sse=13545078.0, rms=22.169 (2.641%) 005: dt: 0.0500, sse=12940778.0, rms=21.644 (2.371%) 006: dt: 0.0500, sse=12410646.0, rms=21.172 (2.180%) 007: dt: 0.0500, sse=11934529.0, rms=20.739 (2.045%) 008: dt: 0.0500, sse=11500117.0, rms=20.336 (1.944%) 009: dt: 0.0500, sse=11099290.0, rms=19.956 (1.865%) 010: dt: 0.0500, sse=10725662.0, rms=19.596 (1.805%) positioning took 1.0 minutes mean border=69.0, 73 (51) missing vertices, mean dist 1.3 [0.1 (%0.0)->2.4 (%100.0))] %19 local maxima, %36 large gradients and %41 min vals, 242 gradients ignored tol=1.0e-04, sigma=2.0, host=lugh., 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=11391674.0, rms=20.231 011: dt: 0.0500, sse=11039211.0, rms=19.896 (1.655%) 012: dt: 0.0500, sse=10706613.0, rms=19.575 (1.615%) 013: dt: 0.0500, sse=10391682.0, rms=19.266 (1.580%) 014: dt: 0.0500, sse=10092639.0, rms=18.967 (1.549%) 015: dt: 0.0500, sse=9808117.0, rms=18.679 (1.521%) 016: dt: 0.0500, sse=9537143.0, rms=18.400 (1.494%) 017: dt: 0.0500, sse=9278654.0, rms=18.130 (1.468%) 018: dt: 0.0500, sse=9032068.0, rms=17.868 (1.443%) 019: dt: 0.0500, sse=8796579.0, rms=17.614 (1.419%) 020: dt: 0.0500, sse=8571208.0, rms=17.368 (1.398%) positioning took 1.0 minutes mean border=68.9, 80 (38) missing vertices, mean dist 1.2 [0.1 (%0.4)->2.0 (%99.6))] %19 local maxima, %36 large gradients and %41 min vals, 235 gradients ignored tol=1.0e-04, sigma=2.0, host=lugh., 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=8645653.0, rms=17.454 021: dt: 0.0500, sse=8426319.0, rms=17.212 (1.386%) 022: dt: 0.0500, sse=8216740.0, rms=16.977 (1.362%) 023: dt: 0.0500, sse=8015595.5, rms=16.749 (1.344%) 024: dt: 0.0500, sse=7823174.0, rms=16.528 (1.321%) 025: dt: 0.0500, sse=7638734.5, rms=16.313 (1.301%) 026: dt: 0.0500, sse=7461733.5, rms=16.104 (1.282%) 027: dt: 0.0500, sse=7291236.5, rms=15.900 (1.267%) 028: dt: 0.0500, sse=7125736.0, rms=15.699 (1.262%) 029: dt: 0.0500, sse=6964901.5, rms=15.502 (1.259%) 030: dt: 0.0500, sse=6808403.5, rms=15.307 (1.256%) positioning took 1.0 minutes mean border=68.8, 94 (28) missing vertices, mean dist 1.0 [0.1 (%5.2)->1.8 (%94.8))] %19 local maxima, %36 large gradients and %40 min vals, 218 gradients ignored tol=1.0e-04, sigma=2.0, host=lugh., 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=6858679.0, rms=15.369 031: dt: 0.5000, sse=5672570.0, rms=13.810 (10.142%) 032: dt: 0.5000, sse=4689161.5, rms=12.365 (10.460%) 033: dt: 0.5000, sse=3833651.0, rms=10.956 (11.399%) 034: dt: 0.5000, sse=3099519.8, rms=9.579 (12.563%) 035: dt: 0.5000, sse=2509247.8, rms=8.310 (13.253%) 036: dt: 0.5000, sse=2056387.5, rms=7.182 (13.571%) 037: dt: 0.5000, sse=1729056.1, rms=6.245 (13.050%) 038: dt: 0.5000, sse=1516270.5, rms=5.546 (11.189%) 039: dt: 0.5000, sse=1384137.9, rms=5.066 (8.660%) 040: dt: 0.5000, sse=1305842.8, rms=4.755 (6.138%) 041: dt: 0.5000, sse=1258274.8, rms=4.558 (4.148%) 042: dt: 0.5000, sse=1228272.2, rms=4.424 (2.926%) 043: dt: 0.5000, sse=1208394.5, rms=4.339 (1.932%) 044: dt: 0.5000, sse=1191900.0, rms=4.261 (1.791%) rms = 4.22, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1183326.6, rms=4.225 (0.858%) 046: dt: 0.2500, sse=1082732.4, rms=3.679 (12.908%) 047: dt: 0.2500, sse=1056857.8, rms=3.539 (3.806%) rms = 3.52, time step reduction 2 of 3 to 0.125... 048: dt: 0.2500, sse=1054357.8, rms=3.523 (0.466%) 049: dt: 0.1250, sse=1039332.1, rms=3.433 (2.548%) rms = 3.42, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1036409.7, rms=3.417 (0.472%) positioning took 3.0 minutes mean border=67.8, 2147 (12) missing vertices, mean dist 0.1 [0.2 (%42.9)->0.5 (%57.1))] %32 local maxima, %26 large gradients and %36 min vals, 153 gradients ignored tol=1.0e-04, sigma=1.0, host=lugh., 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=1254836.6, rms=3.868 051: dt: 0.5000, sse=1217406.0, rms=3.692 (4.562%) 052: dt: 0.5000, sse=1180157.2, rms=3.523 (4.580%) rms = 3.66, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1090986.0, rms=2.948 (16.327%) 054: dt: 0.2500, sse=1063209.5, rms=2.740 (7.052%) rms = 2.70, time step reduction 2 of 3 to 0.125... 055: dt: 0.2500, sse=1057916.5, rms=2.702 (1.370%) 056: dt: 0.1250, sse=1042383.1, rms=2.579 (4.576%) rms = 2.56, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1039851.0, rms=2.560 (0.725%) positioning took 1.5 minutes mean border=67.3, 2257 (8) missing vertices, mean dist 0.1 [0.1 (%43.5)->0.3 (%56.5))] %40 local maxima, %19 large gradients and %35 min vals, 159 gradients ignored tol=1.0e-04, sigma=0.5, host=lugh., 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=1061830.1, rms=2.740 rms = 2.93, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1042059.5, rms=2.593 (5.374%) 059: dt: 0.2500, sse=1034110.5, rms=2.538 (2.134%) rms = 2.52, time step reduction 2 of 3 to 0.125... 060: dt: 0.2500, sse=1031125.7, rms=2.524 (0.558%) rms = 2.48, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=1025840.1, rms=2.477 (1.839%) positioning took 1.0 minutes mean border=66.9, 4765 (8) missing vertices, mean dist 0.1 [0.1 (%45.7)->0.3 (%54.3))] %44 local maxima, %15 large gradients and %34 min vals, 165 gradients ignored tol=1.0e-04, sigma=0.2, host=lugh., nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /home/gc/study/recon-all/400614dclass/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1034591.2, rms=2.539 rms = 2.70, time step reduction 1 of 3 to 0.250... 062: dt: 0.2500, sse=1024083.7, rms=2.456 (3.266%) rms = 2.41, time step reduction 2 of 3 to 0.125... 063: dt: 0.2500, sse=1016651.7, rms=2.411 (1.831%) rms = 2.38, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=1012893.9, rms=2.376 (1.447%) positioning took 0.8 minutes writing curvature file /home/gc/study/recon-all/400614dclass/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/gc/study/recon-all/400614dclass/surf/rh.area.pial vertex spacing 0.98 +- 0.42 (0.05-->14.39) (max @ vno 135758 --> 135945) face area 0.38 +- 0.31 (0.00-->27.24) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 136891 vertices processed 25000 of 136891 vertices processed 50000 of 136891 vertices processed 75000 of 136891 vertices processed 100000 of 136891 vertices processed 125000 of 136891 vertices processed 0 of 136891 vertices processed 25000 of 136891 vertices processed 50000 of 136891 vertices processed 75000 of 136891 vertices processed 100000 of 136891 vertices processed 125000 of 136891 vertices processed thickness calculation complete, 396:807 truncations. 35413 vertices at 0 distance 101501 vertices at 1 distance 76269 vertices at 2 distance 31292 vertices at 3 distance 11350 vertices at 4 distance 4037 vertices at 5 distance 1456 vertices at 6 distance 588 vertices at 7 distance 301 vertices at 8 distance 139 vertices at 9 distance 69 vertices at 10 distance 41 vertices at 11 distance 23 vertices at 12 distance 25 vertices at 13 distance 18 vertices at 14 distance 18 vertices at 15 distance 14 vertices at 16 distance 10 vertices at 17 distance 15 vertices at 18 distance 12 vertices at 19 distance 11 vertices at 20 distance writing curvature file /home/gc/study/recon-all/400614dclass/surf/rh.thickness positioning took 17.2 minutes #-------------------------------------------- #@# Surf Volume lh Thu Sep 7 22:47:54 CEST 2017 /home/gc/study/recon-all/400614dclass/surf /home/gc/study/recon-all/400614dclass/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 400614dclass lh /home/gc/study/recon-all/400614dclass/surf/lh.volume masking with /home/gc/study/recon-all/400614dclass/label/lh.cortex.label Total face volume 239172 Total vertex volume 236306 (mask=0) #@# 400614dclass lh 236306 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Thu Sep 7 22:47:57 CEST 2017 /home/gc/study/recon-all/400614dclass/surf /home/gc/study/recon-all/400614dclass/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 400614dclass rh /home/gc/study/recon-all/400614dclass/surf/rh.volume masking with /home/gc/study/recon-all/400614dclass/label/rh.cortex.label Total face volume 239461 Total vertex volume 236406 (mask=0) #@# 400614dclass rh 236406 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Thu Sep 7 22:48:00 CEST 2017 /home/gc/study/recon-all/400614dclass/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 400614dclass SUBJECTS_DIR is /home/gc/study/recon-all 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 = 146 writing volume /home/gc/study/recon-all/400614dclass/mri/ribbon.mgz mris_volmask took 13.36 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Thu Sep 7 23:01:22 CEST 2017 /home/gc/study/recon-all/400614dclass/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 400614dclass lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/gc/study/recon-all/400614dclass/mri/wm.mgz... reading input surface /home/gc/study/recon-all/400614dclass/surf/lh.white... reading input pial surface /home/gc/study/recon-all/400614dclass/surf/lh.pial... reading input white surface /home/gc/study/recon-all/400614dclass/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 239172 Total vertex volume 236306 (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) = 1420931 mm^3 (det: 1.371007 ) lhCtxGM: 235090.012 234708.000 diff= 382.0 pctdiff= 0.162 rhCtxGM: 235324.034 234754.000 diff= 570.0 pctdiff= 0.242 lhCtxWM: 218327.405 218779.500 diff= -452.1 pctdiff=-0.207 rhCtxWM: 220192.396 220961.500 diff= -769.1 pctdiff=-0.349 SubCortGMVol 60226.000 SupraTentVol 980747.848 (978448.000) diff=2299.848 pctdiff=0.234 SupraTentVolNotVent 971731.848 (969432.000) diff=2299.848 pctdiff=0.237 BrainSegVol 1140377.000 (1136514.000) diff=3863.000 pctdiff=0.339 BrainSegVolNotVent 1126683.000 (1126351.848) diff=331.152 pctdiff=0.029 BrainSegVolNotVent 1126683.000 CerebellumVol 157189.000 VentChorVol 9016.000 3rd4th5thCSF 4678.000 CSFVol 815.000, OptChiasmVol 62.000 MaskVol 1688423.000 1308 901 2416 2.427 0.436 0.091 0.018 10 0.8 bankssts 944 630 2033 2.942 0.480 0.140 0.027 14 1.0 caudalanteriorcingulate 3235 2173 6034 2.573 0.525 0.113 0.023 28 3.0 caudalmiddlefrontal 2403 1530 2961 1.836 0.435 0.137 0.029 30 3.0 cuneus 860 598 2563 3.329 0.918 0.113 0.031 7 0.9 entorhinal 4634 3121 9450 2.728 0.615 0.134 0.033 65 6.3 fusiform 6223 4021 11591 2.575 0.525 0.121 0.023 71 5.8 inferiorparietal 5137 3446 10840 2.674 0.595 0.126 0.029 74 6.0 inferiortemporal 1548 999 2589 2.340 0.851 0.132 0.030 24 1.6 isthmuscingulate 7093 4385 9626 2.053 0.544 0.131 0.030 82 8.7 lateraloccipital 3935 2590 6936 2.607 0.803 0.141 0.043 60 7.3 lateralorbitofrontal 3864 2582 5489 2.048 0.669 0.141 0.032 50 5.2 lingual 2879 1989 4583 2.161 0.638 0.144 0.049 44 5.9 medialorbitofrontal 5049 3395 11903 2.953 0.703 0.128 0.028 68 5.7 middletemporal 862 565 2037 3.194 0.754 0.094 0.019 7 0.6 parahippocampal 2257 1448 3543 2.322 0.474 0.100 0.019 13 1.8 paracentral 2251 1424 4542 2.841 0.583 0.118 0.028 24 2.2 parsopercularis 1035 619 1933 2.529 0.591 0.117 0.039 14 1.5 parsorbitalis 2200 1362 4181 2.716 0.669 0.127 0.038 27 3.6 parstriangularis 2085 1388 2039 1.654 0.432 0.128 0.030 22 2.5 pericalcarine 6494 3953 8619 2.038 0.696 0.104 0.023 57 6.4 postcentral 1694 1158 3425 2.780 0.545 0.141 0.028 25 2.0 posteriorcingulate 8334 4986 14932 2.741 0.612 0.109 0.026 69 8.6 precentral 5404 3638 9248 2.430 0.493 0.118 0.021 57 4.5 precuneus 1278 848 2508 2.864 0.635 0.122 0.035 16 1.9 rostralanteriorcingulate 10025 6510 17133 2.375 0.556 0.133 0.036 126 15.1 rostralmiddlefrontal 10408 6826 23109 2.974 0.592 0.124 0.028 110 11.7 superiorfrontal 8442 5358 13584 2.307 0.453 0.120 0.024 95 7.7 superiorparietal 6243 3976 11076 2.572 0.648 0.104 0.023 57 6.1 superiortemporal 6953 4461 13389 2.694 0.514 0.132 0.031 112 9.5 supramarginal 434 276 935 2.464 0.795 0.168 0.067 10 1.3 frontalpole 621 471 2716 3.766 0.721 0.176 0.057 11 1.5 temporalpole 770 474 1139 2.149 0.372 0.086 0.015 5 0.4 transversetemporal 3461 2305 7136 3.156 0.681 0.126 0.035 34 4.6 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 400614dclass lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /home/gc/study/recon-all/400614dclass/mri/wm.mgz... reading input surface /home/gc/study/recon-all/400614dclass/surf/lh.pial... reading input pial surface /home/gc/study/recon-all/400614dclass/surf/lh.pial... reading input white surface /home/gc/study/recon-all/400614dclass/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 239172 Total vertex volume 236306 (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) = 1420931 mm^3 (det: 1.371007 ) lhCtxGM: 235090.012 234708.000 diff= 382.0 pctdiff= 0.162 rhCtxGM: 235324.034 234754.000 diff= 570.0 pctdiff= 0.242 lhCtxWM: 218327.405 218779.500 diff= -452.1 pctdiff=-0.207 rhCtxWM: 220192.396 220961.500 diff= -769.1 pctdiff=-0.349 SubCortGMVol 60226.000 SupraTentVol 980747.848 (978448.000) diff=2299.848 pctdiff=0.234 SupraTentVolNotVent 971731.848 (969432.000) diff=2299.848 pctdiff=0.237 BrainSegVol 1140377.000 (1136514.000) diff=3863.000 pctdiff=0.339 BrainSegVolNotVent 1126683.000 (1126351.848) diff=331.152 pctdiff=0.029 BrainSegVolNotVent 1126683.000 CerebellumVol 157189.000 VentChorVol 9016.000 3rd4th5thCSF 4678.000 CSFVol 815.000, OptChiasmVol 62.000 MaskVol 1688423.000 1308 1074 2416 2.427 0.436 0.125 0.024 13 1.5 bankssts 944 751 2033 2.942 0.480 0.158 0.044 41 1.3 caudalanteriorcingulate 3235 2452 6034 2.573 0.525 0.122 0.025 35 3.5 caudalmiddlefrontal 2403 1831 2961 1.836 0.435 0.134 0.030 35 3.1 cuneus 860 918 2563 3.329 0.918 0.174 0.040 16 1.6 entorhinal 4634 3750 9450 2.728 0.615 0.129 0.029 83 6.1 fusiform 6223 4828 11591 2.575 0.525 0.130 0.026 81 7.4 inferiorparietal 5137 4523 10840 2.674 0.595 0.136 0.027 71 6.4 inferiortemporal 1548 1220 2589 2.340 0.851 0.149 0.040 46 2.6 isthmuscingulate 7093 5054 9626 2.053 0.544 0.122 0.029 111 9.4 lateraloccipital 3935 2789 6936 2.607 0.803 0.141 0.035 78 6.6 lateralorbitofrontal 3864 2956 5489 2.048 0.669 0.138 0.032 53 5.8 lingual 2879 2266 4583 2.161 0.638 0.137 0.054 301 8.2 medialorbitofrontal 5049 4526 11903 2.953 0.703 0.135 0.030 49 6.6 middletemporal 862 758 2037 3.194 0.754 0.127 0.030 10 1.1 parahippocampal 2257 1638 3543 2.322 0.474 0.104 0.019 22 2.0 paracentral 2251 1714 4542 2.841 0.583 0.130 0.028 27 2.9 parsopercularis 1035 844 1933 2.529 0.591 0.121 0.022 12 1.0 parsorbitalis 2200 1681 4181 2.716 0.669 0.136 0.035 57 3.5 parstriangularis 2085 1173 2039 1.654 0.432 0.103 0.025 25 2.1 pericalcarine 6494 4659 8619 2.038 0.696 0.110 0.020 59 5.6 postcentral 1694 1353 3425 2.780 0.545 0.142 0.040 204 2.4 posteriorcingulate 8334 5723 14932 2.741 0.612 0.105 0.022 80 7.7 precentral 5404 3921 9248 2.430 0.493 0.121 0.026 66 5.7 precuneus 1278 985 2508 2.864 0.635 0.134 0.031 16 1.7 rostralanteriorcingulate 10025 7692 17133 2.375 0.556 0.141 0.032 141 14.9 rostralmiddlefrontal 10408 8415 23109 2.974 0.592 0.130 0.027 127 11.7 superiorfrontal 8442 6321 13584 2.307 0.453 0.126 0.025 136 8.5 superiorparietal 6243 4523 11076 2.572 0.648 0.115 0.024 85 7.2 superiortemporal 6953 5373 13389 2.694 0.514 0.134 0.029 95 9.0 supramarginal 434 457 935 2.464 0.795 0.183 0.042 4 0.9 frontalpole 621 938 2716 3.766 0.721 0.212 0.039 7 1.2 temporalpole 770 628 1139 2.149 0.372 0.107 0.022 3 0.7 transversetemporal 3461 2103 7136 3.156 0.681 0.125 0.035 60 4.9 insula #----------------------------------------- #@# Parcellation Stats rh Thu Sep 7 23:02:37 CEST 2017 /home/gc/study/recon-all/400614dclass/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 400614dclass rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/gc/study/recon-all/400614dclass/mri/wm.mgz... reading input surface /home/gc/study/recon-all/400614dclass/surf/rh.white... reading input pial surface /home/gc/study/recon-all/400614dclass/surf/rh.pial... reading input white surface /home/gc/study/recon-all/400614dclass/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 239461 Total vertex volume 236406 (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) = 1420931 mm^3 (det: 1.371007 ) lhCtxGM: 235090.012 234708.000 diff= 382.0 pctdiff= 0.162 rhCtxGM: 235324.034 234754.000 diff= 570.0 pctdiff= 0.242 lhCtxWM: 218327.405 218779.500 diff= -452.1 pctdiff=-0.207 rhCtxWM: 220192.396 220961.500 diff= -769.1 pctdiff=-0.349 SubCortGMVol 60226.000 SupraTentVol 980747.848 (978448.000) diff=2299.848 pctdiff=0.234 SupraTentVolNotVent 971731.848 (969432.000) diff=2299.848 pctdiff=0.237 BrainSegVol 1140377.000 (1136514.000) diff=3863.000 pctdiff=0.339 BrainSegVolNotVent 1126683.000 (1126351.848) diff=331.152 pctdiff=0.029 BrainSegVolNotVent 1126683.000 CerebellumVol 157189.000 VentChorVol 9016.000 3rd4th5thCSF 4678.000 CSFVol 815.000, OptChiasmVol 62.000 MaskVol 1688423.000 1325 932 2495 2.762 0.507 0.100 0.017 7 0.9 bankssts 992 653 2118 2.982 0.520 0.128 0.023 14 1.0 caudalanteriorcingulate 3551 2319 7264 2.813 0.499 0.114 0.022 32 3.1 caudalmiddlefrontal 2240 1388 2621 1.837 0.431 0.144 0.029 33 2.7 cuneus 632 446 1836 3.232 0.792 0.127 0.036 5 0.9 entorhinal 4526 3148 9360 2.646 0.635 0.135 0.031 62 5.6 fusiform 6498 4108 12323 2.664 0.541 0.121 0.024 75 6.3 inferiorparietal 4702 3084 9386 2.719 0.713 0.122 0.032 52 6.1 inferiortemporal 1048 698 1938 2.430 0.746 0.141 0.037 18 1.3 isthmuscingulate 8450 5244 12486 2.215 0.548 0.133 0.032 102 10.9 lateraloccipital 4248 2874 6897 2.436 0.735 0.148 0.049 59 8.7 lateralorbitofrontal 4058 2711 5729 2.075 0.597 0.146 0.036 55 6.0 lingual 2826 1973 5554 2.516 0.873 0.136 0.042 45 4.4 medialorbitofrontal 5815 3743 13732 3.003 0.653 0.120 0.031 71 7.3 middletemporal 813 517 1925 3.244 0.936 0.103 0.027 9 0.9 parahippocampal 2452 1426 3856 2.543 0.571 0.103 0.019 19 1.8 paracentral 1846 1287 3444 2.542 0.497 0.129 0.032 22 2.3 parsopercularis 1329 861 2641 2.649 0.685 0.143 0.055 22 2.7 parsorbitalis 2013 1361 3838 2.613 0.524 0.136 0.031 25 2.5 parstriangularis 2001 1326 1907 1.647 0.433 0.126 0.027 20 2.2 pericalcarine 6507 4000 9088 2.081 0.629 0.102 0.022 50 5.6 postcentral 1524 982 3244 2.983 0.538 0.130 0.029 20 1.8 posteriorcingulate 8702 5307 14744 2.660 0.596 0.109 0.025 68 8.5 precentral 6491 4342 11001 2.440 0.541 0.127 0.024 73 6.3 precuneus 858 609 2022 2.970 0.591 0.142 0.037 17 1.3 rostralanteriorcingulate 8562 5564 14322 2.346 0.540 0.135 0.038 108 13.4 rostralmiddlefrontal 11100 7213 23697 2.936 0.556 0.117 0.024 100 10.6 superiorfrontal 8391 5390 13693 2.319 0.526 0.117 0.022 84 7.0 superiorparietal 5251 3552 11865 2.957 0.628 0.109 0.022 48 4.7 superiortemporal 5736 3607 9979 2.627 0.516 0.121 0.028 64 6.2 supramarginal 542 335 1359 2.829 0.542 0.201 0.077 15 1.9 frontalpole 682 526 1989 2.940 0.682 0.179 0.063 12 2.1 temporalpole 561 346 819 2.274 0.454 0.134 0.032 7 0.7 transversetemporal 3325 2274 7151 3.095 0.882 0.127 0.035 35 4.6 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 400614dclass rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /home/gc/study/recon-all/400614dclass/mri/wm.mgz... reading input surface /home/gc/study/recon-all/400614dclass/surf/rh.pial... reading input pial surface /home/gc/study/recon-all/400614dclass/surf/rh.pial... reading input white surface /home/gc/study/recon-all/400614dclass/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 239461 Total vertex volume 236406 (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) = 1420931 mm^3 (det: 1.371007 ) lhCtxGM: 235090.012 234708.000 diff= 382.0 pctdiff= 0.162 rhCtxGM: 235324.034 234754.000 diff= 570.0 pctdiff= 0.242 lhCtxWM: 218327.405 218779.500 diff= -452.1 pctdiff=-0.207 rhCtxWM: 220192.396 220961.500 diff= -769.1 pctdiff=-0.349 SubCortGMVol 60226.000 SupraTentVol 980747.848 (978448.000) diff=2299.848 pctdiff=0.234 SupraTentVolNotVent 971731.848 (969432.000) diff=2299.848 pctdiff=0.237 BrainSegVol 1140377.000 (1136514.000) diff=3863.000 pctdiff=0.339 BrainSegVolNotVent 1126683.000 (1126351.848) diff=331.152 pctdiff=0.029 BrainSegVolNotVent 1126683.000 CerebellumVol 157189.000 VentChorVol 9016.000 3rd4th5thCSF 4678.000 CSFVol 815.000, OptChiasmVol 62.000 MaskVol 1688423.000 1325 864 2495 2.762 0.507 0.121 0.028 13 1.8 bankssts 992 800 2118 2.982 0.520 0.165 0.047 40 1.8 caudalanteriorcingulate 3551 2777 7264 2.813 0.499 0.120 0.024 27 3.9 caudalmiddlefrontal 2240 1603 2621 1.837 0.431 0.128 0.029 35 2.7 cuneus 632 682 1836 3.232 0.792 0.178 0.045 12 1.4 entorhinal 4526 3944 9360 2.646 0.635 0.147 0.032 85 6.9 fusiform 6498 4975 12323 2.664 0.541 0.125 0.026 73 7.3 inferiorparietal 4702 3768 9386 2.719 0.713 0.139 0.033 72 7.0 inferiortemporal 1048 852 1938 2.430 0.746 0.145 0.041 18 1.9 isthmuscingulate 8450 6084 12486 2.215 0.548 0.125 0.029 103 10.9 lateraloccipital 4248 3018 6897 2.436 0.735 0.140 0.039 68 7.3 lateralorbitofrontal 4058 2972 5729 2.075 0.597 0.130 0.033 61 6.0 lingual 2826 2461 5554 2.516 0.873 0.155 0.040 45 5.1 medialorbitofrontal 5815 5301 13732 3.003 0.653 0.135 0.028 58 7.7 middletemporal 813 623 1925 3.244 0.936 0.105 0.022 8 0.7 parahippocampal 2452 1611 3856 2.543 0.571 0.105 0.020 23 2.2 paracentral 1846 1466 3444 2.542 0.497 0.137 0.031 23 2.6 parsopercularis 1329 1096 2641 2.649 0.685 0.139 0.038 17 2.3 parsorbitalis 2013 1632 3838 2.613 0.524 0.139 0.028 47 2.7 parstriangularis 2001 1102 1907 1.647 0.433 0.103 0.025 27 2.0 pericalcarine 6507 4831 9088 2.081 0.629 0.115 0.022 47 6.5 postcentral 1524 1223 3244 2.983 0.538 0.146 0.034 32 2.3 posteriorcingulate 8702 5701 14744 2.660 0.596 0.102 0.022 81 8.1 precentral 6491 4598 11001 2.440 0.541 0.128 0.027 95 7.8 precuneus 858 803 2022 2.970 0.591 0.153 0.037 17 1.5 rostralanteriorcingulate 8562 6585 14322 2.346 0.540 0.140 0.033 119 12.9 rostralmiddlefrontal 11100 8601 23697 2.936 0.556 0.121 0.024 167 11.5 superiorfrontal 8391 6375 13693 2.319 0.526 0.126 0.024 89 8.3 superiorparietal 5251 4390 11865 2.957 0.628 0.126 0.026 58 6.1 superiortemporal 5736 3943 9979 2.627 0.516 0.118 0.026 66 6.4 supramarginal 542 595 1359 2.829 0.542 0.216 0.054 8 1.7 frontalpole 682 870 1989 2.940 0.682 0.212 0.049 9 1.5 temporalpole 561 384 819 2.274 0.454 0.112 0.029 3 0.8 transversetemporal 3325 2060 7151 3.095 0.882 0.133 0.035 70 5.2 insula #----------------------------------------- #@# Cortical Parc 2 lh Thu Sep 7 23:03:48 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 400614dclass 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... 20 labels changed using aseg relabeling using gibbs priors... 000: 9023 changed, 136820 examined... 001: 2027 changed, 35177 examined... 002: 564 changed, 10665 examined... 003: 238 changed, 3251 examined... 004: 124 changed, 1372 examined... 005: 51 changed, 672 examined... 006: 28 changed, 302 examined... 007: 14 changed, 146 examined... 008: 12 changed, 91 examined... 009: 5 changed, 52 examined... 010: 3 changed, 29 examined... 011: 1 changed, 17 examined... 012: 3 changed, 9 examined... 013: 1 changed, 10 examined... 014: 0 changed, 7 examined... 2 labels changed using aseg 000: 265 total segments, 181 labels (2453 vertices) changed 001: 90 total segments, 6 labels (18 vertices) changed 002: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 25 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1324 vertices marked for relabeling... 1324 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 19 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Thu Sep 7 23:04:07 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 400614dclass 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... 32 labels changed using aseg relabeling using gibbs priors... 000: 9232 changed, 136891 examined... 001: 2214 changed, 35782 examined... 002: 644 changed, 11489 examined... 003: 250 changed, 3643 examined... 004: 117 changed, 1544 examined... 005: 63 changed, 688 examined... 006: 33 changed, 335 examined... 007: 13 changed, 172 examined... 008: 6 changed, 76 examined... 009: 7 changed, 43 examined... 010: 3 changed, 30 examined... 011: 3 changed, 17 examined... 012: 1 changed, 15 examined... 013: 0 changed, 8 examined... 16 labels changed using aseg 000: 274 total segments, 187 labels (3050 vertices) changed 001: 98 total segments, 11 labels (49 vertices) changed 002: 89 total segments, 2 labels (8 vertices) changed 003: 87 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 34 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1001 vertices marked for relabeling... 1001 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 20 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Thu Sep 7 23:04:27 CEST 2017 /home/gc/study/recon-all/400614dclass/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 400614dclass lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /home/gc/study/recon-all/400614dclass/mri/wm.mgz... reading input surface /home/gc/study/recon-all/400614dclass/surf/lh.white... reading input pial surface /home/gc/study/recon-all/400614dclass/surf/lh.pial... reading input white surface /home/gc/study/recon-all/400614dclass/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 239172 Total vertex volume 236306 (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) = 1420931 mm^3 (det: 1.371007 ) lhCtxGM: 235090.012 234708.000 diff= 382.0 pctdiff= 0.162 rhCtxGM: 235324.034 234754.000 diff= 570.0 pctdiff= 0.242 lhCtxWM: 218327.405 218779.500 diff= -452.1 pctdiff=-0.207 rhCtxWM: 220192.396 220961.500 diff= -769.1 pctdiff=-0.349 SubCortGMVol 60226.000 SupraTentVol 980747.848 (978448.000) diff=2299.848 pctdiff=0.234 SupraTentVolNotVent 971731.848 (969432.000) diff=2299.848 pctdiff=0.237 BrainSegVol 1140377.000 (1136514.000) diff=3863.000 pctdiff=0.339 BrainSegVolNotVent 1126683.000 (1126351.848) diff=331.152 pctdiff=0.029 BrainSegVolNotVent 1126683.000 CerebellumVol 157189.000 VentChorVol 9016.000 3rd4th5thCSF 4678.000 CSFVol 815.000, OptChiasmVol 62.000 MaskVol 1688423.000 1138 767 2119 2.549 0.606 0.150 0.043 15 2.0 G&S_frontomargin 1451 928 2500 2.344 0.476 0.123 0.024 16 1.4 G&S_occipital_inf 1705 972 2651 2.227 0.554 0.103 0.024 14 1.6 G&S_paracentral 1612 1013 3016 2.666 0.609 0.127 0.035 22 2.4 G&S_subcentral 916 546 1368 2.056 0.523 0.137 0.052 12 2.0 G&S_transv_frontopol 2149 1487 4544 2.918 0.597 0.133 0.037 25 3.5 G&S_cingul-Ant 1279 905 2755 3.091 0.497 0.122 0.023 11 1.2 G&S_cingul-Mid-Ant 1269 869 2477 2.814 0.508 0.122 0.024 11 1.2 G&S_cingul-Mid-Post 736 477 1841 2.964 0.585 0.148 0.035 12 1.1 G_cingul-Post-dorsal 324 186 597 2.639 0.803 0.149 0.042 7 0.5 G_cingul-Post-ventral 2229 1386 2788 1.774 0.467 0.132 0.030 27 2.8 G_cuneus 1336 776 3331 3.077 0.525 0.125 0.036 20 1.8 G_front_inf-Opercular 417 246 963 2.783 0.627 0.148 0.059 8 0.9 G_front_inf-Orbital 1194 667 2317 2.613 0.660 0.137 0.052 20 2.5 G_front_inf-Triangul 5631 3593 12024 2.604 0.579 0.137 0.036 83 8.4 G_front_middle 7426 4705 17933 3.046 0.588 0.128 0.031 90 9.3 G_front_sup 670 419 1494 3.259 0.832 0.127 0.039 9 0.8 G_Ins_lg&S_cent_ins 894 584 2513 3.528 0.690 0.144 0.050 12 1.8 G_insular_short 2025 1152 3885 2.527 0.542 0.124 0.027 28 2.2 G_occipital_middle 1470 862 2152 2.168 0.607 0.131 0.034 18 1.9 G_occipital_sup 1745 1165 4180 3.026 0.552 0.147 0.033 28 2.4 G_oc-temp_lat-fusifor 2924 1871 4290 2.026 0.700 0.151 0.037 45 4.6 G_oc-temp_med-Lingual 1843 1220 5072 3.271 0.846 0.136 0.056 61 3.0 G_oc-temp_med-Parahip 2550 1566 5026 2.433 0.814 0.148 0.057 54 6.1 G_orbital 2579 1536 5898 2.904 0.520 0.137 0.030 42 3.2 G_pariet_inf-Angular 3894 2358 7986 2.745 0.534 0.136 0.037 81 6.6 G_pariet_inf-Supramar 3719 2266 6662 2.362 0.446 0.125 0.024 52 3.4 G_parietal_sup 2453 1330 3301 2.047 0.619 0.097 0.021 22 2.1 G_postcentral 3657 1892 7196 2.915 0.619 0.105 0.028 35 3.9 G_precentral 2739 1790 5587 2.493 0.528 0.127 0.024 41 2.6 G_precuneus 1113 752 2135 2.174 0.617 0.155 0.056 22 2.9 G_rectus 760 538 1041 1.942 0.623 0.158 0.064 14 1.8 G_subcallosal 618 374 967 2.126 0.362 0.089 0.014 5 0.4 G_temp_sup-G_T_transv 2251 1305 5131 2.723 0.709 0.129 0.040 37 3.5 G_temp_sup-Lateral 687 497 1706 3.179 0.631 0.091 0.023 3 0.6 G_temp_sup-Plan_polar 1116 775 2071 2.489 0.455 0.093 0.017 7 0.8 G_temp_sup-Plan_tempo 2792 1803 6933 2.812 0.632 0.135 0.038 54 4.1 G_temporal_inf 2857 1809 7833 3.151 0.666 0.137 0.033 48 3.5 G_temporal_middle 278 188 615 3.023 0.506 0.128 0.030 3 0.3 Lat_Fis-ant-Horizont 348 256 506 2.436 0.351 0.116 0.022 2 0.3 Lat_Fis-ant-Vertical 1166 789 1614 2.643 0.383 0.119 0.023 9 1.0 Lat_Fis-post 2212 1330 2292 1.653 0.393 0.136 0.036 27 3.6 Pole_occipital 1741 1178 5355 3.087 0.929 0.160 0.052 33 3.9 Pole_temporal 2325 1603 2523 1.816 0.586 0.126 0.024 23 2.2 S_calcarine 3352 2296 3875 1.951 0.697 0.101 0.021 17 2.8 S_central 1147 812 1676 2.300 0.391 0.101 0.018 7 0.8 S_cingul-Marginalis 471 328 806 2.998 0.420 0.099 0.020 2 0.4 S_circular_insula_ant 1323 899 2069 2.750 0.621 0.085 0.012 5 0.7 S_circular_insula_inf 1803 1230 2825 2.903 0.473 0.112 0.022 10 1.7 S_circular_insula_sup 1213 871 2006 2.519 0.471 0.103 0.011 7 0.6 S_collat_transv_ant 505 342 534 1.973 0.439 0.150 0.038 5 0.9 S_collat_transv_post 2907 1961 4220 2.214 0.477 0.116 0.025 25 3.0 S_front_inf 1114 777 1466 2.158 0.425 0.115 0.024 7 1.1 S_front_middle 2930 2007 4657 2.496 0.414 0.103 0.019 19 2.2 S_front_sup 155 116 295 2.877 0.412 0.150 0.033 1 0.2 S_interm_prim-Jensen 2772 1884 3999 2.352 0.395 0.110 0.018 21 2.0 S_intrapariet&P_trans 827 593 1095 2.163 0.462 0.140 0.027 9 0.8 S_oc_middle&Lunatus 1177 796 1592 2.222 0.337 0.120 0.020 10 1.0 S_oc_sup&transversal 746 530 986 2.155 0.379 0.126 0.024 7 0.6 S_occipital_ant 777 540 1103 2.319 0.330 0.114 0.015 6 0.5 S_oc-temp_lat 1535 1091 2411 2.450 0.483 0.101 0.018 9 0.9 S_oc-temp_med&Lingual 596 403 660 2.027 0.409 0.113 0.024 4 0.6 S_orbital_lateral 739 550 904 2.135 0.684 0.158 0.037 11 1.1 S_orbital_med-olfact 1363 904 2406 2.909 0.644 0.125 0.029 12 1.9 S_orbital-H_Shaped 2146 1420 2962 2.264 0.484 0.109 0.018 16 1.6 S_parieto_occipital 1342 811 1306 2.233 0.760 0.129 0.025 22 1.0 S_pericallosal 2951 2050 4236 2.270 0.473 0.115 0.021 25 2.5 S_postcentral 1264 873 2085 2.677 0.473 0.109 0.020 8 1.0 S_precentral-inf-part 1543 1042 2455 2.718 0.531 0.116 0.022 11 1.4 S_precentral-sup-part 587 405 819 2.377 0.610 0.126 0.032 5 0.7 S_suborbital 1087 762 1544 2.389 0.403 0.123 0.021 9 1.0 S_subparietal 1692 1214 2681 2.610 0.542 0.107 0.017 9 1.2 S_temporal_inf 5582 3874 8933 2.448 0.460 0.105 0.017 43 3.9 S_temporal_sup 511 328 510 1.801 0.313 0.108 0.014 4 0.3 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Thu Sep 7 23:05:03 CEST 2017 /home/gc/study/recon-all/400614dclass/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 400614dclass rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /home/gc/study/recon-all/400614dclass/mri/wm.mgz... reading input surface /home/gc/study/recon-all/400614dclass/surf/rh.white... reading input pial surface /home/gc/study/recon-all/400614dclass/surf/rh.pial... reading input white surface /home/gc/study/recon-all/400614dclass/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 239461 Total vertex volume 236406 (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) = 1420931 mm^3 (det: 1.371007 ) lhCtxGM: 235090.012 234708.000 diff= 382.0 pctdiff= 0.162 rhCtxGM: 235324.034 234754.000 diff= 570.0 pctdiff= 0.242 lhCtxWM: 218327.405 218779.500 diff= -452.1 pctdiff=-0.207 rhCtxWM: 220192.396 220961.500 diff= -769.1 pctdiff=-0.349 SubCortGMVol 60226.000 SupraTentVol 980747.848 (978448.000) diff=2299.848 pctdiff=0.234 SupraTentVolNotVent 971731.848 (969432.000) diff=2299.848 pctdiff=0.237 BrainSegVol 1140377.000 (1136514.000) diff=3863.000 pctdiff=0.339 BrainSegVolNotVent 1126683.000 (1126351.848) diff=331.152 pctdiff=0.029 BrainSegVolNotVent 1126683.000 CerebellumVol 157189.000 VentChorVol 9016.000 3rd4th5thCSF 4678.000 CSFVol 815.000, OptChiasmVol 62.000 MaskVol 1688423.000 1202 800 1965 2.230 0.651 0.161 0.061 20 3.1 G&S_frontomargin 1738 1096 2917 2.400 0.509 0.135 0.031 25 2.3 G&S_occipital_inf 1606 879 2308 2.261 0.499 0.104 0.021 14 1.4 G&S_paracentral 1566 1034 3094 2.701 0.587 0.128 0.037 17 2.1 G&S_subcentral 993 591 1700 2.354 0.523 0.122 0.033 13 1.3 G&S_transv_frontopol 2667 1831 5842 3.002 0.588 0.133 0.034 37 3.6 G&S_cingul-Ant 1235 846 2591 2.938 0.419 0.107 0.018 10 1.0 G&S_cingul-Mid-Ant 1460 989 2903 2.886 0.448 0.124 0.026 14 1.6 G&S_cingul-Mid-Post 447 283 1345 3.206 0.553 0.141 0.035 7 0.5 G_cingul-Post-dorsal 244 158 463 2.527 0.850 0.141 0.043 4 0.3 G_cingul-Post-ventral 2029 1250 2457 1.842 0.489 0.145 0.031 30 2.6 G_cuneus 1479 1010 2941 2.460 0.555 0.140 0.038 22 2.3 G_front_inf-Opercular 458 293 1035 2.946 0.654 0.152 0.045 7 0.8 G_front_inf-Orbital 804 528 1671 2.607 0.504 0.161 0.044 16 1.4 G_front_inf-Triangul 4201 2545 9595 2.761 0.635 0.134 0.034 60 5.6 G_front_middle 8086 5002 18805 3.017 0.581 0.121 0.027 85 8.6 G_front_sup 616 434 1903 3.638 0.950 0.118 0.036 6 0.9 G_Ins_lg&S_cent_ins 654 406 1947 3.474 0.994 0.139 0.050 10 1.4 G_insular_short 2363 1315 4842 2.705 0.483 0.120 0.026 32 2.4 G_occipital_middle 1913 1127 3385 2.346 0.668 0.128 0.030 24 2.1 G_occipital_sup 2160 1425 4850 2.716 0.561 0.154 0.039 41 3.4 G_oc-temp_lat-fusifor 2773 1781 3961 2.003 0.595 0.151 0.040 42 4.3 G_oc-temp_med-Lingual 1270 857 3657 3.357 0.828 0.129 0.042 17 2.3 G_oc-temp_med-Parahip 3198 2031 5960 2.368 0.694 0.159 0.069 62 9.2 G_orbital 2694 1539 5504 2.679 0.579 0.120 0.027 38 2.6 G_pariet_inf-Angular 2857 1717 5458 2.654 0.538 0.122 0.029 38 3.4 G_pariet_inf-Supramar 2607 1617 4952 2.449 0.469 0.127 0.023 35 2.3 G_parietal_sup 2423 1294 3508 2.157 0.531 0.101 0.023 21 2.2 G_postcentral 3429 1792 6928 2.944 0.544 0.101 0.023 29 3.1 G_precentral 2977 1938 5763 2.392 0.508 0.130 0.025 41 2.9 G_precuneus 821 580 1932 2.376 0.714 0.164 0.061 21 2.1 G_rectus 437 314 513 1.903 0.922 0.115 0.035 4 0.6 G_subcallosal 466 292 764 2.401 0.577 0.140 0.035 6 0.6 G_temp_sup-G_T_transv 1767 1090 4781 3.166 0.577 0.120 0.027 26 1.8 G_temp_sup-Lateral 1115 814 2297 2.704 0.979 0.141 0.049 17 2.3 G_temp_sup-Plan_polar 852 556 1723 2.831 0.539 0.104 0.028 8 0.8 G_temp_sup-Plan_tempo 2355 1505 5369 2.750 0.745 0.127 0.039 32 3.7 G_temporal_inf 3651 2242 9519 3.079 0.682 0.127 0.035 55 5.3 G_temporal_middle 212 166 344 2.658 0.405 0.107 0.012 1 0.1 Lat_Fis-ant-Horizont 181 125 301 2.411 0.407 0.063 0.013 0 0.0 Lat_Fis-ant-Vertical 1342 907 1910 2.653 0.440 0.114 0.022 10 1.1 Lat_Fis-post 3256 1985 4120 1.876 0.473 0.139 0.038 39 5.0 Pole_occipital 1909 1413 5834 2.963 0.797 0.170 0.058 33 5.0 Pole_temporal 2103 1485 2454 2.004 0.717 0.137 0.030 23 2.8 S_calcarine 3214 2206 3568 1.901 0.647 0.109 0.023 19 3.1 S_central 1247 833 1967 2.430 0.532 0.109 0.021 12 0.9 S_cingul-Marginalis 577 396 1013 3.109 0.514 0.110 0.025 4 0.5 S_circular_insula_ant 1334 894 2079 2.804 0.659 0.091 0.015 6 0.8 S_circular_insula_inf 1382 940 2234 2.941 0.492 0.111 0.023 8 1.4 S_circular_insula_sup 1176 841 1940 2.588 0.608 0.099 0.013 6 0.6 S_collat_transv_ant 447 307 554 2.264 0.423 0.138 0.029 4 0.5 S_collat_transv_post 1920 1332 2754 2.330 0.389 0.134 0.033 19 2.4 S_front_inf 2102 1425 2953 2.297 0.430 0.125 0.028 19 2.4 S_front_middle 3015 2100 4998 2.536 0.427 0.102 0.018 18 2.2 S_front_sup 441 313 591 2.308 0.402 0.115 0.017 3 0.3 S_interm_prim-Jensen 2989 2037 4356 2.259 0.460 0.105 0.018 20 2.0 S_intrapariet&P_trans 1364 952 1656 2.125 0.423 0.127 0.024 11 1.5 S_oc_middle&Lunatus 1492 1045 1983 2.260 0.499 0.134 0.028 15 1.6 S_oc_sup&transversal 806 545 1314 2.798 0.531 0.132 0.032 9 1.0 S_occipital_ant 962 681 1668 2.591 0.610 0.104 0.017 6 0.6 S_oc-temp_lat 1530 1116 2500 2.507 0.627 0.103 0.016 9 0.9 S_oc-temp_med&Lingual 420 306 704 2.438 0.490 0.138 0.033 5 0.5 S_orbital_lateral 783 594 1042 2.351 0.693 0.131 0.021 7 0.6 S_orbital_med-olfact 1399 944 2264 2.566 0.718 0.129 0.034 13 2.0 S_orbital-H_Shaped 2625 1733 3418 2.201 0.553 0.119 0.020 25 2.0 S_parieto_occipital 1213 734 1252 2.510 0.767 0.139 0.032 23 1.4 S_pericallosal 2613 1744 3501 2.210 0.477 0.097 0.015 15 1.6 S_postcentral 1581 1100 2633 2.572 0.348 0.106 0.018 11 1.2 S_precentral-inf-part 1724 1176 2440 2.503 0.445 0.108 0.018 11 1.3 S_precentral-sup-part 326 237 790 3.073 0.944 0.152 0.038 5 0.4 S_suborbital 1301 911 2044 2.496 0.483 0.122 0.020 10 1.1 S_subparietal 1304 921 1866 2.520 0.474 0.119 0.021 10 1.1 S_temporal_inf 5487 3747 9792 2.810 0.504 0.107 0.020 37 4.5 S_temporal_sup 288 203 421 2.502 0.401 0.144 0.023 3 0.3 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Thu Sep 7 23:05:39 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 400614dclass 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... 1033 labels changed using aseg relabeling using gibbs priors... 000: 1883 changed, 136820 examined... 001: 419 changed, 8837 examined... 002: 110 changed, 2466 examined... 003: 38 changed, 651 examined... 004: 21 changed, 233 examined... 005: 11 changed, 115 examined... 006: 6 changed, 74 examined... 007: 4 changed, 39 examined... 008: 0 changed, 25 examined... 141 labels changed using aseg 000: 55 total segments, 22 labels (223 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... 912 vertices marked for relabeling... 912 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 15 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Thu Sep 7 23:05:54 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 400614dclass 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... 1269 labels changed using aseg relabeling using gibbs priors... 000: 1974 changed, 136891 examined... 001: 463 changed, 9140 examined... 002: 147 changed, 2664 examined... 003: 58 changed, 885 examined... 004: 31 changed, 359 examined... 005: 18 changed, 186 examined... 006: 12 changed, 103 examined... 007: 10 changed, 67 examined... 008: 4 changed, 51 examined... 009: 6 changed, 30 examined... 010: 6 changed, 25 examined... 011: 4 changed, 32 examined... 012: 4 changed, 25 examined... 013: 1 changed, 14 examined... 014: 1 changed, 7 examined... 015: 0 changed, 7 examined... 212 labels changed using aseg 000: 51 total segments, 18 labels (383 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... 451 vertices marked for relabeling... 451 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 15 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Thu Sep 7 23:06:09 CEST 2017 /home/gc/study/recon-all/400614dclass/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 400614dclass lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /home/gc/study/recon-all/400614dclass/mri/wm.mgz... reading input surface /home/gc/study/recon-all/400614dclass/surf/lh.white... reading input pial surface /home/gc/study/recon-all/400614dclass/surf/lh.pial... reading input white surface /home/gc/study/recon-all/400614dclass/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 239172 Total vertex volume 236306 (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) = 1420931 mm^3 (det: 1.371007 ) lhCtxGM: 235090.012 234708.000 diff= 382.0 pctdiff= 0.162 rhCtxGM: 235324.034 234754.000 diff= 570.0 pctdiff= 0.242 lhCtxWM: 218327.405 218779.500 diff= -452.1 pctdiff=-0.207 rhCtxWM: 220192.396 220961.500 diff= -769.1 pctdiff=-0.349 SubCortGMVol 60226.000 SupraTentVol 980747.848 (978448.000) diff=2299.848 pctdiff=0.234 SupraTentVolNotVent 971731.848 (969432.000) diff=2299.848 pctdiff=0.237 BrainSegVol 1140377.000 (1136514.000) diff=3863.000 pctdiff=0.339 BrainSegVolNotVent 1126683.000 (1126351.848) diff=331.152 pctdiff=0.029 BrainSegVolNotVent 1126683.000 CerebellumVol 157189.000 VentChorVol 9016.000 3rd4th5thCSF 4678.000 CSFVol 815.000, OptChiasmVol 62.000 MaskVol 1688423.000 1470 1002 2922 2.977 0.497 0.132 0.025 18 1.5 caudalanteriorcingulate 3520 2362 6540 2.577 0.518 0.116 0.024 32 3.3 caudalmiddlefrontal 3192 2045 3987 1.894 0.467 0.133 0.028 38 3.7 cuneus 774 526 2329 3.373 0.893 0.115 0.034 8 0.8 entorhinal 4153 2826 8481 2.722 0.583 0.134 0.029 55 5.0 fusiform 6316 4052 11824 2.603 0.535 0.123 0.024 74 6.1 inferiorparietal 5329 3530 11430 2.706 0.624 0.126 0.033 80 7.1 inferiortemporal 1528 987 2561 2.351 0.833 0.136 0.031 24 1.8 isthmuscingulate 7027 4338 9473 2.050 0.543 0.131 0.030 81 8.6 lateraloccipital 4600 3052 8121 2.553 0.814 0.150 0.049 79 10.0 lateralorbitofrontal 4000 2650 5603 2.040 0.663 0.141 0.032 52 5.5 lingual 2315 1611 3795 2.154 0.658 0.142 0.048 35 4.5 medialorbitofrontal 6462 4392 14637 2.862 0.682 0.124 0.026 80 6.8 middletemporal 950 628 2187 3.208 0.772 0.113 0.050 43 0.7 parahippocampal 2628 1684 4332 2.385 0.497 0.104 0.019 17 2.2 paracentral 2111 1319 4311 2.887 0.575 0.120 0.029 24 2.2 parsopercularis 919 591 1759 2.645 0.507 0.123 0.038 12 1.3 parsorbitalis 2682 1705 4764 2.627 0.645 0.125 0.036 31 4.0 parstriangularis 2081 1389 2021 1.649 0.430 0.127 0.030 21 2.5 pericalcarine 7384 4505 10015 2.091 0.698 0.105 0.025 68 7.6 postcentral 1878 1269 3644 2.758 0.560 0.137 0.029 26 2.0 posteriorcingulate 8262 4949 14752 2.742 0.608 0.109 0.026 68 8.5 precentral 5383 3615 9444 2.430 0.494 0.119 0.021 60 4.5 precuneus 1878 1239 3679 2.820 0.646 0.127 0.035 23 2.7 rostralanteriorcingulate 7732 4960 13849 2.408 0.575 0.132 0.036 98 11.5 rostralmiddlefrontal 11226 7329 23870 2.843 0.652 0.125 0.030 122 13.8 superiorfrontal 6788 4325 11108 2.337 0.430 0.119 0.023 75 6.0 superiorparietal 7723 5014 15226 2.643 0.725 0.110 0.026 76 8.3 superiortemporal 6480 4182 12424 2.687 0.503 0.132 0.030 104 8.5 supramarginal 774 476 1140 2.148 0.371 0.085 0.015 5 0.4 transversetemporal 2830 1887 6080 3.198 0.676 0.123 0.032 27 3.5 insula #----------------------------------------- #@# Parcellation Stats 3 rh Thu Sep 7 23:06:44 CEST 2017 /home/gc/study/recon-all/400614dclass/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 400614dclass rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /home/gc/study/recon-all/400614dclass/mri/wm.mgz... reading input surface /home/gc/study/recon-all/400614dclass/surf/rh.white... reading input pial surface /home/gc/study/recon-all/400614dclass/surf/rh.pial... reading input white surface /home/gc/study/recon-all/400614dclass/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 239461 Total vertex volume 236406 (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) = 1420931 mm^3 (det: 1.371007 ) lhCtxGM: 235090.012 234708.000 diff= 382.0 pctdiff= 0.162 rhCtxGM: 235324.034 234754.000 diff= 570.0 pctdiff= 0.242 lhCtxWM: 218327.405 218779.500 diff= -452.1 pctdiff=-0.207 rhCtxWM: 220192.396 220961.500 diff= -769.1 pctdiff=-0.349 SubCortGMVol 60226.000 SupraTentVol 980747.848 (978448.000) diff=2299.848 pctdiff=0.234 SupraTentVolNotVent 971731.848 (969432.000) diff=2299.848 pctdiff=0.237 BrainSegVol 1140377.000 (1136514.000) diff=3863.000 pctdiff=0.339 BrainSegVolNotVent 1126683.000 (1126351.848) diff=331.152 pctdiff=0.029 BrainSegVolNotVent 1126683.000 CerebellumVol 157189.000 VentChorVol 9016.000 3rd4th5thCSF 4678.000 CSFVol 815.000, OptChiasmVol 62.000 MaskVol 1688423.000 1072 707 2282 2.989 0.526 0.129 0.023 15 1.0 caudalanteriorcingulate 3708 2414 7455 2.808 0.505 0.114 0.021 34 3.2 caudalmiddlefrontal 2756 1704 3284 1.891 0.498 0.141 0.030 38 3.3 cuneus 576 412 1748 3.305 0.753 0.123 0.029 4 0.6 entorhinal 4119 2864 8175 2.618 0.600 0.133 0.029 55 4.7 fusiform 6519 4112 12257 2.646 0.540 0.122 0.025 76 6.5 inferiorparietal 5134 3405 10679 2.737 0.717 0.125 0.034 59 7.1 inferiortemporal 1069 710 1952 2.424 0.746 0.139 0.036 18 1.3 isthmuscingulate 8425 5224 12237 2.195 0.538 0.133 0.032 102 10.7 lateraloccipital 4853 3221 8078 2.386 0.738 0.154 0.054 78 11.3 lateralorbitofrontal 4023 2683 5643 2.070 0.593 0.146 0.037 54 5.9 lingual 2222 1584 4553 2.425 0.932 0.149 0.047 42 4.1 medialorbitofrontal 6817 4413 15759 2.992 0.639 0.120 0.030 81 8.4 middletemporal 866 549 2018 3.230 0.942 0.104 0.033 11 1.4 parahippocampal 2690 1560 4297 2.567 0.569 0.104 0.019 21 2.1 paracentral 2316 1565 4151 2.478 0.494 0.132 0.032 28 3.1 parsopercularis 1055 677 2179 2.710 0.629 0.126 0.050 16 1.9 parsorbitalis 1916 1309 3610 2.680 0.504 0.142 0.036 26 2.6 parstriangularis 1992 1315 1910 1.655 0.432 0.126 0.028 20 2.2 pericalcarine 7318 4513 10118 2.080 0.616 0.102 0.021 58 6.2 postcentral 1651 1066 3446 2.947 0.580 0.132 0.030 22 2.1 posteriorcingulate 8162 4967 14126 2.686 0.600 0.108 0.025 64 7.9 precentral 6735 4496 11489 2.421 0.551 0.127 0.024 77 6.4 precuneus 1096 783 2353 2.946 0.658 0.131 0.033 18 1.4 rostralanteriorcingulate 6203 4052 10484 2.390 0.537 0.133 0.036 72 8.9 rostralmiddlefrontal 13858 9025 28309 2.812 0.598 0.120 0.027 137 14.8 superiorfrontal 6813 4399 11506 2.383 0.495 0.116 0.021 67 5.8 superiorparietal 6859 4738 15520 2.917 0.634 0.118 0.029 69 8.5 superiortemporal 5411 3406 9401 2.634 0.519 0.120 0.028 60 5.8 supramarginal 544 339 798 2.262 0.441 0.137 0.032 7 0.7 transversetemporal 2900 1981 6588 3.206 0.848 0.118 0.030 25 3.4 insula #----------------------------------------- #@# WM/GM Contrast lh Thu Sep 7 23:07:19 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts pctsurfcon --s 400614dclass --lh-only Log file is /home/gc/study/recon-all/400614dclass/scripts/pctsurfcon.log Thu Sep 7 23:07:19 CEST 2017 setenv SUBJECTS_DIR /home/gc/study/recon-all cd /home/gc/study/recon-all/400614dclass/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux lugh.fisica.uniud.it 2.6.32-642.4.2.el6.x86_64 #1 SMP Tue Aug 23 11:15:56 CDT 2016 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /home/gc/study/recon-all/400614dclass/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/gc/study/recon-all/400614dclass/surf/tmp.pctsurfcon.4170/lh.wm.mgh --regheader 400614dclass --cortex srcvol = /home/gc/study/recon-all/400614dclass/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/gc/study/recon-all/400614dclass/mri/orig.mgz as target reference. -------- original matrix ----------- -0.02666 0.99835 -0.05078 -0.00003; 0.99652 0.02253 -0.08027 0.00000; 0.07900 0.05274 0.99548 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/gc/study/recon-all/400614dclass/label/lh.cortex.label Reading surface /home/gc/study/recon-all/400614dclass/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 = 76652 Masking with /home/gc/study/recon-all/400614dclass/label/lh.cortex.label Writing to /home/gc/study/recon-all/400614dclass/surf/tmp.pctsurfcon.4170/lh.wm.mgh Dim: 136820 1 1 mri_vol2surf --mov /home/gc/study/recon-all/400614dclass/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/gc/study/recon-all/400614dclass/surf/tmp.pctsurfcon.4170/lh.gm.mgh --projfrac 0.3 --regheader 400614dclass --cortex srcvol = /home/gc/study/recon-all/400614dclass/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/gc/study/recon-all/400614dclass/mri/orig.mgz as target reference. -------- original matrix ----------- -0.02666 0.99835 -0.05078 -0.00003; 0.99652 0.02253 -0.08027 0.00000; 0.07900 0.05274 0.99548 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/gc/study/recon-all/400614dclass/label/lh.cortex.label Reading surface /home/gc/study/recon-all/400614dclass/surf/lh.white Done reading source surface Reading thickness /home/gc/study/recon-all/400614dclass/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 = 92636 Masking with /home/gc/study/recon-all/400614dclass/label/lh.cortex.label Writing to /home/gc/study/recon-all/400614dclass/surf/tmp.pctsurfcon.4170/lh.gm.mgh Dim: 136820 1 1 mri_concat /home/gc/study/recon-all/400614dclass/surf/tmp.pctsurfcon.4170/lh.wm.mgh /home/gc/study/recon-all/400614dclass/surf/tmp.pctsurfcon.4170/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/gc/study/recon-all/400614dclass/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /home/gc/study/recon-all/400614dclass/surf/lh.w-g.pct.mgh mri_segstats --in /home/gc/study/recon-all/400614dclass/surf/lh.w-g.pct.mgh --annot 400614dclass lh aparc --sum /home/gc/study/recon-all/400614dclass/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /home/gc/study/recon-all/400614dclass/surf/lh.w-g.pct.mgh --annot 400614dclass lh aparc --sum /home/gc/study/recon-all/400614dclass/stats/lh.w-g.pct.stats --snr sysname Linux hostname lugh.fisica.uniud.it machine x86_64 user gc UseRobust 0 Constructing seg from annotation Reading annotation /home/gc/study/recon-all/400614dclass/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /home/gc/study/recon-all/400614dclass/surf/lh.w-g.pct.mgh Vertex Area is 0.650533 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# WM/GM Contrast rh Thu Sep 7 23:07:25 CEST 2017 /home/gc/study/recon-all/400614dclass/scripts pctsurfcon --s 400614dclass --rh-only Log file is /home/gc/study/recon-all/400614dclass/scripts/pctsurfcon.log Thu Sep 7 23:07:25 CEST 2017 setenv SUBJECTS_DIR /home/gc/study/recon-all cd /home/gc/study/recon-all/400614dclass/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux lugh.fisica.uniud.it 2.6.32-642.4.2.el6.x86_64 #1 SMP Tue Aug 23 11:15:56 CDT 2016 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /home/gc/study/recon-all/400614dclass/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/gc/study/recon-all/400614dclass/surf/tmp.pctsurfcon.4226/rh.wm.mgh --regheader 400614dclass --cortex srcvol = /home/gc/study/recon-all/400614dclass/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/gc/study/recon-all/400614dclass/mri/orig.mgz as target reference. -------- original matrix ----------- -0.02666 0.99835 -0.05078 -0.00003; 0.99652 0.02253 -0.08027 0.00000; 0.07900 0.05274 0.99548 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/gc/study/recon-all/400614dclass/label/rh.cortex.label Reading surface /home/gc/study/recon-all/400614dclass/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 = 76789 Masking with /home/gc/study/recon-all/400614dclass/label/rh.cortex.label Writing to /home/gc/study/recon-all/400614dclass/surf/tmp.pctsurfcon.4226/rh.wm.mgh Dim: 136891 1 1 mri_vol2surf --mov /home/gc/study/recon-all/400614dclass/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/gc/study/recon-all/400614dclass/surf/tmp.pctsurfcon.4226/rh.gm.mgh --projfrac 0.3 --regheader 400614dclass --cortex srcvol = /home/gc/study/recon-all/400614dclass/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /home/gc/study/recon-all/400614dclass/mri/orig.mgz as target reference. -------- original matrix ----------- -0.02666 0.99835 -0.05078 -0.00003; 0.99652 0.02253 -0.08027 0.00000; 0.07900 0.05274 0.99548 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /home/gc/study/recon-all/400614dclass/label/rh.cortex.label Reading surface /home/gc/study/recon-all/400614dclass/surf/rh.white Done reading source surface Reading thickness /home/gc/study/recon-all/400614dclass/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 = 92425 Masking with /home/gc/study/recon-all/400614dclass/label/rh.cortex.label Writing to /home/gc/study/recon-all/400614dclass/surf/tmp.pctsurfcon.4226/rh.gm.mgh Dim: 136891 1 1 mri_concat /home/gc/study/recon-all/400614dclass/surf/tmp.pctsurfcon.4226/rh.wm.mgh /home/gc/study/recon-all/400614dclass/surf/tmp.pctsurfcon.4226/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/gc/study/recon-all/400614dclass/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /home/gc/study/recon-all/400614dclass/surf/rh.w-g.pct.mgh mri_segstats --in /home/gc/study/recon-all/400614dclass/surf/rh.w-g.pct.mgh --annot 400614dclass rh aparc --sum /home/gc/study/recon-all/400614dclass/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /home/gc/study/recon-all/400614dclass/surf/rh.w-g.pct.mgh --annot 400614dclass rh aparc --sum /home/gc/study/recon-all/400614dclass/stats/rh.w-g.pct.stats --snr sysname Linux hostname lugh.fisica.uniud.it machine x86_64 user gc UseRobust 0 Constructing seg from annotation Reading annotation /home/gc/study/recon-all/400614dclass/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /home/gc/study/recon-all/400614dclass/surf/rh.w-g.pct.mgh Vertex Area is 0.652088 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# Relabel Hypointensities Thu Sep 7 23:07:30 CEST 2017 /home/gc/study/recon-all/400614dclass/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 3366 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 2724 voxels changed to hypointensity... 6031 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Thu Sep 7 23:07:52 CEST 2017 /home/gc/study/recon-all/400614dclass mri_aparc2aseg --s 400614dclass --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/gc/study/recon-all subject 400614dclass outvol /home/gc/study/recon-all/400614dclass/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading lh pial surface /home/gc/study/recon-all/400614dclass/surf/lh.pial Loading lh annotations from /home/gc/study/recon-all/400614dclass/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading rh pial surface /home/gc/study/recon-all/400614dclass/surf/rh.pial Loading rh annotations from /home/gc/study/recon-all/400614dclass/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/gc/study/recon-all/400614dclass/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /home/gc/study/recon-all/400614dclass/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 7.19 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 --> 77 rescaling Left_Lateral_Ventricle from 13 --> 35 rescaling Left_Inf_Lat_Vent from 34 --> 40 rescaling Left_Cerebellum_White_Matter from 86 --> 91 rescaling Left_Cerebellum_Cortex from 60 --> 76 rescaling Left_Thalamus from 94 --> 102 rescaling Left_Thalamus_Proper from 84 --> 96 rescaling Left_Caudate from 75 --> 90 rescaling Left_Putamen from 80 --> 92 rescaling Left_Pallidum from 98 --> 99 rescaling Third_Ventricle from 25 --> 52 rescaling Fourth_Ventricle from 22 --> 34 rescaling Brain_Stem from 81 --> 88 rescaling Left_Hippocampus from 57 --> 71 rescaling Left_Amygdala from 56 --> 79 rescaling CSF from 32 --> 75 rescaling Left_Accumbens_area from 62 --> 72 rescaling Left_VentralDC from 87 --> 96 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 77 rescaling Right_Lateral_Ventricle from 13 --> 28 rescaling Right_Inf_Lat_Vent from 25 --> 31 rescaling Right_Cerebellum_White_Matter from 87 --> 91 rescaling Right_Cerebellum_Cortex from 59 --> 76 rescaling Right_Thalamus_Proper from 85 --> 92 rescaling Right_Caudate from 62 --> 83 rescaling Right_Putamen from 80 --> 89 rescaling Right_Pallidum from 97 --> 99 rescaling Right_Hippocampus from 53 --> 75 rescaling Right_Amygdala from 55 --> 80 rescaling Right_Accumbens_area from 65 --> 82 rescaling Right_VentralDC from 86 --> 102 rescaling Fifth_Ventricle from 40 --> 63 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 54 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 = 469012 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 118 changed. pass 2: 19 changed. pass 3: 5 changed. pass 4: 1 changed. pass 5: 1 changed. pass 6: 1 changed. pass 7: 0 changed. nchanged = 0 Writing output aseg to /home/gc/study/recon-all/400614dclass/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Thu Sep 7 23:13:43 CEST 2017 /home/gc/study/recon-all/400614dclass mri_aparc2aseg --s 400614dclass --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/gc/study/recon-all subject 400614dclass outvol /home/gc/study/recon-all/400614dclass/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading lh pial surface /home/gc/study/recon-all/400614dclass/surf/lh.pial Loading lh annotations from /home/gc/study/recon-all/400614dclass/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading rh pial surface /home/gc/study/recon-all/400614dclass/surf/rh.pial Loading rh annotations from /home/gc/study/recon-all/400614dclass/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/gc/study/recon-all/400614dclass/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /home/gc/study/recon-all/400614dclass/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 7.19 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 --> 77 rescaling Left_Lateral_Ventricle from 13 --> 35 rescaling Left_Inf_Lat_Vent from 34 --> 40 rescaling Left_Cerebellum_White_Matter from 86 --> 91 rescaling Left_Cerebellum_Cortex from 60 --> 76 rescaling Left_Thalamus from 94 --> 102 rescaling Left_Thalamus_Proper from 84 --> 96 rescaling Left_Caudate from 75 --> 90 rescaling Left_Putamen from 80 --> 92 rescaling Left_Pallidum from 98 --> 99 rescaling Third_Ventricle from 25 --> 52 rescaling Fourth_Ventricle from 22 --> 34 rescaling Brain_Stem from 81 --> 88 rescaling Left_Hippocampus from 57 --> 71 rescaling Left_Amygdala from 56 --> 79 rescaling CSF from 32 --> 75 rescaling Left_Accumbens_area from 62 --> 72 rescaling Left_VentralDC from 87 --> 96 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 77 rescaling Right_Lateral_Ventricle from 13 --> 28 rescaling Right_Inf_Lat_Vent from 25 --> 31 rescaling Right_Cerebellum_White_Matter from 87 --> 91 rescaling Right_Cerebellum_Cortex from 59 --> 76 rescaling Right_Thalamus_Proper from 85 --> 92 rescaling Right_Caudate from 62 --> 83 rescaling Right_Putamen from 80 --> 89 rescaling Right_Pallidum from 97 --> 99 rescaling Right_Hippocampus from 53 --> 75 rescaling Right_Amygdala from 55 --> 80 rescaling Right_Accumbens_area from 65 --> 82 rescaling Right_VentralDC from 86 --> 102 rescaling Fifth_Ventricle from 40 --> 63 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 54 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 = 469109 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 118 changed. pass 2: 19 changed. pass 3: 5 changed. pass 4: 1 changed. pass 5: 1 changed. pass 6: 1 changed. pass 7: 0 changed. nchanged = 0 Writing output aseg to /home/gc/study/recon-all/400614dclass/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Thu Sep 7 23:19:46 CEST 2017 /home/gc/study/recon-all/400614dclass mri_aparc2aseg --s 400614dclass --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/gc/study/recon-all subject 400614dclass outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading lh pial surface /home/gc/study/recon-all/400614dclass/surf/lh.pial Loading lh annotations from /home/gc/study/recon-all/400614dclass/label/lh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading rh pial surface /home/gc/study/recon-all/400614dclass/surf/rh.pial Loading rh annotations from /home/gc/study/recon-all/400614dclass/label/rh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/gc/study/recon-all/400614dclass/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /home/gc/study/recon-all/400614dclass/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 7.19 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 --> 77 rescaling Left_Lateral_Ventricle from 13 --> 35 rescaling Left_Inf_Lat_Vent from 34 --> 40 rescaling Left_Cerebellum_White_Matter from 86 --> 91 rescaling Left_Cerebellum_Cortex from 60 --> 76 rescaling Left_Thalamus from 94 --> 102 rescaling Left_Thalamus_Proper from 84 --> 96 rescaling Left_Caudate from 75 --> 90 rescaling Left_Putamen from 80 --> 92 rescaling Left_Pallidum from 98 --> 99 rescaling Third_Ventricle from 25 --> 52 rescaling Fourth_Ventricle from 22 --> 34 rescaling Brain_Stem from 81 --> 88 rescaling Left_Hippocampus from 57 --> 71 rescaling Left_Amygdala from 56 --> 79 rescaling CSF from 32 --> 75 rescaling Left_Accumbens_area from 62 --> 72 rescaling Left_VentralDC from 87 --> 96 rescaling Right_Cerebral_White_Matter from 105 --> 101 rescaling Right_Cerebral_Cortex from 58 --> 77 rescaling Right_Lateral_Ventricle from 13 --> 28 rescaling Right_Inf_Lat_Vent from 25 --> 31 rescaling Right_Cerebellum_White_Matter from 87 --> 91 rescaling Right_Cerebellum_Cortex from 59 --> 76 rescaling Right_Thalamus_Proper from 85 --> 92 rescaling Right_Caudate from 62 --> 83 rescaling Right_Putamen from 80 --> 89 rescaling Right_Pallidum from 97 --> 99 rescaling Right_Hippocampus from 53 --> 75 rescaling Right_Amygdala from 55 --> 80 rescaling Right_Accumbens_area from 65 --> 82 rescaling Right_VentralDC from 86 --> 102 rescaling Fifth_Ventricle from 40 --> 63 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 54 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 = 469109 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 118 changed. pass 2: 19 changed. pass 3: 5 changed. pass 4: 1 changed. pass 5: 1 changed. pass 6: 1 changed. pass 7: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Thu Sep 7 23:25:42 CEST 2017 /home/gc/study/recon-all/400614dclass/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Thu Sep 7 23:25:42 CEST 2017 setenv SUBJECTS_DIR /home/gc/study/recon-all cd /home/gc/study/recon-all/400614dclass/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 lugh.fisica.uniud.it 2.6.32-642.4.2.el6.x86_64 #1 SMP Tue Aug 23 11:15:56 CDT 2016 x86_64 x86_64 x86_64 GNU/Linux mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /home/gc/study/recon-all/400614dclass/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 lugh.fisica.uniud.it machine x86_64 user gc input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done Started at Thu Sep 7 23:25:42 CEST 2017 Ended at Thu Sep 7 23:25:49 CEST 2017 Apas2aseg-Run-Time-Sec 7 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Thu Sep 7 23:25:49 CEST 2017 /home/gc/study/recon-all/400614dclass 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 400614dclass $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 400614dclass sysname Linux hostname lugh.fisica.uniud.it machine x86_64 user gc UseRobust 0 atlas_icv (eTIV) = 1420931 mm^3 (det: 1.371007 ) Computing euler number orig.nofix lheno = -90, rheno = -94 orig.nofix lhholes = 46, rhholes = 48 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 235090.012 234708.000 diff= 382.0 pctdiff= 0.162 rhCtxGM: 235324.034 234754.000 diff= 570.0 pctdiff= 0.242 lhCtxWM: 218327.405 218779.500 diff= -452.1 pctdiff=-0.207 rhCtxWM: 220192.396 220961.500 diff= -769.1 pctdiff=-0.349 SubCortGMVol 60226.000 SupraTentVol 980747.848 (978448.000) diff=2299.848 pctdiff=0.234 SupraTentVolNotVent 971731.848 (969432.000) diff=2299.848 pctdiff=0.237 BrainSegVol 1140377.000 (1136514.000) diff=3863.000 pctdiff=0.339 BrainSegVolNotVent 1126683.000 (1126351.848) diff=331.152 pctdiff=0.029 BrainSegVolNotVent 1126683.000 CerebellumVol 157189.000 VentChorVol 9016.000 3rd4th5thCSF 4678.000 CSFVol 815.000, OptChiasmVol 62.000 MaskVol 1688423.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Thu Sep 7 23:29:38 CEST 2017 /home/gc/study/recon-all/400614dclass mri_aparc2aseg --s 400614dclass --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /home/gc/study/recon-all subject 400614dclass outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /home/gc/study/recon-all/400614dclass/mri/aparc+aseg.mgz Reading lh white surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading lh pial surface /home/gc/study/recon-all/400614dclass/surf/lh.pial Loading lh annotations from /home/gc/study/recon-all/400614dclass/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading rh pial surface /home/gc/study/recon-all/400614dclass/surf/rh.pial Loading rh annotations from /home/gc/study/recon-all/400614dclass/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/gc/study/recon-all/400614dclass/mri/ribbon.mgz Loading filled from /home/gc/study/recon-all/400614dclass/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 6457 vertices from left hemi Ripped 7294 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /home/gc/study/recon-all/400614dclass/mri/aseg.mgz Loading Ctx Seg File /home/gc/study/recon-all/400614dclass/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 = 906753 Used brute-force search on 193 voxels Fixing Parahip LH WM Found 10 clusters 0 k 1.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 2.000000 5 k 2.000000 6 k 31.000000 7 k 1.000000 8 k 1266.000000 9 k 1.000000 Fixing Parahip RH WM Found 5 clusters 0 k 1218.000000 1 k 1.000000 2 k 1.000000 3 k 28.000000 4 k 1.000000 Writing output aseg to mri/wmparc.mgz mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 400614dclass --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 400614dclass --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname lugh.fisica.uniud.it machine x86_64 user gc UseRobust 0 atlas_icv (eTIV) = 1420931 mm^3 (det: 1.371007 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 235090.012 234708.000 diff= 382.0 pctdiff= 0.162 rhCtxGM: 235324.034 234754.000 diff= 570.0 pctdiff= 0.242 lhCtxWM: 218327.405 218779.500 diff= -452.1 pctdiff=-0.207 rhCtxWM: 220192.396 220961.500 diff= -769.1 pctdiff=-0.349 SubCortGMVol 60226.000 SupraTentVol 980747.848 (978448.000) diff=2299.848 pctdiff=0.234 SupraTentVolNotVent 971731.848 (969432.000) diff=2299.848 pctdiff=0.237 BrainSegVol 1140377.000 (1136514.000) diff=3863.000 pctdiff=0.339 BrainSegVolNotVent 1126683.000 (1126351.848) diff=331.152 pctdiff=0.029 BrainSegVolNotVent 1126683.000 CerebellumVol 157189.000 VentChorVol 9016.000 3rd4th5thCSF 4678.000 CSFVol 815.000, OptChiasmVol 62.000 MaskVol 1688423.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done /home/gc/study/recon-all/400614dclass/label #-------------------------------------------- #@# BA_exvivo Labels lh Thu Sep 7 23:40:50 CEST 2017 mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.BA1_exvivo.label --trgsubject 400614dclass --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 399 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4528 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.BA2_exvivo.label --trgsubject 400614dclass --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 651 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8560 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.BA3a_exvivo.label --trgsubject 400614dclass --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 189 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4266 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.BA3b_exvivo.label --trgsubject 400614dclass --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 449 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6432 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.BA4a_exvivo.label --trgsubject 400614dclass --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 801 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6585 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.BA4p_exvivo.label --trgsubject 400614dclass --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 531 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4601 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.BA6_exvivo.label --trgsubject 400614dclass --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 1492 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 15081 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.BA44_exvivo.label --trgsubject 400614dclass --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 312 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4493 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.BA45_exvivo.label --trgsubject 400614dclass --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 1172 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4594 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.V1_exvivo.label --trgsubject 400614dclass --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 1392 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6033 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.V2_exvivo.label --trgsubject 400614dclass --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 2462 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 10576 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.MT_exvivo.label --trgsubject 400614dclass --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 379 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2397 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject 400614dclass --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 282 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1572 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject 400614dclass --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 299 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1498 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.BA1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 114 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1128 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.BA2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 127 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2219 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.BA3a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 60 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1564 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.BA3b_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 140 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2136 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.BA4a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 438 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2757 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.BA4p_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 120 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1669 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.BA6_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 744 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7779 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.BA44_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 107 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2019 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.BA45_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 442 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1593 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.V1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 934 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4339 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.V2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 1227 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4561 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.MT_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 113 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 626 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 125 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 595 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./lh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/lh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136820 Number of reverse mapping hits = 160 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 610 mri_label2label: Done mris_label2annot --s 400614dclass --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /home/gc/study/recon-all/400614dclass/label cmdline mris_label2annot --s 400614dclass --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 lugh.fisica.uniud.it machine x86_64 user gc subject 400614dclass hemi lh SUBJECTS_DIR /home/gc/study/recon-all ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /home/gc/study/recon-all/400614dclass/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 93932 unhit vertices Writing annot to /home/gc/study/recon-all/400614dclass/label/lh.BA_exvivo.annot mris_label2annot --s 400614dclass --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /home/gc/study/recon-all/400614dclass/label cmdline mris_label2annot --s 400614dclass --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 lugh.fisica.uniud.it machine x86_64 user gc subject 400614dclass hemi lh SUBJECTS_DIR /home/gc/study/recon-all ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /home/gc/study/recon-all/400614dclass/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 111175 unhit vertices Writing annot to /home/gc/study/recon-all/400614dclass/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 400614dclass lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /home/gc/study/recon-all/400614dclass/mri/wm.mgz... reading input surface /home/gc/study/recon-all/400614dclass/surf/lh.white... reading input pial surface /home/gc/study/recon-all/400614dclass/surf/lh.pial... reading input white surface /home/gc/study/recon-all/400614dclass/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 239172 Total vertex volume 236306 (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) = 1420931 mm^3 (det: 1.371007 ) lhCtxGM: 235090.012 234708.000 diff= 382.0 pctdiff= 0.162 rhCtxGM: 235324.034 234754.000 diff= 570.0 pctdiff= 0.242 lhCtxWM: 218327.405 218779.500 diff= -452.1 pctdiff=-0.207 rhCtxWM: 220192.396 220961.500 diff= -769.1 pctdiff=-0.349 SubCortGMVol 60226.000 SupraTentVol 980747.848 (978448.000) diff=2299.848 pctdiff=0.234 SupraTentVolNotVent 971731.848 (969432.000) diff=2299.848 pctdiff=0.237 BrainSegVol 1140377.000 (1136514.000) diff=3863.000 pctdiff=0.339 BrainSegVolNotVent 1126683.000 (1126351.848) diff=331.152 pctdiff=0.029 BrainSegVolNotVent 1126683.000 CerebellumVol 157189.000 VentChorVol 9016.000 3rd4th5thCSF 4678.000 CSFVol 815.000, OptChiasmVol 62.000 MaskVol 1688423.000 1284 620 1779 2.155 0.569 0.114 0.029 17 1.5 BA1_exvivo 4058 2654 6016 2.312 0.505 0.113 0.025 37 4.3 BA2_exvivo 1146 767 1095 1.834 0.604 0.139 0.030 11 1.3 BA3a_exvivo 2612 1629 3128 1.823 0.730 0.102 0.024 24 2.7 BA3b_exvivo 2013 1123 3509 2.708 0.578 0.092 0.022 13 1.6 BA4a_exvivo 1543 989 2368 2.468 0.614 0.106 0.027 9 1.8 BA4p_exvivo 9592 5902 21063 2.990 0.580 0.116 0.026 95 10.1 BA6_exvivo 1909 1251 4023 2.877 0.599 0.125 0.031 21 2.3 BA44_exvivo 3615 2217 6579 2.560 0.609 0.128 0.037 45 5.7 BA45_exvivo 3634 2364 3679 1.608 0.417 0.130 0.031 40 4.8 V1_exvivo 7796 4931 10010 1.937 0.546 0.141 0.033 99 10.8 V2_exvivo 1976 1249 3074 2.316 0.502 0.120 0.022 23 1.8 MT_exvivo 774 507 2206 3.443 0.827 0.092 0.019 5 0.6 perirhinal_exvivo 936 666 2772 3.200 0.768 0.160 0.047 17 2.0 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 400614dclass lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /home/gc/study/recon-all/400614dclass/mri/wm.mgz... reading input surface /home/gc/study/recon-all/400614dclass/surf/lh.white... reading input pial surface /home/gc/study/recon-all/400614dclass/surf/lh.pial... reading input white surface /home/gc/study/recon-all/400614dclass/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 239172 Total vertex volume 236306 (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) = 1420931 mm^3 (det: 1.371007 ) lhCtxGM: 235090.012 234708.000 diff= 382.0 pctdiff= 0.162 rhCtxGM: 235324.034 234754.000 diff= 570.0 pctdiff= 0.242 lhCtxWM: 218327.405 218779.500 diff= -452.1 pctdiff=-0.207 rhCtxWM: 220192.396 220961.500 diff= -769.1 pctdiff=-0.349 SubCortGMVol 60226.000 SupraTentVol 980747.848 (978448.000) diff=2299.848 pctdiff=0.234 SupraTentVolNotVent 971731.848 (969432.000) diff=2299.848 pctdiff=0.237 BrainSegVol 1140377.000 (1136514.000) diff=3863.000 pctdiff=0.339 BrainSegVolNotVent 1126683.000 (1126351.848) diff=331.152 pctdiff=0.029 BrainSegVolNotVent 1126683.000 CerebellumVol 157189.000 VentChorVol 9016.000 3rd4th5thCSF 4678.000 CSFVol 815.000, OptChiasmVol 62.000 MaskVol 1688423.000 846 372 1129 2.201 0.584 0.107 0.026 10 0.9 BA1_exvivo 1477 965 2276 2.216 0.528 0.088 0.015 8 0.8 BA2_exvivo 946 636 816 1.704 0.475 0.138 0.029 9 1.0 BA3a_exvivo 1495 1006 1387 1.381 0.265 0.078 0.013 5 0.8 BA3b_exvivo 2114 1125 3649 2.766 0.554 0.088 0.024 14 1.8 BA4a_exvivo 1174 797 1778 2.383 0.595 0.109 0.027 6 1.4 BA4p_exvivo 5519 3338 12133 3.015 0.591 0.112 0.024 49 5.3 BA6_exvivo 1263 805 2797 3.015 0.573 0.125 0.033 15 1.5 BA44_exvivo 1452 806 2700 2.615 0.634 0.131 0.044 22 2.8 BA45_exvivo 3759 2486 3883 1.600 0.418 0.127 0.030 39 4.8 V1_exvivo 4105 2587 4683 1.764 0.456 0.148 0.037 58 6.4 V2_exvivo 525 320 859 2.296 0.526 0.121 0.025 6 0.4 MT_exvivo 411 280 1255 3.389 0.765 0.076 0.012 1 0.2 perirhinal_exvivo 559 386 1420 3.142 0.792 0.162 0.037 11 0.8 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Thu Sep 7 23:46:26 CEST 2017 mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.BA1_exvivo.label --trgsubject 400614dclass --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 295 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4257 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.BA2_exvivo.label --trgsubject 400614dclass --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 411 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7098 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.BA3a_exvivo.label --trgsubject 400614dclass --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 173 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4153 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.BA3b_exvivo.label --trgsubject 400614dclass --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 252 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4774 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.BA4a_exvivo.label --trgsubject 400614dclass --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 812 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6559 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.BA4p_exvivo.label --trgsubject 400614dclass --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 379 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4852 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.BA6_exvivo.label --trgsubject 400614dclass --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 1869 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 14125 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.BA44_exvivo.label --trgsubject 400614dclass --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 821 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7733 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.BA45_exvivo.label --trgsubject 400614dclass --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 797 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6152 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.V1_exvivo.label --trgsubject 400614dclass --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 1064 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5791 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.V2_exvivo.label --trgsubject 400614dclass --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 2272 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10288 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.MT_exvivo.label --trgsubject 400614dclass --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 595 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2527 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject 400614dclass --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 93 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1131 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject 400614dclass --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 78 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 830 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 90 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 966 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 159 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2847 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 67 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1765 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 113 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2296 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 121 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1509 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 136 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1625 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 1058 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 8017 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 129 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1141 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 162 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1340 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 667 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 3899 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 1010 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4447 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 315 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 55 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 749 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /home/gc/study/recon-all/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject 400614dclass --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /home/gc/study/recon-all/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 400614dclass trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/gc/study/recon-all FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /home/gc/study/recon-all/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /home/gc/study/recon-all/400614dclass/surf/rh.white Reading target registration /home/gc/study/recon-all/400614dclass/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 136891 Number of reverse mapping hits = 45 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 336 mri_label2label: Done mris_label2annot --s 400614dclass --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /home/gc/study/recon-all/400614dclass/label cmdline mris_label2annot --s 400614dclass --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 lugh.fisica.uniud.it machine x86_64 user gc subject 400614dclass hemi rh SUBJECTS_DIR /home/gc/study/recon-all ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /home/gc/study/recon-all/400614dclass/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 94355 unhit vertices Writing annot to /home/gc/study/recon-all/400614dclass/label/rh.BA_exvivo.annot mris_label2annot --s 400614dclass --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /home/gc/study/recon-all/400614dclass/label cmdline mris_label2annot --s 400614dclass --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 lugh.fisica.uniud.it machine x86_64 user gc subject 400614dclass hemi rh SUBJECTS_DIR /home/gc/study/recon-all ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /home/gc/study/recon-all/400614dclass/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 113010 unhit vertices Writing annot to /home/gc/study/recon-all/400614dclass/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 400614dclass rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /home/gc/study/recon-all/400614dclass/mri/wm.mgz... reading input surface /home/gc/study/recon-all/400614dclass/surf/rh.white... reading input pial surface /home/gc/study/recon-all/400614dclass/surf/rh.pial... reading input white surface /home/gc/study/recon-all/400614dclass/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 239461 Total vertex volume 236406 (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) = 1420931 mm^3 (det: 1.371007 ) lhCtxGM: 235090.012 234708.000 diff= 382.0 pctdiff= 0.162 rhCtxGM: 235324.034 234754.000 diff= 570.0 pctdiff= 0.242 lhCtxWM: 218327.405 218779.500 diff= -452.1 pctdiff=-0.207 rhCtxWM: 220192.396 220961.500 diff= -769.1 pctdiff=-0.349 SubCortGMVol 60226.000 SupraTentVol 980747.848 (978448.000) diff=2299.848 pctdiff=0.234 SupraTentVolNotVent 971731.848 (969432.000) diff=2299.848 pctdiff=0.237 BrainSegVol 1140377.000 (1136514.000) diff=3863.000 pctdiff=0.339 BrainSegVolNotVent 1126683.000 (1126351.848) diff=331.152 pctdiff=0.029 BrainSegVolNotVent 1126683.000 CerebellumVol 157189.000 VentChorVol 9016.000 3rd4th5thCSF 4678.000 CSFVol 815.000, OptChiasmVol 62.000 MaskVol 1688423.000 1045 514 1563 2.221 0.481 0.111 0.025 10 1.1 BA1_exvivo 3379 2131 4846 2.252 0.489 0.092 0.017 19 2.2 BA2_exvivo 1116 764 948 1.673 0.392 0.128 0.030 9 1.3 BA3a_exvivo 2039 1297 2238 1.616 0.429 0.106 0.025 16 2.0 BA3b_exvivo 1870 936 3091 2.746 0.462 0.082 0.018 10 1.4 BA4a_exvivo 1334 914 2121 2.457 0.520 0.110 0.025 8 1.3 BA4p_exvivo 9789 6001 19894 2.915 0.571 0.107 0.022 79 8.5 BA6_exvivo 3734 2503 6819 2.606 0.501 0.126 0.030 41 4.5 BA44_exvivo 3903 2601 7129 2.503 0.592 0.137 0.039 54 5.8 BA45_exvivo 3454 2216 3980 1.744 0.477 0.126 0.030 34 4.4 V1_exvivo 7706 4917 9833 1.990 0.543 0.146 0.036 106 10.8 V2_exvivo 2225 1424 4015 2.597 0.529 0.130 0.028 27 2.4 MT_exvivo 529 377 1692 3.302 0.877 0.105 0.030 3 0.7 perirhinal_exvivo 413 289 930 3.297 0.997 0.116 0.024 3 0.3 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 400614dclass rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /home/gc/study/recon-all/400614dclass/mri/wm.mgz... reading input surface /home/gc/study/recon-all/400614dclass/surf/rh.white... reading input pial surface /home/gc/study/recon-all/400614dclass/surf/rh.pial... reading input white surface /home/gc/study/recon-all/400614dclass/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 239461 Total vertex volume 236406 (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) = 1420931 mm^3 (det: 1.371007 ) lhCtxGM: 235090.012 234708.000 diff= 382.0 pctdiff= 0.162 rhCtxGM: 235324.034 234754.000 diff= 570.0 pctdiff= 0.242 lhCtxWM: 218327.405 218779.500 diff= -452.1 pctdiff=-0.207 rhCtxWM: 220192.396 220961.500 diff= -769.1 pctdiff=-0.349 SubCortGMVol 60226.000 SupraTentVol 980747.848 (978448.000) diff=2299.848 pctdiff=0.234 SupraTentVolNotVent 971731.848 (969432.000) diff=2299.848 pctdiff=0.237 BrainSegVol 1140377.000 (1136514.000) diff=3863.000 pctdiff=0.339 BrainSegVolNotVent 1126683.000 (1126351.848) diff=331.152 pctdiff=0.029 BrainSegVolNotVent 1126683.000 CerebellumVol 157189.000 VentChorVol 9016.000 3rd4th5thCSF 4678.000 CSFVol 815.000, OptChiasmVol 62.000 MaskVol 1688423.000 701 339 962 2.102 0.499 0.105 0.025 7 0.7 BA1_exvivo 1970 1159 2934 2.266 0.458 0.081 0.014 10 1.1 BA2_exvivo 1010 681 827 1.706 0.394 0.131 0.031 8 1.2 BA3a_exvivo 1605 1065 1575 1.477 0.326 0.096 0.019 11 1.2 BA3b_exvivo 1110 537 1782 2.714 0.463 0.090 0.020 8 0.9 BA4a_exvivo 1150 803 1812 2.423 0.541 0.117 0.027 7 1.4 BA4p_exvivo 6356 3860 12644 2.886 0.563 0.110 0.024 54 5.9 BA6_exvivo 901 644 1924 2.599 0.470 0.159 0.040 16 1.5 BA44_exvivo 1007 675 1892 2.421 0.512 0.132 0.031 13 1.3 BA45_exvivo 3293 2104 3737 1.739 0.490 0.125 0.030 32 4.1 V1_exvivo 3917 2512 4677 1.875 0.491 0.157 0.041 60 6.5 V2_exvivo 261 184 434 2.696 0.526 0.149 0.035 3 0.4 MT_exvivo 322 220 1050 3.487 0.814 0.094 0.019 1 0.2 perirhinal_exvivo 278 204 587 3.327 0.819 0.124 0.025 2 0.3 entorhinal_exvivo Started at Thu Sep 7 11:44:40 CEST 2017 Ended at Thu Sep 7 23:51:51 CEST 2017 #@#%# recon-all-run-time-hours 12.120 recon-all -s 400614dclass finished without error at Thu Sep 7 23:51:51 CEST 2017