Sa 10. Mär 21:13:50 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs /cm/shared/apps/freesurfer/6.0.0/bin/recon-all -i 44538_T1_MPRAGE.nii.gz -subject 44538_T1_fs -all subjid 44538_T1_fs setenv SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Actual FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux node005 2.6.32-696.16.1.el6.x86_64 #1 SMP Tue Nov 14 14:23:46 CST 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 1310720 kbytes coredumpsize 0 kbytes memoryuse 2883584 kbytes vmemoryuse unlimited descriptors 8192 memorylocked unlimited maxproc 1024 total used free shared buffers cached Mem: 24729588 16852524 7877064 4095060 0 10543292 -/+ buffers/cache: 6309232 18420356 Swap: 0 0 0 ######################################## 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: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.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: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.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: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.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: 2018/03/10-20:13:50-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.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: 2018/03/10-20:13:51-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:51-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:51-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:51-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:51-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/10-20:13:51-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: annadan1111 Machine: node005 Platform: Linux PlatformVersion: 2.6.32-696.16.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /cm/shared/apps/freesurfer/6.0.0/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 /cm/shared/apps/freesurfer/6.0.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /scratch/annadan1111/MABT1T2/test3/44538_T1_fs mri_convert /scratch/annadan1111/MABT1T2/test3/44538_T1_MPRAGE.nii.gz /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/orig/001.mgz mri_convert.bin /scratch/annadan1111/MABT1T2/test3/44538_T1_MPRAGE.nii.gz /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /scratch/annadan1111/MABT1T2/test3/44538_T1_MPRAGE.nii.gz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99959, -0.0134742, 0.0252487) j_ras = (0.0154732, 0.996616, -0.0807281) k_ras = (-0.0240755, 0.0810857, 0.996416) writing to /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sa 10. Mär 21:13:57 CET 2018 Found 1 runs /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/orig/001.mgz /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/rawavg.mgz /scratch/annadan1111/MABT1T2/test3/44538_T1_fs mri_convert /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/rawavg.mgz /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/orig.mgz --conform mri_convert.bin /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/rawavg.mgz /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/rawavg.mgz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99959, -0.0134742, 0.0252487) j_ras = (0.0154732, 0.996616, -0.0807281) k_ras = (-0.0240755, 0.0810857, 0.996416) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/orig.mgz... mri_add_xform_to_header -c /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/transforms/talairach.xfm /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/orig.mgz /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sa 10. Mär 21:14:08 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri /cm/shared/apps/freesurfer/6.0.0/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 node005 2.6.32-696.16.1.el6.x86_64 #1 SMP Tue Nov 14 14:23:46 CST 2017 x86_64 x86_64 x86_64 GNU/Linux Sa 10. Mär 21:14:08 CET 2018 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.72824 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.72824/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.72824/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.49246e-10, 0) j_ras = (-1.86265e-09, 7.45058e-09, -1) k_ras = (4.65661e-10, 1, -7.45058e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.72824/nu0.mnc... -------------------------------------------------------- Iteration 1 Sa 10. Mär 21:14:11 CET 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.72824/nu0.mnc ./tmp.mri_nu_correct.mni.72824/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.72824/0/ -iterations 1000 -distance 50 [annadan1111@node005:/scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/] [2018-03-10 21:14:11] running: /cm/shared/apps/freesurfer/6.0.0/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.72824/0/ ./tmp.mri_nu_correct.mni.72824/nu0.mnc ./tmp.mri_nu_correct.mni.72824/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 41 CV of field change: 0.000950835 mri_convert ./tmp.mri_nu_correct.mni.72824/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.72824/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.72824/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.49246e-10, 0) j_ras = (-1.86265e-09, 7.45058e-09, -1) k_ras = (4.65661e-10, 1, -7.45058e-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... Sa 10. Mär 21:15:26 CET 2018 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Sa 10. Mär 21:15:26 CET 2018 Ended at Sa 10. Mär 21:16:15 CET 2018 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sa 10. Mär 21:16:17 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6512, pval=0.3663 >= threshold=0.0050) awk -f /cm/shared/apps/freesurfer/6.0.0/bin/extract_talairach_avi_QA.awk /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/transforms/talairach_avi.log tal_QC_AZS /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/transforms/talairach_avi.log TalAviQA: 0.97930 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Sa 10. Mär 21:16:17 CET 2018 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri /cm/shared/apps/freesurfer/6.0.0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux node005 2.6.32-696.16.1.el6.x86_64 #1 SMP Tue Nov 14 14:23:46 CST 2017 x86_64 x86_64 x86_64 GNU/Linux Sa 10. Mär 21:16:18 CET 2018 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.73909 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.73909/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.73909/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.49246e-10, 0) j_ras = (-1.86265e-09, 7.45058e-09, -1) k_ras = (4.65661e-10, 1, -7.45058e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.73909/nu0.mnc... -------------------------------------------------------- Iteration 1 Sa 10. Mär 21:16:20 CET 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.73909/nu0.mnc ./tmp.mri_nu_correct.mni.73909/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.73909/0/ [annadan1111@node005:/scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/] [2018-03-10 21:16:21] running: /cm/shared/apps/freesurfer/6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.73909/0/ ./tmp.mri_nu_correct.mni.73909/nu0.mnc ./tmp.mri_nu_correct.mni.73909/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 42 CV of field change: 0.000946236 -------------------------------------------------------- Iteration 2 Sa 10. Mär 21:17:16 CET 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.73909/nu1.mnc ./tmp.mri_nu_correct.mni.73909/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.73909/1/ [annadan1111@node005:/scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/] [2018-03-10 21:17:16] running: /cm/shared/apps/freesurfer/6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.73909/1/ ./tmp.mri_nu_correct.mni.73909/nu1.mnc ./tmp.mri_nu_correct.mni.73909/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 12 CV of field change: 0.000935269 mri_binarize --i ./tmp.mri_nu_correct.mni.73909/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.73909/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.73909/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.73909/ones.mgz sysname Linux hostname node005 machine x86_64 user annadan1111 input ./tmp.mri_nu_correct.mni.73909/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.73909/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.73909/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.73909/sum.junk --avgwf ./tmp.mri_nu_correct.mni.73909/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.73909/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.73909/sum.junk --avgwf ./tmp.mri_nu_correct.mni.73909/input.mean.dat sysname Linux hostname node005 machine x86_64 user annadan1111 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.73909/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.73909/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.73909/ones.mgz --i ./tmp.mri_nu_correct.mni.73909/nu2.mnc --sum ./tmp.mri_nu_correct.mni.73909/sum.junk --avgwf ./tmp.mri_nu_correct.mni.73909/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.73909/ones.mgz --i ./tmp.mri_nu_correct.mni.73909/nu2.mnc --sum ./tmp.mri_nu_correct.mni.73909/sum.junk --avgwf ./tmp.mri_nu_correct.mni.73909/output.mean.dat sysname Linux hostname node005 machine x86_64 user annadan1111 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.73909/ones.mgz Loading ./tmp.mri_nu_correct.mni.73909/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.73909/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.73909/nu2.mnc ./tmp.mri_nu_correct.mni.73909/nu2.mnc mul .97100487956334435321 Saving result to './tmp.mri_nu_correct.mni.73909/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.73909/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.73909/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.73909/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.49246e-10, 0) j_ras = (-1.86265e-09, 7.45058e-09, -1) k_ras = (4.65661e-10, 1, -7.45058e-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 8 seconds. mapping ( 9, 112) to ( 3, 110) Sa 10. Mär 21:18:41 CET 2018 mri_nu_correct.mni done mri_add_xform_to_header -c /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sa 10. Mär 21:18:42 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 1.07512 -0.01822 0.01626 2.02299; 0.03428 1.02865 -0.01637 -30.57877; -0.03482 0.04334 1.12353 -47.29532; 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 = 18 Starting OpenSpline(): npoints = 18 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 81 (81), valley at 53 (53) csf peak at 34, setting threshold to 65 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 82 (82), valley at 53 (53) csf peak at 35, setting threshold to 66 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 Sa 10. Mär 21:21:28 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri mri_em_register -rusage /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /cm/shared/apps/freesurfer/6.0.0/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 '/cm/shared/apps/freesurfer/6.0.0/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=11.0 skull bounding box = (48, 50, 24) --> (208, 229, 222) using (101, 110, 123) as brain centroid... mean wm in atlas = 108, using box (81,88,99) --> (120, 132,147) to find MRI wm before smoothing, mri peak at 109 robust fit to distribution - 109 +- 3.5 after smoothing, mri peak at 109, scaling input intensities by 0.991 scaling channel 0 by 0.990826 initial log_p = -4.515 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.416813 @ (-9.091, -9.091, -9.091) max log p = -4.357569 @ (4.545, 4.545, -4.545) max log p = -4.276699 @ (2.273, -6.818, 2.273) max log p = -4.247693 @ (1.136, 1.136, 1.136) max log p = -4.247693 @ (0.000, 0.000, 0.000) max log p = -4.247693 @ (0.000, 0.000, 0.000) Found translation: (-1.1, -10.2, -10.2): log p = -4.248 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.112, old_max_log_p =-4.248 (thresh=-4.2) 1.06375 0.00000 0.00000 -9.16960; 0.00000 1.07500 0.00000 -21.65739; 0.00000 0.00000 1.07500 -19.31356; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.099, old_max_log_p =-4.112 (thresh=-4.1) 1.05465 0.14032 0.00000 -29.40715; -0.14926 1.14574 0.00000 -6.12944; 0.00000 0.00000 1.07500 -19.31356; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.027, old_max_log_p =-4.099 (thresh=-4.1) 1.06511 -0.01043 0.00000 -8.72974; -0.01110 1.24082 0.00000 -37.53654; 0.00000 0.00000 0.99438 -9.54581; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.027, old_max_log_p =-4.027 (thresh=-4.0) 1.06511 -0.01043 0.00000 -8.72974; -0.01110 1.24082 0.00000 -37.53654; 0.00000 0.00000 0.99438 -9.54581; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.971, old_max_log_p =-4.027 (thresh=-4.0) 1.06511 -0.01043 0.00000 -10.60474; -0.01088 1.21603 -0.03439 -31.65511; -0.00035 0.03908 1.03111 -19.65595; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.971, old_max_log_p =-3.971 (thresh=-4.0) 1.06511 -0.01043 0.00000 -10.60474; -0.01088 1.21603 -0.03439 -31.65511; -0.00035 0.03908 1.03111 -19.65595; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.956, old_max_log_p =-3.971 (thresh=-4.0) 1.06762 -0.02015 0.00865 -10.55005; -0.00212 1.21334 -0.02580 -32.01776; -0.00898 0.02920 1.03011 -16.97511; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.955, old_max_log_p =-3.956 (thresh=-4.0) 1.06639 -0.03027 0.00043 -7.91379; 0.00661 1.21171 -0.02577 -32.43710; -0.00025 0.02900 1.02894 -17.92759; 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 1.06639 -0.03027 0.00043 -7.91379; 0.00661 1.21171 -0.02577 -32.43710; -0.00025 0.02900 1.02894 -17.92759; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.06639 -0.03027 0.00043 -7.91379; 0.00661 1.21171 -0.02577 -32.43710; -0.00025 0.02900 1.02894 -17.92759; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.06639 -0.03027 0.00043 -7.91379; 0.00661 1.21171 -0.02577 -32.43710; -0.00025 0.02900 1.02894 -17.92759; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.955 (old=-4.515) transform before final EM align: 1.06639 -0.03027 0.00043 -7.91379; 0.00661 1.21171 -0.02577 -32.43710; -0.00025 0.02900 1.02894 -17.92759; 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 1.06639 -0.03027 0.00043 -7.91379; 0.00661 1.21171 -0.02577 -32.43710; -0.00025 0.02900 1.02894 -17.92759; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.06639 -0.03027 0.00043 -7.91379; 0.00661 1.21171 -0.02577 -32.43710; -0.00025 0.02900 1.02894 -17.92759; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.3 tol 0.000000 final transform: 1.06639 -0.03027 0.00043 -7.91379; 0.00661 1.21171 -0.02577 -32.43710; -0.00025 0.02900 1.02894 -17.92759; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1618.530945 mri_em_register stimesec 2.345643 mri_em_register ru_maxrss 609808 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157445 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 6578 mri_em_register ru_oublock 3 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 117 mri_em_register ru_nivcsw 47924 registration took 27 minutes and 5 seconds. mri_watershed -rusage /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/touch/rusage.mri_watershed.dat -T1 -brain_atlas /cm/shared/apps/freesurfer/6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=129 y=131 z=118 r=75 first estimation of the main basin volume: 1835127 voxels Looking for seedpoints 2 found in the cerebellum 17 found in the rest of the brain global maximum in x=156, y=114, z=83, Imax=255 CSF=21, 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=8768783058 voxels, voxel volume =1.000 = 8768783058 mmm3 = 8768783.360 cm3 done. PostAnalyze...Basin Prior 3 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=128,y=126, z=116, r=9648 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=27 , nb = 43802 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=8 , nb = -1057942460 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=6 , nb = 1089449747 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=32 , nb = -1070020399 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=30 , nb = 1065701352 OTHER CSF_MIN=0, CSF_intensity=4, CSF_MAX=10 , nb = 1078044476 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 27, 45, 58, 76 after analyzing : 27, 53, 58, 58 RIGHT_CER before analyzing : 8, 12, 46, 91 after analyzing : 8, 34, 46, 48 LEFT_CER before analyzing : 6, 11, 59, 91 after analyzing : 6, 43, 59, 55 RIGHT_BRAIN before analyzing : 32, 47, 58, 77 after analyzing : 32, 54, 58, 59 LEFT_BRAIN before analyzing : 30, 48, 59, 75 after analyzing : 30, 55, 59, 60 OTHER before analyzing : 10, 15, 23, 32 after analyzing : 10, 21, 25, 23 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...63 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.009 curvature mean = 69.179, std = 6.769 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.60, sigma = 6.84 after rotation: sse = 4.60, sigma = 6.84 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 4.90, its var is 6.12 before Erosion-Dilatation 1.70% of inacurate vertices after Erosion-Dilatation 1.86% 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...44 iterations mri_strip_skull: done peeling brain Brain Size = 1680012 voxels, voxel volume = 1.000 mm3 = 1680012 mmm3 = 1680.012 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 27.721785 mri_watershed stimesec 0.391940 mri_watershed ru_maxrss 825436 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 212093 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 12700 mri_watershed ru_oublock 2574 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 169 mri_watershed ru_nivcsw 505 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sa 10. Mär 21:49:03 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri mri_em_register -rusage /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /cm/shared/apps/freesurfer/6.0.0/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 '/cm/shared/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=26.0 skull bounding box = (62, 63, 37) --> (194, 183, 206) using (106, 103, 122) as brain centroid... mean wm in atlas = 107, using box (90,88,101) --> (122, 117,142) to find MRI wm before smoothing, mri peak at 109 robust fit to distribution - 109 +- 3.6 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 initial log_p = -4.131 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.828626 @ (-9.091, -9.091, -9.091) max log p = -3.747200 @ (4.545, 4.545, 4.545) max log p = -3.685573 @ (2.273, -2.273, -2.273) max log p = -3.652903 @ (-1.136, -1.136, -1.136) max log p = -3.649687 @ (0.568, -1.705, -0.568) max log p = -3.647266 @ (-2.557, 1.420, 0.284) Found translation: (-5.4, -8.2, -8.2): log p = -3.647 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.606, old_max_log_p =-3.647 (thresh=-3.6) 1.00000 0.00000 0.00000 -5.39773; 0.00000 1.07500 0.00000 -17.80329; 0.00000 0.00000 1.00000 -8.23864; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.606, old_max_log_p =-3.606 (thresh=-3.6) 1.00000 0.00000 0.00000 -5.39773; 0.00000 1.07500 0.00000 -17.80329; 0.00000 0.00000 1.00000 -8.23864; 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=-3.493, old_max_log_p =-3.606 (thresh=-3.6) 1.05582 0.03699 0.03341 -19.46851; -0.03456 1.09395 -0.03569 -9.71526; -0.03331 0.03450 1.01696 -12.08526; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.490, old_max_log_p =-3.493 (thresh=-3.5) 1.07626 0.00120 0.03299 -17.58301; -0.00206 1.07396 0.03137 -21.06540; -0.03098 -0.03713 1.01711 -3.39627; 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=-3.468, old_max_log_p =-3.490 (thresh=-3.5) 1.08005 0.00120 0.03311 -18.09078; -0.00206 1.07145 0.03130 -20.73644; -0.03109 -0.03726 1.02069 -3.77922; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.462, old_max_log_p =-3.468 (thresh=-3.5) 1.07879 0.00120 0.03307 -17.92106; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02309 -4.03521; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.462, old_max_log_p =-3.462 (thresh=-3.5) 1.07879 0.00120 0.03307 -17.92106; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02309 -4.03521; 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 1.07879 0.00120 0.03307 -17.92106; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02309 -4.03521; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.07879 0.00120 0.03307 -17.92106; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02309 -4.03521; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.07879 0.00120 0.03307 -17.92106; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02309 -4.03521; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.462 (old=-4.131) transform before final EM align: 1.07879 0.00120 0.03307 -17.92106; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02309 -4.03521; 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 1.07879 0.00120 0.03307 -17.92106; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02309 -4.03521; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.07879 0.00120 0.03307 -17.92106; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02309 -4.03521; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.0 tol 0.000000 final transform: 1.07879 0.00120 0.03307 -17.92106; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02309 -4.03521; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1209.573116 mri_em_register stimesec 1.619753 mri_em_register ru_maxrss 599028 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 159338 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 9153 mri_em_register ru_oublock 3 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 139 mri_em_register ru_nivcsw 26994 registration took 20 minutes and 14 seconds. #-------------------------------------- #@# CA Normalize Sa 10. Mär 22:09:17 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /cm/shared/apps/freesurfer/6.0.0/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 '/cm/shared/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=26.0 skull bounding box = (62, 63, 37) --> (194, 183, 206) using (106, 103, 122) as brain centroid... mean wm in atlas = 107, using box (90,88,101) --> (122, 117,142) to find MRI wm before smoothing, mri peak at 109 robust fit to distribution - 109 +- 3.6 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 using 246344 sample points... INFO: compute sample coordinates transform 1.07879 0.00120 0.03307 -17.92106; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02309 -4.03521; 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 (130, 65, 39) --> (191, 176, 203) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 7821 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (70, 65, 38) --> (131, 176, 202) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 9 of 7489 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (132, 146, 62) --> (177, 185, 114) Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 310 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (90, 146, 58) --> (131, 185, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 18 of 61 (29.5%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (115, 138, 95) --> (146, 203, 126) Brain_Stem: limiting intensities to 93.0 --> 132.0 0 of 529 (0.0%) samples deleted using 16210 total control points for intensity normalization... bias field = 0.976 +- 0.050 217 of 16183 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (130, 65, 39) --> (191, 176, 203) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 7 of 7944 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (70, 65, 38) --> (131, 176, 202) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 8 of 7650 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (132, 146, 62) --> (177, 185, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 330 (0.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (90, 146, 58) --> (131, 185, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 75 of 107 (70.1%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (115, 138, 95) --> (146, 203, 126) Brain_Stem: limiting intensities to 88.0 --> 132.0 1 of 587 (0.2%) samples deleted using 16618 total control points for intensity normalization... bias field = 1.009 +- 0.044 172 of 16450 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (130, 65, 39) --> (191, 176, 203) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 132.0 20 of 7941 (0.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (70, 65, 38) --> (131, 176, 202) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 10 of 7689 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (132, 146, 62) --> (177, 185, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 104 of 419 (24.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (90, 146, 58) --> (131, 185, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 96 of 149 (64.4%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (115, 138, 95) --> (146, 203, 126) Brain_Stem: limiting intensities to 88.0 --> 132.0 7 of 587 (1.2%) samples deleted using 16785 total control points for intensity normalization... bias field = 1.006 +- 0.040 140 of 16434 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 40 seconds. #-------------------------------------- #@# CA Reg Sa 10. Mär 22:10:56 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri mri_ca_register -rusage /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /cm/shared/apps/freesurfer/6.0.0/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 '/cm/shared/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.18 (predicted orig area = 6.8) 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=0.834, neg=0, invalid=762 0001: dt=236.058947, rms=0.746 (10.512%), neg=0, invalid=762 0002: dt=138.400000, rms=0.718 (3.748%), neg=0, invalid=762 0003: dt=321.333333, rms=0.704 (1.916%), neg=0, invalid=762 0004: dt=129.472000, rms=0.700 (0.678%), neg=0, invalid=762 0005: dt=369.920000, rms=0.696 (0.555%), neg=0, invalid=762 0006: dt=129.472000, rms=0.694 (0.296%), neg=0, invalid=762 0007: dt=443.904000, rms=0.691 (0.421%), neg=0, invalid=762 0008: dt=110.976000, rms=0.689 (0.303%), neg=0, invalid=762 0009: dt=1183.744000, rms=0.684 (0.630%), neg=0, invalid=762 0010: dt=93.159763, rms=0.681 (0.414%), neg=0, invalid=762 0011: dt=1479.680000, rms=0.678 (0.486%), neg=0, invalid=762 0012: dt=110.976000, rms=0.676 (0.381%), neg=0, invalid=762 0013: dt=129.472000, rms=0.675 (0.013%), neg=0, invalid=762 0014: dt=129.472000, rms=0.675 (0.045%), neg=0, invalid=762 0015: dt=129.472000, rms=0.675 (0.063%), neg=0, invalid=762 0016: dt=129.472000, rms=0.674 (0.108%), neg=0, invalid=762 0017: dt=129.472000, rms=0.673 (0.131%), neg=0, invalid=762 0018: dt=129.472000, rms=0.672 (0.140%), neg=0, invalid=762 0019: dt=129.472000, rms=0.671 (0.136%), neg=0, invalid=762 0020: dt=129.472000, rms=0.670 (0.128%), neg=0, invalid=762 0021: dt=129.472000, rms=0.669 (0.132%), neg=0, invalid=762 0022: dt=129.472000, rms=0.669 (0.128%), neg=0, invalid=762 0023: dt=129.472000, rms=0.668 (0.109%), neg=0, invalid=762 0024: dt=129.472000, rms=0.667 (0.100%), neg=0, invalid=762 0025: dt=2071.552000, rms=0.666 (0.227%), neg=0, invalid=762 0026: dt=55.488000, rms=0.666 (0.029%), neg=0, invalid=762 0027: dt=55.488000, rms=0.665 (0.014%), neg=0, invalid=762 0028: dt=55.488000, rms=0.665 (0.006%), neg=0, invalid=762 0029: dt=55.488000, rms=0.665 (0.010%), neg=0, invalid=762 0030: dt=55.488000, rms=0.665 (0.026%), neg=0, invalid=762 0031: dt=55.488000, rms=0.665 (0.044%), neg=0, invalid=762 0032: dt=55.488000, rms=0.665 (0.050%), neg=0, invalid=762 0033: dt=55.488000, rms=0.664 (0.033%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.665, neg=0, invalid=762 0034: dt=295.936000, rms=0.660 (0.668%), neg=0, invalid=762 0035: dt=27.744000, rms=0.660 (0.023%), neg=0, invalid=762 0036: dt=27.744000, rms=0.660 (0.001%), neg=0, invalid=762 0037: dt=27.744000, rms=0.660 (-0.031%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.669, neg=0, invalid=762 0038: dt=31.104000, rms=0.667 (0.289%), neg=0, invalid=762 0039: dt=227.868132, rms=0.658 (1.238%), neg=0, invalid=762 0040: dt=84.099174, rms=0.651 (1.154%), neg=0, invalid=762 0041: dt=58.494624, rms=0.646 (0.676%), neg=0, invalid=762 0042: dt=9.072000, rms=0.646 (0.055%), neg=0, invalid=762 0043: dt=9.072000, rms=0.646 (0.026%), neg=0, invalid=762 0044: dt=9.072000, rms=0.646 (0.011%), neg=0, invalid=762 0045: dt=9.072000, rms=0.646 (0.002%), neg=0, invalid=762 0046: dt=204.000000, rms=0.640 (0.963%), neg=0, invalid=762 0047: dt=9.072000, rms=0.638 (0.184%), neg=0, invalid=762 0048: dt=9.072000, rms=0.638 (0.069%), neg=0, invalid=762 0049: dt=9.072000, rms=0.638 (-0.076%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.639, neg=0, invalid=762 0050: dt=36.288000, rms=0.637 (0.281%), neg=0, invalid=762 0051: dt=248.832000, rms=0.630 (1.070%), neg=0, invalid=762 0052: dt=22.292135, rms=0.629 (0.124%), neg=0, invalid=762 0053: dt=22.292135, rms=0.629 (0.011%), neg=0, invalid=762 0054: dt=22.292135, rms=0.629 (-0.030%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.655, neg=0, invalid=762 0055: dt=30.631829, rms=0.648 (1.022%), neg=0, invalid=762 0056: dt=76.044944, rms=0.633 (2.343%), neg=0, invalid=762 0057: dt=9.600000, rms=0.631 (0.339%), neg=0, invalid=762 0058: dt=4.800000, rms=0.631 (0.039%), neg=0, invalid=762 0059: dt=4.800000, rms=0.631 (0.004%), neg=0, invalid=762 0060: dt=4.800000, rms=0.631 (-0.041%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.631, neg=0, invalid=762 0061: dt=11.200000, rms=0.630 (0.209%), neg=0, invalid=762 0062: dt=32.000000, rms=0.629 (0.150%), neg=0, invalid=762 0063: dt=32.000000, rms=0.628 (0.188%), neg=0, invalid=762 0064: dt=32.000000, rms=0.627 (0.146%), neg=0, invalid=762 0065: dt=32.000000, rms=0.626 (0.080%), neg=0, invalid=762 0066: dt=32.000000, rms=0.625 (0.162%), neg=0, invalid=762 0067: dt=32.000000, rms=0.624 (0.258%), neg=0, invalid=762 0068: dt=32.000000, rms=0.622 (0.256%), neg=0, invalid=762 0069: dt=32.000000, rms=0.621 (0.171%), neg=0, invalid=762 0070: dt=32.000000, rms=0.620 (0.113%), neg=0, invalid=762 0071: dt=32.000000, rms=0.620 (0.092%), neg=0, invalid=762 0072: dt=25.600000, rms=0.620 (0.022%), neg=0, invalid=762 0073: dt=25.600000, rms=0.620 (0.011%), neg=0, invalid=762 0074: dt=25.600000, rms=0.620 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.655, neg=0, invalid=762 0075: dt=0.000000, rms=0.654 (0.080%), neg=0, invalid=762 0076: dt=0.000000, rms=0.654 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.655, neg=0, invalid=762 0077: dt=0.000000, rms=0.654 (0.080%), neg=0, invalid=762 0078: dt=0.000000, rms=0.654 (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=0.723, neg=0, invalid=762 0079: dt=1.104651, rms=0.711 (1.690%), neg=0, invalid=762 0080: dt=0.779614, rms=0.709 (0.288%), neg=0, invalid=762 0081: dt=0.448000, rms=0.709 (0.066%), neg=0, invalid=762 0082: dt=0.448000, rms=0.709 (0.020%), neg=0, invalid=762 0083: dt=0.448000, rms=0.709 (-0.080%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.709, neg=0, invalid=762 0084: dt=0.448000, rms=0.708 (0.144%), neg=0, invalid=762 0085: dt=0.448000, rms=0.708 (0.027%), neg=0, invalid=762 0086: dt=0.448000, rms=0.708 (0.011%), neg=0, invalid=762 0087: dt=0.448000, rms=0.708 (-0.047%), 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=0.657, neg=0, invalid=762 0088: dt=0.656757, rms=0.646 (1.739%), neg=0, invalid=762 0089: dt=0.064000, rms=0.646 (0.070%), neg=0, invalid=762 0090: dt=0.064000, rms=0.646 (-0.053%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.646, neg=0, invalid=762 0091: dt=0.028000, rms=0.645 (0.094%), neg=0, invalid=762 0092: dt=0.001750, rms=0.645 (-0.001%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.11891 (29) Left_Lateral_Ventricle (4): linear fit = 1.51 x + 0.0 (1793 voxels, overlap=0.274) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (1793 voxels, peak = 30), gca=30.0 gca peak = 0.15565 (16) mri peak = 0.10626 (29) Right_Lateral_Ventricle (43): linear fit = 1.84 x + 0.0 (1606 voxels, overlap=0.098) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1606 voxels, peak = 29), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.09855 (98) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (1053 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (1053 voxels, peak = 99), gca=99.4 gca peak = 0.20183 (93) mri peak = 0.12897 (101) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (1037 voxels, overlap=0.870) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (1037 voxels, peak = 97), gca=97.2 gca peak = 0.21683 (55) mri peak = 0.12064 (74) Right_Hippocampus (53): linear fit = 1.34 x + 0.0 (1200 voxels, overlap=0.012) Right_Hippocampus (53): linear fit = 1.34 x + 0.0 (1200 voxels, peak = 73), gca=73.4 gca peak = 0.30730 (58) mri peak = 0.12403 (75) Left_Hippocampus (17): linear fit = 1.26 x + 0.0 (1179 voxels, overlap=0.012) Left_Hippocampus (17): linear fit = 1.26 x + 0.0 (1179 voxels, peak = 73), gca=73.4 gca peak = 0.11430 (101) mri peak = 0.14841 (105) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (70103 voxels, overlap=0.549) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (70103 voxels, peak = 105), gca=104.5 gca peak = 0.12076 (102) mri peak = 0.15941 (106) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (72682 voxels, overlap=0.353) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (72682 voxels, peak = 107), gca=106.6 gca peak = 0.14995 (59) mri peak = 0.04771 (74) Left_Cerebral_Cortex (3): linear fit = 1.26 x + 0.0 (40525 voxels, overlap=0.002) Left_Cerebral_Cortex (3): linear fit = 1.26 x + 0.0 (40525 voxels, peak = 75), gca=74.6 gca peak = 0.15082 (58) mri peak = 0.05432 (74) Right_Cerebral_Cortex (42): linear fit = 1.28 x + 0.0 (40500 voxels, overlap=0.001) Right_Cerebral_Cortex (42): linear fit = 1.28 x + 0.0 (40500 voxels, peak = 75), gca=74.5 gca peak = 0.14161 (67) mri peak = 0.16989 (86) Right_Caudate (50): linear fit = 1.27 x + 0.0 (517 voxels, overlap=0.013) Right_Caudate (50): linear fit = 1.27 x + 0.0 (517 voxels, peak = 85), gca=85.4 gca peak = 0.15243 (71) mri peak = 0.18042 (87) Left_Caudate (11): linear fit = 1.21 x + 0.0 (1106 voxels, overlap=0.005) Left_Caudate (11): linear fit = 1.21 x + 0.0 (1106 voxels, peak = 86), gca=85.6 gca peak = 0.13336 (57) mri peak = 0.05089 (75) Left_Cerebellum_Cortex (8): linear fit = 1.40 x + 0.0 (23523 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.40 x + 0.0 (23523 voxels, peak = 80), gca=80.1 gca peak = 0.13252 (56) mri peak = 0.04373 (75) Right_Cerebellum_Cortex (47): linear fit = 1.41 x + 0.0 (25084 voxels, overlap=0.002) Right_Cerebellum_Cortex (47): linear fit = 1.41 x + 0.0 (25084 voxels, peak = 79), gca=79.2 gca peak = 0.18181 (84) mri peak = 0.08522 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (9829 voxels, overlap=0.570) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (9829 voxels, peak = 94), gca=93.7 gca peak = 0.20573 (83) mri peak = 0.06878 (78) Right_Cerebellum_White_Matter (46): linear fit = 0.94 x + 0.0 (7336 voxels, overlap=0.867) Right_Cerebellum_White_Matter (46): linear fit = 0.94 x + 0.0 (7336 voxels, peak = 78), gca=77.6 gca peak = 0.21969 (57) mri peak = 0.16979 (74) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (556 voxels, overlap=0.040) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (556 voxels, peak = 74), gca=73.8 gca peak = 0.39313 (56) mri peak = 0.09843 (75) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (500 voxels, overlap=0.021) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (500 voxels, peak = 73), gca=72.5 gca peak = 0.14181 (85) mri peak = 0.08937 (97) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (5836 voxels, overlap=0.338) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (5836 voxels, peak = 96), gca=96.5 gca peak = 0.11978 (83) mri peak = 0.07506 (94) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4139 voxels, overlap=0.541) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4139 voxels, peak = 93), gca=92.5 gca peak = 0.13399 (79) mri peak = 0.13129 (92) Left_Putamen (12): linear fit = 1.15 x + 0.0 (2538 voxels, overlap=0.005) Left_Putamen (12): linear fit = 1.15 x + 0.0 (2538 voxels, peak = 91), gca=91.2 gca peak = 0.14159 (79) mri peak = 0.10043 (92) Right_Putamen (51): linear fit = 1.15 x + 0.0 (2764 voxels, overlap=0.019) Right_Putamen (51): linear fit = 1.15 x + 0.0 (2764 voxels, peak = 91), gca=91.2 gca peak = 0.10025 (80) mri peak = 0.14813 (91) Brain_Stem (16): linear fit = 1.14 x + 0.0 (10819 voxels, overlap=0.011) Brain_Stem (16): linear fit = 1.14 x + 0.0 (10819 voxels, peak = 92), gca=91.6 gca peak = 0.13281 (86) mri peak = 0.11288 (95) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1258 voxels, overlap=0.111) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1258 voxels, peak = 94), gca=94.2 gca peak = 0.12801 (89) mri peak = 0.12948 (97) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1435 voxels, overlap=0.084) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1435 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) mri peak = 1.00000 (29) gca peak = 0.15061 (21) mri peak = 0.33355 (28) Fourth_Ventricle (15): linear fit = 1.30 x + 0.0 (715 voxels, overlap=0.063) Fourth_Ventricle (15): linear fit = 1.30 x + 0.0 (715 voxels, peak = 27), gca=27.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.29 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 1.43 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.658, neg=0, invalid=762 0093: dt=112.625407, rms=0.627 (4.748%), neg=0, invalid=762 0094: dt=231.536680, rms=0.618 (1.380%), neg=0, invalid=762 0095: dt=443.904000, rms=0.612 (1.006%), neg=0, invalid=762 0096: dt=110.976000, rms=0.610 (0.287%), neg=0, invalid=762 0097: dt=295.936000, rms=0.608 (0.263%), neg=0, invalid=762 0098: dt=110.976000, rms=0.608 (0.127%), neg=0, invalid=762 0099: dt=517.888000, rms=0.606 (0.300%), neg=0, invalid=762 0100: dt=73.984000, rms=0.605 (0.185%), neg=0, invalid=762 0101: dt=443.904000, rms=0.604 (0.131%), neg=0, invalid=762 0102: dt=129.472000, rms=0.603 (0.184%), neg=0, invalid=762 0103: dt=129.472000, rms=0.603 (0.056%), neg=0, invalid=762 0104: dt=517.888000, rms=0.601 (0.179%), neg=0, invalid=762 0105: dt=73.984000, rms=0.601 (0.108%), neg=0, invalid=762 0106: dt=517.888000, rms=0.600 (0.129%), neg=0, invalid=762 0107: dt=129.472000, rms=0.599 (0.131%), neg=0, invalid=762 0108: dt=110.976000, rms=0.599 (0.022%), neg=0, invalid=762 0109: dt=110.976000, rms=0.599 (0.051%), neg=0, invalid=762 0110: dt=110.976000, rms=0.598 (0.074%), neg=0, invalid=762 0111: dt=110.976000, rms=0.598 (0.092%), neg=0, invalid=762 0112: dt=110.976000, rms=0.597 (0.098%), neg=0, invalid=762 0113: dt=110.976000, rms=0.597 (0.121%), neg=0, invalid=762 0114: dt=110.976000, rms=0.596 (0.136%), neg=0, invalid=762 0115: dt=110.976000, rms=0.595 (0.150%), neg=0, invalid=762 0116: dt=110.976000, rms=0.594 (0.139%), neg=0, invalid=762 0117: dt=110.976000, rms=0.593 (0.124%), neg=0, invalid=762 0118: dt=110.976000, rms=0.593 (0.122%), neg=0, invalid=762 0119: dt=110.976000, rms=0.592 (0.115%), neg=0, invalid=762 0120: dt=110.976000, rms=0.591 (0.105%), neg=0, invalid=762 0121: dt=110.976000, rms=0.591 (0.096%), neg=0, invalid=762 0122: dt=110.976000, rms=0.590 (0.091%), neg=0, invalid=762 0123: dt=110.976000, rms=0.590 (0.095%), neg=0, invalid=762 0124: dt=110.976000, rms=0.589 (0.097%), neg=0, invalid=762 0125: dt=110.976000, rms=0.588 (0.088%), neg=0, invalid=762 0126: dt=110.976000, rms=0.588 (0.077%), neg=0, invalid=762 0127: dt=110.976000, rms=0.588 (0.067%), neg=0, invalid=762 0128: dt=110.976000, rms=0.587 (0.064%), neg=0, invalid=762 0129: dt=110.976000, rms=0.587 (0.065%), neg=0, invalid=762 0130: dt=110.976000, rms=0.586 (0.066%), neg=0, invalid=762 0131: dt=110.976000, rms=0.586 (0.057%), neg=0, invalid=762 0132: dt=110.976000, rms=0.586 (0.051%), neg=0, invalid=762 0133: dt=110.976000, rms=0.586 (0.047%), neg=0, invalid=762 0134: dt=110.976000, rms=0.585 (0.050%), neg=0, invalid=762 0135: dt=110.976000, rms=0.585 (0.049%), neg=0, invalid=762 0136: dt=110.976000, rms=0.585 (0.048%), neg=0, invalid=762 0137: dt=110.976000, rms=0.584 (0.047%), neg=0, invalid=762 0138: dt=110.976000, rms=0.584 (0.047%), neg=0, invalid=762 0139: dt=110.976000, rms=0.584 (0.052%), neg=0, invalid=762 0140: dt=110.976000, rms=0.584 (0.049%), neg=0, invalid=762 0141: dt=110.976000, rms=0.583 (0.048%), neg=0, invalid=762 0142: dt=110.976000, rms=0.583 (0.044%), neg=0, invalid=762 0143: dt=110.976000, rms=0.583 (0.044%), neg=0, invalid=762 0144: dt=110.976000, rms=0.583 (0.046%), neg=0, invalid=762 0145: dt=110.976000, rms=0.582 (0.048%), neg=0, invalid=762 0146: dt=110.976000, rms=0.582 (0.047%), neg=0, invalid=762 0147: dt=110.976000, rms=0.582 (0.045%), neg=0, invalid=762 0148: dt=110.976000, rms=0.581 (0.040%), neg=0, invalid=762 0149: dt=110.976000, rms=0.581 (0.038%), neg=0, invalid=762 0150: dt=110.976000, rms=0.581 (0.039%), neg=0, invalid=762 0151: dt=110.976000, rms=0.581 (0.040%), neg=0, invalid=762 0152: dt=110.976000, rms=0.581 (0.036%), neg=0, invalid=762 0153: dt=110.976000, rms=0.580 (0.036%), neg=0, invalid=762 0154: dt=110.976000, rms=0.580 (0.031%), neg=0, invalid=762 0155: dt=110.976000, rms=0.580 (0.031%), neg=0, invalid=762 0156: dt=110.976000, rms=0.580 (0.031%), neg=0, invalid=762 0157: dt=110.976000, rms=0.580 (0.031%), neg=0, invalid=762 0158: dt=110.976000, rms=0.579 (0.030%), neg=0, invalid=762 0159: dt=110.976000, rms=0.579 (0.032%), neg=0, invalid=762 0160: dt=110.976000, rms=0.579 (0.029%), neg=0, invalid=762 0161: dt=110.976000, rms=0.579 (0.029%), neg=0, invalid=762 0162: dt=110.976000, rms=0.579 (0.027%), neg=0, invalid=762 0163: dt=110.976000, rms=0.579 (0.025%), neg=0, invalid=762 0164: dt=110.976000, rms=0.578 (0.027%), neg=0, invalid=762 0165: dt=110.976000, rms=0.578 (0.028%), neg=0, invalid=762 0166: dt=110.976000, rms=0.578 (0.028%), neg=0, invalid=762 0167: dt=110.976000, rms=0.578 (0.027%), neg=0, invalid=762 0168: dt=110.976000, rms=0.578 (0.025%), neg=0, invalid=762 0169: dt=110.976000, rms=0.578 (0.023%), neg=0, invalid=762 0170: dt=5918.720000, rms=0.577 (0.068%), neg=0, invalid=762 0171: dt=110.976000, rms=0.577 (0.038%), neg=0, invalid=762 0172: dt=110.976000, rms=0.577 (0.015%), neg=0, invalid=762 0173: dt=110.976000, rms=0.577 (0.004%), neg=0, invalid=762 0174: dt=110.976000, rms=0.577 (-0.006%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.577, neg=0, invalid=762 0175: dt=443.904000, rms=0.576 (0.271%), neg=0, invalid=762 0176: dt=92.480000, rms=0.576 (0.020%), neg=0, invalid=762 0177: dt=92.480000, rms=0.576 (0.011%), neg=0, invalid=762 0178: dt=92.480000, rms=0.575 (0.012%), neg=0, invalid=762 0179: dt=92.480000, rms=0.575 (0.016%), neg=0, invalid=762 0180: dt=92.480000, rms=0.575 (0.042%), neg=0, invalid=762 0181: dt=92.480000, rms=0.575 (0.055%), neg=0, invalid=762 0182: dt=92.480000, rms=0.574 (0.055%), neg=0, invalid=762 0183: dt=92.480000, rms=0.574 (0.030%), neg=0, invalid=762 0184: dt=92.480000, rms=0.574 (0.023%), neg=0, invalid=762 0185: dt=92.480000, rms=0.574 (0.015%), neg=0, invalid=762 0186: dt=517.888000, rms=0.574 (0.048%), neg=0, invalid=762 0187: dt=55.488000, rms=0.574 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.576, neg=0, invalid=762 0188: dt=124.416000, rms=0.574 (0.327%), neg=0, invalid=762 0189: dt=331.776000, rms=0.566 (1.409%), neg=0, invalid=762 0190: dt=36.288000, rms=0.564 (0.351%), neg=0, invalid=762 0191: dt=36.288000, rms=0.564 (0.095%), neg=0, invalid=762 0192: dt=145.152000, rms=0.562 (0.240%), neg=0, invalid=762 0193: dt=331.776000, rms=0.558 (0.817%), neg=0, invalid=762 0194: dt=47.333333, rms=0.556 (0.268%), neg=0, invalid=762 0195: dt=82.944000, rms=0.556 (0.067%), neg=0, invalid=762 0196: dt=580.608000, rms=0.551 (0.879%), neg=0, invalid=762 0197: dt=36.288000, rms=0.550 (0.127%), neg=0, invalid=762 0198: dt=36.288000, rms=0.550 (0.025%), neg=0, invalid=762 0199: dt=36.288000, rms=0.550 (0.028%), neg=0, invalid=762 0200: dt=36.288000, rms=0.550 (0.057%), neg=0, invalid=762 0201: dt=36.288000, rms=0.549 (0.092%), neg=0, invalid=762 0202: dt=36.288000, rms=0.548 (0.137%), neg=0, invalid=762 0203: dt=36.288000, rms=0.547 (0.167%), neg=0, invalid=762 0204: dt=36.288000, rms=0.546 (0.177%), neg=0, invalid=762 0205: dt=36.288000, rms=0.545 (0.171%), neg=0, invalid=762 0206: dt=36.288000, rms=0.545 (0.158%), neg=0, invalid=762 0207: dt=36.288000, rms=0.544 (0.146%), neg=0, invalid=762 0208: dt=36.288000, rms=0.543 (0.141%), neg=0, invalid=762 0209: dt=36.288000, rms=0.543 (0.034%), neg=0, invalid=762 0210: dt=36.288000, rms=0.543 (0.055%), neg=0, invalid=762 0211: dt=36.288000, rms=0.542 (0.068%), neg=0, invalid=762 0212: dt=36.288000, rms=0.542 (0.069%), neg=0, invalid=762 0213: dt=36.288000, rms=0.542 (0.013%), neg=0, invalid=762 0214: dt=36.288000, rms=0.542 (0.024%), neg=0, invalid=762 0215: dt=9.072000, rms=0.542 (0.006%), neg=0, invalid=762 0216: dt=6.480000, rms=0.542 (0.004%), neg=0, invalid=762 0217: dt=0.202500, rms=0.542 (0.000%), neg=0, invalid=762 0218: dt=0.101250, rms=0.542 (0.000%), neg=0, invalid=762 0219: dt=0.003164, rms=0.542 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.542, neg=0, invalid=762 0220: dt=145.152000, rms=0.538 (0.632%), neg=0, invalid=762 0221: dt=82.944000, rms=0.538 (0.151%), neg=0, invalid=762 0222: dt=145.152000, rms=0.537 (0.147%), neg=0, invalid=762 0223: dt=67.472868, rms=0.536 (0.113%), neg=0, invalid=762 0224: dt=124.416000, rms=0.536 (0.103%), neg=0, invalid=762 0225: dt=62.208000, rms=0.535 (0.092%), neg=0, invalid=762 0226: dt=145.152000, rms=0.535 (0.113%), neg=0, invalid=762 0227: dt=62.208000, rms=0.534 (0.070%), neg=0, invalid=762 0228: dt=145.152000, rms=0.534 (0.089%), neg=0, invalid=762 0229: dt=62.208000, rms=0.533 (0.069%), neg=0, invalid=762 0230: dt=145.152000, rms=0.533 (0.077%), neg=0, invalid=762 0231: dt=36.288000, rms=0.533 (0.051%), neg=0, invalid=762 0232: dt=497.664000, rms=0.532 (0.177%), neg=0, invalid=762 0233: dt=36.288000, rms=0.531 (0.129%), neg=0, invalid=762 0234: dt=82.944000, rms=0.531 (0.053%), neg=0, invalid=762 0235: dt=82.944000, rms=0.530 (0.040%), neg=0, invalid=762 0236: dt=82.944000, rms=0.530 (0.040%), neg=0, invalid=762 0237: dt=82.944000, rms=0.530 (0.079%), neg=0, invalid=762 0238: dt=82.944000, rms=0.529 (0.101%), neg=0, invalid=762 0239: dt=82.944000, rms=0.529 (0.144%), neg=0, invalid=762 0240: dt=82.944000, rms=0.528 (0.132%), neg=0, invalid=762 0241: dt=82.944000, rms=0.527 (0.159%), neg=0, invalid=762 0242: dt=82.944000, rms=0.526 (0.146%), neg=0, invalid=762 0243: dt=82.944000, rms=0.525 (0.160%), neg=0, invalid=762 0244: dt=82.944000, rms=0.525 (0.145%), neg=0, invalid=762 0245: dt=82.944000, rms=0.524 (0.169%), neg=0, invalid=762 0246: dt=82.944000, rms=0.523 (0.146%), neg=0, invalid=762 0247: dt=82.944000, rms=0.522 (0.145%), neg=0, invalid=762 0248: dt=82.944000, rms=0.522 (0.124%), neg=0, invalid=762 0249: dt=82.944000, rms=0.521 (0.128%), neg=0, invalid=762 0250: dt=82.944000, rms=0.520 (0.132%), neg=0, invalid=762 0251: dt=82.944000, rms=0.520 (0.130%), neg=0, invalid=762 0252: dt=82.944000, rms=0.519 (0.122%), neg=0, invalid=762 0253: dt=82.944000, rms=0.518 (0.110%), neg=0, invalid=762 0254: dt=82.944000, rms=0.518 (0.117%), neg=0, invalid=762 0255: dt=82.944000, rms=0.517 (0.110%), neg=0, invalid=762 0256: dt=82.944000, rms=0.517 (0.109%), neg=0, invalid=762 0257: dt=82.944000, rms=0.516 (0.096%), neg=0, invalid=762 0258: dt=82.944000, rms=0.516 (0.094%), neg=0, invalid=762 0259: dt=82.944000, rms=0.515 (0.086%), neg=0, invalid=762 0260: dt=82.944000, rms=0.515 (0.079%), neg=0, invalid=762 0261: dt=82.944000, rms=0.514 (0.078%), neg=0, invalid=762 0262: dt=82.944000, rms=0.514 (0.075%), neg=0, invalid=762 0263: dt=82.944000, rms=0.514 (0.076%), neg=0, invalid=762 0264: dt=82.944000, rms=0.513 (0.068%), neg=0, invalid=762 0265: dt=82.944000, rms=0.513 (0.061%), neg=0, invalid=762 0266: dt=82.944000, rms=0.513 (0.056%), neg=0, invalid=762 0267: dt=82.944000, rms=0.512 (0.065%), neg=0, invalid=762 0268: dt=82.944000, rms=0.512 (0.065%), neg=0, invalid=762 0269: dt=82.944000, rms=0.512 (0.061%), neg=0, invalid=762 0270: dt=82.944000, rms=0.511 (0.048%), neg=0, invalid=762 0271: dt=82.944000, rms=0.511 (0.054%), neg=0, invalid=762 0272: dt=82.944000, rms=0.511 (0.053%), neg=0, invalid=762 0273: dt=82.944000, rms=0.511 (0.063%), neg=0, invalid=762 0274: dt=82.944000, rms=0.510 (0.052%), neg=0, invalid=762 0275: dt=82.944000, rms=0.510 (0.048%), neg=0, invalid=762 0276: dt=82.944000, rms=0.510 (0.040%), neg=0, invalid=762 0277: dt=82.944000, rms=0.510 (0.042%), neg=0, invalid=762 0278: dt=82.944000, rms=0.509 (0.049%), neg=0, invalid=762 0279: dt=82.944000, rms=0.509 (0.041%), neg=0, invalid=762 0280: dt=82.944000, rms=0.509 (0.042%), neg=0, invalid=762 0281: dt=82.944000, rms=0.509 (0.037%), neg=0, invalid=762 0282: dt=82.944000, rms=0.509 (0.039%), neg=0, invalid=762 0283: dt=82.944000, rms=0.508 (0.033%), neg=0, invalid=762 0284: dt=82.944000, rms=0.508 (0.039%), neg=0, invalid=762 0285: dt=82.944000, rms=0.508 (0.031%), neg=0, invalid=762 0286: dt=82.944000, rms=0.508 (0.031%), neg=0, invalid=762 0287: dt=82.944000, rms=0.508 (0.029%), neg=0, invalid=762 0288: dt=82.944000, rms=0.508 (0.034%), neg=0, invalid=762 0289: dt=82.944000, rms=0.507 (0.039%), neg=0, invalid=762 0290: dt=82.944000, rms=0.507 (0.030%), neg=0, invalid=762 0291: dt=82.944000, rms=0.507 (0.021%), neg=0, invalid=762 0292: dt=82.944000, rms=0.507 (0.023%), neg=0, invalid=762 0293: dt=82.944000, rms=0.507 (0.032%), neg=0, invalid=762 0294: dt=82.944000, rms=0.507 (0.035%), neg=0, invalid=762 0295: dt=82.944000, rms=0.507 (0.030%), neg=0, invalid=762 0296: dt=82.944000, rms=0.506 (0.018%), neg=0, invalid=762 0297: dt=82.944000, rms=0.506 (0.017%), neg=0, invalid=762 0298: dt=145.152000, rms=0.506 (0.012%), neg=0, invalid=762 0299: dt=145.152000, rms=0.506 (-0.013%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.517, neg=0, invalid=762 0300: dt=11.200000, rms=0.517 (0.106%), neg=0, invalid=762 0301: dt=11.200000, rms=0.517 (0.031%), neg=0, invalid=762 0302: dt=11.200000, rms=0.516 (0.031%), neg=0, invalid=762 0303: dt=11.200000, rms=0.516 (0.017%), neg=0, invalid=762 0304: dt=11.200000, rms=0.516 (-0.019%), neg=0, invalid=762 0305: dt=44.800000, rms=0.516 (0.146%), neg=0, invalid=762 0306: dt=44.800000, rms=0.515 (0.215%), neg=0, invalid=762 0307: dt=44.800000, rms=0.513 (0.254%), neg=0, invalid=762 0308: dt=11.200000, rms=0.513 (0.058%), neg=0, invalid=762 0309: dt=11.200000, rms=0.513 (0.059%), neg=0, invalid=762 0310: dt=2.800000, rms=0.513 (0.016%), neg=0, invalid=762 0311: dt=2.800000, rms=0.512 (0.014%), neg=0, invalid=762 0312: dt=0.175000, rms=0.512 (0.001%), neg=0, invalid=762 0313: dt=0.087500, rms=0.512 (0.000%), neg=0, invalid=762 0314: dt=0.043750, rms=0.512 (0.000%), neg=0, invalid=762 0315: dt=0.031250, rms=0.512 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.513, neg=0, invalid=762 0316: dt=84.150082, rms=0.506 (1.245%), neg=0, invalid=762 0317: dt=25.600000, rms=0.505 (0.225%), neg=0, invalid=762 0318: dt=95.299270, rms=0.504 (0.254%), neg=0, invalid=762 0319: dt=32.000000, rms=0.503 (0.230%), neg=0, invalid=762 0320: dt=44.800000, rms=0.502 (0.227%), neg=0, invalid=762 0321: dt=32.000000, rms=0.501 (0.104%), neg=0, invalid=762 0322: dt=38.400000, rms=0.500 (0.152%), neg=0, invalid=762 0323: dt=32.000000, rms=0.500 (0.093%), neg=0, invalid=762 0324: dt=38.400000, rms=0.499 (0.137%), neg=0, invalid=762 0325: dt=32.000000, rms=0.499 (0.083%), neg=0, invalid=762 0326: dt=44.800000, rms=0.498 (0.129%), neg=0, invalid=762 0327: dt=25.600000, rms=0.498 (0.080%), neg=0, invalid=762 0328: dt=102.400000, rms=0.497 (0.181%), neg=0, invalid=762 0329: dt=25.600000, rms=0.496 (0.114%), neg=0, invalid=762 0330: dt=128.000000, rms=0.495 (0.211%), neg=0, invalid=762 0331: dt=25.600000, rms=0.495 (0.128%), neg=0, invalid=762 0332: dt=102.400000, rms=0.494 (0.145%), neg=0, invalid=762 0333: dt=25.600000, rms=0.493 (0.095%), neg=0, invalid=762 0334: dt=44.800000, rms=0.493 (0.090%), neg=0, invalid=762 0335: dt=44.800000, rms=0.493 (0.050%), neg=0, invalid=762 0336: dt=32.000000, rms=0.492 (0.060%), neg=0, invalid=762 0337: dt=32.000000, rms=0.492 (0.044%), neg=0, invalid=762 0338: dt=32.000000, rms=0.492 (0.044%), neg=0, invalid=762 0339: dt=32.000000, rms=0.492 (0.089%), neg=0, invalid=762 0340: dt=32.000000, rms=0.491 (0.107%), neg=0, invalid=762 0341: dt=32.000000, rms=0.491 (0.040%), neg=0, invalid=762 0342: dt=32.000000, rms=0.490 (0.078%), neg=0, invalid=762 0343: dt=4.000000, rms=0.490 (0.015%), neg=0, invalid=762 0344: dt=1.000000, rms=0.490 (0.006%), neg=0, invalid=762 0345: dt=0.500000, rms=0.490 (0.002%), neg=0, invalid=762 0346: dt=0.031250, rms=0.490 (0.000%), neg=0, invalid=762 0347: dt=0.015625, rms=0.490 (0.000%), neg=0, invalid=762 0348: dt=0.000488, rms=0.490 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.511, neg=0, invalid=762 0349: dt=0.000000, rms=0.511 (0.045%), neg=0, invalid=762 0350: dt=0.000000, rms=0.511 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.511, neg=0, invalid=762 0351: dt=0.000000, rms=0.511 (0.045%), neg=0, invalid=762 0352: dt=0.000000, rms=0.511 (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=0.552, neg=0, invalid=762 0353: dt=1.931973, rms=0.546 (0.923%), neg=0, invalid=762 0354: dt=0.768000, rms=0.546 (0.058%), neg=0, invalid=762 0355: dt=0.320000, rms=0.546 (0.005%), neg=0, invalid=762 0356: dt=0.320000, rms=0.546 (-0.004%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.546, neg=0, invalid=762 0357: dt=1.792000, rms=0.545 (0.254%), neg=0, invalid=762 0358: dt=0.768000, rms=0.545 (0.020%), neg=0, invalid=762 0359: dt=0.768000, rms=0.545 (-0.003%), 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=0.506, neg=0, invalid=762 0360: dt=1.280000, rms=0.479 (5.278%), neg=0, invalid=762 0361: dt=0.000000, rms=0.479 (0.011%), neg=0, invalid=762 0362: dt=0.050000, rms=0.479 (-0.128%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.480, neg=0, invalid=762 0363: dt=0.000000, rms=0.479 (0.072%), neg=0, invalid=762 0364: dt=0.000000, rms=0.479 (0.000%), neg=0, invalid=762 0365: dt=0.050000, rms=0.479 (-0.058%), 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=0.473, neg=0, invalid=762 0366: dt=0.000000, rms=0.472 (0.074%), neg=0, invalid=762 0367: dt=0.000000, rms=0.472 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.473, neg=0, invalid=762 0368: dt=92.480000, rms=0.472 (0.095%), neg=0, invalid=762 0369: dt=295.936000, rms=0.472 (0.051%), neg=0, invalid=762 0370: dt=295.936000, rms=0.472 (0.066%), neg=0, invalid=762 0371: dt=295.936000, rms=0.472 (-0.086%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.472, neg=0, invalid=762 0372: dt=31.104000, rms=0.471 (0.147%), neg=0, invalid=762 0373: dt=36.288000, rms=0.471 (0.049%), neg=0, invalid=762 0374: dt=36.288000, rms=0.471 (0.054%), neg=0, invalid=762 0375: dt=36.288000, rms=0.471 (0.047%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0376: dt=36.288000, rms=0.471 (0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.471, neg=0, invalid=762 0377: dt=119.422680, rms=0.467 (0.917%), neg=0, invalid=762 0378: dt=36.288000, rms=0.466 (0.217%), neg=0, invalid=762 0379: dt=36.288000, rms=0.465 (0.067%), neg=0, invalid=762 0380: dt=36.288000, rms=0.465 (0.091%), neg=0, invalid=762 0381: dt=36.288000, rms=0.464 (0.133%), neg=0, invalid=762 0382: dt=36.288000, rms=0.464 (0.164%), neg=0, invalid=762 0383: dt=36.288000, rms=0.463 (0.171%), neg=0, invalid=762 0384: dt=36.288000, rms=0.462 (0.163%), neg=0, invalid=762 0385: dt=36.288000, rms=0.461 (0.157%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0386: dt=36.288000, rms=0.461 (0.137%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0387: dt=36.288000, rms=0.460 (0.106%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0388: dt=36.288000, rms=0.460 (0.091%), neg=0, invalid=762 0389: dt=145.152000, rms=0.460 (0.047%), neg=0, invalid=762 0390: dt=145.152000, rms=0.460 (-0.060%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.461, neg=0, invalid=762 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0391: dt=25.600000, rms=0.459 (0.410%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 10 iterations, nbhd size=1, neg = 0 0392: dt=64.703297, rms=0.457 (0.509%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0393: dt=32.000000, rms=0.455 (0.327%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0394: dt=38.400000, rms=0.454 (0.292%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0395: dt=25.600000, rms=0.453 (0.195%), neg=0, invalid=762 0396: dt=25.600000, rms=0.452 (0.183%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0397: dt=25.600000, rms=0.451 (0.232%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 9 iterations, nbhd size=1, neg = 0 0398: dt=25.600000, rms=0.450 (0.261%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 10 iterations, nbhd size=1, neg = 0 0399: dt=25.600000, rms=0.449 (0.234%), neg=0, invalid=762 iter 0, gcam->neg = 16 after 11 iterations, nbhd size=1, neg = 0 0400: dt=25.600000, rms=0.448 (0.213%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 9 iterations, nbhd size=1, neg = 0 0401: dt=25.600000, rms=0.447 (0.188%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 9 iterations, nbhd size=1, neg = 0 0402: dt=25.600000, rms=0.446 (0.196%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 12 iterations, nbhd size=1, neg = 0 0403: dt=25.600000, rms=0.445 (0.159%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 12 iterations, nbhd size=1, neg = 0 0404: dt=25.600000, rms=0.445 (0.125%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 11 iterations, nbhd size=1, neg = 0 0405: dt=25.600000, rms=0.444 (0.137%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 10 iterations, nbhd size=1, neg = 0 0406: dt=25.600000, rms=0.444 (0.131%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 0407: dt=25.600000, rms=0.443 (0.103%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 0408: dt=25.600000, rms=0.443 (0.106%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 11 iterations, nbhd size=1, neg = 0 0409: dt=25.600000, rms=0.442 (0.076%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0410: dt=32.000000, rms=0.442 (0.019%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0411: dt=32.000000, rms=0.442 (0.039%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0412: dt=32.000000, rms=0.442 (0.040%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0413: dt=32.000000, rms=0.442 (0.015%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0414: dt=32.000000, rms=0.442 (0.039%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0415: dt=32.000000, rms=0.442 (0.031%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.442, neg=0, invalid=762 iter 0, gcam->neg = 5 after 9 iterations, nbhd size=1, neg = 0 0416: dt=71.262411, rms=0.437 (1.143%), neg=0, invalid=762 0417: dt=23.667590, rms=0.436 (0.284%), neg=0, invalid=762 0418: dt=44.800000, rms=0.435 (0.146%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0419: dt=44.800000, rms=0.435 (0.053%), neg=0, invalid=762 0420: dt=44.800000, rms=0.434 (0.216%), neg=0, invalid=762 0421: dt=44.800000, rms=0.434 (0.052%), neg=0, invalid=762 0422: dt=44.800000, rms=0.433 (0.158%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0423: dt=44.800000, rms=0.433 (-0.075%), neg=0, invalid=762 0424: dt=25.600000, rms=0.433 (0.059%), neg=0, invalid=762 0425: dt=44.800000, rms=0.432 (0.047%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.442, neg=0, invalid=762 0426: dt=0.000000, rms=0.442 (0.065%), neg=0, invalid=762 0427: dt=0.000000, rms=0.442 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.442, neg=0, invalid=762 0428: dt=2.880000, rms=0.442 (0.107%), neg=0, invalid=762 0429: dt=1.008000, rms=0.442 (0.013%), neg=0, invalid=762 0430: dt=1.008000, rms=0.442 (0.003%), neg=0, invalid=762 0431: dt=1.008000, rms=0.442 (-0.009%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.459, neg=0, invalid=762 0432: dt=0.448000, rms=0.458 (0.144%), neg=0, invalid=762 0433: dt=0.384000, rms=0.458 (0.017%), neg=0, invalid=762 0434: dt=0.384000, rms=0.458 (-0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.459, neg=0, invalid=762 0435: dt=1.024000, rms=0.458 (0.201%), neg=0, invalid=762 0436: dt=0.384000, rms=0.458 (0.010%), neg=0, invalid=762 0437: dt=0.384000, rms=0.458 (-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=0.440, neg=0, invalid=762 iter 0, gcam->neg = 333 after 13 iterations, nbhd size=1, neg = 0 0438: dt=1.954645, rms=0.421 (4.354%), neg=0, invalid=762 0439: dt=0.064000, rms=0.421 (0.035%), neg=0, invalid=762 0440: dt=0.064000, rms=0.421 (-0.024%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.421, neg=0, invalid=762 0441: dt=0.080000, rms=0.420 (0.131%), neg=0, invalid=762 0442: dt=0.001750, rms=0.420 (0.001%), neg=0, invalid=762 0443: dt=0.001750, rms=0.420 (0.000%), neg=0, invalid=762 0444: dt=0.001750, rms=0.420 (0.000%), neg=0, invalid=762 0445: dt=0.001750, rms=0.420 (-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=0.411, neg=0, invalid=762 0446: dt=0.000000, rms=0.411 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.411, neg=0, invalid=762 0447: dt=23.120000, rms=0.411 (0.001%), neg=0, invalid=762 0448: dt=8.092000, rms=0.411 (0.000%), neg=0, invalid=762 0449: dt=8.092000, rms=0.411 (0.000%), neg=0, invalid=762 0450: dt=8.092000, rms=0.411 (-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=0.411, neg=0, invalid=762 0451: dt=0.000000, rms=0.411 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.411, neg=0, invalid=762 0452: dt=62.208000, rms=0.411 (0.034%), neg=0, invalid=762 0453: dt=145.152000, rms=0.410 (0.067%), neg=0, invalid=762 0454: dt=103.680000, rms=0.410 (0.019%), neg=0, invalid=762 0455: dt=103.680000, rms=0.410 (0.041%), neg=0, invalid=762 0456: dt=103.680000, rms=0.410 (0.050%), neg=0, invalid=762 0457: dt=103.680000, rms=0.410 (0.018%), neg=0, invalid=762 0458: dt=103.680000, rms=0.410 (0.048%), neg=0, invalid=762 0459: dt=103.680000, rms=0.409 (0.050%), neg=0, invalid=762 0460: dt=103.680000, rms=0.409 (0.017%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.410, neg=0, invalid=762 0461: dt=6.400000, rms=0.410 (0.021%), neg=0, invalid=762 0462: dt=2.000000, rms=0.410 (0.001%), neg=0, invalid=762 0463: dt=2.000000, rms=0.410 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.410, neg=0, invalid=762 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0464: dt=139.934732, rms=0.406 (0.948%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0465: dt=22.461538, rms=0.405 (0.263%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0466: dt=44.800000, rms=0.405 (0.070%), neg=0, invalid=762 0467: dt=44.800000, rms=0.404 (0.103%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0468: dt=44.800000, rms=0.403 (0.188%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0469: dt=44.800000, rms=0.403 (0.188%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0470: dt=44.800000, rms=0.402 (0.211%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 3 iterations, nbhd size=0, neg = 0 0471: dt=44.800000, rms=0.401 (0.214%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 9 iterations, nbhd size=1, neg = 0 0472: dt=44.800000, rms=0.400 (0.174%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 10 iterations, nbhd size=1, neg = 0 0473: dt=44.800000, rms=0.400 (0.114%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 4 iterations, nbhd size=0, neg = 0 0474: dt=44.800000, rms=0.399 (0.117%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 0475: dt=44.800000, rms=0.399 (0.106%), neg=0, invalid=762 0476: dt=32.000000, rms=0.399 (0.012%), neg=0, invalid=762 0477: dt=32.000000, rms=0.399 (0.005%), neg=0, invalid=762 0478: dt=32.000000, rms=0.399 (0.002%), neg=0, invalid=762 0479: dt=32.000000, rms=0.399 (0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.404, neg=0, invalid=762 0480: dt=0.000000, rms=0.404 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.404, neg=0, invalid=762 0481: dt=4.032000, rms=0.403 (0.040%), neg=0, invalid=762 0482: dt=3.333333, rms=0.403 (0.013%), neg=0, invalid=762 0483: dt=3.333333, rms=0.403 (0.004%), neg=0, invalid=762 0484: dt=3.333333, rms=0.403 (-0.024%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.411, neg=0, invalid=762 0485: dt=0.000000, rms=0.411 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.411, neg=0, invalid=762 0486: dt=0.000000, rms=0.411 (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=0.398, neg=0, invalid=762 iter 0, gcam->neg = 254 after 17 iterations, nbhd size=1, neg = 0 0487: dt=1.174079, rms=0.392 (1.560%), neg=0, invalid=762 0488: dt=0.000027, rms=0.392 (0.000%), neg=0, invalid=762 0489: dt=0.000027, rms=0.392 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.392, neg=0, invalid=762 0490: dt=0.112000, rms=0.392 (0.084%), neg=0, invalid=762 0491: dt=0.112000, rms=0.392 (0.044%), neg=0, invalid=762 0492: dt=0.112000, rms=0.391 (0.032%), neg=0, invalid=762 0493: dt=0.112000, rms=0.391 (0.007%), neg=0, invalid=762 0494: dt=0.112000, rms=0.391 (-0.060%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 3 hours, 30 minutes and 35 seconds. mri_ca_register utimesec 12612.317636 mri_ca_register stimesec 8.528703 mri_ca_register ru_maxrss 1335468 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4667555 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 5335 mri_ca_register ru_oublock 62930 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 243 mri_ca_register ru_nivcsw 164023 FSRUNTIME@ mri_ca_register 3.5096 hours 1 threads #-------------------------------------- #@# SubCort Seg So 11. Mär 01:41:31 CET 2018 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /cm/shared/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname node005 machine x86_64 setenv SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test3 cd /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /cm/shared/apps/freesurfer/6.0.0/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 /cm/shared/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 6.77 Atlas used for the 3D morph was /cm/shared/apps/freesurfer/6.0.0/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 = 0.12088 (29) Left_Lateral_Ventricle (4): linear fit = 1.48 x + 0.0 (3639 voxels, overlap=0.186) Left_Lateral_Ventricle (4): linear fit = 1.48 x + 0.0 (3639 voxels, peak = 30), gca=29.5 gca peak = 0.17677 (13) mri peak = 0.13018 (29) Right_Lateral_Ventricle (43): linear fit = 2.08 x + 0.0 (3239 voxels, overlap=0.132) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (3239 voxels, peak = 27), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.15775 (98) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (729 voxels, overlap=0.953) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (729 voxels, peak = 99), gca=99.3 gca peak = 0.16930 (96) mri peak = 0.25076 (101) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (662 voxels, overlap=0.353) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (662 voxels, peak = 100), gca=100.3 gca peak = 0.24553 (55) mri peak = 0.12250 (74) Right_Hippocampus (53): linear fit = 1.34 x + 0.0 (1201 voxels, overlap=0.017) Right_Hippocampus (53): linear fit = 1.34 x + 0.0 (1201 voxels, peak = 73), gca=73.4 gca peak = 0.30264 (59) mri peak = 0.13813 (75) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (1240 voxels, overlap=0.018) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (1240 voxels, peak = 76), gca=76.4 gca peak = 0.07580 (103) mri peak = 0.17298 (105) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (39313 voxels, overlap=0.495) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (39313 voxels, peak = 106), gca=105.6 gca peak = 0.07714 (104) mri peak = 0.17396 (106) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (41290 voxels, overlap=0.354) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (41290 voxels, peak = 107), gca=106.6 gca peak = 0.09712 (58) mri peak = 0.06546 (72) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (44992 voxels, overlap=0.022) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (44992 voxels, peak = 72), gca=72.2 gca peak = 0.11620 (58) mri peak = 0.06617 (72) Right_Cerebral_Cortex (42): linear fit = 1.25 x + 0.0 (45288 voxels, overlap=0.008) Right_Cerebral_Cortex (42): linear fit = 1.25 x + 0.0 (45288 voxels, peak = 72), gca=72.2 gca peak = 0.30970 (66) mri peak = 0.15745 (87) Right_Caudate (50): linear fit = 1.29 x + 0.0 (1429 voxels, overlap=0.015) Right_Caudate (50): linear fit = 1.29 x + 0.0 (1429 voxels, peak = 85), gca=85.5 gca peak = 0.15280 (69) mri peak = 0.16134 (87) Left_Caudate (11): linear fit = 1.23 x + 0.0 (1465 voxels, overlap=0.016) Left_Caudate (11): linear fit = 1.23 x + 0.0 (1465 voxels, peak = 85), gca=84.5 gca peak = 0.13902 (56) mri peak = 0.08374 (78) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (33490 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (33490 voxels, peak = 77), gca=77.0 gca peak = 0.14777 (55) mri peak = 0.09542 (76) Right_Cerebellum_Cortex (47): linear fit = 1.38 x + 0.0 (28995 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.38 x + 0.0 (28995 voxels, peak = 76), gca=75.6 gca peak = 0.16765 (84) mri peak = 0.21830 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (6538 voxels, overlap=0.002) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (6538 voxels, peak = 93), gca=92.8 gca peak = 0.18739 (84) mri peak = 0.11787 (94) Right_Cerebellum_White_Matter (46): linear fit = 1.11 x + 0.0 (11418 voxels, overlap=0.557) Right_Cerebellum_White_Matter (46): linear fit = 1.11 x + 0.0 (11418 voxels, peak = 93), gca=92.8 gca peak = 0.29869 (57) mri peak = 0.17195 (75) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (562 voxels, overlap=0.036) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (562 voxels, peak = 74), gca=73.8 gca peak = 0.33601 (57) mri peak = 0.13214 (75) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (560 voxels, overlap=0.039) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (560 voxels, peak = 74), gca=74.4 gca peak = 0.11131 (90) mri peak = 0.08664 (97) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (4780 voxels, overlap=0.528) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (4780 voxels, peak = 98), gca=97.7 gca peak = 0.11793 (83) mri peak = 0.08268 (95) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4226 voxels, overlap=0.426) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4226 voxels, peak = 93), gca=92.5 gca peak = 0.08324 (81) mri peak = 0.16897 (92) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1811 voxels, overlap=0.007) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1811 voxels, peak = 94), gca=93.6 gca peak = 0.10360 (77) mri peak = 0.12615 (92) Right_Putamen (51): linear fit = 1.16 x + 0.0 (2061 voxels, overlap=0.070) Right_Putamen (51): linear fit = 1.16 x + 0.0 (2061 voxels, peak = 90), gca=89.7 gca peak = 0.08424 (78) mri peak = 0.12024 (91) Brain_Stem (16): linear fit = 1.12 x + 0.0 (12475 voxels, overlap=0.159) Brain_Stem (16): linear fit = 1.12 x + 0.0 (12475 voxels, peak = 87), gca=87.0 gca peak = 0.12631 (89) mri peak = 0.10896 (98) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1498 voxels, overlap=0.205) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1498 voxels, peak = 97), gca=97.5 gca peak = 0.14500 (87) mri peak = 0.10121 (96) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1817 voxels, overlap=0.082) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1817 voxels, peak = 96), gca=96.1 gca peak = 0.14975 (24) mri peak = 0.10600 (30) Third_Ventricle (14): linear fit = 1.23 x + 0.0 (74 voxels, overlap=0.597) Third_Ventricle (14): linear fit = 1.23 x + 0.0 (74 voxels, peak = 29), gca=29.4 gca peak = 0.19357 (14) mri peak = 0.19674 (27) Fourth_Ventricle (15): linear fit = 1.76 x + 0.0 (249 voxels, overlap=0.172) Fourth_Ventricle (15): linear fit = 1.76 x + 0.0 (249 voxels, peak = 25), gca=24.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak 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 1.29 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.40 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15663 (27) mri peak = 0.12088 (29) Left_Lateral_Ventricle (4): linear fit = 0.99 x + 0.0 (3639 voxels, overlap=0.759) Left_Lateral_Ventricle (4): linear fit = 0.99 x + 0.0 (3639 voxels, peak = 27), gca=26.6 gca peak = 0.13981 (19) mri peak = 0.13018 (29) Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (3239 voxels, overlap=0.308) Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (3239 voxels, peak = 27), gca=26.7 gca peak = 0.29122 (100) mri peak = 0.15775 (98) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (729 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (729 voxels, peak = 100), gca=100.5 gca peak = 0.17230 (100) mri peak = 0.25076 (101) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (662 voxels, overlap=0.877) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (662 voxels, peak = 100), gca=99.5 gca peak = 0.22461 (74) mri peak = 0.12250 (74) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1201 voxels, overlap=0.943) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1201 voxels, peak = 73), gca=72.9 gca peak = 0.26484 (73) mri peak = 0.13813 (75) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1240 voxels, overlap=1.001) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1240 voxels, peak = 72), gca=71.9 gca peak = 0.07614 (105) mri peak = 0.17298 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (39313 voxels, overlap=0.612) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (39313 voxels, peak = 105), gca=105.0 gca peak = 0.07686 (107) mri peak = 0.17396 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (41290 voxels, overlap=0.492) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (41290 voxels, peak = 107), gca=107.0 gca peak = 0.07950 (72) mri peak = 0.06546 (72) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (44992 voxels, overlap=0.921) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (44992 voxels, peak = 72), gca=72.0 gca peak = 0.09549 (72) mri peak = 0.06617 (72) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (45288 voxels, overlap=0.917) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (45288 voxels, peak = 72), gca=72.0 gca peak = 0.21563 (85) mri peak = 0.15745 (87) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1429 voxels, overlap=0.998) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1429 voxels, peak = 85), gca=85.0 gca peak = 0.13452 (95) mri peak = 0.16134 (87) Left_Caudate (11): linear fit = 0.94 x + 0.0 (1465 voxels, overlap=0.630) Left_Caudate (11): linear fit = 0.94 x + 0.0 (1465 voxels, peak = 89), gca=88.8 gca peak = 0.10646 (76) mri peak = 0.08374 (78) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (33490 voxels, overlap=0.888) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (33490 voxels, peak = 76), gca=76.0 gca peak = 0.11437 (75) mri peak = 0.09542 (76) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (28995 voxels, overlap=0.873) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (28995 voxels, peak = 75), gca=75.0 gca peak = 0.14173 (93) mri peak = 0.21830 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6538 voxels, overlap=0.691) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6538 voxels, peak = 94), gca=94.4 gca peak = 0.16627 (93) mri peak = 0.11787 (94) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (11418 voxels, overlap=0.980) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (11418 voxels, peak = 93), gca=92.5 gca peak = 0.29270 (75) mri peak = 0.17195 (75) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (562 voxels, overlap=0.999) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (562 voxels, peak = 74), gca=73.9 gca peak = 0.29565 (74) mri peak = 0.13214 (75) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (560 voxels, overlap=0.999) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (560 voxels, peak = 75), gca=75.1 gca peak = 0.10206 (97) mri peak = 0.08664 (97) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4780 voxels, overlap=0.893) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4780 voxels, peak = 98), gca=98.5 gca peak = 0.10424 (90) mri peak = 0.08268 (95) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4226 voxels, overlap=0.937) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4226 voxels, peak = 90), gca=90.0 gca peak = 0.07366 (87) mri peak = 0.16897 (92) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1811 voxels, overlap=0.605) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1811 voxels, peak = 86), gca=85.7 gca peak = 0.08180 (87) mri peak = 0.12615 (92) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2061 voxels, overlap=0.761) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2061 voxels, peak = 87), gca=86.6 gca peak = 0.08176 (87) mri peak = 0.12024 (91) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12475 voxels, overlap=0.606) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12475 voxels, peak = 87), gca=86.6 gca peak = 0.12269 (92) mri peak = 0.10896 (98) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1498 voxels, overlap=0.742) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1498 voxels, peak = 93), gca=93.4 gca peak = 0.14981 (96) mri peak = 0.10121 (96) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1817 voxels, overlap=0.786) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1817 voxels, peak = 95), gca=94.6 gca peak = 0.12950 (31) mri peak = 0.10600 (30) Third_Ventricle (14): linear fit = 1.04 x + 0.0 (74 voxels, overlap=0.950) Third_Ventricle (14): linear fit = 1.04 x + 0.0 (74 voxels, peak = 32), gca=32.4 gca peak = 0.14735 (21) mri peak = 0.19674 (27) Fourth_Ventricle (15): linear fit = 1.29 x + 0.0 (249 voxels, overlap=0.351) Fourth_Ventricle (15): linear fit = 1.29 x + 0.0 (249 voxels, peak = 27), gca=27.2 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.17746 (35) gca peak Left_Thalamus = 0.36646 (105) gca peak CSF = 0.23763 (51) gca peak Left_Accumbens_area = 0.69378 (76) gca peak Left_undetermined = 0.96707 (34) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.11818 (35) gca peak Right_Inf_Lat_Vent = 0.24572 (31) gca peak Right_Accumbens_area = 0.29821 (84) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14504 (37) gca peak Fifth_Ventricle = 0.51669 (43) gca peak WM_hypointensities = 0.08625 (78) gca peak non_WM_hypointensities = 0.07502 (56) gca peak Optic_Chiasm = 0.68730 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.18 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 50814 voxels changed in iteration 0 of unlikely voxel relabeling 212 voxels changed in iteration 1 of unlikely voxel relabeling 31 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 45143 gm and wm labels changed (%41 to gray, %59 to white out of all changed labels) 422 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 63428 changed. image ll: -2.103, PF=0.500 pass 2: 16787 changed. image ll: -2.102, PF=0.500 pass 3: 5520 changed. pass 4: 2203 changed. 35881 voxels changed in iteration 0 of unlikely voxel relabeling 334 voxels changed in iteration 1 of unlikely voxel relabeling 14 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6666 voxels changed in iteration 0 of unlikely voxel relabeling 156 voxels changed in iteration 1 of unlikely voxel relabeling 5 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5209 voxels changed in iteration 0 of unlikely voxel relabeling 43 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 4304 voxels changed in iteration 0 of unlikely voxel relabeling 39 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 4059.390878 mri_ca_label stimesec 1.886713 mri_ca_label ru_maxrss 2089808 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 1027184 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 65685 mri_ca_label ru_oublock 404 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 535 mri_ca_label ru_nivcsw 71347 auto-labeling took 67 minutes and 47 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/transforms/cc_up.lta 44538_T1_fs will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/transforms/cc_up.lta reading aseg from /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/aseg.auto_noCCseg.mgz reading norm from /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/norm.mgz 24001 voxels in left wm, 30407 in right wm, xrange [126, 132] searching rotation angles z=[-8 6], y=[-6 8] searching scale 1 Z rot -8.0 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 global minimum found at slice 129.0, rotations (1.12, -0.70) final transformation (x=129.0, yr=1.121, zr=-0.705): 0.99973 0.01230 0.01957 -4.63974; -0.01230 0.99992 -0.00024 18.62330; -0.01957 0.00000 0.99981 12.54684; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 111 118 eigenvectors: 0.00002 -0.00621 0.99998; 0.13779 -0.99044 -0.00615; 0.99046 0.13779 0.00084; writing aseg with callosum to /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/aseg.auto.mgz... corpus callosum segmentation took 0.6 minutes #-------------------------------------- #@# Merge ASeg So 11. Mär 02:49:54 CET 2018 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 So 11. Mär 02:49:54 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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... 557 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 83 (83), valley at 60 (60) csf peak at 40, setting threshold to 68 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 81 (81), valley at 59 (59) csf peak at 37, setting threshold to 66 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 54 seconds. #-------------------------------------------- #@# Mask BFS So 11. Mär 02:53:50 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1621434 voxels in mask (pct= 9.66) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation So 11. Mär 02:53:53 CET 2018 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 (103.0): 103.3 +- 6.0 [79.0 --> 125.0] GM (78.0) : 75.0 +- 13.3 [30.0 --> 95.0] setting bottom of white matter range to 88.3 setting top of gray matter range to 101.7 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... 4111 sparsely connected voxels removed... thickening thin strands.... 20 segments, 2313 filled 280 bright non-wm voxels segmented. 4200 diagonally connected voxels added... white matter segmentation took 2.0 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.63 minutes reading wm segmentation from wm.seg.mgz... 309 voxels added to wm to prevent paths from MTL structures to cortex 3213 additional wm voxels added 0 additional wm voxels added SEG EDIT: 51160 voxels turned on, 98081 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 18 found - 18 modified | TOTAL: 18 pass 2 (xy+): 0 found - 18 modified | TOTAL: 18 pass 1 (xy-): 12 found - 12 modified | TOTAL: 30 pass 2 (xy-): 0 found - 12 modified | TOTAL: 30 pass 1 (yz+): 9 found - 9 modified | TOTAL: 39 pass 2 (yz+): 0 found - 9 modified | TOTAL: 39 pass 1 (yz-): 22 found - 22 modified | TOTAL: 61 pass 2 (yz-): 0 found - 22 modified | TOTAL: 61 pass 1 (xz+): 22 found - 22 modified | TOTAL: 83 pass 2 (xz+): 0 found - 22 modified | TOTAL: 83 pass 1 (xz-): 19 found - 19 modified | TOTAL: 102 pass 2 (xz-): 0 found - 19 modified | TOTAL: 102 Iteration Number : 1 pass 1 (+++): 12 found - 12 modified | TOTAL: 12 pass 2 (+++): 0 found - 12 modified | TOTAL: 12 pass 1 (+++): 8 found - 8 modified | TOTAL: 20 pass 2 (+++): 0 found - 8 modified | TOTAL: 20 pass 1 (+++): 16 found - 16 modified | TOTAL: 36 pass 2 (+++): 0 found - 16 modified | TOTAL: 36 pass 1 (+++): 8 found - 8 modified | TOTAL: 44 pass 2 (+++): 0 found - 8 modified | TOTAL: 44 Iteration Number : 1 pass 1 (++): 57 found - 57 modified | TOTAL: 57 pass 2 (++): 0 found - 57 modified | TOTAL: 57 pass 1 (+-): 62 found - 62 modified | TOTAL: 119 pass 2 (+-): 0 found - 62 modified | TOTAL: 119 pass 1 (--): 65 found - 65 modified | TOTAL: 184 pass 2 (--): 0 found - 65 modified | TOTAL: 184 pass 1 (-+): 58 found - 58 modified | TOTAL: 242 pass 2 (-+): 0 found - 58 modified | TOTAL: 242 Iteration Number : 2 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 1 found - 1 modified | TOTAL: 5 pass 2 (xy-): 0 found - 1 modified | TOTAL: 5 pass 1 (yz+): 3 found - 3 modified | TOTAL: 8 pass 2 (yz+): 0 found - 3 modified | TOTAL: 8 pass 1 (yz-): 5 found - 5 modified | TOTAL: 13 pass 2 (yz-): 0 found - 5 modified | TOTAL: 13 pass 1 (xz+): 4 found - 4 modified | TOTAL: 17 pass 2 (xz+): 0 found - 4 modified | TOTAL: 17 pass 1 (xz-): 3 found - 3 modified | TOTAL: 20 pass 2 (xz-): 0 found - 3 modified | TOTAL: 20 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 0 found - 0 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 1 found - 2 modified | TOTAL: 4 pass 3 (--): 0 found - 2 modified | TOTAL: 4 pass 1 (-+): 3 found - 3 modified | TOTAL: 7 pass 2 (-+): 0 found - 3 modified | TOTAL: 7 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 = 415 (out of 498036: 0.083327) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill So 11. Mär 02:56:32 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 1.07879 0.00120 0.03307 -17.92105; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02309 -4.03522; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.07879 0.00120 0.03307 -17.92105; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02309 -4.03522; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1307 (min = 350, max = 1400), aspect = 0.43 (min = 0.10, max = 0.75) no need to search using seed (125, 106, 93), TAL = (3.0, -35.0, 22.0) talairach voxel to voxel transform 0.92610 -0.00208 -0.02987 16.43368; 0.00095 0.93451 -0.02855 18.97367; 0.02824 0.03405 0.97548 5.13724; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 106, 93) --> (3.0, -35.0, 22.0) done. writing output to filled.mgz... filling took 0.8 minutes talairach cc position changed to (3.00, -35.00, 22.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, -35.00, 22.00) SRC: (112.53, 115.48, 102.49) search lh wm seed point around talairach space (-15.00, -35.00, 22.00), SRC: (145.87, 115.51, 103.50) 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 So 11. Mär 02:57:20 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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+): 2 found - 2 modified | TOTAL: 3 pass 2 (yz+): 0 found - 2 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 2 found - 2 modified | TOTAL: 6 pass 2 (xz+): 0 found - 2 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 239030: 0.003347) 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: 74 vertices, 96 faces slice 50: 3221 vertices, 3379 faces slice 60: 8664 vertices, 8859 faces slice 70: 14411 vertices, 14647 faces slice 80: 22278 vertices, 22580 faces slice 90: 30230 vertices, 30481 faces slice 100: 38630 vertices, 38939 faces slice 110: 48902 vertices, 49267 faces slice 120: 60676 vertices, 61102 faces slice 130: 71788 vertices, 72209 faces slice 140: 81792 vertices, 82186 faces slice 150: 90464 vertices, 90835 faces slice 160: 97908 vertices, 98257 faces slice 170: 104724 vertices, 105040 faces slice 180: 110325 vertices, 110604 faces slice 190: 114494 vertices, 114731 faces slice 200: 116456 vertices, 116587 faces slice 210: 116570 vertices, 116682 faces slice 220: 116570 vertices, 116682 faces slice 230: 116570 vertices, 116682 faces slice 240: 116570 vertices, 116682 faces slice 250: 116570 vertices, 116682 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... 116570 voxel in cpt #1: X=-112 [v=116570,e=350046,f=233364] located at (-27.070541, -11.040696, 6.398181) For the whole surface: X=-112 [v=116570,e=350046,f=233364] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh So 11. Mär 02:57:27 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 5 found - 5 modified | TOTAL: 6 pass 2 (yz+): 0 found - 5 modified | TOTAL: 6 pass 1 (yz-): 0 found - 0 modified | TOTAL: 6 pass 1 (xz+): 1 found - 1 modified | TOTAL: 7 pass 2 (xz+): 0 found - 1 modified | TOTAL: 7 pass 1 (xz-): 2 found - 2 modified | TOTAL: 9 pass 2 (xz-): 0 found - 2 modified | TOTAL: 9 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 = 9 (out of 239442: 0.003759) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 599 vertices, 654 faces slice 50: 3969 vertices, 4123 faces slice 60: 9493 vertices, 9702 faces slice 70: 15914 vertices, 16152 faces slice 80: 24077 vertices, 24427 faces slice 90: 32941 vertices, 33234 faces slice 100: 42233 vertices, 42556 faces slice 110: 53320 vertices, 53730 faces slice 120: 64872 vertices, 65316 faces slice 130: 76142 vertices, 76603 faces slice 140: 86443 vertices, 86848 faces slice 150: 94255 vertices, 94600 faces slice 160: 101033 vertices, 101428 faces slice 170: 107696 vertices, 108019 faces slice 180: 113491 vertices, 113790 faces slice 190: 117516 vertices, 117739 faces slice 200: 119056 vertices, 119195 faces slice 210: 119098 vertices, 119224 faces slice 220: 119098 vertices, 119224 faces slice 230: 119098 vertices, 119224 faces slice 240: 119098 vertices, 119224 faces slice 250: 119098 vertices, 119224 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... 119098 voxel in cpt #1: X=-126 [v=119098,e=357672,f=238448] located at (25.474869, -13.314925, 8.357327) For the whole surface: X=-126 [v=119098,e=357672,f=238448] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh So 11. Mär 02:57:34 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 So 11. Mär 02:57:39 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 So 11. Mär 02:57:44 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 45.1 mm, total surface area = 60913 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.6 minutes step 000: RMS=0.161 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.080 (target=0.015) step 020: RMS=0.070 (target=0.015) step 025: RMS=0.062 (target=0.015) step 030: RMS=0.056 (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=0.046 (target=0.015) step 060: RMS=0.046 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 33.950838 mris_inflate stimesec 0.057991 mris_inflate ru_maxrss 150904 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 20245 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 9227 mris_inflate ru_oublock 8204 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 107 mris_inflate ru_nivcsw 149 #-------------------------------------------- #@# Inflation1 rh So 11. Mär 02:58:18 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 45.0 mm, total surface area = 61692 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.6 minutes step 000: RMS=0.164 (target=0.015) step 005: RMS=0.126 (target=0.015) step 010: RMS=0.097 (target=0.015) step 015: RMS=0.084 (target=0.015) step 020: RMS=0.075 (target=0.015) step 025: RMS=0.067 (target=0.015) step 030: RMS=0.061 (target=0.015) step 035: RMS=0.056 (target=0.015) step 040: RMS=0.054 (target=0.015) step 045: RMS=0.052 (target=0.015) step 050: RMS=0.051 (target=0.015) step 055: RMS=0.050 (target=0.015) step 060: RMS=0.050 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 34.615737 mris_inflate stimesec 0.052991 mris_inflate ru_maxrss 154268 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 20578 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 9406 mris_inflate ru_oublock 8382 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 112 mris_inflate ru_nivcsw 90 #-------------------------------------------- #@# QSphere lh So 11. Mär 02:58:53 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.06 +- 0.61 (0.00-->8.14) (max @ vno 36519 --> 36528) face area 0.03 +- 0.03 (-0.24-->0.94) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.329... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.449, avgs=0 005/300: dt: 0.9000, rms radial error=177.190, avgs=0 010/300: dt: 0.9000, rms radial error=176.632, avgs=0 015/300: dt: 0.9000, rms radial error=175.900, avgs=0 020/300: dt: 0.9000, rms radial error=175.068, avgs=0 025/300: dt: 0.9000, rms radial error=174.177, avgs=0 030/300: dt: 0.9000, rms radial error=173.254, avgs=0 035/300: dt: 0.9000, rms radial error=172.315, avgs=0 040/300: dt: 0.9000, rms radial error=171.369, avgs=0 045/300: dt: 0.9000, rms radial error=170.421, avgs=0 050/300: dt: 0.9000, rms radial error=169.473, avgs=0 055/300: dt: 0.9000, rms radial error=168.526, avgs=0 060/300: dt: 0.9000, rms radial error=167.584, avgs=0 065/300: dt: 0.9000, rms radial error=166.646, avgs=0 070/300: dt: 0.9000, rms radial error=165.713, avgs=0 075/300: dt: 0.9000, rms radial error=164.784, avgs=0 080/300: dt: 0.9000, rms radial error=163.860, avgs=0 085/300: dt: 0.9000, rms radial error=162.941, avgs=0 090/300: dt: 0.9000, rms radial error=162.027, avgs=0 095/300: dt: 0.9000, rms radial error=161.117, avgs=0 100/300: dt: 0.9000, rms radial error=160.212, avgs=0 105/300: dt: 0.9000, rms radial error=159.312, avgs=0 110/300: dt: 0.9000, rms radial error=158.417, avgs=0 115/300: dt: 0.9000, rms radial error=157.526, avgs=0 120/300: dt: 0.9000, rms radial error=156.641, avgs=0 125/300: dt: 0.9000, rms radial error=155.760, avgs=0 130/300: dt: 0.9000, rms radial error=154.884, avgs=0 135/300: dt: 0.9000, rms radial error=154.013, avgs=0 140/300: dt: 0.9000, rms radial error=153.147, avgs=0 145/300: dt: 0.9000, rms radial error=152.285, avgs=0 150/300: dt: 0.9000, rms radial error=151.428, avgs=0 155/300: dt: 0.9000, rms radial error=150.576, avgs=0 160/300: dt: 0.9000, rms radial error=149.729, avgs=0 165/300: dt: 0.9000, rms radial error=148.886, avgs=0 170/300: dt: 0.9000, rms radial error=148.047, avgs=0 175/300: dt: 0.9000, rms radial error=147.214, avgs=0 180/300: dt: 0.9000, rms radial error=146.384, avgs=0 185/300: dt: 0.9000, rms radial error=145.560, avgs=0 190/300: dt: 0.9000, rms radial error=144.739, avgs=0 195/300: dt: 0.9000, rms radial error=143.924, avgs=0 200/300: dt: 0.9000, rms radial error=143.112, avgs=0 205/300: dt: 0.9000, rms radial error=142.306, avgs=0 210/300: dt: 0.9000, rms radial error=141.503, avgs=0 215/300: dt: 0.9000, rms radial error=140.705, avgs=0 220/300: dt: 0.9000, rms radial error=139.912, avgs=0 225/300: dt: 0.9000, rms radial error=139.123, avgs=0 230/300: dt: 0.9000, rms radial error=138.338, avgs=0 235/300: dt: 0.9000, rms radial error=137.558, avgs=0 240/300: dt: 0.9000, rms radial error=136.782, avgs=0 245/300: dt: 0.9000, rms radial error=136.010, avgs=0 250/300: dt: 0.9000, rms radial error=135.243, avgs=0 255/300: dt: 0.9000, rms radial error=134.480, avgs=0 260/300: dt: 0.9000, rms radial error=133.721, avgs=0 265/300: dt: 0.9000, rms radial error=132.966, avgs=0 270/300: dt: 0.9000, rms radial error=132.216, avgs=0 275/300: dt: 0.9000, rms radial error=131.470, avgs=0 280/300: dt: 0.9000, rms radial error=130.728, avgs=0 285/300: dt: 0.9000, rms radial error=129.990, avgs=0 290/300: dt: 0.9000, rms radial error=129.256, avgs=0 295/300: dt: 0.9000, rms radial error=128.526, avgs=0 300/300: dt: 0.9000, rms radial error=127.801, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 13400.01 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 2 (K=40.0), pass 1, starting sse = 2168.74 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00036 epoch 3 (K=160.0), pass 1, starting sse = 224.94 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00471 epoch 4 (K=640.0), pass 1, starting sse = 20.13 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/15 = 0.00660 final distance error %26.25 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.06 hours mris_sphere utimesec 225.310747 mris_sphere stimesec 0.067989 mris_sphere ru_maxrss 151100 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 20289 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 9228 mris_sphere ru_oublock 8205 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 108 mris_sphere ru_nivcsw 4150 FSRUNTIME@ mris_sphere 0.0627 hours 1 threads #-------------------------------------------- #@# QSphere rh So 11. Mär 03:02:39 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.05 +- 0.61 (0.00-->7.68) (max @ vno 40990 --> 41903) face area 0.03 +- 0.03 (-0.14-->0.67) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.328... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.310, avgs=0 005/300: dt: 0.9000, rms radial error=177.049, avgs=0 010/300: dt: 0.9000, rms radial error=176.491, avgs=0 015/300: dt: 0.9000, rms radial error=175.758, avgs=0 020/300: dt: 0.9000, rms radial error=174.923, avgs=0 025/300: dt: 0.9000, rms radial error=174.031, avgs=0 030/300: dt: 0.9000, rms radial error=173.106, avgs=0 035/300: dt: 0.9000, rms radial error=172.170, avgs=0 040/300: dt: 0.9000, rms radial error=171.226, avgs=0 045/300: dt: 0.9000, rms radial error=170.280, avgs=0 050/300: dt: 0.9000, rms radial error=169.334, avgs=0 055/300: dt: 0.9000, rms radial error=168.390, avgs=0 060/300: dt: 0.9000, rms radial error=167.450, avgs=0 065/300: dt: 0.9000, rms radial error=166.514, avgs=0 070/300: dt: 0.9000, rms radial error=165.583, avgs=0 075/300: dt: 0.9000, rms radial error=164.657, avgs=0 080/300: dt: 0.9000, rms radial error=163.735, avgs=0 085/300: dt: 0.9000, rms radial error=162.818, avgs=0 090/300: dt: 0.9000, rms radial error=161.907, avgs=0 095/300: dt: 0.9000, rms radial error=160.999, avgs=0 100/300: dt: 0.9000, rms radial error=160.097, avgs=0 105/300: dt: 0.9000, rms radial error=159.200, avgs=0 110/300: dt: 0.9000, rms radial error=158.307, avgs=0 115/300: dt: 0.9000, rms radial error=157.419, avgs=0 120/300: dt: 0.9000, rms radial error=156.535, avgs=0 125/300: dt: 0.9000, rms radial error=155.657, avgs=0 130/300: dt: 0.9000, rms radial error=154.783, avgs=0 135/300: dt: 0.9000, rms radial error=153.914, avgs=0 140/300: dt: 0.9000, rms radial error=153.049, avgs=0 145/300: dt: 0.9000, rms radial error=152.189, avgs=0 150/300: dt: 0.9000, rms radial error=151.333, avgs=0 155/300: dt: 0.9000, rms radial error=150.482, avgs=0 160/300: dt: 0.9000, rms radial error=149.636, avgs=0 165/300: dt: 0.9000, rms radial error=148.795, avgs=0 170/300: dt: 0.9000, rms radial error=147.957, avgs=0 175/300: dt: 0.9000, rms radial error=147.125, avgs=0 180/300: dt: 0.9000, rms radial error=146.296, avgs=0 185/300: dt: 0.9000, rms radial error=145.473, avgs=0 190/300: dt: 0.9000, rms radial error=144.654, avgs=0 195/300: dt: 0.9000, rms radial error=143.839, avgs=0 200/300: dt: 0.9000, rms radial error=143.029, avgs=0 205/300: dt: 0.9000, rms radial error=142.223, avgs=0 210/300: dt: 0.9000, rms radial error=141.421, avgs=0 215/300: dt: 0.9000, rms radial error=140.624, avgs=0 220/300: dt: 0.9000, rms radial error=139.832, avgs=0 225/300: dt: 0.9000, rms radial error=139.044, avgs=0 230/300: dt: 0.9000, rms radial error=138.260, avgs=0 235/300: dt: 0.9000, rms radial error=137.480, avgs=0 240/300: dt: 0.9000, rms radial error=136.705, avgs=0 245/300: dt: 0.9000, rms radial error=135.935, avgs=0 250/300: dt: 0.9000, rms radial error=135.168, avgs=0 255/300: dt: 0.9000, rms radial error=134.406, avgs=0 260/300: dt: 0.9000, rms radial error=133.648, avgs=0 265/300: dt: 0.9000, rms radial error=132.894, avgs=0 270/300: dt: 0.9000, rms radial error=132.144, avgs=0 275/300: dt: 0.9000, rms radial error=131.399, avgs=0 280/300: dt: 0.9000, rms radial error=130.657, avgs=0 285/300: dt: 0.9000, rms radial error=129.920, avgs=0 290/300: dt: 0.9000, rms radial error=129.187, avgs=0 295/300: dt: 0.9000, rms radial error=128.458, avgs=0 300/300: dt: 0.9000, rms radial error=127.734, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 13739.31 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 = 2242.42 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00022 epoch 3 (K=160.0), pass 1, starting sse = 238.20 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/11 = 0.00919 epoch 4 (K=640.0), pass 1, starting sse = 18.70 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/15 = 0.00703 final distance error %26.33 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.06 hours mris_sphere utimesec 229.686082 mris_sphere stimesec 0.077988 mris_sphere ru_maxrss 154460 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 20618 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 9407 mris_sphere ru_oublock 8383 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 113 mris_sphere ru_nivcsw 3257 FSRUNTIME@ mris_sphere 0.0639 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh So 11. Mär 03:06:29 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh So 11. Mär 03:06:29 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh So 11. Mär 03:06:29 CET 2018 mris_fix_topology -rusage /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 44538_T1_fs 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=-112 (nv=116570, nf=233364, ne=350046, g=57) 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... 7287 ambiguous faces found in tessellation segmenting defects... 55 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 1 into 0 -merging segment 17 into 15 -merging segment 26 into 25 -merging segment 33 into 29 -merging segment 48 into 35 50 defects to be corrected 0 vertices coincident reading input surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.5789 (-4.2894) -vertex loglikelihood: -5.7030 (-2.8515) -normal dot loglikelihood: -3.6596 (-3.6596) -quad curv loglikelihood: -6.5181 (-3.2590) Total Loglikelihood : -24.4595 CORRECTING DEFECT 0 (vertices=451, convex hull=220, v0=9498) After retessellation of defect 0 (v0=9498), euler #=-49 (112176,334768,222543) : difference with theory (-47) = 2 CORRECTING DEFECT 1 (vertices=25, convex hull=54, v0=13773) After retessellation of defect 1 (v0=13773), euler #=-48 (112185,334814,222581) : difference with theory (-46) = 2 CORRECTING DEFECT 2 (vertices=5, convex hull=21, v0=16420) After retessellation of defect 2 (v0=16420), euler #=-47 (112185,334818,222586) : difference with theory (-45) = 2 CORRECTING DEFECT 3 (vertices=46, convex hull=90, v0=22030) After retessellation of defect 3 (v0=22030), euler #=-46 (112212,334934,222676) : difference with theory (-44) = 2 CORRECTING DEFECT 4 (vertices=52, convex hull=72, v0=24755) After retessellation of defect 4 (v0=24755), euler #=-45 (112231,335023,222747) : difference with theory (-43) = 2 CORRECTING DEFECT 5 (vertices=24, convex hull=58, v0=27117) After retessellation of defect 5 (v0=27117), euler #=-44 (112243,335080,222793) : difference with theory (-42) = 2 CORRECTING DEFECT 6 (vertices=27, convex hull=74, v0=28083) After retessellation of defect 6 (v0=28083), euler #=-43 (112257,335152,222852) : difference with theory (-41) = 2 CORRECTING DEFECT 7 (vertices=27, convex hull=73, v0=30997) After retessellation of defect 7 (v0=30997), euler #=-42 (112274,335229,222913) : difference with theory (-40) = 2 CORRECTING DEFECT 8 (vertices=26, convex hull=66, v0=32386) After retessellation of defect 8 (v0=32386), euler #=-41 (112290,335302,222971) : difference with theory (-39) = 2 CORRECTING DEFECT 9 (vertices=81, convex hull=102, v0=33852) After retessellation of defect 9 (v0=33852), euler #=-40 (112347,335517,223130) : difference with theory (-38) = 2 CORRECTING DEFECT 10 (vertices=20, convex hull=51, v0=35186) After retessellation of defect 10 (v0=35186), euler #=-39 (112358,335568,223171) : difference with theory (-37) = 2 CORRECTING DEFECT 11 (vertices=202, convex hull=206, v0=38272) After retessellation of defect 11 (v0=38272), euler #=-40 (112389,335787,223358) : difference with theory (-36) = 4 CORRECTING DEFECT 12 (vertices=22, convex hull=50, v0=39613) After retessellation of defect 12 (v0=39613), euler #=-39 (112399,335834,223396) : difference with theory (-35) = 4 CORRECTING DEFECT 13 (vertices=24, convex hull=64, v0=41624) After retessellation of defect 13 (v0=41624), euler #=-38 (112415,335910,223457) : difference with theory (-34) = 4 CORRECTING DEFECT 14 (vertices=110, convex hull=89, v0=42126) After retessellation of defect 14 (v0=42126), euler #=-36 (112443,336036,223557) : difference with theory (-33) = 3 CORRECTING DEFECT 15 (vertices=44, convex hull=84, v0=44378) After retessellation of defect 15 (v0=44378), euler #=-35 (112472,336163,223656) : difference with theory (-32) = 3 CORRECTING DEFECT 16 (vertices=56, convex hull=96, v0=47932) After retessellation of defect 16 (v0=47932), euler #=-34 (112493,336261,223734) : difference with theory (-31) = 3 CORRECTING DEFECT 17 (vertices=31, convex hull=70, v0=48889) After retessellation of defect 17 (v0=48889), euler #=-33 (112514,336351,223804) : difference with theory (-30) = 3 CORRECTING DEFECT 18 (vertices=60, convex hull=85, v0=50311) After retessellation of defect 18 (v0=50311), euler #=-32 (112548,336491,223911) : difference with theory (-29) = 3 CORRECTING DEFECT 19 (vertices=49, convex hull=78, v0=67191) After retessellation of defect 19 (v0=67191), euler #=-31 (112566,336575,223978) : difference with theory (-28) = 3 CORRECTING DEFECT 20 (vertices=30, convex hull=56, v0=69241) After retessellation of defect 20 (v0=69241), euler #=-30 (112584,336647,224033) : difference with theory (-27) = 3 CORRECTING DEFECT 21 (vertices=266, convex hull=90, v0=69277) After retessellation of defect 21 (v0=69277), euler #=-29 (112601,336736,224106) : difference with theory (-26) = 3 CORRECTING DEFECT 22 (vertices=27, convex hull=55, v0=70967) After retessellation of defect 22 (v0=70967), euler #=-28 (112610,336784,224146) : difference with theory (-25) = 3 CORRECTING DEFECT 23 (vertices=73, convex hull=112, v0=72695) After retessellation of defect 23 (v0=72695), euler #=-26 (112635,336912,224251) : difference with theory (-24) = 2 CORRECTING DEFECT 24 (vertices=34, convex hull=66, v0=72785) After retessellation of defect 24 (v0=72785), euler #=-25 (112644,336964,224295) : difference with theory (-23) = 2 CORRECTING DEFECT 25 (vertices=29, convex hull=28, v0=75347) After retessellation of defect 25 (v0=75347), euler #=-24 (112649,336988,224315) : difference with theory (-22) = 2 CORRECTING DEFECT 26 (vertices=139, convex hull=148, v0=76821) After retessellation of defect 26 (v0=76821), euler #=-22 (112702,337213,224489) : difference with theory (-21) = 1 CORRECTING DEFECT 27 (vertices=69, convex hull=82, v0=77798) After retessellation of defect 27 (v0=77798), euler #=-21 (112716,337292,224555) : difference with theory (-20) = 1 CORRECTING DEFECT 28 (vertices=38, convex hull=82, v0=77961) After retessellation of defect 28 (v0=77961), euler #=-20 (112739,337395,224636) : difference with theory (-19) = 1 CORRECTING DEFECT 29 (vertices=66, convex hull=82, v0=78820) After retessellation of defect 29 (v0=78820), euler #=-19 (112752,337473,224702) : difference with theory (-18) = 1 CORRECTING DEFECT 30 (vertices=97, convex hull=144, v0=79491) After retessellation of defect 30 (v0=79491), euler #=-18 (112807,337707,224882) : difference with theory (-17) = 1 CORRECTING DEFECT 31 (vertices=913, convex hull=402, v0=80466) L defect detected... After retessellation of defect 31 (v0=80466), euler #=-16 (113038,338604,225550) : difference with theory (-16) = 0 CORRECTING DEFECT 32 (vertices=39, convex hull=64, v0=82429) After retessellation of defect 32 (v0=82429), euler #=-15 (113060,338695,225620) : difference with theory (-15) = 0 CORRECTING DEFECT 33 (vertices=515, convex hull=116, v0=82717) After retessellation of defect 33 (v0=82717), euler #=-14 (113109,338895,225772) : difference with theory (-14) = 0 CORRECTING DEFECT 34 (vertices=25, convex hull=53, v0=84156) After retessellation of defect 34 (v0=84156), euler #=-13 (113121,338947,225813) : difference with theory (-13) = 0 CORRECTING DEFECT 35 (vertices=26, convex hull=30, v0=85122) After retessellation of defect 35 (v0=85122), euler #=-12 (113126,338970,225832) : difference with theory (-12) = 0 CORRECTING DEFECT 36 (vertices=81, convex hull=118, v0=86057) After retessellation of defect 36 (v0=86057), euler #=-11 (113158,339118,225949) : difference with theory (-11) = 0 CORRECTING DEFECT 37 (vertices=72, convex hull=55, v0=89505) After retessellation of defect 37 (v0=89505), euler #=-10 (113182,339218,226026) : difference with theory (-10) = 0 CORRECTING DEFECT 38 (vertices=23, convex hull=55, v0=89529) After retessellation of defect 38 (v0=89529), euler #=-9 (113194,339275,226072) : difference with theory (-9) = 0 CORRECTING DEFECT 39 (vertices=162, convex hull=117, v0=89570) After retessellation of defect 39 (v0=89570), euler #=-8 (113216,339392,226168) : difference with theory (-8) = 0 CORRECTING DEFECT 40 (vertices=19, convex hull=40, v0=92637) After retessellation of defect 40 (v0=92637), euler #=-7 (113226,339440,226207) : difference with theory (-7) = 0 CORRECTING DEFECT 41 (vertices=37, convex hull=81, v0=92747) After retessellation of defect 41 (v0=92747), euler #=-6 (113246,339537,226285) : difference with theory (-6) = 0 CORRECTING DEFECT 42 (vertices=41, convex hull=68, v0=94447) After retessellation of defect 42 (v0=94447), euler #=-5 (113266,339623,226352) : difference with theory (-5) = 0 CORRECTING DEFECT 43 (vertices=41, convex hull=65, v0=94616) After retessellation of defect 43 (v0=94616), euler #=-4 (113288,339717,226425) : difference with theory (-4) = 0 CORRECTING DEFECT 44 (vertices=21, convex hull=57, v0=96255) After retessellation of defect 44 (v0=96255), euler #=-3 (113297,339761,226461) : difference with theory (-3) = 0 CORRECTING DEFECT 45 (vertices=25, convex hull=58, v0=103345) After retessellation of defect 45 (v0=103345), euler #=-2 (113313,339830,226515) : difference with theory (-2) = 0 CORRECTING DEFECT 46 (vertices=29, convex hull=67, v0=103567) After retessellation of defect 46 (v0=103567), euler #=-1 (113326,339892,226565) : difference with theory (-1) = 0 CORRECTING DEFECT 47 (vertices=55, convex hull=95, v0=108371) After retessellation of defect 47 (v0=108371), euler #=0 (113354,340017,226663) : difference with theory (0) = 0 CORRECTING DEFECT 48 (vertices=68, convex hull=70, v0=111922) After retessellation of defect 48 (v0=111922), euler #=1 (113370,340094,226725) : difference with theory (1) = 0 CORRECTING DEFECT 49 (vertices=29, convex hull=29, v0=116466) After retessellation of defect 49 (v0=116466), euler #=2 (113373,340113,226742) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.25 (0.05-->10.86) (max @ vno 94371 --> 95841) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.25 (0.05-->10.86) (max @ vno 94371 --> 95841) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 141 mutations (31.8%), 303 crossovers (68.2%), 390 vertices were eliminated building final representation... 3197 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=113373, nf=226742, ne=340113, g=0) writing corrected surface to /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 37.9 minutes 0 defective edges removing intersecting faces 000: 374 intersecting 001: 34 intersecting mris_fix_topology utimesec 2268.860080 mris_fix_topology stimesec 0.149977 mris_fix_topology ru_maxrss 375728 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 51803 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 20625 mris_fix_topology ru_oublock 10704 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 340 mris_fix_topology ru_nivcsw 35452 FSRUNTIME@ mris_fix_topology lh 0.6311 hours 1 threads #@# Fix Topology rh So 11. Mär 03:44:21 CET 2018 mris_fix_topology -rusage /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 44538_T1_fs 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=-126 (nv=119098, nf=238448, ne=357672, g=64) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 7083 ambiguous faces found in tessellation segmenting defects... 72 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 26 into 23 -merging segment 60 into 55 70 defects to be corrected 0 vertices coincident reading input surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.7438 (-4.3719) -vertex loglikelihood: -5.7032 (-2.8516) -normal dot loglikelihood: -3.5985 (-3.5985) -quad curv loglikelihood: -6.5320 (-3.2660) Total Loglikelihood : -24.5775 CORRECTING DEFECT 0 (vertices=28, convex hull=57, v0=5006) After retessellation of defect 0 (v0=5006), euler #=-68 (114712,342170,227390) : difference with theory (-67) = 1 CORRECTING DEFECT 1 (vertices=51, convex hull=82, v0=10777) After retessellation of defect 1 (v0=10777), euler #=-67 (114733,342268,227468) : difference with theory (-66) = 1 CORRECTING DEFECT 2 (vertices=75, convex hull=51, v0=11241) After retessellation of defect 2 (v0=11241), euler #=-66 (114744,342322,227512) : difference with theory (-65) = 1 CORRECTING DEFECT 3 (vertices=25, convex hull=53, v0=12710) After retessellation of defect 3 (v0=12710), euler #=-65 (114755,342376,227556) : difference with theory (-64) = 1 CORRECTING DEFECT 4 (vertices=41, convex hull=88, v0=15934) After retessellation of defect 4 (v0=15934), euler #=-64 (114781,342492,227647) : difference with theory (-63) = 1 CORRECTING DEFECT 5 (vertices=45, convex hull=45, v0=16073) After retessellation of defect 5 (v0=16073), euler #=-63 (114793,342547,227691) : difference with theory (-62) = 1 CORRECTING DEFECT 6 (vertices=63, convex hull=98, v0=16118) After retessellation of defect 6 (v0=16118), euler #=-62 (114830,342700,227808) : difference with theory (-61) = 1 CORRECTING DEFECT 7 (vertices=153, convex hull=56, v0=17060) After retessellation of defect 7 (v0=17060), euler #=-61 (114845,342772,227866) : difference with theory (-60) = 1 CORRECTING DEFECT 8 (vertices=67, convex hull=77, v0=17585) After retessellation of defect 8 (v0=17585), euler #=-60 (114879,342903,227964) : difference with theory (-59) = 1 CORRECTING DEFECT 9 (vertices=52, convex hull=111, v0=17955) After retessellation of defect 9 (v0=17955), euler #=-59 (114897,343004,228048) : difference with theory (-58) = 1 CORRECTING DEFECT 10 (vertices=29, convex hull=84, v0=19486) After retessellation of defect 10 (v0=19486), euler #=-58 (114906,343067,228103) : difference with theory (-57) = 1 CORRECTING DEFECT 11 (vertices=27, convex hull=52, v0=20445) After retessellation of defect 11 (v0=20445), euler #=-57 (114918,343124,228149) : difference with theory (-56) = 1 CORRECTING DEFECT 12 (vertices=5, convex hull=21, v0=23835) After retessellation of defect 12 (v0=23835), euler #=-56 (114918,343130,228156) : difference with theory (-55) = 1 CORRECTING DEFECT 13 (vertices=45, convex hull=75, v0=23883) After retessellation of defect 13 (v0=23883), euler #=-55 (114946,343244,228243) : difference with theory (-54) = 1 CORRECTING DEFECT 14 (vertices=40, convex hull=69, v0=28952) After retessellation of defect 14 (v0=28952), euler #=-54 (114966,343330,228310) : difference with theory (-53) = 1 CORRECTING DEFECT 15 (vertices=34, convex hull=62, v0=32564) After retessellation of defect 15 (v0=32564), euler #=-53 (114986,343415,228376) : difference with theory (-52) = 1 CORRECTING DEFECT 16 (vertices=78, convex hull=88, v0=32959) After retessellation of defect 16 (v0=32959), euler #=-52 (115023,343565,228490) : difference with theory (-51) = 1 CORRECTING DEFECT 17 (vertices=29, convex hull=69, v0=33089) After retessellation of defect 17 (v0=33089), euler #=-51 (115043,343652,228558) : difference with theory (-50) = 1 CORRECTING DEFECT 18 (vertices=26, convex hull=66, v0=34074) After retessellation of defect 18 (v0=34074), euler #=-50 (115054,343713,228609) : difference with theory (-49) = 1 CORRECTING DEFECT 19 (vertices=20, convex hull=58, v0=36931) After retessellation of defect 19 (v0=36931), euler #=-49 (115068,343779,228662) : difference with theory (-48) = 1 CORRECTING DEFECT 20 (vertices=151, convex hull=159, v0=40114) After retessellation of defect 20 (v0=40114), euler #=-48 (115078,343880,228754) : difference with theory (-47) = 1 CORRECTING DEFECT 21 (vertices=7, convex hull=29, v0=41119) After retessellation of defect 21 (v0=41119), euler #=-47 (115082,343899,228770) : difference with theory (-46) = 1 CORRECTING DEFECT 22 (vertices=32, convex hull=87, v0=41365) After retessellation of defect 22 (v0=41365), euler #=-46 (115105,344000,228849) : difference with theory (-45) = 1 CORRECTING DEFECT 23 (vertices=63, convex hull=81, v0=44109) After retessellation of defect 23 (v0=44109), euler #=-44 (115115,344065,228906) : difference with theory (-44) = 0 CORRECTING DEFECT 24 (vertices=11, convex hull=38, v0=45258) After retessellation of defect 24 (v0=45258), euler #=-43 (115117,344088,228928) : difference with theory (-43) = 0 CORRECTING DEFECT 25 (vertices=8, convex hull=29, v0=45945) After retessellation of defect 25 (v0=45945), euler #=-42 (115119,344103,228942) : difference with theory (-42) = 0 CORRECTING DEFECT 26 (vertices=7, convex hull=17, v0=48365) After retessellation of defect 26 (v0=48365), euler #=-41 (115120,344109,228948) : difference with theory (-41) = 0 CORRECTING DEFECT 27 (vertices=32, convex hull=59, v0=51498) After retessellation of defect 27 (v0=51498), euler #=-40 (115137,344183,229006) : difference with theory (-40) = 0 CORRECTING DEFECT 28 (vertices=24, convex hull=65, v0=51679) After retessellation of defect 28 (v0=51679), euler #=-39 (115153,344261,229069) : difference with theory (-39) = 0 CORRECTING DEFECT 29 (vertices=27, convex hull=51, v0=61602) After retessellation of defect 29 (v0=61602), euler #=-38 (115167,344322,229117) : difference with theory (-38) = 0 CORRECTING DEFECT 30 (vertices=105, convex hull=85, v0=63776) After retessellation of defect 30 (v0=63776), euler #=-37 (115177,344384,229170) : difference with theory (-37) = 0 CORRECTING DEFECT 31 (vertices=9, convex hull=23, v0=65578) After retessellation of defect 31 (v0=65578), euler #=-36 (115178,344393,229179) : difference with theory (-36) = 0 CORRECTING DEFECT 32 (vertices=20, convex hull=44, v0=68809) After retessellation of defect 32 (v0=68809), euler #=-35 (115187,344435,229213) : difference with theory (-35) = 0 CORRECTING DEFECT 33 (vertices=35, convex hull=76, v0=68873) After retessellation of defect 33 (v0=68873), euler #=-34 (115208,344531,229289) : difference with theory (-34) = 0 CORRECTING DEFECT 34 (vertices=460, convex hull=81, v0=69399) After retessellation of defect 34 (v0=69399), euler #=-34 (115217,344603,229352) : difference with theory (-33) = 1 CORRECTING DEFECT 35 (vertices=68, convex hull=103, v0=69594) After retessellation of defect 35 (v0=69594), euler #=-33 (115253,344756,229470) : difference with theory (-32) = 1 CORRECTING DEFECT 36 (vertices=13, convex hull=32, v0=71545) After retessellation of defect 36 (v0=71545), euler #=-32 (115258,344784,229494) : difference with theory (-31) = 1 CORRECTING DEFECT 37 (vertices=45, convex hull=97, v0=71880) After retessellation of defect 37 (v0=71880), euler #=-31 (115275,344875,229569) : difference with theory (-30) = 1 CORRECTING DEFECT 38 (vertices=80, convex hull=133, v0=72473) After retessellation of defect 38 (v0=72473), euler #=-30 (115324,345084,229730) : difference with theory (-29) = 1 CORRECTING DEFECT 39 (vertices=39, convex hull=66, v0=74456) After retessellation of defect 39 (v0=74456), euler #=-29 (115341,345160,229790) : difference with theory (-28) = 1 CORRECTING DEFECT 40 (vertices=176, convex hull=207, v0=74567) After retessellation of defect 40 (v0=74567), euler #=-28 (115371,345351,229952) : difference with theory (-27) = 1 CORRECTING DEFECT 41 (vertices=21, convex hull=21, v0=74917) After retessellation of defect 41 (v0=74917), euler #=-27 (115374,345365,229964) : difference with theory (-26) = 1 CORRECTING DEFECT 42 (vertices=425, convex hull=150, v0=78375) After retessellation of defect 42 (v0=78375), euler #=-26 (115448,345655,230181) : difference with theory (-25) = 1 CORRECTING DEFECT 43 (vertices=51, convex hull=71, v0=79427) After retessellation of defect 43 (v0=79427), euler #=-25 (115472,345759,230262) : difference with theory (-24) = 1 CORRECTING DEFECT 44 (vertices=6, convex hull=16, v0=81382) After retessellation of defect 44 (v0=81382), euler #=-24 (115474,345767,230269) : difference with theory (-23) = 1 CORRECTING DEFECT 45 (vertices=29, convex hull=60, v0=82618) After retessellation of defect 45 (v0=82618), euler #=-23 (115483,345817,230311) : difference with theory (-22) = 1 CORRECTING DEFECT 46 (vertices=30, convex hull=23, v0=83057) After retessellation of defect 46 (v0=83057), euler #=-22 (115487,345834,230325) : difference with theory (-21) = 1 CORRECTING DEFECT 47 (vertices=33, convex hull=39, v0=83334) After retessellation of defect 47 (v0=83334), euler #=-21 (115498,345877,230358) : difference with theory (-20) = 1 CORRECTING DEFECT 48 (vertices=29, convex hull=69, v0=85485) After retessellation of defect 48 (v0=85485), euler #=-20 (115516,345958,230422) : difference with theory (-19) = 1 CORRECTING DEFECT 49 (vertices=119, convex hull=59, v0=86260) After retessellation of defect 49 (v0=86260), euler #=-19 (115524,346006,230463) : difference with theory (-18) = 1 CORRECTING DEFECT 50 (vertices=27, convex hull=57, v0=87488) After retessellation of defect 50 (v0=87488), euler #=-18 (115535,346062,230509) : difference with theory (-17) = 1 CORRECTING DEFECT 51 (vertices=80, convex hull=108, v0=88274) After retessellation of defect 51 (v0=88274), euler #=-17 (115577,346238,230644) : difference with theory (-16) = 1 CORRECTING DEFECT 52 (vertices=73, convex hull=67, v0=88583) After retessellation of defect 52 (v0=88583), euler #=-16 (115591,346308,230701) : difference with theory (-15) = 1 CORRECTING DEFECT 53 (vertices=21, convex hull=68, v0=89942) After retessellation of defect 53 (v0=89942), euler #=-15 (115600,346361,230746) : difference with theory (-14) = 1 CORRECTING DEFECT 54 (vertices=110, convex hull=95, v0=91440) After retessellation of defect 54 (v0=91440), euler #=-13 (115626,346478,230839) : difference with theory (-13) = 0 CORRECTING DEFECT 55 (vertices=26, convex hull=60, v0=92123) After retessellation of defect 55 (v0=92123), euler #=-12 (115638,346537,230887) : difference with theory (-12) = 0 CORRECTING DEFECT 56 (vertices=60, convex hull=95, v0=92178) After retessellation of defect 56 (v0=92178), euler #=-11 (115662,346651,230978) : difference with theory (-11) = 0 CORRECTING DEFECT 57 (vertices=61, convex hull=45, v0=92887) After retessellation of defect 57 (v0=92887), euler #=-10 (115673,346701,231018) : difference with theory (-10) = 0 CORRECTING DEFECT 58 (vertices=139, convex hull=122, v0=93455) After retessellation of defect 58 (v0=93455), euler #=-9 (115715,346879,231155) : difference with theory (-9) = 0 CORRECTING DEFECT 59 (vertices=61, convex hull=75, v0=99348) After retessellation of defect 59 (v0=99348), euler #=-8 (115741,346988,231239) : difference with theory (-8) = 0 CORRECTING DEFECT 60 (vertices=364, convex hull=63, v0=101005) After retessellation of defect 60 (v0=101005), euler #=-7 (115774,347112,231331) : difference with theory (-7) = 0 CORRECTING DEFECT 61 (vertices=27, convex hull=73, v0=106238) After retessellation of defect 61 (v0=106238), euler #=-6 (115790,347184,231388) : difference with theory (-6) = 0 CORRECTING DEFECT 62 (vertices=28, convex hull=57, v0=107005) After retessellation of defect 62 (v0=107005), euler #=-5 (115806,347255,231444) : difference with theory (-5) = 0 CORRECTING DEFECT 63 (vertices=30, convex hull=65, v0=107243) After retessellation of defect 63 (v0=107243), euler #=-4 (115821,347327,231502) : difference with theory (-4) = 0 CORRECTING DEFECT 64 (vertices=43, convex hull=87, v0=109160) After retessellation of defect 64 (v0=109160), euler #=-3 (115850,347450,231597) : difference with theory (-3) = 0 CORRECTING DEFECT 65 (vertices=40, convex hull=51, v0=110148) After retessellation of defect 65 (v0=110148), euler #=-2 (115861,347502,231639) : difference with theory (-2) = 0 CORRECTING DEFECT 66 (vertices=6, convex hull=23, v0=114840) After retessellation of defect 66 (v0=114840), euler #=-1 (115862,347511,231648) : difference with theory (-1) = 0 CORRECTING DEFECT 67 (vertices=46, convex hull=40, v0=115295) After retessellation of defect 67 (v0=115295), euler #=0 (115868,347545,231677) : difference with theory (0) = 0 CORRECTING DEFECT 68 (vertices=34, convex hull=59, v0=117163) After retessellation of defect 68 (v0=117163), euler #=1 (115883,347611,231729) : difference with theory (1) = 0 CORRECTING DEFECT 69 (vertices=35, convex hull=90, v0=117804) After retessellation of defect 69 (v0=117804), euler #=2 (115906,347712,231808) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.25 (0.08-->11.26) (max @ vno 89536 --> 93903) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.25 (0.08-->11.26) (max @ vno 89536 --> 93903) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 214 mutations (34.1%), 413 crossovers (65.9%), 267 vertices were eliminated building final representation... 3192 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=115906, nf=231808, ne=347712, g=0) writing corrected surface to /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 37.5 minutes 0 defective edges removing intersecting faces 000: 399 intersecting 001: 19 intersecting mris_fix_topology utimesec 2248.518173 mris_fix_topology stimesec 0.244962 mris_fix_topology ru_maxrss 379088 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 50682 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 20804 mris_fix_topology ru_oublock 10942 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 299 mris_fix_topology ru_nivcsw 87105 FSRUNTIME@ mris_fix_topology rh 0.6257 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 113373 - 340113 + 226742 = 2 --> 0 holes F =2V-4: 226742 = 226746-4 (0) 2E=3F: 680226 = 680226 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 115906 - 347712 + 231808 = 2 --> 0 holes F =2V-4: 231808 = 231812-4 (0) 2E=3F: 695424 = 695424 (0) total defect index = 0 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 17 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 28 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh So 11. Mär 04:22:03 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/filled.mgz... reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/brain.finalsurfs.mgz... reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/../mri/aseg.presurf.mgz... reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/wm.mgz... 17245 bright wm thresholded. 350 bright non-wm voxels segmented. reading original surface position from /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.orig... computing class statistics... border white: 216839 voxels (1.29%) border gray 244104 voxels (1.45%) WM (102.0): 102.3 +- 5.8 [70.0 --> 110.0] GM (85.0) : 83.8 +- 10.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 72.5 (was 70) setting MAX_BORDER_WHITE to 110.8 (was 105) setting MIN_BORDER_WHITE to 83.0 (was 85) setting MAX_CSF to 62.0 (was 40) setting MAX_GRAY to 99.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 72.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 51.5 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.23 (0.03-->3.97) (max @ vno 11117 --> 112118) face area 0.28 +- 0.13 (0.00-->3.23) mean absolute distance = 0.81 +- 1.02 3290 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-5.2, GM=83+-6.1 mean inside = 99.1, mean outside = 87.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=90.4, 64 (64) missing vertices, mean dist 0.3 [0.7 (%35.5)->0.8 (%64.5))] %63 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=node0, 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 0.91 +- 0.26 (0.08-->4.82) (max @ vno 85022 --> 112842) face area 0.28 +- 0.14 (0.00-->3.74) mean absolute distance = 0.42 +- 0.72 3116 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1526898.1, rms=7.026 001: dt: 0.5000, sse=986091.4, rms=5.031 (28.400%) 002: dt: 0.5000, sse=739537.7, rms=3.731 (25.827%) 003: dt: 0.5000, sse=624068.2, rms=2.931 (21.448%) 004: dt: 0.5000, sse=571715.9, rms=2.470 (15.740%) 005: dt: 0.5000, sse=547672.2, rms=2.227 (9.811%) 006: dt: 0.5000, sse=536914.3, rms=2.106 (5.447%) 007: dt: 0.5000, sse=532763.9, rms=2.043 (2.974%) rms = 2.02, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=530759.3, rms=2.016 (1.357%) 009: dt: 0.2500, sse=495763.1, rms=1.447 (28.190%) 010: dt: 0.2500, sse=491336.0, rms=1.366 (5.631%) rms = 1.36, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=491406.4, rms=1.358 (0.558%) rms = 1.35, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=490263.9, rms=1.345 (0.958%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=92.3, 53 (3) missing vertices, mean dist -0.2 [0.5 (%67.6)->0.3 (%32.4))] %75 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=node0, 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 (0.11-->5.44) (max @ vno 85022 --> 112842) face area 0.35 +- 0.17 (0.00-->4.74) mean absolute distance = 0.33 +- 0.50 3416 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=777063.8, rms=3.152 013: dt: 0.5000, sse=650110.6, rms=2.002 (36.484%) 014: dt: 0.5000, sse=621821.4, rms=1.667 (16.754%) 015: dt: 0.5000, sse=614064.9, rms=1.609 (3.451%) rms = 1.62, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=600556.6, rms=1.358 (15.621%) 017: dt: 0.2500, sse=595373.8, rms=1.239 (8.748%) rms = 1.22, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=594771.7, rms=1.222 (1.399%) rms = 1.21, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=594461.4, rms=1.209 (1.060%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 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=93.7, 41 (2) missing vertices, mean dist -0.2 [0.4 (%65.3)->0.3 (%34.7))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=node0, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.07-->5.52) (max @ vno 85022 --> 112842) face area 0.34 +- 0.17 (0.00-->4.46) mean absolute distance = 0.28 +- 0.40 2949 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=657804.8, rms=2.231 020: dt: 0.5000, sse=597442.0, rms=1.464 (34.366%) 021: dt: 0.5000, sse=588331.4, rms=1.365 (6.781%) rms = 1.46, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=579499.4, rms=1.180 (13.522%) 023: dt: 0.2500, sse=576928.3, rms=1.110 (5.938%) rms = 1.11, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=577720.9, rms=1.109 (0.117%) rms = 1.10, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=577689.3, rms=1.101 (0.707%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=94.2, 51 (1) missing vertices, mean dist -0.1 [0.3 (%55.2)->0.3 (%44.8))] %87 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=node0, 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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=581627.2, rms=1.325 026: dt: 0.5000, sse=560917.1, rms=0.927 (30.014%) rms = 1.22, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=556778.6, rms=0.857 (7.575%) rms = 0.88, time step reduction 2 of 3 to 0.125... rms = 0.85, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=556287.5, rms=0.853 (0.451%) positioning took 0.4 minutes generating cortex label... 4 non-cortical segments detected only using segment with 7540 vertices erasing segment 1 (vno[0] = 50877) erasing segment 2 (vno[0] = 81091) erasing segment 3 (vno[0] = 81855) writing cortex label to /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label/lh.cortex.label... writing curvature file /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.curv writing smoothed area to lh.area writing curvature file /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.area vertex spacing 0.89 +- 0.26 (0.03-->5.55) (max @ vno 85022 --> 112842) face area 0.34 +- 0.16 (0.00-->4.47) refinement took 4.3 minutes #-------------------------------------------- #@# Make White Surf rh So 11. Mär 04:26:22 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/filled.mgz... reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/brain.finalsurfs.mgz... reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/../mri/aseg.presurf.mgz... reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/wm.mgz... 17245 bright wm thresholded. 350 bright non-wm voxels segmented. reading original surface position from /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.orig... computing class statistics... border white: 216839 voxels (1.29%) border gray 244104 voxels (1.45%) WM (102.0): 102.3 +- 5.8 [70.0 --> 110.0] GM (85.0) : 83.8 +- 10.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 73.5 (was 70) setting MAX_BORDER_WHITE to 109.8 (was 105) setting MIN_BORDER_WHITE to 84.0 (was 85) setting MAX_CSF to 63.0 (was 40) setting MAX_GRAY to 98.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 73.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 52.5 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.23 (0.02-->4.05) (max @ vno 89536 --> 94479) face area 0.28 +- 0.13 (0.00-->3.52) mean absolute distance = 0.77 +- 0.93 3516 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=84+-5.2 mean inside = 99.1, mean outside = 87.2 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=90.9, 87 (87) missing vertices, mean dist 0.3 [0.7 (%35.8)->0.8 (%64.2))] %61 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=node0, 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 0.91 +- 0.26 (0.04-->4.80) (max @ vno 39199 --> 40087) face area 0.28 +- 0.14 (0.00-->2.52) mean absolute distance = 0.39 +- 0.66 3509 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1520920.6, rms=6.865 001: dt: 0.5000, sse=974211.8, rms=4.881 (28.901%) 002: dt: 0.5000, sse=738294.0, rms=3.626 (25.703%) 003: dt: 0.5000, sse=628131.6, rms=2.872 (20.803%) 004: dt: 0.5000, sse=583904.3, rms=2.447 (14.813%) 005: dt: 0.5000, sse=558261.9, rms=2.227 (8.956%) 006: dt: 0.5000, sse=548182.8, rms=2.130 (4.382%) 007: dt: 0.5000, sse=543787.8, rms=2.080 (2.352%) rms = 2.05, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=542364.9, rms=2.048 (1.526%) 009: dt: 0.2500, sse=509456.9, rms=1.532 (25.180%) 010: dt: 0.2500, sse=503980.0, rms=1.455 (5.062%) rms = 1.44, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=503124.9, rms=1.444 (0.754%) rms = 1.43, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=502331.4, rms=1.425 (1.271%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=92.6, 67 (20) missing vertices, mean dist -0.2 [0.4 (%66.5)->0.3 (%33.5))] %74 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=node0, 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-->4.92) (max @ vno 39199 --> 40087) face area 0.34 +- 0.17 (0.00-->3.29) mean absolute distance = 0.33 +- 0.49 4148 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=749955.3, rms=2.876 013: dt: 0.5000, sse=644339.6, rms=1.823 (36.618%) 014: dt: 0.5000, sse=623254.4, rms=1.571 (13.810%) rms = 1.60, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=608374.9, rms=1.387 (11.689%) 016: dt: 0.2500, sse=604123.4, rms=1.300 (6.293%) rms = 1.28, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=604339.1, rms=1.276 (1.842%) rms = 1.26, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=601700.0, rms=1.263 (1.032%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=93.9, 58 (10) missing vertices, mean dist -0.2 [0.4 (%64.7)->0.2 (%35.3))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=node0, 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 (0.08-->4.96) (max @ vno 39199 --> 40087) face area 0.34 +- 0.16 (0.00-->3.57) mean absolute distance = 0.29 +- 0.40 3430 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=665247.6, rms=2.229 019: dt: 0.5000, sse=608211.1, rms=1.520 (31.838%) 020: dt: 0.5000, sse=602623.9, rms=1.401 (7.795%) rms = 1.51, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=590323.8, rms=1.226 (12.536%) 022: dt: 0.2500, sse=586862.8, rms=1.163 (5.107%) rms = 1.16, time step reduction 2 of 3 to 0.125... rms = 1.16, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=586185.4, rms=1.158 (0.468%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=94.5, 69 (9) missing vertices, mean dist -0.1 [0.3 (%55.6)->0.3 (%44.4))] %86 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=node0, 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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=591180.0, rms=1.394 024: dt: 0.5000, sse=569111.1, rms=0.996 (28.556%) rms = 1.29, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=564845.7, rms=0.906 (9.055%) rms = 0.92, 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=564364.1, rms=0.900 (0.625%) positioning took 0.4 minutes generating cortex label... 12 non-cortical segments detected only using segment with 7639 vertices erasing segment 0 (vno[0] = 28057) erasing segment 2 (vno[0] = 43780) erasing segment 3 (vno[0] = 44845) erasing segment 4 (vno[0] = 74167) erasing segment 5 (vno[0] = 83279) erasing segment 6 (vno[0] = 84306) erasing segment 7 (vno[0] = 85288) erasing segment 8 (vno[0] = 86215) erasing segment 9 (vno[0] = 86943) erasing segment 10 (vno[0] = 88777) erasing segment 11 (vno[0] = 90666) writing cortex label to /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label/rh.cortex.label... writing curvature file /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.curv writing smoothed area to rh.area writing curvature file /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.area vertex spacing 0.89 +- 0.26 (0.02-->5.03) (max @ vno 39199 --> 40087) face area 0.33 +- 0.16 (0.00-->3.83) refinement took 4.1 minutes #-------------------------------------------- #@# Smooth2 lh So 11. Mär 04:30:26 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 So 11. Mär 04:30:31 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 So 11. Mär 04:30:35 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_inflate -rusage /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 45.1 mm, total surface area = 68762 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.181 (target=0.015) step 005: RMS=0.124 (target=0.015) step 010: RMS=0.092 (target=0.015) step 015: RMS=0.076 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.024 (target=0.015) inflation complete. inflation took 0.6 minutes mris_inflate utimesec 33.807860 mris_inflate stimesec 0.053991 mris_inflate ru_maxrss 146864 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 19865 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 8999 mris_inflate ru_oublock 8861 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 132 mris_inflate ru_nivcsw 109 #-------------------------------------------- #@# Inflation2 rh So 11. Mär 04:31:09 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_inflate -rusage /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 45.0 mm, total surface area = 69327 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.183 (target=0.015) step 005: RMS=0.127 (target=0.015) step 010: RMS=0.095 (target=0.015) step 015: RMS=0.079 (target=0.015) step 020: RMS=0.065 (target=0.015) step 025: RMS=0.055 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.040 (target=0.015) step 040: RMS=0.035 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. inflation took 0.6 minutes mris_inflate utimesec 34.424766 mris_inflate stimesec 0.058991 mris_inflate ru_maxrss 150216 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 20200 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 9177 mris_inflate ru_oublock 9059 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 130 mris_inflate ru_nivcsw 138 #-------------------------------------------- #@# Curv .H and .K lh So 11. Mär 04:31:44 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf mris_curvature -w lh.white.preaparc total integrated curvature = 6.138*4pi (77.138) --> -5 handles ICI = 166.0, FI = 1390.4, variation=23059.994 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 94 vertices thresholded to be in k1 ~ [-0.18 0.58], k2 ~ [-0.14 0.07] total integrated curvature = 0.569*4pi (7.149) --> 0 handles ICI = 1.4, FI = 7.6, variation=135.934 86 vertices thresholded to be in [-0.03 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 108 vertices thresholded to be in [-0.11 0.26] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.024 done. #-------------------------------------------- #@# Curv .H and .K rh So 11. Mär 04:33:01 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf mris_curvature -w rh.white.preaparc total integrated curvature = 4.104*4pi (51.571) --> -3 handles ICI = 181.5, FI = 1486.2, variation=24868.595 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 132 vertices thresholded to be in k1 ~ [-0.60 0.31], k2 ~ [-0.19 0.25] total integrated curvature = 0.551*4pi (6.926) --> 0 handles ICI = 1.3, FI = 7.3, variation=129.544 114 vertices thresholded to be in [-0.08 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 86 vertices thresholded to be in [-0.20 0.12] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.021 done. #----------------------------------------- #@# Curvature Stats lh So 11. Mär 04:34:20 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 44538_T1_fs 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 [ 44538_T1_fs/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 [ 198 ] Gb_filter = 0 WARN: S lookup min: -0.339618 WARN: S explicit min: 0.000000 vertex = 146 #----------------------------------------- #@# Curvature Stats rh So 11. Mär 04:34:23 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 44538_T1_fs 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 [ 44538_T1_fs/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 [ 221 ] Gb_filter = 0 WARN: S lookup min: -0.237444 WARN: S explicit min: 0.000000 vertex = 577 #-------------------------------------------- #@# Sphere lh So 11. Mär 04:34:27 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_sphere -rusage /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 0.307... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=node0, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.76 pass 1: epoch 2 of 3 starting distance error %19.66 unfolding complete - removing small folds... starting distance error %19.63 removing remaining folds... final distance error %19.65 MRISunfold() return, current seed 1234 -01: dt=0.0000, 72 negative triangles 198: dt=0.9900, 72 negative triangles 199: dt=0.9900, 24 negative triangles 200: dt=0.9900, 23 negative triangles 201: dt=0.9900, 16 negative triangles 202: dt=0.9900, 19 negative triangles 203: dt=0.9900, 18 negative triangles 204: dt=0.9900, 14 negative triangles 205: dt=0.9900, 6 negative triangles 206: dt=0.9900, 11 negative triangles 207: dt=0.9900, 6 negative triangles 208: dt=0.9900, 10 negative triangles 209: dt=0.9900, 8 negative triangles 210: dt=0.9900, 6 negative triangles 211: dt=0.9900, 3 negative triangles 212: dt=0.9900, 5 negative triangles 213: dt=0.9900, 2 negative triangles 214: dt=0.9900, 6 negative triangles 215: dt=0.9900, 1 negative triangles 216: dt=0.9900, 2 negative triangles 217: dt=0.9900, 2 negative triangles 218: dt=0.9900, 2 negative triangles 219: dt=0.9900, 1 negative triangles 220: dt=0.9900, 2 negative triangles 221: dt=0.9900, 1 negative triangles 222: dt=0.9900, 1 negative triangles 223: dt=0.9900, 1 negative triangles 224: dt=0.9900, 1 negative triangles 225: dt=0.9405, 3 negative triangles 226: dt=0.9405, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.72 hours mris_sphere utimesec 2573.972696 mris_sphere stimesec 0.306953 mris_sphere ru_maxrss 201756 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 33723 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 13096 mris_sphere ru_oublock 7976 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 130 mris_sphere ru_nivcsw 47813 FSRUNTIME@ mris_sphere 0.7161 hours 1 threads #-------------------------------------------- #@# Sphere rh So 11. Mär 05:17:25 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_sphere -rusage /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 0.307... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=node0, 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 %19.09 pass 1: epoch 2 of 3 starting distance error %19.04 unfolding complete - removing small folds... starting distance error %18.95 removing remaining folds... final distance error %18.98 MRISunfold() return, current seed 1234 -01: dt=0.0000, 127 negative triangles 274: dt=0.9900, 127 negative triangles 275: dt=0.9900, 32 negative triangles 276: dt=0.9900, 22 negative triangles 277: dt=0.9900, 29 negative triangles 278: dt=0.9900, 24 negative triangles 279: dt=0.9900, 16 negative triangles 280: dt=0.9900, 27 negative triangles 281: dt=0.9900, 20 negative triangles 282: dt=0.9900, 11 negative triangles 283: dt=0.9900, 6 negative triangles 284: dt=0.9900, 7 negative triangles 285: dt=0.9900, 5 negative triangles 286: dt=0.9900, 2 negative triangles 287: dt=0.9900, 5 negative triangles 288: dt=0.9900, 4 negative triangles 289: dt=0.9900, 2 negative triangles 290: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.83 hours mris_sphere utimesec 2988.382696 mris_sphere stimesec 0.309952 mris_sphere ru_maxrss 207404 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 34343 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 13274 mris_sphere ru_oublock 8154 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 103 mris_sphere ru_nivcsw 47236 FSRUNTIME@ mris_sphere 0.8313 hours 1 threads #-------------------------------------------- #@# Surf Reg lh So 11. Mär 06:07:18 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_register -curv -rusage /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /cm/shared/apps/freesurfer/6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts cmdline mris_register -curv -rusage /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /cm/shared/apps/freesurfer/6.0.0/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 /cm/shared/apps/freesurfer/6.0.0/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=node0, 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=node0, 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 = 5.387 curvature mean = 0.047, std = 0.812 curvature mean = 0.015, std = 0.881 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 16.00) sse = 250350.4, tmin=0.9646 d=32.00 min @ (0.00, 8.00, 0.00) sse = 165736.2, tmin=1.9649 d=8.00 min @ (2.00, 0.00, 0.00) sse = 163136.5, tmin=3.9701 d=4.00 min @ (-1.00, 0.00, 0.00) sse = 162437.4, tmin=4.9841 d=2.00 min @ (0.50, 0.50, 0.00) sse = 161778.9, tmin=5.9971 d=1.00 min @ (0.00, 0.00, 0.25) sse = 161730.9, tmin=7.0146 d=0.50 min @ (0.00, 0.00, -0.12) sse = 161708.3, tmin=8.0406 tol=1.0e+00, sigma=0.5, host=node0, 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 8.04 min curvature mean = 0.005, std = 0.846 curvature mean = 0.006, std = 0.956 curvature mean = 0.003, std = 0.859 curvature mean = 0.002, std = 0.983 curvature mean = 0.002, std = 0.862 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.031, std = 0.285 curvature mean = 0.038, std = 0.251 curvature mean = 0.064, std = 0.372 curvature mean = 0.032, std = 0.314 curvature mean = 0.038, std = 0.554 curvature mean = 0.031, std = 0.342 curvature mean = 0.022, std = 0.690 curvature mean = 0.030, std = 0.354 curvature mean = 0.008, std = 0.794 MRISregister() return, current seed 0 -01: dt=0.0000, 30 negative triangles 102: dt=0.9900, 30 negative triangles expanding nbhd size to 1 103: dt=0.9900, 47 negative triangles 104: dt=0.9900, 25 negative triangles 105: dt=0.9900, 26 negative triangles 106: dt=0.9900, 23 negative triangles 107: dt=0.9900, 25 negative triangles 108: dt=0.9900, 22 negative triangles 109: dt=0.9900, 16 negative triangles 110: dt=0.9900, 12 negative triangles 111: dt=0.9900, 13 negative triangles 112: dt=0.9900, 14 negative triangles 113: dt=0.9900, 10 negative triangles 114: dt=0.9900, 9 negative triangles 115: dt=0.9900, 8 negative triangles 116: dt=0.9900, 7 negative triangles 117: dt=0.9900, 7 negative triangles 118: dt=0.9900, 9 negative triangles 119: dt=0.9900, 6 negative triangles 120: dt=0.9900, 6 negative triangles 121: dt=0.9900, 7 negative triangles 122: dt=0.9900, 5 negative triangles 123: dt=0.9900, 5 negative triangles 124: dt=0.9900, 6 negative triangles 125: dt=0.9900, 6 negative triangles 126: dt=0.9900, 5 negative triangles 127: dt=0.9900, 4 negative triangles 128: dt=0.9900, 3 negative triangles 129: dt=0.9900, 3 negative triangles 130: dt=0.9900, 2 negative triangles 131: dt=0.9900, 1 negative triangles 132: dt=0.9900, 1 negative triangles 133: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.65 hours mris_register utimesec 2332.107465 mris_register stimesec 0.286956 mris_register ru_maxrss 201780 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 27554 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 23060 mris_register ru_oublock 7977 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 209 mris_register ru_nivcsw 4292 FSRUNTIME@ mris_register 0.6483 hours 1 threads #-------------------------------------------- #@# Surf Reg rh So 11. Mär 06:46:12 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_register -curv -rusage /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /cm/shared/apps/freesurfer/6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts cmdline mris_register -curv -rusage /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /cm/shared/apps/freesurfer/6.0.0/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 /cm/shared/apps/freesurfer/6.0.0/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=node0, 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=node0, 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 = 5.442 curvature mean = 0.045, std = 0.808 curvature mean = 0.016, std = 0.883 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 16.00) sse = 279254.6, tmin=0.9590 d=32.00 min @ (8.00, 8.00, 0.00) sse = 204399.2, tmin=1.9533 d=16.00 min @ (0.00, 0.00, 4.00) sse = 199926.1, tmin=2.9584 d=8.00 min @ (-2.00, 0.00, -2.00) sse = 195648.4, tmin=3.9734 d=4.00 min @ (1.00, 0.00, 0.00) sse = 194618.3, tmin=4.9965 d=2.00 min @ (0.00, 0.50, 0.00) sse = 194430.4, tmin=6.0234 d=1.00 min @ (0.00, 0.00, 0.25) sse = 194382.8, tmin=7.0452 d=0.50 min @ (0.00, 0.12, 0.12) sse = 194376.5, tmin=8.0694 tol=1.0e+00, sigma=0.5, host=node0, 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 8.07 min curvature mean = 0.016, std = 0.839 curvature mean = 0.005, std = 0.958 curvature mean = 0.014, std = 0.851 curvature mean = 0.002, std = 0.983 curvature mean = 0.013, std = 0.854 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.035, std = 0.319 curvature mean = 0.034, std = 0.244 curvature mean = 0.064, std = 0.342 curvature mean = 0.028, std = 0.306 curvature mean = 0.042, std = 0.500 curvature mean = 0.027, std = 0.334 curvature mean = 0.025, std = 0.625 curvature mean = 0.027, std = 0.345 curvature mean = 0.010, std = 0.728 MRISregister() return, current seed 0 -01: dt=0.0000, 30 negative triangles 105: dt=0.9900, 30 negative triangles expanding nbhd size to 1 106: dt=0.9900, 34 negative triangles 107: dt=0.9900, 30 negative triangles 108: dt=0.9900, 25 negative triangles 109: dt=0.9900, 26 negative triangles 110: dt=0.9900, 26 negative triangles 111: dt=0.9900, 21 negative triangles 112: dt=0.9900, 22 negative triangles 113: dt=0.9900, 19 negative triangles 114: dt=0.9900, 19 negative triangles 115: dt=0.9900, 16 negative triangles 116: dt=0.9900, 15 negative triangles 117: dt=0.9900, 12 negative triangles 118: dt=0.9900, 17 negative triangles 119: dt=0.9900, 14 negative triangles 120: dt=0.9900, 10 negative triangles 121: dt=0.9900, 11 negative triangles 122: dt=0.9900, 8 negative triangles 123: dt=0.9900, 10 negative triangles 124: dt=0.9900, 8 negative triangles 125: dt=0.9900, 6 negative triangles 126: dt=0.9900, 6 negative triangles 127: dt=0.9900, 5 negative triangles 128: dt=0.9900, 5 negative triangles 129: dt=0.9900, 2 negative triangles 130: dt=0.9900, 2 negative triangles 131: dt=0.9900, 3 negative triangles 132: dt=0.9900, 1 negative triangles 133: dt=0.9900, 2 negative triangles 134: dt=0.9900, 1 negative triangles 135: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.74 hours mris_register utimesec 2663.613069 mris_register stimesec 0.296954 mris_register ru_maxrss 203516 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 26220 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 23278 mris_register ru_oublock 8156 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 170 mris_register ru_nivcsw 3130 FSRUNTIME@ mris_register 0.7402 hours 1 threads #-------------------------------------------- #@# Jacobian white lh So 11. Mär 07:30:36 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 So 11. Mär 07:30:38 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 So 11. Mär 07:30:40 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mrisp_paint -a 5 /cm/shared/apps/freesurfer/6.0.0/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 /cm/shared/apps/freesurfer/6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh So 11. Mär 07:30:41 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mrisp_paint -a 5 /cm/shared/apps/freesurfer/6.0.0/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 /cm/shared/apps/freesurfer/6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh So 11. Mär 07:30:42 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 44538_T1_fs lh ../surf/lh.sphere.reg /cm/shared/apps/freesurfer/6.0.0/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 /cm/shared/apps/freesurfer/6.0.0/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... 1056 labels changed using aseg relabeling using gibbs priors... 000: 2624 changed, 113373 examined... 001: 612 changed, 11249 examined... 002: 136 changed, 3479 examined... 003: 48 changed, 813 examined... 004: 25 changed, 309 examined... 005: 12 changed, 168 examined... 006: 1 changed, 72 examined... 007: 1 changed, 5 examined... 008: 0 changed, 7 examined... 213 labels changed using aseg 000: 96 total segments, 57 labels (173 vertices) changed 001: 39 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... 1676 vertices marked for relabeling... 1676 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 12 seconds. #----------------------------------------- #@# Cortical Parc rh So 11. Mär 07:30:54 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 44538_T1_fs rh ../surf/rh.sphere.reg /cm/shared/apps/freesurfer/6.0.0/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 /cm/shared/apps/freesurfer/6.0.0/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... 924 labels changed using aseg relabeling using gibbs priors... 000: 2370 changed, 115906 examined... 001: 562 changed, 10439 examined... 002: 141 changed, 3171 examined... 003: 52 changed, 828 examined... 004: 18 changed, 299 examined... 005: 9 changed, 111 examined... 006: 4 changed, 42 examined... 007: 2 changed, 18 examined... 008: 1 changed, 15 examined... 009: 0 changed, 5 examined... 202 labels changed using aseg 000: 86 total segments, 49 labels (208 vertices) changed 001: 38 total segments, 1 labels (1 vertices) changed 002: 37 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... 1248 vertices marked for relabeling... 1248 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 12 seconds. #-------------------------------------------- #@# Make Pial Surf lh So 11. Mär 07:31:07 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/filled.mgz... reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/brain.finalsurfs.mgz... reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/../mri/aseg.presurf.mgz... reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/wm.mgz... 17245 bright wm thresholded. 350 bright non-wm voxels segmented. reading original surface position from /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.orig... computing class statistics... border white: 216839 voxels (1.29%) border gray 244104 voxels (1.45%) WM (102.0): 102.3 +- 5.8 [70.0 --> 110.0] GM (85.0) : 83.8 +- 10.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 72.5 (was 70) setting MAX_BORDER_WHITE to 110.8 (was 105) setting MIN_BORDER_WHITE to 83.0 (was 85) setting MAX_CSF to 62.0 (was 40) setting MAX_GRAY to 99.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 72.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 51.5 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-5.2, GM=83+-6.1 mean inside = 99.1, mean outside = 87.0 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.26 (0.03-->5.55) (max @ vno 85022 --> 112842) face area 0.34 +- 0.16 (0.00-->4.46) mean absolute distance = 0.70 +- 0.98 2621 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 190 points - only 0.00% unknown deleting segment 3 with 10 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 24 points - only 0.00% unknown mean border=90.2, 100 (100) missing vertices, mean dist 0.4 [1.0 (%16.8)->0.6 (%83.2))] %61 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=node0, 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 +- 0.27 (0.09-->5.47) (max @ vno 85022 --> 112842) face area 0.34 +- 0.17 (0.00-->4.41) mean absolute distance = 0.41 +- 0.71 3003 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1138180.2, rms=5.280 001: dt: 0.5000, sse=770642.0, rms=3.281 (37.858%) 002: dt: 0.5000, sse=653797.3, rms=2.323 (29.189%) 003: dt: 0.5000, sse=623236.6, rms=2.006 (13.643%) 004: dt: 0.5000, sse=611879.4, rms=1.864 (7.098%) rms = 1.85, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=610543.0, rms=1.853 (0.591%) 006: dt: 0.2500, sse=588464.7, rms=1.454 (21.505%) 007: dt: 0.2500, sse=587400.1, rms=1.394 (4.139%) rms = 1.38, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=584932.6, rms=1.380 (0.999%) rms = 1.37, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=584338.2, rms=1.366 (1.051%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 169 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown deleting segment 2 with 17 points - only 0.00% unknown mean border=92.2, 43 (7) missing vertices, mean dist -0.2 [0.5 (%67.9)->0.3 (%32.1))] %75 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=node0, 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 (0.07-->5.65) (max @ vno 85022 --> 112842) face area 0.35 +- 0.18 (0.00-->4.70) mean absolute distance = 0.33 +- 0.50 3487 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=770218.5, rms=3.018 010: dt: 0.5000, sse=658737.6, rms=1.877 (37.796%) 011: dt: 0.5000, sse=623651.5, rms=1.545 (17.692%) rms = 1.54, time step reduction 1 of 3 to 0.250... 012: dt: 0.5000, sse=623393.8, rms=1.541 (0.300%) 013: dt: 0.2500, sse=604967.9, rms=1.199 (22.174%) rms = 1.17, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=603555.3, rms=1.169 (2.488%) rms = 1.16, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=603045.5, rms=1.160 (0.756%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 180 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 4 with 17 points - only 0.00% unknown mean border=93.6, 45 (4) missing vertices, mean dist -0.2 [0.4 (%65.6)->0.2 (%34.4))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=node0, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.26 (0.08-->5.65) (max @ vno 85022 --> 112842) face area 0.34 +- 0.17 (0.00-->4.38) mean absolute distance = 0.28 +- 0.40 3078 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=663027.6, rms=2.215 016: dt: 0.5000, sse=606698.8, rms=1.438 (35.077%) 017: dt: 0.5000, sse=594882.4, rms=1.337 (7.053%) rms = 1.44, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=586155.3, rms=1.151 (13.891%) 019: dt: 0.2500, sse=584871.8, rms=1.086 (5.669%) rms = 1.09, time step reduction 2 of 3 to 0.125... rms = 1.08, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=583869.2, rms=1.081 (0.462%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 179 points - only 0.00% unknown deleting segment 1 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 4 with 18 points - only 0.00% unknown mean border=94.2, 40 (4) missing vertices, mean dist -0.1 [0.3 (%55.8)->0.2 (%44.2))] %87 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=node0, 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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=589036.3, rms=1.340 021: dt: 0.5000, sse=577977.9, rms=0.960 (28.339%) rms = 1.24, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=565958.9, rms=0.860 (10.442%) rms = 0.87, time step reduction 2 of 3 to 0.125... rms = 0.85, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=564610.2, rms=0.853 (0.762%) positioning took 0.4 minutes generating cortex label... 5 non-cortical segments detected only using segment with 7527 vertices erasing segment 1 (vno[0] = 50877) erasing segment 2 (vno[0] = 68858) erasing segment 3 (vno[0] = 81091) erasing segment 4 (vno[0] = 81855) writing cortex label to /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label/lh.cortex.label... writing curvature file /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.curv writing smoothed area to lh.area writing curvature file /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.area vertex spacing 0.90 +- 0.27 (0.03-->5.71) (max @ vno 85022 --> 112842) face area 0.34 +- 0.17 (0.00-->4.12) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 3 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=70.8, 114 (114) missing vertices, mean dist 1.9 [1.0 (%0.0)->3.3 (%100.0))] %19 local maxima, %36 large gradients and %40 min vals, 357 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=node0, 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=13068693.0, rms=24.179 001: dt: 0.0500, sse=11896138.0, rms=23.020 (4.795%) 002: dt: 0.0500, sse=11043561.0, rms=22.138 (3.829%) 003: dt: 0.0500, sse=10382655.0, rms=21.430 (3.200%) 004: dt: 0.0500, sse=9841674.0, rms=20.832 (2.790%) 005: dt: 0.0500, sse=9383174.0, rms=20.312 (2.499%) 006: dt: 0.0500, sse=8982809.0, rms=19.846 (2.294%) 007: dt: 0.0500, sse=8625478.0, rms=19.420 (2.143%) 008: dt: 0.0500, sse=8301816.0, rms=19.027 (2.026%) 009: dt: 0.0500, sse=8005003.5, rms=18.659 (1.935%) 010: dt: 0.0500, sse=7729833.5, rms=18.311 (1.865%) positioning took 0.8 minutes mean border=70.6, 76 (53) missing vertices, mean dist 1.7 [0.4 (%0.0)->2.8 (%100.0))] %20 local maxima, %35 large gradients and %39 min vals, 347 gradients ignored tol=1.0e-04, sigma=2.0, host=node0, 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=8444960.0, rms=19.200 011: dt: 0.0500, sse=8185989.0, rms=18.882 (1.655%) 012: dt: 0.0500, sse=7943065.0, rms=18.579 (1.605%) 013: dt: 0.0500, sse=7714448.0, rms=18.289 (1.560%) 014: dt: 0.0500, sse=7498598.0, rms=18.011 (1.520%) 015: dt: 0.0500, sse=7294265.0, rms=17.744 (1.484%) 016: dt: 0.0500, sse=7100469.5, rms=17.487 (1.451%) 017: dt: 0.0500, sse=6916861.0, rms=17.239 (1.415%) 018: dt: 0.0500, sse=6742522.0, rms=17.001 (1.383%) 019: dt: 0.0500, sse=6576637.5, rms=16.771 (1.353%) 020: dt: 0.0500, sse=6418497.0, rms=16.548 (1.326%) positioning took 0.8 minutes mean border=70.4, 83 (39) missing vertices, mean dist 1.5 [0.1 (%0.5)->2.5 (%99.5))] %21 local maxima, %36 large gradients and %38 min vals, 344 gradients ignored tol=1.0e-04, sigma=2.0, host=node0, 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=6540010.5, rms=16.724 021: dt: 0.0500, sse=6385218.0, rms=16.506 (1.305%) 022: dt: 0.0500, sse=6237553.0, rms=16.295 (1.278%) 023: dt: 0.0500, sse=6095818.5, rms=16.090 (1.259%) 024: dt: 0.0500, sse=5960489.0, rms=15.891 (1.234%) 025: dt: 0.0500, sse=5831320.5, rms=15.699 (1.207%) 026: dt: 0.0500, sse=5707698.0, rms=15.513 (1.184%) 027: dt: 0.0500, sse=5588902.5, rms=15.332 (1.166%) 028: dt: 0.0500, sse=5473448.0, rms=15.154 (1.161%) 029: dt: 0.0500, sse=5361519.5, rms=14.980 (1.152%) 030: dt: 0.0500, sse=5252865.0, rms=14.808 (1.145%) positioning took 0.8 minutes mean border=70.3, 134 (31) missing vertices, mean dist 1.3 [0.1 (%5.3)->2.3 (%94.7))] %21 local maxima, %36 large gradients and %37 min vals, 330 gradients ignored tol=1.0e-04, sigma=2.0, host=node0, 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=5354167.0, rms=14.967 031: dt: 0.5000, sse=4547140.5, rms=13.642 (8.856%) 032: dt: 0.5000, sse=3922620.0, rms=12.514 (8.269%) 033: dt: 0.5000, sse=3430073.2, rms=11.547 (7.727%) 034: dt: 0.5000, sse=3027088.8, rms=10.685 (7.465%) 035: dt: 0.5000, sse=2706908.5, rms=9.947 (6.904%) 036: dt: 0.5000, sse=2427949.5, rms=9.253 (6.981%) 037: dt: 0.5000, sse=2202107.8, rms=8.652 (6.493%) 038: dt: 0.5000, sse=1999203.0, rms=8.071 (6.717%) 039: dt: 0.5000, sse=1832495.1, rms=7.563 (6.294%) 040: dt: 0.5000, sse=1680180.0, rms=7.065 (6.589%) 041: dt: 0.5000, sse=1561041.1, rms=6.654 (5.818%) 042: dt: 0.5000, sse=1452829.5, rms=6.253 (6.023%) 043: dt: 0.5000, sse=1374603.8, rms=5.950 (4.844%) 044: dt: 0.5000, sse=1303490.8, rms=5.657 (4.924%) 045: dt: 0.5000, sse=1256589.9, rms=5.459 (3.506%) 046: dt: 0.5000, sse=1211018.9, rms=5.256 (3.722%) 047: dt: 0.5000, sse=1185378.9, rms=5.139 (2.214%) 048: dt: 0.5000, sse=1155761.6, rms=5.000 (2.711%) 049: dt: 0.5000, sse=1141508.2, rms=4.934 (1.317%) 050: dt: 0.5000, sse=1121854.2, rms=4.838 (1.944%) rms = 4.81, time step reduction 1 of 3 to 0.250... 051: dt: 0.5000, sse=1115208.9, rms=4.809 (0.593%) 052: dt: 0.2500, sse=1035749.0, rms=4.354 (9.467%) 053: dt: 0.2500, sse=1012873.0, rms=4.229 (2.874%) rms = 4.23, time step reduction 2 of 3 to 0.125... rms = 4.19, time step reduction 3 of 3 to 0.062... 054: dt: 0.1250, sse=1006558.8, rms=4.191 (0.897%) positioning took 2.9 minutes mean border=68.8, 1925 (3) missing vertices, mean dist 0.2 [0.2 (%37.4)->0.6 (%62.6))] %37 local maxima, %24 large gradients and %33 min vals, 308 gradients ignored tol=1.0e-04, sigma=1.0, host=node0, 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=1311578.2, rms=4.726 055: dt: 0.5000, sse=1223423.2, rms=4.270 (9.638%) 056: dt: 0.5000, sse=1162088.8, rms=3.947 (7.574%) rms = 4.07, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=1089363.5, rms=3.436 (12.930%) 058: dt: 0.2500, sse=1065703.8, rms=3.253 (5.324%) rms = 3.22, time step reduction 2 of 3 to 0.125... 059: dt: 0.2500, sse=1061466.4, rms=3.222 (0.970%) 060: dt: 0.1250, sse=1042066.8, rms=3.066 (4.836%) rms = 3.04, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=1038252.3, rms=3.038 (0.931%) positioning took 1.1 minutes mean border=68.1, 2470 (1) missing vertices, mean dist 0.1 [0.2 (%39.7)->0.4 (%60.3))] %46 local maxima, %15 large gradients and %32 min vals, 321 gradients ignored tol=1.0e-04, sigma=0.5, host=node0, 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=1064551.6, rms=3.209 rms = 3.51, time step reduction 1 of 3 to 0.250... 062: dt: 0.2500, sse=1044382.1, rms=3.050 (4.943%) 063: dt: 0.2500, sse=1036569.8, rms=2.995 (1.803%) rms = 3.00, time step reduction 2 of 3 to 0.125... rms = 2.97, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=1033904.9, rms=2.972 (0.780%) positioning took 0.6 minutes mean border=67.6, 4798 (1) missing vertices, mean dist 0.1 [0.2 (%43.7)->0.3 (%56.3))] %48 local maxima, %12 large gradients and %30 min vals, 326 gradients ignored tol=1.0e-04, sigma=0.2, host=node0, 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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1041100.3, rms=3.011 rms = 3.28, time step reduction 1 of 3 to 0.250... 065: dt: 0.2500, sse=1028737.3, rms=2.910 (3.356%) 066: dt: 0.2500, sse=1019174.8, rms=2.853 (1.959%) rms = 2.86, time step reduction 2 of 3 to 0.125... rms = 2.83, time step reduction 3 of 3 to 0.062... 067: dt: 0.1250, sse=1016810.6, rms=2.830 (0.778%) positioning took 0.7 minutes writing curvature file /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.area.pial vertex spacing 1.06 +- 0.50 (0.08-->7.05) (max @ vno 72913 --> 72890) face area 0.44 +- 0.38 (0.00-->6.87) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 113373 vertices processed 25000 of 113373 vertices processed 50000 of 113373 vertices processed 75000 of 113373 vertices processed 100000 of 113373 vertices processed 0 of 113373 vertices processed 25000 of 113373 vertices processed 50000 of 113373 vertices processed 75000 of 113373 vertices processed 100000 of 113373 vertices processed thickness calculation complete, 1897:5534 truncations. 20892 vertices at 0 distance 64518 vertices at 1 distance 66028 vertices at 2 distance 37146 vertices at 3 distance 15725 vertices at 4 distance 5871 vertices at 5 distance 2252 vertices at 6 distance 924 vertices at 7 distance 404 vertices at 8 distance 204 vertices at 9 distance 111 vertices at 10 distance 90 vertices at 11 distance 79 vertices at 12 distance 51 vertices at 13 distance 53 vertices at 14 distance 40 vertices at 15 distance 46 vertices at 16 distance 19 vertices at 17 distance 19 vertices at 18 distance 16 vertices at 19 distance 16 vertices at 20 distance writing curvature file /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.thickness positioning took 13.4 minutes #-------------------------------------------- #@# Make Pial Surf rh So 11. Mär 07:44:32 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/filled.mgz... reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/brain.finalsurfs.mgz... reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/../mri/aseg.presurf.mgz... reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/wm.mgz... 17245 bright wm thresholded. 350 bright non-wm voxels segmented. reading original surface position from /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.orig... computing class statistics... border white: 216839 voxels (1.29%) border gray 244104 voxels (1.45%) WM (102.0): 102.3 +- 5.8 [70.0 --> 110.0] GM (85.0) : 83.8 +- 10.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 73.5 (was 70) setting MAX_BORDER_WHITE to 109.8 (was 105) setting MIN_BORDER_WHITE to 84.0 (was 85) setting MAX_CSF to 63.0 (was 40) setting MAX_GRAY to 98.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 73.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 52.5 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104+-4.3, GM=84+-5.2 mean inside = 99.1, mean outside = 87.2 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.26 (0.02-->5.03) (max @ vno 39199 --> 40087) face area 0.33 +- 0.16 (0.00-->3.82) mean absolute distance = 0.65 +- 0.91 2542 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 22 points - only 0.00% unknown deleting segment 6 with 126 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown deleting segment 8 with 26 points - only 0.00% unknown mean border=90.8, 116 (116) missing vertices, mean dist 0.3 [1.0 (%16.4)->0.6 (%83.6))] %59 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=node0, 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 0.91 +- 0.27 (0.02-->5.29) (max @ vno 39199 --> 40087) face area 0.33 +- 0.17 (0.00-->3.45) mean absolute distance = 0.38 +- 0.65 3168 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1085541.2, rms=4.954 001: dt: 0.5000, sse=753949.5, rms=3.070 (38.040%) 002: dt: 0.5000, sse=656308.1, rms=2.247 (26.787%) 003: dt: 0.5000, sse=631857.6, rms=2.000 (10.993%) 004: dt: 0.5000, sse=619472.1, rms=1.872 (6.398%) rms = 1.87, time step reduction 1 of 3 to 0.250... 005: dt: 0.5000, sse=622452.6, rms=1.869 (0.176%) 006: dt: 0.2500, sse=598074.6, rms=1.487 (20.423%) 007: dt: 0.2500, sse=595068.8, rms=1.431 (3.799%) rms = 1.42, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=594962.9, rms=1.422 (0.634%) rms = 1.41, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=593520.8, rms=1.409 (0.920%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 19 points - only 47.37% unknown deleting segment 2 with 7 points - only 0.00% unknown deleting segment 3 with 105 points - only 0.00% unknown deleting segment 4 with 11 points - only 0.00% unknown mean border=92.5, 73 (16) missing vertices, mean dist -0.2 [0.4 (%66.3)->0.3 (%33.7))] %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=node0, 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-->5.58) (max @ vno 39199 --> 40087) face area 0.35 +- 0.18 (0.00-->3.91) mean absolute distance = 0.33 +- 0.49 4116 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=739195.3, rms=2.712 010: dt: 0.5000, sse=642889.8, rms=1.694 (37.534%) 011: dt: 0.5000, sse=622780.8, rms=1.483 (12.473%) rms = 1.55, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=613355.4, rms=1.305 (11.947%) 013: dt: 0.2500, sse=612034.4, rms=1.233 (5.555%) rms = 1.23, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=610056.7, rms=1.225 (0.619%) rms = 1.22, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=609740.8, rms=1.216 (0.797%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 19 points - only 47.37% unknown deleting segment 1 with 26 points - only 0.00% unknown deleting segment 2 with 111 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 50.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 11 points - only 0.00% unknown removing 4 vertex label from ripped group mean border=93.8, 76 (11) missing vertices, mean dist -0.2 [0.4 (%64.9)->0.2 (%35.1))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=node0, 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 (0.06-->5.48) (max @ vno 39199 --> 40087) face area 0.34 +- 0.17 (0.00-->4.05) mean absolute distance = 0.29 +- 0.40 3315 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=670070.9, rms=2.204 016: dt: 0.5000, sse=615717.9, rms=1.498 (32.060%) 017: dt: 0.5000, sse=603449.2, rms=1.373 (8.312%) rms = 1.49, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=594959.6, rms=1.197 (12.837%) 019: dt: 0.2500, sse=593134.4, rms=1.140 (4.736%) rms = 1.14, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=592873.4, rms=1.139 (0.088%) rms = 1.13, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=592050.8, rms=1.131 (0.698%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 26 points - only 0.00% unknown deleting segment 1 with 121 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 4 with 11 points - only 0.00% unknown mean border=94.4, 81 (8) missing vertices, mean dist -0.1 [0.3 (%55.5)->0.3 (%44.5))] %86 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=node0, 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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=595410.1, rms=1.371 022: dt: 0.5000, sse=576951.4, rms=0.947 (30.949%) rms = 1.25, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=569553.0, rms=0.878 (7.314%) rms = 0.91, time step reduction 2 of 3 to 0.125... rms = 0.87, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=569099.4, rms=0.873 (0.472%) positioning took 0.4 minutes generating cortex label... 10 non-cortical segments detected only using segment with 7656 vertices erasing segment 0 (vno[0] = 28057) erasing segment 2 (vno[0] = 71866) erasing segment 3 (vno[0] = 83279) erasing segment 4 (vno[0] = 84306) erasing segment 5 (vno[0] = 85288) erasing segment 6 (vno[0] = 86215) erasing segment 7 (vno[0] = 86943) erasing segment 8 (vno[0] = 88777) erasing segment 9 (vno[0] = 90666) writing cortex label to /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label/rh.cortex.label... writing curvature file /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.curv writing smoothed area to rh.area writing curvature file /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.area vertex spacing 0.89 +- 0.27 (0.02-->5.51) (max @ vno 39199 --> 40087) face area 0.33 +- 0.17 (0.00-->3.99) 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 19 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=71.6, 137 (137) missing vertices, mean dist 1.9 [0.2 (%0.0)->3.4 (%100.0))] %20 local maxima, %34 large gradients and %41 min vals, 497 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=node0, 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=12878184.0, rms=23.735 001: dt: 0.0500, sse=11732930.0, rms=22.606 (4.758%) 002: dt: 0.0500, sse=10897840.0, rms=21.745 (3.807%) 003: dt: 0.0500, sse=10250596.0, rms=21.053 (3.180%) 004: dt: 0.0500, sse=9722242.0, rms=20.472 (2.764%) 005: dt: 0.0500, sse=9273696.0, rms=19.964 (2.478%) 006: dt: 0.0500, sse=8882385.0, rms=19.511 (2.272%) 007: dt: 0.0500, sse=8533517.0, rms=19.097 (2.119%) 008: dt: 0.0500, sse=8216857.5, rms=18.714 (2.007%) 009: dt: 0.0500, sse=7926449.5, rms=18.355 (1.916%) 010: dt: 0.0500, sse=7657654.0, rms=18.017 (1.843%) positioning took 0.8 minutes mean border=71.4, 105 (62) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.9 (%100.0))] %21 local maxima, %34 large gradients and %40 min vals, 464 gradients ignored tol=1.0e-04, sigma=2.0, host=node0, 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=8384619.0, rms=18.917 011: dt: 0.0500, sse=8130955.0, rms=18.607 (1.635%) 012: dt: 0.0500, sse=7892545.5, rms=18.312 (1.588%) 013: dt: 0.0500, sse=7668203.0, rms=18.029 (1.543%) 014: dt: 0.0500, sse=7455848.0, rms=17.758 (1.507%) 015: dt: 0.0500, sse=7254722.5, rms=17.496 (1.471%) 016: dt: 0.0500, sse=7063723.5, rms=17.244 (1.439%) 017: dt: 0.0500, sse=6881941.0, rms=17.001 (1.411%) 018: dt: 0.0500, sse=6709259.0, rms=16.767 (1.379%) 019: dt: 0.0500, sse=6544237.0, rms=16.540 (1.355%) 020: dt: 0.0500, sse=6386873.5, rms=16.320 (1.328%) positioning took 0.8 minutes mean border=71.2, 115 (37) missing vertices, mean dist 1.5 [0.1 (%0.5)->2.6 (%99.5))] %22 local maxima, %34 large gradients and %39 min vals, 459 gradients ignored tol=1.0e-04, sigma=2.0, host=node0, 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=6528259.0, rms=16.521 021: dt: 0.0500, sse=6373492.5, rms=16.305 (1.309%) 022: dt: 0.0500, sse=6225567.5, rms=16.096 (1.285%) 023: dt: 0.0500, sse=6082639.0, rms=15.891 (1.274%) 024: dt: 0.0500, sse=5946706.0, rms=15.693 (1.244%) 025: dt: 0.0500, sse=5816640.5, rms=15.501 (1.220%) 026: dt: 0.0500, sse=5691753.0, rms=15.315 (1.201%) 027: dt: 0.0500, sse=5571504.5, rms=15.134 (1.186%) 028: dt: 0.0500, sse=5455685.0, rms=14.957 (1.170%) 029: dt: 0.0500, sse=5343179.5, rms=14.783 (1.164%) 030: dt: 0.0500, sse=5234190.0, rms=14.612 (1.155%) positioning took 0.8 minutes mean border=71.0, 160 (35) missing vertices, mean dist 1.3 [0.1 (%5.5)->2.4 (%94.5))] %22 local maxima, %34 large gradients and %38 min vals, 450 gradients ignored tol=1.0e-04, sigma=2.0, host=node0, 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=5334803.5, rms=14.769 031: dt: 0.5000, sse=4535656.0, rms=13.467 (8.817%) 032: dt: 0.5000, sse=3934130.0, rms=12.391 (7.990%) 033: dt: 0.5000, sse=3458127.8, rms=11.467 (7.452%) 034: dt: 0.5000, sse=3082563.2, rms=10.676 (6.900%) 035: dt: 0.5000, sse=2777441.5, rms=9.988 (6.448%) 036: dt: 0.5000, sse=2523277.5, rms=9.372 (6.169%) 037: dt: 0.5000, sse=2296533.5, rms=8.790 (6.209%) 038: dt: 0.5000, sse=2096683.8, rms=8.239 (6.264%) 039: dt: 0.5000, sse=1916997.9, rms=7.715 (6.358%) 040: dt: 0.5000, sse=1755407.6, rms=7.209 (6.564%) 041: dt: 0.5000, sse=1614626.5, rms=6.741 (6.492%) 042: dt: 0.5000, sse=1500580.0, rms=6.333 (6.059%) 043: dt: 0.5000, sse=1408408.1, rms=5.986 (5.468%) 044: dt: 0.5000, sse=1337100.6, rms=5.700 (4.779%) 045: dt: 0.5000, sse=1281234.2, rms=5.470 (4.033%) 046: dt: 0.5000, sse=1241521.8, rms=5.296 (3.189%) 047: dt: 0.5000, sse=1210327.2, rms=5.160 (2.559%) 048: dt: 0.5000, sse=1186175.6, rms=5.048 (2.175%) 049: dt: 0.5000, sse=1167601.9, rms=4.964 (1.658%) 050: dt: 0.5000, sse=1151598.1, rms=4.887 (1.566%) rms = 4.84, time step reduction 1 of 3 to 0.250... 051: dt: 0.5000, sse=1140795.1, rms=4.839 (0.980%) 052: dt: 0.2500, sse=1064828.8, rms=4.415 (8.754%) 053: dt: 0.2500, sse=1042641.2, rms=4.297 (2.673%) rms = 4.31, time step reduction 2 of 3 to 0.125... rms = 4.25, time step reduction 3 of 3 to 0.062... 054: dt: 0.1250, sse=1035160.2, rms=4.254 (1.000%) positioning took 2.9 minutes mean border=69.5, 2096 (11) missing vertices, mean dist 0.2 [0.2 (%36.4)->0.6 (%63.6))] %37 local maxima, %22 large gradients and %33 min vals, 331 gradients ignored tol=1.0e-04, sigma=1.0, host=node0, 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=1363598.2, rms=4.871 055: dt: 0.5000, sse=1264101.8, rms=4.380 (10.095%) 056: dt: 0.5000, sse=1195027.1, rms=4.027 (8.044%) rms = 4.13, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=1120028.8, rms=3.523 (12.513%) 058: dt: 0.2500, sse=1096186.0, rms=3.344 (5.082%) rms = 3.32, time step reduction 2 of 3 to 0.125... 059: dt: 0.2500, sse=1092637.4, rms=3.320 (0.721%) 060: dt: 0.1250, sse=1068940.5, rms=3.140 (5.435%) rms = 3.11, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=1064188.4, rms=3.106 (1.069%) positioning took 1.2 minutes mean border=68.7, 2573 (8) missing vertices, mean dist 0.1 [0.2 (%38.1)->0.4 (%61.9))] %47 local maxima, %13 large gradients and %32 min vals, 317 gradients ignored tol=1.0e-04, sigma=0.5, host=node0, 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=1094904.6, rms=3.295 rms = 3.60, time step reduction 1 of 3 to 0.250... 062: dt: 0.2500, sse=1072631.2, rms=3.127 (5.078%) 063: dt: 0.2500, sse=1063734.6, rms=3.066 (1.950%) rms = 3.06, time step reduction 2 of 3 to 0.125... 064: dt: 0.2500, sse=1061792.0, rms=3.061 (0.168%) 065: dt: 0.1250, sse=1049317.5, rms=2.959 (3.328%) rms = 2.94, time step reduction 3 of 3 to 0.062... 066: dt: 0.1250, sse=1046218.8, rms=2.939 (0.690%) positioning took 1.0 minutes mean border=68.3, 5001 (8) missing vertices, mean dist 0.1 [0.2 (%43.0)->0.3 (%57.0))] %48 local maxima, %11 large gradients and %31 min vals, 323 gradients ignored tol=1.0e-04, sigma=0.2, host=node0, 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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1055441.5, rms=2.967 rms = 3.22, time step reduction 1 of 3 to 0.250... 067: dt: 0.2500, sse=1045082.2, rms=2.884 (2.799%) rms = 2.84, time step reduction 2 of 3 to 0.125... 068: dt: 0.2500, sse=1037873.4, rms=2.844 (1.384%) rms = 2.80, time step reduction 3 of 3 to 0.062... 069: dt: 0.1250, sse=1032490.8, rms=2.795 (1.700%) positioning took 0.6 minutes writing curvature file /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.area.pial vertex spacing 1.05 +- 0.51 (0.08-->7.61) (max @ vno 73975 --> 73966) face area 0.43 +- 0.39 (0.00-->7.83) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 115906 vertices processed 25000 of 115906 vertices processed 50000 of 115906 vertices processed 75000 of 115906 vertices processed 100000 of 115906 vertices processed 0 of 115906 vertices processed 25000 of 115906 vertices processed 50000 of 115906 vertices processed 75000 of 115906 vertices processed 100000 of 115906 vertices processed thickness calculation complete, 2005:5847 truncations. 20838 vertices at 0 distance 62881 vertices at 1 distance 66017 vertices at 2 distance 39709 vertices at 3 distance 17759 vertices at 4 distance 6905 vertices at 5 distance 2675 vertices at 6 distance 1061 vertices at 7 distance 509 vertices at 8 distance 275 vertices at 9 distance 140 vertices at 10 distance 111 vertices at 11 distance 63 vertices at 12 distance 56 vertices at 13 distance 42 vertices at 14 distance 27 vertices at 15 distance 21 vertices at 16 distance 18 vertices at 17 distance 19 vertices at 18 distance 16 vertices at 19 distance 32 vertices at 20 distance writing curvature file /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.thickness positioning took 14.3 minutes #-------------------------------------------- #@# Surf Volume lh So 11. Mär 07:58:53 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 44538_T1_fs lh /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.volume masking with /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label/lh.cortex.label Total face volume 251239 Total vertex volume 247453 (mask=0) #@# 44538_T1_fs lh 247453 vertexvol Done #-------------------------------------------- #@# Surf Volume rh So 11. Mär 07:58:56 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 44538_T1_fs rh /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.volume masking with /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label/rh.cortex.label Total face volume 255880 Total vertex volume 251876 (mask=0) #@# 44538_T1_fs rh 251876 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask So 11. Mär 07:58:59 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 44538_T1_fs SUBJECTS_DIR is /scratch/annadan1111/MABT1T2/test3 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 = 124 writing volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/ribbon.mgz mris_volmask took 11.70 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh So 11. Mär 08:10:41 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 44538_T1_fs lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white... reading input pial surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 251239 Total vertex volume 247453 (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) = 1565239 mm^3 (det: 1.244605 ) lhCtxGM: 246418.054 246126.000 diff= 292.1 pctdiff= 0.119 rhCtxGM: 250283.102 250399.000 diff= -115.9 pctdiff=-0.046 lhCtxWM: 199638.904 200177.000 diff= -538.1 pctdiff=-0.270 rhCtxWM: 198959.974 199531.000 diff= -571.0 pctdiff=-0.287 SubCortGMVol 58698.000 SupraTentVol 980279.034 (978426.000) diff=1853.034 pctdiff=0.189 SupraTentVolNotVent 956798.034 (954945.000) diff=1853.034 pctdiff=0.194 BrainSegVol 1136768.000 (1134094.000) diff=2674.000 pctdiff=0.235 BrainSegVolNotVent 1109214.000 (1108126.034) diff=1087.966 pctdiff=0.098 BrainSegVolNotVent 1109214.000 CerebellumVol 154114.000 VentChorVol 23481.000 3rd4th5thCSF 4073.000 CSFVol 1399.000, OptChiasmVol 155.000 MaskVol 1668967.000 1056 742 1917 2.768 0.379 0.111 0.025 9 1.1 bankssts 764 472 1665 3.140 0.667 0.132 0.028 11 0.9 caudalanteriorcingulate 2559 1756 5760 2.839 0.555 0.128 0.034 31 3.8 caudalmiddlefrontal 1890 1215 2443 1.882 0.532 0.139 0.036 25 2.7 cuneus 580 390 1960 3.358 0.949 0.120 0.037 5 0.8 entorhinal 4182 2831 10261 3.018 0.760 0.133 0.043 55 7.0 fusiform 5350 3744 14402 2.966 0.788 0.134 0.034 78 7.5 inferiorparietal 4771 3285 15322 3.380 0.923 0.140 0.041 76 7.8 inferiortemporal 1428 905 2679 2.609 0.918 0.119 0.039 18 2.0 isthmuscingulate 6897 4513 11928 2.369 0.672 0.138 0.035 97 9.9 lateraloccipital 3646 2499 8941 3.229 0.955 0.136 0.043 48 7.1 lateralorbitofrontal 4168 2672 6185 2.151 0.793 0.138 0.041 55 6.6 lingual 2305 1585 5849 3.130 0.900 0.127 0.039 34 3.5 medialorbitofrontal 3809 2647 12112 3.284 0.863 0.128 0.035 53 5.6 middletemporal 914 580 2014 2.974 0.828 0.087 0.019 4 0.7 parahippocampal 2043 1298 3671 2.609 0.635 0.124 0.036 20 2.8 paracentral 1935 1358 5205 3.059 0.666 0.135 0.035 29 2.8 parsopercularis 990 691 4025 3.770 0.815 0.154 0.043 18 1.6 parsorbitalis 1756 1239 4721 2.828 0.749 0.134 0.038 26 3.1 parstriangularis 1610 1073 1229 1.324 0.347 0.135 0.035 21 2.3 pericalcarine 5586 3688 9548 2.212 0.703 0.123 0.034 62 7.8 postcentral 1584 1067 3300 2.606 0.864 0.136 0.034 22 2.1 posteriorcingulate 7155 4506 13321 2.662 0.686 0.114 0.032 64 9.3 precentral 4608 3178 10021 2.783 0.659 0.122 0.031 50 5.4 precuneus 906 601 3207 3.681 0.943 0.132 0.045 12 1.6 rostralanteriorcingulate 5809 3972 16751 3.183 0.829 0.144 0.046 90 10.9 rostralmiddlefrontal 8465 5966 23098 3.207 0.708 0.133 0.036 103 12.6 superiorfrontal 5717 3929 11255 2.423 0.629 0.130 0.031 63 7.2 superiorparietal 4511 3069 12464 3.183 0.751 0.115 0.028 45 4.9 superiortemporal 3571 2510 8996 3.016 0.651 0.134 0.037 47 5.3 supramarginal 427 297 1857 3.918 0.596 0.196 0.097 16 1.6 frontalpole 592 390 2754 4.121 0.669 0.136 0.040 7 1.1 temporalpole 528 339 877 2.658 0.424 0.121 0.032 4 0.7 transversetemporal 3340 2205 7695 3.278 1.069 0.106 0.030 24 3.9 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 44538_T1_fs lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.pial... reading input pial surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 251239 Total vertex volume 247453 (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) = 1565239 mm^3 (det: 1.244605 ) lhCtxGM: 246418.054 246126.000 diff= 292.1 pctdiff= 0.119 rhCtxGM: 250283.102 250399.000 diff= -115.9 pctdiff=-0.046 lhCtxWM: 199638.904 200177.000 diff= -538.1 pctdiff=-0.270 rhCtxWM: 198959.974 199531.000 diff= -571.0 pctdiff=-0.287 SubCortGMVol 58698.000 SupraTentVol 980279.034 (978426.000) diff=1853.034 pctdiff=0.189 SupraTentVolNotVent 956798.034 (954945.000) diff=1853.034 pctdiff=0.194 BrainSegVol 1136768.000 (1134094.000) diff=2674.000 pctdiff=0.235 BrainSegVolNotVent 1109214.000 (1108126.034) diff=1087.966 pctdiff=0.098 BrainSegVolNotVent 1109214.000 CerebellumVol 154114.000 VentChorVol 23481.000 3rd4th5thCSF 4073.000 CSFVol 1399.000, OptChiasmVol 155.000 MaskVol 1668967.000 1056 656 1917 2.768 0.379 0.121 0.031 13 1.6 bankssts 764 598 1665 3.140 0.667 0.171 0.044 25 1.4 caudalanteriorcingulate 2559 2238 5760 2.839 0.555 0.143 0.031 31 3.8 caudalmiddlefrontal 1890 1432 2443 1.882 0.532 0.130 0.027 21 2.4 cuneus 580 753 1960 3.358 0.949 0.167 0.036 6 1.0 entorhinal 4182 3681 10261 3.018 0.760 0.145 0.033 65 6.0 fusiform 5350 5511 14402 2.966 0.788 0.165 0.033 83 8.1 inferiorparietal 4771 5118 15322 3.380 0.923 0.169 0.037 71 8.3 inferiortemporal 1428 1089 2679 2.609 0.918 0.133 0.035 20 1.9 isthmuscingulate 6897 5599 11928 2.369 0.672 0.133 0.034 94 9.7 lateraloccipital 3646 3018 8941 3.229 0.955 0.140 0.034 73 5.8 lateralorbitofrontal 4168 3169 6185 2.151 0.793 0.133 0.035 53 6.4 lingual 2305 2079 5849 3.130 0.900 0.152 0.039 76 4.2 medialorbitofrontal 3809 4134 12112 3.284 0.863 0.169 0.040 93 7.4 middletemporal 914 810 2014 2.974 0.828 0.128 0.028 7 1.3 parahippocampal 2043 1492 3671 2.609 0.635 0.123 0.028 29 2.5 paracentral 1935 1913 5205 3.059 0.666 0.162 0.034 24 3.0 parsopercularis 990 1291 4025 3.770 0.815 0.203 0.040 15 1.6 parsorbitalis 1756 1926 4721 2.828 0.749 0.191 0.038 30 3.3 parstriangularis 1610 920 1229 1.324 0.347 0.100 0.027 20 1.9 pericalcarine 5586 4774 9548 2.212 0.703 0.133 0.026 53 6.0 postcentral 1584 1352 3300 2.606 0.864 0.153 0.039 58 2.6 posteriorcingulate 7155 5142 13321 2.662 0.686 0.110 0.024 87 6.9 precentral 4608 3877 10021 2.783 0.659 0.145 0.035 70 7.3 precuneus 906 1008 3207 3.681 0.943 0.186 0.041 13 1.4 rostralanteriorcingulate 5809 5844 16751 3.183 0.829 0.184 0.043 91 12.0 rostralmiddlefrontal 8465 7909 23098 3.207 0.708 0.151 0.032 112 11.7 superiorfrontal 5717 4971 11255 2.423 0.629 0.147 0.030 69 7.7 superiorparietal 4511 4299 12464 3.183 0.751 0.144 0.032 71 6.0 superiortemporal 3571 3267 8996 3.016 0.651 0.154 0.035 51 5.4 supramarginal 427 634 1857 3.918 0.596 0.219 0.038 5 0.7 frontalpole 592 882 2754 4.121 0.669 0.200 0.038 7 1.0 temporalpole 528 349 877 2.658 0.424 0.104 0.027 3 0.6 transversetemporal 3340 2122 7695 3.278 1.069 0.121 0.051 70 9.3 insula #----------------------------------------- #@# Parcellation Stats rh So 11. Mär 08:11:50 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 44538_T1_fs rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white... reading input pial surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 255880 Total vertex volume 251876 (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) = 1565239 mm^3 (det: 1.244605 ) lhCtxGM: 246418.054 246126.000 diff= 292.1 pctdiff= 0.119 rhCtxGM: 250283.102 250399.000 diff= -115.9 pctdiff=-0.046 lhCtxWM: 199638.904 200177.000 diff= -538.1 pctdiff=-0.270 rhCtxWM: 198959.974 199531.000 diff= -571.0 pctdiff=-0.287 SubCortGMVol 58698.000 SupraTentVol 980279.034 (978426.000) diff=1853.034 pctdiff=0.189 SupraTentVolNotVent 956798.034 (954945.000) diff=1853.034 pctdiff=0.194 BrainSegVol 1136768.000 (1134094.000) diff=2674.000 pctdiff=0.235 BrainSegVolNotVent 1109214.000 (1108126.034) diff=1087.966 pctdiff=0.098 BrainSegVolNotVent 1109214.000 CerebellumVol 154114.000 VentChorVol 23481.000 3rd4th5thCSF 4073.000 CSFVol 1399.000, OptChiasmVol 155.000 MaskVol 1668967.000 1140 811 2468 3.137 0.560 0.114 0.026 8 1.3 bankssts 867 539 2031 3.038 0.904 0.147 0.055 17 1.7 caudalanteriorcingulate 2111 1453 4694 2.887 0.652 0.127 0.035 21 3.2 caudalmiddlefrontal 1966 1207 2508 1.922 0.634 0.137 0.034 25 2.9 cuneus 572 366 2005 3.658 0.767 0.129 0.050 7 1.1 entorhinal 4403 2980 10499 2.986 0.782 0.144 0.048 67 8.8 fusiform 6282 4378 15764 2.943 0.719 0.136 0.037 90 10.2 inferiorparietal 3938 2692 11535 3.367 0.893 0.138 0.044 59 6.7 inferiortemporal 1256 796 2552 2.882 1.039 0.131 0.036 17 1.8 isthmuscingulate 6150 3955 11270 2.429 0.759 0.140 0.038 80 9.4 lateraloccipital 3099 2100 8540 3.431 0.788 0.142 0.046 43 5.9 lateralorbitofrontal 4277 2719 6443 2.121 0.739 0.136 0.044 64 6.8 lingual 2590 1723 6237 2.995 0.972 0.119 0.040 37 3.8 medialorbitofrontal 4306 3000 14315 3.503 0.795 0.132 0.037 64 6.5 middletemporal 989 632 1915 2.720 0.681 0.104 0.027 6 1.1 parahippocampal 2250 1415 3783 2.446 0.555 0.125 0.041 26 3.5 paracentral 1452 978 3816 3.118 0.723 0.126 0.037 15 2.1 parsopercularis 1318 906 4485 3.677 0.777 0.165 0.057 25 3.3 parsorbitalis 1758 1231 4684 2.919 0.800 0.135 0.040 23 2.9 parstriangularis 1593 1089 1207 1.312 0.331 0.142 0.039 21 2.7 pericalcarine 5627 3638 9542 2.305 0.724 0.113 0.031 53 6.9 postcentral 1462 990 3547 2.803 1.070 0.150 0.052 26 2.7 posteriorcingulate 6460 4132 12076 2.596 0.660 0.121 0.040 71 10.6 precentral 5130 3426 10367 2.613 0.703 0.122 0.033 58 6.9 precuneus 647 409 1757 3.787 0.727 0.142 0.048 12 1.1 rostralanteriorcingulate 6366 4302 19153 3.201 0.839 0.143 0.050 109 12.9 rostralmiddlefrontal 8908 6089 25202 3.360 0.778 0.132 0.039 115 13.9 superiorfrontal 6917 4645 13027 2.402 0.569 0.122 0.030 79 8.2 superiorparietal 4780 3206 11963 3.104 0.822 0.114 0.033 98 6.9 superiortemporal 4520 3027 11363 3.122 0.670 0.133 0.036 59 6.7 supramarginal 410 264 1862 3.958 0.785 0.163 0.057 11 1.0 frontalpole 558 404 3333 4.306 0.521 0.152 0.072 48 1.7 temporalpole 538 290 835 2.301 0.474 0.115 0.053 6 1.0 transversetemporal 3047 2021 7084 3.339 0.902 0.116 0.037 28 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 44538_T1_fs rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.pial... reading input pial surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 255880 Total vertex volume 251876 (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) = 1565239 mm^3 (det: 1.244605 ) lhCtxGM: 246418.054 246126.000 diff= 292.1 pctdiff= 0.119 rhCtxGM: 250283.102 250399.000 diff= -115.9 pctdiff=-0.046 lhCtxWM: 199638.904 200177.000 diff= -538.1 pctdiff=-0.270 rhCtxWM: 198959.974 199531.000 diff= -571.0 pctdiff=-0.287 SubCortGMVol 58698.000 SupraTentVol 980279.034 (978426.000) diff=1853.034 pctdiff=0.189 SupraTentVolNotVent 956798.034 (954945.000) diff=1853.034 pctdiff=0.194 BrainSegVol 1136768.000 (1134094.000) diff=2674.000 pctdiff=0.235 BrainSegVolNotVent 1109214.000 (1108126.034) diff=1087.966 pctdiff=0.098 BrainSegVolNotVent 1109214.000 CerebellumVol 154114.000 VentChorVol 23481.000 3rd4th5thCSF 4073.000 CSFVol 1399.000, OptChiasmVol 155.000 MaskVol 1668967.000 1140 719 2468 3.137 0.560 0.114 0.033 16 1.5 bankssts 867 748 2031 3.038 0.904 0.168 0.043 39 1.3 caudalanteriorcingulate 2111 1813 4694 2.887 0.652 0.152 0.033 32 3.4 caudalmiddlefrontal 1966 1447 2508 1.922 0.634 0.128 0.030 41 2.3 cuneus 572 671 2005 3.658 0.767 0.137 0.030 4 0.7 entorhinal 4403 3816 10499 2.986 0.782 0.139 0.034 71 6.6 fusiform 6282 5825 15764 2.943 0.719 0.154 0.033 94 9.6 inferiorparietal 3938 3790 11535 3.367 0.893 0.156 0.036 75 6.3 inferiortemporal 1256 965 2552 2.882 1.039 0.131 0.032 27 1.8 isthmuscingulate 6150 5199 11270 2.429 0.759 0.131 0.029 79 7.9 lateraloccipital 3099 2661 8540 3.431 0.788 0.149 0.037 56 5.3 lateralorbitofrontal 4277 3297 6443 2.121 0.739 0.135 0.047 73 10.5 lingual 2590 2291 6237 2.995 0.972 0.147 0.036 43 3.9 medialorbitofrontal 4306 4786 14315 3.503 0.795 0.168 0.034 57 7.1 middletemporal 989 776 1915 2.720 0.681 0.123 0.028 10 1.3 parahippocampal 2250 1631 3783 2.446 0.555 0.124 0.030 27 2.6 paracentral 1452 1364 3816 3.118 0.723 0.153 0.031 26 1.9 parsopercularis 1318 1471 4485 3.677 0.777 0.180 0.037 17 2.4 parsorbitalis 1758 1765 4684 2.919 0.800 0.176 0.042 30 3.2 parstriangularis 1593 938 1207 1.312 0.331 0.111 0.036 44 2.6 pericalcarine 5627 4521 9542 2.305 0.724 0.120 0.024 43 5.8 postcentral 1462 1341 3547 2.803 1.070 0.190 0.052 49 3.7 posteriorcingulate 6460 4839 12076 2.596 0.660 0.119 0.028 92 7.7 precentral 5130 4247 10367 2.613 0.703 0.143 0.033 77 7.7 precuneus 647 588 1757 3.787 0.727 0.153 0.041 21 1.0 rostralanteriorcingulate 6366 6999 19153 3.201 0.839 0.191 0.042 102 13.2 rostralmiddlefrontal 8908 8232 25202 3.360 0.778 0.154 0.034 125 13.0 superiorfrontal 6917 5920 13027 2.402 0.569 0.137 0.028 92 8.3 superiorparietal 4780 4209 11963 3.104 0.822 0.135 0.033 84 7.0 superiortemporal 4520 3955 11363 3.122 0.670 0.143 0.034 61 6.6 supramarginal 410 600 1862 3.958 0.785 0.241 0.039 8 0.8 frontalpole 558 1013 3333 4.306 0.521 0.237 0.054 11 1.1 temporalpole 538 413 835 2.301 0.474 0.106 0.030 2 0.6 transversetemporal 3047 1855 7084 3.339 0.902 0.119 0.035 58 4.3 insula #----------------------------------------- #@# Cortical Parc 2 lh So 11. Mär 08:13:04 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 44538_T1_fs lh ../surf/lh.sphere.reg /cm/shared/apps/freesurfer/6.0.0/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 /cm/shared/apps/freesurfer/6.0.0/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... 68 labels changed using aseg relabeling using gibbs priors... 000: 7371 changed, 113373 examined... 001: 1736 changed, 29098 examined... 002: 501 changed, 9258 examined... 003: 203 changed, 2812 examined... 004: 109 changed, 1206 examined... 005: 59 changed, 609 examined... 006: 29 changed, 319 examined... 007: 17 changed, 164 examined... 008: 8 changed, 94 examined... 009: 7 changed, 54 examined... 010: 1 changed, 37 examined... 011: 0 changed, 8 examined... 33 labels changed using aseg 000: 231 total segments, 149 labels (1700 vertices) changed 001: 85 total segments, 3 labels (48 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 32 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1118 vertices marked for relabeling... 1118 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 17 seconds. #----------------------------------------- #@# Cortical Parc 2 rh So 11. Mär 08:13:21 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 44538_T1_fs rh ../surf/rh.sphere.reg /cm/shared/apps/freesurfer/6.0.0/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 /cm/shared/apps/freesurfer/6.0.0/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... 31 labels changed using aseg relabeling using gibbs priors... 000: 7318 changed, 115906 examined... 001: 1671 changed, 28933 examined... 002: 493 changed, 8813 examined... 003: 192 changed, 2840 examined... 004: 83 changed, 1118 examined... 005: 30 changed, 443 examined... 006: 16 changed, 175 examined... 007: 6 changed, 83 examined... 008: 2 changed, 34 examined... 009: 3 changed, 14 examined... 010: 1 changed, 17 examined... 011: 0 changed, 7 examined... 30 labels changed using aseg 000: 211 total segments, 130 labels (1470 vertices) changed 001: 87 total segments, 6 labels (17 vertices) changed 002: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 32 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 790 vertices marked for relabeling... 790 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 17 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh So 11. Mär 08:13:38 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 44538_T1_fs lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white... reading input pial surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 251239 Total vertex volume 247453 (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) = 1565239 mm^3 (det: 1.244605 ) lhCtxGM: 246418.054 246126.000 diff= 292.1 pctdiff= 0.119 rhCtxGM: 250283.102 250399.000 diff= -115.9 pctdiff=-0.046 lhCtxWM: 199638.904 200177.000 diff= -538.1 pctdiff=-0.270 rhCtxWM: 198959.974 199531.000 diff= -571.0 pctdiff=-0.287 SubCortGMVol 58698.000 SupraTentVol 980279.034 (978426.000) diff=1853.034 pctdiff=0.189 SupraTentVolNotVent 956798.034 (954945.000) diff=1853.034 pctdiff=0.194 BrainSegVol 1136768.000 (1134094.000) diff=2674.000 pctdiff=0.235 BrainSegVolNotVent 1109214.000 (1108126.034) diff=1087.966 pctdiff=0.098 BrainSegVolNotVent 1109214.000 CerebellumVol 154114.000 VentChorVol 23481.000 3rd4th5thCSF 4073.000 CSFVol 1399.000, OptChiasmVol 155.000 MaskVol 1668967.000 849 598 2714 3.586 1.037 0.160 0.055 15 1.9 G&S_frontomargin 1534 1018 2714 2.400 0.585 0.141 0.032 23 2.0 G&S_occipital_inf 1642 980 2536 2.241 0.604 0.133 0.041 19 2.8 G&S_paracentral 1180 782 3154 3.107 0.575 0.131 0.037 16 1.6 G&S_subcentral 630 451 2300 3.457 0.561 0.174 0.068 19 1.7 G&S_transv_frontopol 1612 1108 4722 3.432 0.754 0.123 0.037 16 2.3 G&S_cingul-Ant 1040 720 2380 3.071 0.640 0.133 0.031 13 1.3 G&S_cingul-Mid-Ant 1190 824 2372 2.612 0.620 0.118 0.028 10 1.3 G&S_cingul-Mid-Post 642 408 2079 3.441 0.813 0.157 0.066 14 1.6 G_cingul-Post-dorsal 202 131 454 2.965 0.869 0.127 0.038 2 0.2 G_cingul-Post-ventral 1713 1094 2418 1.901 0.625 0.146 0.039 25 2.7 G_cuneus 1202 819 3957 3.364 0.546 0.147 0.042 26 2.0 G_front_inf-Opercular 412 273 1622 3.679 0.622 0.171 0.039 9 0.6 G_front_inf-Orbital 962 654 3529 3.308 0.665 0.154 0.055 22 2.5 G_front_inf-Triangul 3182 2162 10446 3.211 0.715 0.150 0.050 61 6.4 G_front_middle 6200 4301 19050 3.309 0.708 0.141 0.043 88 11.1 G_front_sup 659 421 1737 3.648 0.933 0.116 0.039 7 1.0 G_Ins_lg&S_cent_ins 567 373 2319 4.275 0.594 0.101 0.029 4 0.6 G_insular_short 2226 1520 6485 2.998 0.846 0.154 0.045 47 4.4 G_occipital_middle 1099 721 2049 2.381 0.531 0.129 0.030 11 1.4 G_occipital_sup 1813 1180 5043 3.082 0.782 0.141 0.055 32 3.9 G_oc-temp_lat-fusifor 3035 1896 4371 2.017 0.814 0.144 0.045 45 5.3 G_oc-temp_med-Lingual 1225 775 3376 3.202 0.880 0.108 0.031 11 1.5 G_oc-temp_med-Parahip 2380 1624 8278 3.399 1.051 0.165 0.059 52 6.4 G_orbital 1984 1392 6553 3.177 0.810 0.147 0.039 38 3.2 G_pariet_inf-Angular 1713 1192 5235 3.167 0.650 0.146 0.048 32 3.0 G_pariet_inf-Supramar 2020 1452 5010 2.637 0.663 0.152 0.039 32 3.3 G_parietal_sup 2315 1453 4494 2.372 0.643 0.139 0.043 33 3.9 G_postcentral 2688 1576 5848 2.810 0.699 0.113 0.038 30 3.9 G_precentral 2344 1590 6678 2.973 0.652 0.132 0.037 36 3.1 G_precuneus 841 590 2685 3.122 1.033 0.162 0.063 22 2.1 G_rectus 721 433 1279 2.575 1.375 0.093 0.036 6 0.8 G_subcallosal 348 219 692 2.837 0.432 0.119 0.033 3 0.5 G_temp_sup-G_T_transv 1525 1083 6465 3.641 0.735 0.148 0.038 26 2.2 G_temp_sup-Lateral 597 437 1855 3.433 0.643 0.088 0.018 3 0.5 G_temp_sup-Plan_polar 672 463 1851 3.170 0.636 0.128 0.036 9 1.0 G_temp_sup-Plan_tempo 3024 2040 11127 3.474 0.981 0.150 0.049 59 5.9 G_temporal_inf 2059 1408 8917 3.674 0.793 0.147 0.048 43 4.1 G_temporal_middle 323 230 492 2.150 0.436 0.099 0.020 1 0.2 Lat_Fis-ant-Horizont 336 257 631 2.705 0.561 0.118 0.022 2 0.3 Lat_Fis-ant-Vertical 798 547 1126 2.689 0.554 0.121 0.028 6 1.0 Lat_Fis-post 2008 1200 2803 2.130 0.617 0.138 0.036 29 2.8 Pole_occipital 1448 1033 6242 3.981 0.767 0.146 0.044 21 2.3 Pole_temporal 2064 1395 2198 1.827 0.785 0.124 0.031 21 2.7 S_calcarine 3204 2168 3821 1.998 0.633 0.112 0.027 21 3.8 S_central 1017 699 1521 2.479 0.547 0.110 0.025 7 1.0 S_cingul-Marginalis 517 358 977 3.293 0.417 0.089 0.018 2 0.4 S_circular_insula_ant 1339 878 2371 3.142 0.852 0.089 0.018 5 1.0 S_circular_insula_inf 1579 1075 2412 2.756 0.597 0.108 0.024 8 1.7 S_circular_insula_sup 791 556 1888 3.190 0.768 0.125 0.035 8 1.2 S_collat_transv_ant 331 225 342 2.022 0.619 0.150 0.030 4 0.5 S_collat_transv_post 1491 1029 2597 2.626 0.499 0.115 0.024 10 1.5 S_front_inf 1064 724 2150 2.795 0.689 0.124 0.035 9 1.6 S_front_middle 2091 1476 4903 3.102 0.689 0.130 0.036 23 3.0 S_front_sup 159 113 277 2.687 0.377 0.123 0.018 1 0.2 S_interm_prim-Jensen 2304 1598 3552 2.343 0.496 0.114 0.023 17 2.3 S_intrapariet&P_trans 945 665 1353 2.078 0.516 0.122 0.026 7 1.0 S_oc_middle&Lunatus 892 622 1299 2.233 0.492 0.107 0.019 6 0.7 S_oc_sup&transversal 495 346 980 2.687 0.533 0.119 0.029 5 0.5 S_occipital_ant 1006 682 1733 2.880 0.516 0.108 0.026 6 0.9 S_oc-temp_lat 1830 1261 3046 2.571 0.567 0.108 0.023 11 1.7 S_oc-temp_med&Lingual 400 279 624 2.650 0.531 0.128 0.030 3 0.5 S_orbital_lateral 543 439 933 2.726 0.589 0.126 0.022 4 0.4 S_orbital_med-olfact 1327 897 3176 3.596 0.981 0.118 0.034 11 2.0 S_orbital-H_Shaped 1817 1227 2646 2.329 0.749 0.116 0.026 16 1.9 S_parieto_occipital 1264 751 1117 2.124 0.826 0.112 0.024 15 1.0 S_pericallosal 2105 1438 3298 2.432 0.588 0.116 0.030 16 2.4 S_postcentral 1083 762 2163 2.781 0.551 0.105 0.022 7 0.9 S_precentral-inf-part 1292 891 1942 2.567 0.377 0.103 0.023 6 1.2 S_precentral-sup-part 579 383 1210 3.263 0.825 0.110 0.021 4 0.5 S_suborbital 773 534 1246 2.604 0.496 0.117 0.029 5 0.8 S_subparietal 1254 886 2031 2.827 0.586 0.128 0.024 12 1.5 S_temporal_inf 4716 3279 9130 2.806 0.610 0.108 0.025 35 4.7 S_temporal_sup 245 163 426 2.499 0.364 0.086 0.017 1 0.2 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh So 11. Mär 08:14:18 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 44538_T1_fs rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white... reading input pial surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 255880 Total vertex volume 251876 (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) = 1565239 mm^3 (det: 1.244605 ) lhCtxGM: 246418.054 246126.000 diff= 292.1 pctdiff= 0.119 rhCtxGM: 250283.102 250399.000 diff= -115.9 pctdiff=-0.046 lhCtxWM: 199638.904 200177.000 diff= -538.1 pctdiff=-0.270 rhCtxWM: 198959.974 199531.000 diff= -571.0 pctdiff=-0.287 SubCortGMVol 58698.000 SupraTentVol 980279.034 (978426.000) diff=1853.034 pctdiff=0.189 SupraTentVolNotVent 956798.034 (954945.000) diff=1853.034 pctdiff=0.194 BrainSegVol 1136768.000 (1134094.000) diff=2674.000 pctdiff=0.235 BrainSegVolNotVent 1109214.000 (1108126.034) diff=1087.966 pctdiff=0.098 BrainSegVolNotVent 1109214.000 CerebellumVol 154114.000 VentChorVol 23481.000 3rd4th5thCSF 4073.000 CSFVol 1399.000, OptChiasmVol 155.000 MaskVol 1668967.000 849 578 3141 3.561 0.899 0.159 0.058 17 2.1 G&S_frontomargin 1140 780 2622 2.787 0.829 0.144 0.038 16 1.8 G&S_occipital_inf 1410 822 2223 2.278 0.530 0.119 0.039 17 2.0 G&S_paracentral 1196 819 2823 3.049 0.498 0.141 0.042 17 1.9 G&S_subcentral 881 599 3443 3.677 0.754 0.159 0.058 17 2.1 G&S_transv_frontopol 2446 1591 6307 3.561 0.783 0.131 0.040 33 3.6 G&S_cingul-Ant 1043 706 2619 3.229 0.761 0.128 0.044 14 1.8 G&S_cingul-Mid-Ant 1334 902 2845 2.827 0.756 0.141 0.051 20 2.3 G&S_cingul-Mid-Post 458 310 1831 3.698 0.921 0.182 0.060 10 1.3 G_cingul-Post-dorsal 321 188 776 3.338 0.869 0.131 0.039 4 0.4 G_cingul-Post-ventral 1813 1119 2461 1.903 0.662 0.139 0.037 24 2.8 G_cuneus 1037 702 3653 3.476 0.577 0.150 0.047 17 1.9 G_front_inf-Opercular 556 388 1953 3.312 0.650 0.173 0.069 13 1.7 G_front_inf-Orbital 604 421 2234 3.370 0.804 0.149 0.054 9 1.2 G_front_inf-Triangul 3308 2212 12340 3.407 0.734 0.163 0.064 79 8.5 G_front_middle 5968 4013 18451 3.385 0.783 0.141 0.046 94 10.6 G_front_sup 574 406 1959 4.031 0.881 0.125 0.053 7 1.1 G_Ins_lg&S_cent_ins 480 300 1865 4.047 0.840 0.113 0.038 5 0.7 G_insular_short 1479 1035 4529 3.158 0.741 0.145 0.040 23 2.3 G_occipital_middle 1357 837 2614 2.472 0.539 0.128 0.036 16 1.9 G_occipital_sup 2252 1434 6130 2.929 0.851 0.156 0.061 47 6.1 G_oc-temp_lat-fusifor 2849 1781 4446 2.072 0.786 0.142 0.048 51 4.7 G_oc-temp_med-Lingual 1184 736 3331 3.220 0.864 0.119 0.043 12 2.1 G_oc-temp_med-Parahip 2299 1570 8760 3.797 0.760 0.170 0.063 49 6.0 G_orbital 2322 1626 8462 3.347 0.675 0.167 0.055 56 5.8 G_pariet_inf-Angular 2203 1469 6931 3.449 0.602 0.147 0.042 37 3.7 G_pariet_inf-Supramar 2262 1587 5488 2.601 0.535 0.138 0.037 39 3.4 G_parietal_sup 1950 1139 3854 2.472 0.712 0.116 0.036 23 2.8 G_postcentral 2538 1506 5956 2.786 0.698 0.128 0.055 42 5.6 G_precentral 2154 1434 5901 2.859 0.670 0.136 0.041 36 3.6 G_precuneus 758 496 2475 3.023 0.998 0.148 0.065 19 2.0 G_rectus 432 283 571 2.103 0.879 0.078 0.031 3 0.3 G_subcallosal 425 229 781 2.388 0.491 0.119 0.057 5 0.7 G_temp_sup-G_T_transv 1626 1096 5857 3.535 0.644 0.147 0.046 29 3.0 G_temp_sup-Lateral 783 535 1890 3.307 0.832 0.109 0.044 44 1.5 G_temp_sup-Plan_polar 747 490 1414 2.587 0.729 0.074 0.014 3 0.4 G_temp_sup-Plan_tempo 2118 1394 7464 3.562 0.922 0.152 0.055 42 4.6 G_temporal_inf 2500 1739 10330 3.734 0.708 0.151 0.046 53 4.6 G_temporal_middle 335 238 472 2.119 0.419 0.109 0.022 2 0.3 Lat_Fis-ant-Horizont 121 81 208 2.834 0.507 0.128 0.034 1 0.2 Lat_Fis-ant-Vertical 1307 841 1797 2.610 0.710 0.119 0.043 61 2.8 Lat_Fis-post 2920 1793 4155 1.993 0.752 0.133 0.036 34 4.6 Pole_occipital 1486 1088 7411 4.098 0.659 0.149 0.052 23 3.0 Pole_temporal 2044 1369 2306 1.964 0.825 0.131 0.039 22 3.2 S_calcarine 2766 1919 3221 1.951 0.562 0.114 0.030 18 3.4 S_central 1068 730 1683 2.533 0.583 0.111 0.030 8 1.3 S_cingul-Marginalis 650 434 1250 3.433 0.688 0.100 0.023 3 0.6 S_circular_insula_ant 1112 719 1574 2.718 0.572 0.093 0.021 5 1.0 S_circular_insula_inf 1357 913 2220 2.886 0.541 0.103 0.022 7 1.4 S_circular_insula_sup 862 586 1575 2.912 0.845 0.115 0.027 6 1.0 S_collat_transv_ant 350 244 412 1.924 0.491 0.147 0.038 4 0.5 S_collat_transv_post 1243 852 2525 2.782 0.772 0.119 0.034 12 1.8 S_front_inf 1714 1180 3092 2.585 0.629 0.117 0.025 13 1.9 S_front_middle 2009 1378 3935 2.979 0.640 0.111 0.026 13 2.1 S_front_sup 239 173 396 2.568 0.564 0.125 0.025 2 0.2 S_interm_prim-Jensen 2813 1927 4248 2.293 0.497 0.115 0.027 25 3.0 S_intrapariet&P_trans 502 360 865 2.539 0.515 0.138 0.038 6 0.6 S_oc_middle&Lunatus 1108 726 1410 2.295 0.509 0.135 0.031 11 1.4 S_oc_sup&transversal 692 498 1286 2.772 0.489 0.131 0.033 7 0.8 S_occipital_ant 1194 823 2153 3.058 0.563 0.134 0.037 15 1.6 S_oc-temp_lat 1840 1279 2880 2.533 0.542 0.107 0.023 11 1.6 S_oc-temp_med&Lingual 434 295 738 2.775 0.425 0.106 0.022 2 0.4 S_orbital_lateral 522 371 1005 2.881 0.562 0.111 0.023 3 0.5 S_orbital_med-olfact 1042 718 2357 3.351 0.857 0.123 0.037 9 1.6 S_orbital-H_Shaped 2517 1597 3425 2.229 0.682 0.119 0.028 23 2.9 S_parieto_occipital 1219 750 1132 2.259 0.976 0.119 0.025 15 0.9 S_pericallosal 2458 1667 3355 2.269 0.481 0.104 0.024 14 2.5 S_postcentral 1208 826 1935 2.748 0.499 0.099 0.019 5 1.0 S_precentral-inf-part 1064 728 1521 2.336 0.500 0.116 0.027 6 1.3 S_precentral-sup-part 316 217 646 3.348 1.075 0.104 0.023 2 0.3 S_suborbital 797 562 1387 2.581 0.575 0.117 0.026 5 0.8 S_subparietal 910 659 2076 3.409 0.776 0.125 0.030 7 1.1 S_temporal_inf 5479 3779 10082 2.899 0.589 0.104 0.022 34 5.0 S_temporal_sup 306 211 414 2.381 0.490 0.131 0.028 2 0.4 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh So 11. Mär 08:15:00 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 44538_T1_fs lh ../surf/lh.sphere.reg /cm/shared/apps/freesurfer/6.0.0/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 /cm/shared/apps/freesurfer/6.0.0/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... 1317 labels changed using aseg relabeling using gibbs priors... 000: 1756 changed, 113373 examined... 001: 406 changed, 8187 examined... 002: 120 changed, 2361 examined... 003: 59 changed, 704 examined... 004: 35 changed, 312 examined... 005: 23 changed, 180 examined... 006: 23 changed, 133 examined... 007: 23 changed, 116 examined... 008: 13 changed, 111 examined... 009: 9 changed, 81 examined... 010: 10 changed, 49 examined... 011: 11 changed, 59 examined... 012: 7 changed, 52 examined... 013: 4 changed, 41 examined... 014: 3 changed, 23 examined... 015: 3 changed, 15 examined... 016: 2 changed, 15 examined... 017: 2 changed, 12 examined... 018: 1 changed, 15 examined... 019: 1 changed, 7 examined... 020: 0 changed, 8 examined... 335 labels changed using aseg 000: 50 total segments, 17 labels (162 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 9 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 799 vertices marked for relabeling... 799 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 14 seconds. #----------------------------------------- #@# Cortical Parc 3 rh So 11. Mär 08:15:14 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 44538_T1_fs rh ../surf/rh.sphere.reg /cm/shared/apps/freesurfer/6.0.0/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 /cm/shared/apps/freesurfer/6.0.0/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... 1418 labels changed using aseg relabeling using gibbs priors... 000: 1781 changed, 115906 examined... 001: 424 changed, 8261 examined... 002: 141 changed, 2374 examined... 003: 71 changed, 854 examined... 004: 46 changed, 417 examined... 005: 28 changed, 249 examined... 006: 23 changed, 158 examined... 007: 23 changed, 110 examined... 008: 17 changed, 125 examined... 009: 13 changed, 86 examined... 010: 14 changed, 74 examined... 011: 13 changed, 73 examined... 012: 7 changed, 61 examined... 013: 5 changed, 37 examined... 014: 7 changed, 28 examined... 015: 5 changed, 29 examined... 016: 2 changed, 21 examined... 017: 0 changed, 10 examined... 378 labels changed using aseg 000: 51 total segments, 18 labels (130 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 5 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 573 vertices marked for relabeling... 573 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 14 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh So 11. Mär 08:15:29 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 44538_T1_fs lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white... reading input pial surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 251239 Total vertex volume 247453 (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) = 1565239 mm^3 (det: 1.244605 ) lhCtxGM: 246418.054 246126.000 diff= 292.1 pctdiff= 0.119 rhCtxGM: 250283.102 250399.000 diff= -115.9 pctdiff=-0.046 lhCtxWM: 199638.904 200177.000 diff= -538.1 pctdiff=-0.270 rhCtxWM: 198959.974 199531.000 diff= -571.0 pctdiff=-0.287 SubCortGMVol 58698.000 SupraTentVol 980279.034 (978426.000) diff=1853.034 pctdiff=0.189 SupraTentVolNotVent 956798.034 (954945.000) diff=1853.034 pctdiff=0.194 BrainSegVol 1136768.000 (1134094.000) diff=2674.000 pctdiff=0.235 BrainSegVolNotVent 1109214.000 (1108126.034) diff=1087.966 pctdiff=0.098 BrainSegVolNotVent 1109214.000 CerebellumVol 154114.000 VentChorVol 23481.000 3rd4th5thCSF 4073.000 CSFVol 1399.000, OptChiasmVol 155.000 MaskVol 1668967.000 1282 827 2753 3.061 0.684 0.132 0.031 17 1.6 caudalanteriorcingulate 2711 1858 6021 2.833 0.544 0.127 0.034 32 3.8 caudalmiddlefrontal 2573 1656 3567 1.968 0.565 0.132 0.032 31 3.3 cuneus 568 380 1942 3.275 0.994 0.123 0.039 5 1.0 entorhinal 3704 2491 8707 2.999 0.716 0.132 0.041 47 5.9 fusiform 5380 3793 14620 2.944 0.797 0.135 0.034 79 7.6 inferiorparietal 4915 3381 15586 3.345 0.946 0.139 0.043 75 8.3 inferiortemporal 1405 884 2622 2.602 0.940 0.123 0.041 18 2.0 isthmuscingulate 6948 4542 11976 2.358 0.666 0.137 0.034 97 9.7 lateraloccipital 3814 2611 10202 3.384 1.036 0.142 0.047 55 7.9 lateralorbitofrontal 4233 2714 6292 2.150 0.790 0.138 0.041 56 6.6 lingual 2076 1420 5450 3.051 1.115 0.135 0.046 35 3.7 medialorbitofrontal 5109 3533 15347 3.258 0.819 0.129 0.035 71 7.4 middletemporal 965 610 2124 2.975 0.847 0.086 0.019 4 0.7 parahippocampal 2426 1565 4478 2.630 0.655 0.125 0.036 23 3.4 paracentral 1858 1284 4869 3.041 0.657 0.135 0.035 29 2.7 parsopercularis 1142 778 3510 3.321 0.802 0.137 0.032 16 1.5 parsorbitalis 1987 1401 5220 2.875 0.731 0.136 0.040 29 3.4 parstriangularis 1582 1054 1211 1.345 0.385 0.136 0.036 21 2.3 pericalcarine 6326 4204 11043 2.255 0.708 0.127 0.036 70 9.2 postcentral 1763 1185 3557 2.614 0.839 0.136 0.037 25 2.6 posteriorcingulate 7055 4446 13179 2.678 0.691 0.114 0.032 63 9.2 precentral 4401 3057 9838 2.799 0.659 0.122 0.030 47 5.0 precuneus 1306 857 3901 3.487 0.963 0.125 0.039 15 2.0 rostralanteriorcingulate 4225 2874 12125 3.099 0.791 0.140 0.044 61 7.8 rostralmiddlefrontal 9150 6456 26721 3.269 0.727 0.138 0.041 131 15.0 superiorfrontal 4461 3083 8692 2.436 0.622 0.131 0.031 51 5.6 superiorparietal 5809 3966 16451 3.209 0.779 0.116 0.029 58 6.6 superiortemporal 3155 2223 7930 3.034 0.662 0.135 0.038 41 4.6 supramarginal 525 337 871 2.673 0.414 0.121 0.031 4 0.7 transversetemporal 2623 1757 6647 3.508 0.912 0.097 0.025 14 2.7 insula #----------------------------------------- #@# Parcellation Stats 3 rh So 11. Mär 08:16:09 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 44538_T1_fs rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white... reading input pial surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 255880 Total vertex volume 251876 (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) = 1565239 mm^3 (det: 1.244605 ) lhCtxGM: 246418.054 246126.000 diff= 292.1 pctdiff= 0.119 rhCtxGM: 250283.102 250399.000 diff= -115.9 pctdiff=-0.046 lhCtxWM: 199638.904 200177.000 diff= -538.1 pctdiff=-0.270 rhCtxWM: 198959.974 199531.000 diff= -571.0 pctdiff=-0.287 SubCortGMVol 58698.000 SupraTentVol 980279.034 (978426.000) diff=1853.034 pctdiff=0.189 SupraTentVolNotVent 956798.034 (954945.000) diff=1853.034 pctdiff=0.194 BrainSegVol 1136768.000 (1134094.000) diff=2674.000 pctdiff=0.235 BrainSegVolNotVent 1109214.000 (1108126.034) diff=1087.966 pctdiff=0.098 BrainSegVolNotVent 1109214.000 CerebellumVol 154114.000 VentChorVol 23481.000 3rd4th5thCSF 4073.000 CSFVol 1399.000, OptChiasmVol 155.000 MaskVol 1668967.000 986 612 2301 2.978 0.939 0.142 0.052 19 1.8 caudalanteriorcingulate 2342 1592 5243 2.865 0.687 0.129 0.039 29 3.9 caudalmiddlefrontal 2614 1573 3610 2.034 0.690 0.128 0.032 30 3.5 cuneus 530 333 1858 3.640 0.773 0.125 0.050 6 1.0 entorhinal 4007 2684 9002 2.919 0.766 0.142 0.048 60 8.2 fusiform 6170 4297 15718 2.958 0.723 0.138 0.038 92 10.2 inferiorparietal 4451 3057 13602 3.406 0.873 0.142 0.046 69 7.9 inferiortemporal 1237 783 2547 2.923 0.998 0.129 0.035 15 1.7 isthmuscingulate 6037 3896 10814 2.379 0.738 0.140 0.037 78 9.1 lateraloccipital 3381 2288 10107 3.500 0.802 0.148 0.051 52 7.5 lateralorbitofrontal 4249 2694 6414 2.127 0.735 0.136 0.045 63 6.7 lingual 1738 1161 4876 3.149 1.065 0.121 0.045 28 3.0 medialorbitofrontal 5216 3623 16208 3.420 0.779 0.127 0.034 71 7.4 middletemporal 1076 686 2062 2.703 0.702 0.106 0.028 8 1.3 parahippocampal 2260 1424 3820 2.450 0.558 0.121 0.040 26 3.4 paracentral 1692 1136 4342 3.077 0.739 0.128 0.039 18 2.5 parsopercularis 1242 848 3952 3.446 0.852 0.153 0.049 20 2.5 parsorbitalis 1579 1119 4146 2.905 0.810 0.135 0.041 20 2.6 parstriangularis 1563 1072 1181 1.311 0.334 0.143 0.039 21 2.6 pericalcarine 6108 3982 10354 2.306 0.723 0.114 0.031 57 7.6 postcentral 1567 1069 3859 2.836 1.016 0.155 0.053 29 3.0 posteriorcingulate 6129 3902 11602 2.624 0.659 0.120 0.039 65 9.9 precentral 5247 3544 10765 2.611 0.697 0.124 0.032 60 7.0 precuneus 1001 629 2187 3.326 1.033 0.128 0.040 15 1.4 rostralanteriorcingulate 4507 3059 13236 3.187 0.800 0.145 0.049 75 9.0 rostralmiddlefrontal 11391 7747 32385 3.323 0.806 0.134 0.040 156 18.4 superiorfrontal 5666 3836 10880 2.424 0.562 0.120 0.030 65 6.6 superiorparietal 6163 4185 16843 3.217 0.845 0.119 0.037 154 9.8 superiortemporal 4260 2854 10514 3.104 0.673 0.133 0.037 54 6.4 supramarginal 517 276 778 2.298 0.460 0.115 0.055 5 1.0 transversetemporal 2734 1839 6668 3.419 0.894 0.111 0.033 22 3.6 insula #----------------------------------------- #@# WM/GM Contrast lh So 11. Mär 08:16:49 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts pctsurfcon --s 44538_T1_fs --lh-only Log file is /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts/pctsurfcon.log So 11. Mär 08:16:50 CET 2018 setenv SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test3 cd /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts /cm/shared/apps/freesurfer/6.0.0/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux node005 2.6.32-696.16.1.el6.x86_64 #1 SMP Tue Nov 14 14:23:46 CST 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 mri_vol2surf --mov /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/tmp.pctsurfcon.63917/lh.wm.mgh --regheader 44538_T1_fs --cortex srcvol = /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99959 0.01347 -0.02525 0.00002; -0.02408 0.08109 0.99642 -0.00004; -0.01547 -0.99662 0.08073 -0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label/lh.cortex.label Reading surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 = 63013 Masking with /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label/lh.cortex.label Writing to /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/tmp.pctsurfcon.63917/lh.wm.mgh Dim: 113373 1 1 mri_vol2surf --mov /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/tmp.pctsurfcon.63917/lh.gm.mgh --projfrac 0.3 --regheader 44538_T1_fs --cortex srcvol = /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99959 0.01347 -0.02525 0.00002; -0.02408 0.08109 0.99642 -0.00004; -0.01547 -0.99662 0.08073 -0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label/lh.cortex.label Reading surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Done reading source surface Reading thickness /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 = 73648 Masking with /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label/lh.cortex.label Writing to /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/tmp.pctsurfcon.63917/lh.gm.mgh Dim: 113373 1 1 mri_concat /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/tmp.pctsurfcon.63917/lh.wm.mgh /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/tmp.pctsurfcon.63917/lh.gm.mgh --paired-diff-norm --mul 100 --o /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.w-g.pct.mgh mri_segstats --in /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.w-g.pct.mgh --annot 44538_T1_fs lh aparc --sum /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.w-g.pct.mgh --annot 44538_T1_fs lh aparc --sum /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/stats/lh.w-g.pct.stats --snr sysname Linux hostname node005 machine x86_64 user annadan1111 UseRobust 0 Constructing seg from annotation Reading annotation /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.w-g.pct.mgh Vertex Area is 0.675096 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 So 11. Mär 08:16:55 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts pctsurfcon --s 44538_T1_fs --rh-only Log file is /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts/pctsurfcon.log So 11. Mär 08:16:55 CET 2018 setenv SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test3 cd /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/scripts /cm/shared/apps/freesurfer/6.0.0/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux node005 2.6.32-696.16.1.el6.x86_64 #1 SMP Tue Nov 14 14:23:46 CST 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 mri_vol2surf --mov /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/tmp.pctsurfcon.63971/rh.wm.mgh --regheader 44538_T1_fs --cortex srcvol = /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99959 0.01347 -0.02525 0.00002; -0.02408 0.08109 0.99642 -0.00004; -0.01547 -0.99662 0.08073 -0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label/rh.cortex.label Reading surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 = 63948 Masking with /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label/rh.cortex.label Writing to /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/tmp.pctsurfcon.63971/rh.wm.mgh Dim: 115906 1 1 mri_vol2surf --mov /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/tmp.pctsurfcon.63971/rh.gm.mgh --projfrac 0.3 --regheader 44538_T1_fs --cortex srcvol = /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99959 0.01347 -0.02525 0.00002; -0.02408 0.08109 0.99642 -0.00004; -0.01547 -0.99662 0.08073 -0.00003; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label/rh.cortex.label Reading surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Done reading source surface Reading thickness /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 = 74311 Masking with /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label/rh.cortex.label Writing to /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/tmp.pctsurfcon.63971/rh.gm.mgh Dim: 115906 1 1 mri_concat /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/tmp.pctsurfcon.63971/rh.wm.mgh /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/tmp.pctsurfcon.63971/rh.gm.mgh --paired-diff-norm --mul 100 --o /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.w-g.pct.mgh mri_segstats --in /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.w-g.pct.mgh --annot 44538_T1_fs rh aparc --sum /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.w-g.pct.mgh --annot 44538_T1_fs rh aparc --sum /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/stats/rh.w-g.pct.stats --snr sysname Linux hostname node005 machine x86_64 user annadan1111 UseRobust 0 Constructing seg from annotation Reading annotation /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.w-g.pct.mgh Vertex Area is 0.666801 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 So 11. Mär 08:17:01 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 1488 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 1730 voxels changed to hypointensity... 3186 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc So 11. Mär 08:17:25 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs mri_aparc2aseg --s 44538_T1_fs --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /cm/shared/apps/freesurfer/6.0.0/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: /cm/shared/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test3 subject 44538_T1_fs outvol /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading lh pial surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.pial Loading lh annotations from /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading rh pial surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.pial Loading rh annotations from /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.77 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 107 rescaling Left_Cerebral_Cortex from 61 --> 72 rescaling Left_Lateral_Ventricle from 13 --> 27 rescaling Left_Inf_Lat_Vent from 34 --> 34 rescaling Left_Cerebellum_White_Matter from 86 --> 94 rescaling Left_Cerebellum_Cortex from 60 --> 76 rescaling Left_Thalamus from 94 --> 104 rescaling Left_Thalamus_Proper from 84 --> 98 rescaling Left_Caudate from 75 --> 89 rescaling Left_Putamen from 80 --> 86 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 32 rescaling Fourth_Ventricle from 22 --> 27 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 72 rescaling Left_Amygdala from 56 --> 74 rescaling CSF from 32 --> 60 rescaling Left_Accumbens_area from 62 --> 71 rescaling Left_VentralDC from 87 --> 95 rescaling Right_Cerebral_White_Matter from 105 --> 105 rescaling Right_Cerebral_Cortex from 58 --> 72 rescaling Right_Lateral_Ventricle from 13 --> 27 rescaling Right_Inf_Lat_Vent from 25 --> 31 rescaling Right_Cerebellum_White_Matter from 87 --> 93 rescaling Right_Cerebellum_Cortex from 59 --> 75 rescaling Right_Thalamus_Proper from 85 --> 90 rescaling Right_Caudate from 62 --> 85 rescaling Right_Putamen from 80 --> 87 rescaling Right_Pallidum from 97 --> 100 rescaling Right_Hippocampus from 53 --> 73 rescaling Right_Amygdala from 55 --> 75 rescaling Right_Accumbens_area from 65 --> 84 rescaling Right_VentralDC from 86 --> 93 rescaling Fifth_Ventricle from 40 --> 51 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 56 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 = 495390 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: 12 changed. pass 3: 2 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s So 11. Mär 08:22:30 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs mri_aparc2aseg --s 44538_T1_fs --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /cm/shared/apps/freesurfer/6.0.0/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: /cm/shared/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test3 subject 44538_T1_fs outvol /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading lh pial surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.pial Loading lh annotations from /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading rh pial surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.pial Loading rh annotations from /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.77 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 107 rescaling Left_Cerebral_Cortex from 61 --> 72 rescaling Left_Lateral_Ventricle from 13 --> 27 rescaling Left_Inf_Lat_Vent from 34 --> 34 rescaling Left_Cerebellum_White_Matter from 86 --> 94 rescaling Left_Cerebellum_Cortex from 60 --> 76 rescaling Left_Thalamus from 94 --> 104 rescaling Left_Thalamus_Proper from 84 --> 98 rescaling Left_Caudate from 75 --> 89 rescaling Left_Putamen from 80 --> 86 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 32 rescaling Fourth_Ventricle from 22 --> 27 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 72 rescaling Left_Amygdala from 56 --> 74 rescaling CSF from 32 --> 60 rescaling Left_Accumbens_area from 62 --> 71 rescaling Left_VentralDC from 87 --> 95 rescaling Right_Cerebral_White_Matter from 105 --> 105 rescaling Right_Cerebral_Cortex from 58 --> 72 rescaling Right_Lateral_Ventricle from 13 --> 27 rescaling Right_Inf_Lat_Vent from 25 --> 31 rescaling Right_Cerebellum_White_Matter from 87 --> 93 rescaling Right_Cerebellum_Cortex from 59 --> 75 rescaling Right_Thalamus_Proper from 85 --> 90 rescaling Right_Caudate from 62 --> 85 rescaling Right_Putamen from 80 --> 87 rescaling Right_Pallidum from 97 --> 100 rescaling Right_Hippocampus from 53 --> 73 rescaling Right_Amygdala from 55 --> 75 rescaling Right_Accumbens_area from 65 --> 84 rescaling Right_VentralDC from 86 --> 93 rescaling Fifth_Ventricle from 40 --> 51 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 56 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 = 495379 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: 12 changed. pass 3: 2 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas So 11. Mär 08:27:30 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs mri_aparc2aseg --s 44538_T1_fs --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /cm/shared/apps/freesurfer/6.0.0/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: /cm/shared/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test3 subject 44538_T1_fs outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading lh pial surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.pial Loading lh annotations from /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading rh pial surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.pial Loading rh annotations from /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 6.77 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 107 rescaling Left_Cerebral_Cortex from 61 --> 72 rescaling Left_Lateral_Ventricle from 13 --> 27 rescaling Left_Inf_Lat_Vent from 34 --> 34 rescaling Left_Cerebellum_White_Matter from 86 --> 94 rescaling Left_Cerebellum_Cortex from 60 --> 76 rescaling Left_Thalamus from 94 --> 104 rescaling Left_Thalamus_Proper from 84 --> 98 rescaling Left_Caudate from 75 --> 89 rescaling Left_Putamen from 80 --> 86 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 32 rescaling Fourth_Ventricle from 22 --> 27 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 72 rescaling Left_Amygdala from 56 --> 74 rescaling CSF from 32 --> 60 rescaling Left_Accumbens_area from 62 --> 71 rescaling Left_VentralDC from 87 --> 95 rescaling Right_Cerebral_White_Matter from 105 --> 105 rescaling Right_Cerebral_Cortex from 58 --> 72 rescaling Right_Lateral_Ventricle from 13 --> 27 rescaling Right_Inf_Lat_Vent from 25 --> 31 rescaling Right_Cerebellum_White_Matter from 87 --> 93 rescaling Right_Cerebellum_Cortex from 59 --> 75 rescaling Right_Thalamus_Proper from 85 --> 90 rescaling Right_Caudate from 62 --> 85 rescaling Right_Putamen from 80 --> 87 rescaling Right_Pallidum from 97 --> 100 rescaling Right_Hippocampus from 53 --> 73 rescaling Right_Amygdala from 55 --> 75 rescaling Right_Accumbens_area from 65 --> 84 rescaling Right_VentralDC from 86 --> 93 rescaling Fifth_Ventricle from 40 --> 51 rescaling WM_hypointensities from 78 --> 78 rescaling non_WM_hypointensities from 40 --> 56 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 = 495379 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: 12 changed. pass 3: 2 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz #----------------------------------------- #@# APas-to-ASeg So 11. Mär 08:32:34 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz So 11. Mär 08:32:34 CET 2018 setenv SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test3 cd /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri /cm/shared/apps/freesurfer/6.0.0/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 node005 2.6.32-696.16.1.el6.x86_64 #1 SMP Tue Nov 14 14:23:46 CST 2017 x86_64 x86_64 x86_64 GNU/Linux mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 node005 machine x86_64 user annadan1111 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 So 11. Mär 08:32:34 CET 2018 Ended at So 11. Mär 08:32:42 CET 2018 Apas2aseg-Run-Time-Sec 8 apas2aseg Done #-------------------------------------------- #@# ASeg Stats So 11. Mär 08:32:42 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs 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 /cm/shared/apps/freesurfer/6.0.0/ASegStatsLUT.txt --subject 44538_T1_fs $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 /cm/shared/apps/freesurfer/6.0.0/ASegStatsLUT.txt --subject 44538_T1_fs sysname Linux hostname node005 machine x86_64 user annadan1111 UseRobust 0 atlas_icv (eTIV) = 1565239 mm^3 (det: 1.244605 ) Computing euler number orig.nofix lheno = -112, rheno = -126 orig.nofix lhholes = 57, rhholes = 64 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 246418.054 246126.000 diff= 292.1 pctdiff= 0.119 rhCtxGM: 250283.102 250399.000 diff= -115.9 pctdiff=-0.046 lhCtxWM: 199638.904 200177.000 diff= -538.1 pctdiff=-0.270 rhCtxWM: 198959.974 199531.000 diff= -571.0 pctdiff=-0.287 SubCortGMVol 58698.000 SupraTentVol 980279.034 (978426.000) diff=1853.034 pctdiff=0.189 SupraTentVolNotVent 956798.034 (954945.000) diff=1853.034 pctdiff=0.194 BrainSegVol 1136768.000 (1134094.000) diff=2674.000 pctdiff=0.235 BrainSegVolNotVent 1109214.000 (1108126.034) diff=1087.966 pctdiff=0.098 BrainSegVolNotVent 1109214.000 CerebellumVol 154114.000 VentChorVol 23481.000 3rd4th5thCSF 4073.000 CSFVol 1399.000, OptChiasmVol 155.000 MaskVol 1668967.000 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 So 11. Mär 08:36:37 CET 2018 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs mri_aparc2aseg --s 44538_T1_fs --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test3 subject 44538_T1_fs outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/aparc+aseg.mgz Reading lh white surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading lh pial surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.pial Loading lh annotations from /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading rh pial surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.pial Loading rh annotations from /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/ribbon.mgz Loading filled from /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 7921 vertices from left hemi Ripped 8219 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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/aseg.mgz Loading Ctx Seg File /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 = 892846 Used brute-force search on 205 voxels Fixing Parahip LH WM Found 9 clusters 0 k 1.000000 1 k 3.000000 2 k 1260.000000 3 k 3.000000 4 k 2.000000 5 k 1.000000 6 k 3.000000 7 k 3.000000 8 k 1.000000 Fixing Parahip RH WM Found 9 clusters 0 k 1.000000 1 k 35.000000 2 k 1488.000000 3 k 3.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 2.000000 8 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 44538_T1_fs --surf-wm-vol --ctab /cm/shared/apps/freesurfer/6.0.0/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 44538_T1_fs --surf-wm-vol --ctab /cm/shared/apps/freesurfer/6.0.0/WMParcStatsLUT.txt --etiv sysname Linux hostname node005 machine x86_64 user annadan1111 UseRobust 0 atlas_icv (eTIV) = 1565239 mm^3 (det: 1.244605 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 246418.054 246126.000 diff= 292.1 pctdiff= 0.119 rhCtxGM: 250283.102 250399.000 diff= -115.9 pctdiff=-0.046 lhCtxWM: 199638.904 200177.000 diff= -538.1 pctdiff=-0.270 rhCtxWM: 198959.974 199531.000 diff= -571.0 pctdiff=-0.287 SubCortGMVol 58698.000 SupraTentVol 980279.034 (978426.000) diff=1853.034 pctdiff=0.189 SupraTentVolNotVent 956798.034 (954945.000) diff=1853.034 pctdiff=0.194 BrainSegVol 1136768.000 (1134094.000) diff=2674.000 pctdiff=0.235 BrainSegVolNotVent 1109214.000 (1108126.034) diff=1087.966 pctdiff=0.098 BrainSegVolNotVent 1109214.000 CerebellumVol 154114.000 VentChorVol 23481.000 3rd4th5thCSF 4073.000 CSFVol 1399.000, OptChiasmVol 155.000 MaskVol 1668967.000 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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label #-------------------------------------------- #@# BA_exvivo Labels lh So 11. Mär 08:46:37 CET 2018 mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA1_exvivo.label --trgsubject 44538_T1_fs --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 259 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4388 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA2_exvivo.label --trgsubject 44538_T1_fs --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 244 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8153 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA3a_exvivo.label --trgsubject 44538_T1_fs --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 121 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4198 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA3b_exvivo.label --trgsubject 44538_T1_fs --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 255 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6238 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA4a_exvivo.label --trgsubject 44538_T1_fs --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 595 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6379 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA4p_exvivo.label --trgsubject 44538_T1_fs --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 443 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4513 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA6_exvivo.label --trgsubject 44538_T1_fs --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 791 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14380 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA44_exvivo.label --trgsubject 44538_T1_fs --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 156 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4337 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA45_exvivo.label --trgsubject 44538_T1_fs --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 376 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3798 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.V1_exvivo.label --trgsubject 44538_T1_fs --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 949 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5590 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.V2_exvivo.label --trgsubject 44538_T1_fs --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 1996 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 10110 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.MT_exvivo.label --trgsubject 44538_T1_fs --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 388 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2406 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject 44538_T1_fs --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 68 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1358 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject 44538_T1_fs --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 41 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1240 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 56 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1070 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 114 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2206 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 40 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1544 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 128 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2124 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 322 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2641 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 151 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1700 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 424 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7459 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 88 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2000 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 168 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1319 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 680 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4085 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 914 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4248 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 109 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 622 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 21 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 491 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 99.9999 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 113373 Number of reverse mapping hits = 12 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 462 mri_label2label: Done mris_label2annot --s 44538_T1_fs --hemi lh --ctab /cm/shared/apps/freesurfer/6.0.0/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 /cm/shared/apps/freesurfer/6.0.0/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label cmdline mris_label2annot --s 44538_T1_fs --hemi lh --ctab /cm/shared/apps/freesurfer/6.0.0/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 node005 machine x86_64 user annadan1111 subject 44538_T1_fs hemi lh SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test3 ColorTable /cm/shared/apps/freesurfer/6.0.0/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 77393 unhit vertices Writing annot to /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label/lh.BA_exvivo.annot mris_label2annot --s 44538_T1_fs --hemi lh --ctab /cm/shared/apps/freesurfer/6.0.0/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 /cm/shared/apps/freesurfer/6.0.0/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label cmdline mris_label2annot --s 44538_T1_fs --hemi lh --ctab /cm/shared/apps/freesurfer/6.0.0/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 node005 machine x86_64 user annadan1111 subject 44538_T1_fs hemi lh SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test3 ColorTable /cm/shared/apps/freesurfer/6.0.0/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 91262 unhit vertices Writing annot to /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 44538_T1_fs lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white... reading input pial surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 251239 Total vertex volume 247453 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /cm/shared/apps/freesurfer/6.0.0/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) = 1565239 mm^3 (det: 1.244605 ) lhCtxGM: 246418.054 246126.000 diff= 292.1 pctdiff= 0.119 rhCtxGM: 250283.102 250399.000 diff= -115.9 pctdiff=-0.046 lhCtxWM: 199638.904 200177.000 diff= -538.1 pctdiff=-0.270 rhCtxWM: 198959.974 199531.000 diff= -571.0 pctdiff=-0.287 SubCortGMVol 58698.000 SupraTentVol 980279.034 (978426.000) diff=1853.034 pctdiff=0.189 SupraTentVolNotVent 956798.034 (954945.000) diff=1853.034 pctdiff=0.194 BrainSegVol 1136768.000 (1134094.000) diff=2674.000 pctdiff=0.235 BrainSegVolNotVent 1109214.000 (1108126.034) diff=1087.966 pctdiff=0.098 BrainSegVolNotVent 1109214.000 CerebellumVol 154114.000 VentChorVol 23481.000 3rd4th5thCSF 4073.000 CSFVol 1399.000, OptChiasmVol 155.000 MaskVol 1668967.000 1095 660 2060 2.376 0.657 0.135 0.041 14 1.7 BA1_exvivo 2951 2023 5753 2.559 0.619 0.127 0.034 31 3.8 BA2_exvivo 1012 745 1006 1.666 0.406 0.131 0.031 8 1.2 BA3a_exvivo 2145 1417 3216 1.998 0.749 0.125 0.036 22 3.4 BA3b_exvivo 1774 1042 3013 2.660 0.556 0.120 0.040 18 2.7 BA4a_exvivo 1538 889 2276 2.558 0.566 0.105 0.030 12 1.9 BA4p_exvivo 7841 5360 19087 2.934 0.663 0.126 0.036 85 11.2 BA6_exvivo 1770 1238 4813 3.134 0.649 0.132 0.033 27 2.3 BA44_exvivo 2411 1667 6982 3.017 0.737 0.138 0.041 37 4.3 BA45_exvivo 3088 1971 3211 1.621 0.685 0.129 0.033 36 4.1 V1_exvivo 7241 4652 10234 2.087 0.616 0.142 0.038 99 11.0 V2_exvivo 1984 1378 4332 2.785 0.621 0.130 0.032 28 2.6 MT_exvivo 550 345 1821 3.595 0.704 0.120 0.037 5 0.8 perirhinal_exvivo 580 393 1450 3.046 0.940 0.106 0.027 4 0.6 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 44538_T1_fs lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white... reading input pial surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 251239 Total vertex volume 247453 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /cm/shared/apps/freesurfer/6.0.0/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) = 1565239 mm^3 (det: 1.244605 ) lhCtxGM: 246418.054 246126.000 diff= 292.1 pctdiff= 0.119 rhCtxGM: 250283.102 250399.000 diff= -115.9 pctdiff=-0.046 lhCtxWM: 199638.904 200177.000 diff= -538.1 pctdiff=-0.270 rhCtxWM: 198959.974 199531.000 diff= -571.0 pctdiff=-0.287 SubCortGMVol 58698.000 SupraTentVol 980279.034 (978426.000) diff=1853.034 pctdiff=0.189 SupraTentVolNotVent 956798.034 (954945.000) diff=1853.034 pctdiff=0.194 BrainSegVol 1136768.000 (1134094.000) diff=2674.000 pctdiff=0.235 BrainSegVolNotVent 1109214.000 (1108126.034) diff=1087.966 pctdiff=0.098 BrainSegVolNotVent 1109214.000 CerebellumVol 154114.000 VentChorVol 23481.000 3rd4th5thCSF 4073.000 CSFVol 1399.000, OptChiasmVol 155.000 MaskVol 1668967.000 679 418 1388 2.461 0.553 0.143 0.044 10 1.1 BA1_exvivo 1363 945 2681 2.455 0.527 0.132 0.033 16 1.9 BA2_exvivo 857 649 830 1.642 0.367 0.142 0.034 7 1.2 BA3a_exvivo 1425 954 1669 1.649 0.381 0.113 0.032 12 2.0 BA3b_exvivo 1811 1018 2915 2.667 0.524 0.112 0.039 18 2.7 BA4a_exvivo 1198 725 1796 2.498 0.548 0.104 0.026 8 1.4 BA4p_exvivo 4580 3093 11107 2.855 0.694 0.129 0.040 52 7.1 BA6_exvivo 1168 821 3388 3.212 0.561 0.145 0.041 23 1.9 BA44_exvivo 976 683 3326 3.152 0.728 0.156 0.052 21 2.3 BA45_exvivo 3295 2110 3687 1.683 0.721 0.130 0.032 38 4.3 V1_exvivo 3669 2341 5020 2.001 0.609 0.150 0.042 58 6.0 V2_exvivo 521 380 1073 2.501 0.582 0.153 0.041 12 1.0 MT_exvivo 266 174 921 3.511 0.675 0.116 0.030 2 0.4 perirhinal_exvivo 303 215 748 2.857 0.829 0.087 0.017 1 0.3 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh So 11. Mär 08:51:13 CET 2018 mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA1_exvivo.label --trgsubject 44538_T1_fs --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 242 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4204 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA2_exvivo.label --trgsubject 44538_T1_fs --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 282 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6969 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA3a_exvivo.label --trgsubject 44538_T1_fs --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 121 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4101 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA3b_exvivo.label --trgsubject 44538_T1_fs --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 211 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4733 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA4a_exvivo.label --trgsubject 44538_T1_fs --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 343 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6090 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA4p_exvivo.label --trgsubject 44538_T1_fs --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 195 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4668 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA6_exvivo.label --trgsubject 44538_T1_fs --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 820 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13076 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA44_exvivo.label --trgsubject 44538_T1_fs --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 261 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7173 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA45_exvivo.label --trgsubject 44538_T1_fs --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 655 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6010 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.V1_exvivo.label --trgsubject 44538_T1_fs --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 772 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5499 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.V2_exvivo.label --trgsubject 44538_T1_fs --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 1907 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 9923 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.MT_exvivo.label --trgsubject 44538_T1_fs --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 304 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2236 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject 44538_T1_fs --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 111 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1149 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject 44538_T1_fs --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 68 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 820 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 64 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 940 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 129 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2817 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 57 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1755 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 110 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2293 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 132 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1520 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 88 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1577 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 413 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7372 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 75 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1087 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 74 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1252 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 424 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 3656 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 990 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4427 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 67 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 335 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 69 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 763 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject 44538_T1_fs --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test3/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 44538_T1_fs 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 /scratch/annadan1111/MABT1T2/test3 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /scratch/annadan1111/MABT1T2/test3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 115906 Number of reverse mapping hits = 28 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 319 mri_label2label: Done mris_label2annot --s 44538_T1_fs --hemi rh --ctab /cm/shared/apps/freesurfer/6.0.0/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 /cm/shared/apps/freesurfer/6.0.0/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label cmdline mris_label2annot --s 44538_T1_fs --hemi rh --ctab /cm/shared/apps/freesurfer/6.0.0/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 node005 machine x86_64 user annadan1111 subject 44538_T1_fs hemi rh SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test3 ColorTable /cm/shared/apps/freesurfer/6.0.0/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 80836 unhit vertices Writing annot to /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label/rh.BA_exvivo.annot mris_label2annot --s 44538_T1_fs --hemi rh --ctab /cm/shared/apps/freesurfer/6.0.0/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 /cm/shared/apps/freesurfer/6.0.0/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 /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/label cmdline mris_label2annot --s 44538_T1_fs --hemi rh --ctab /cm/shared/apps/freesurfer/6.0.0/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 node005 machine x86_64 user annadan1111 subject 44538_T1_fs hemi rh SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test3 ColorTable /cm/shared/apps/freesurfer/6.0.0/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 95733 unhit vertices Writing annot to /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/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 44538_T1_fs rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white... reading input pial surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 255880 Total vertex volume 251876 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /cm/shared/apps/freesurfer/6.0.0/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) = 1565239 mm^3 (det: 1.244605 ) lhCtxGM: 246418.054 246126.000 diff= 292.1 pctdiff= 0.119 rhCtxGM: 250283.102 250399.000 diff= -115.9 pctdiff=-0.046 lhCtxWM: 199638.904 200177.000 diff= -538.1 pctdiff=-0.270 rhCtxWM: 198959.974 199531.000 diff= -571.0 pctdiff=-0.287 SubCortGMVol 58698.000 SupraTentVol 980279.034 (978426.000) diff=1853.034 pctdiff=0.189 SupraTentVolNotVent 956798.034 (954945.000) diff=1853.034 pctdiff=0.194 BrainSegVol 1136768.000 (1134094.000) diff=2674.000 pctdiff=0.235 BrainSegVolNotVent 1109214.000 (1108126.034) diff=1087.966 pctdiff=0.098 BrainSegVolNotVent 1109214.000 CerebellumVol 154114.000 VentChorVol 23481.000 3rd4th5thCSF 4073.000 CSFVol 1399.000, OptChiasmVol 155.000 MaskVol 1668967.000 901 490 1764 2.516 0.582 0.120 0.045 11 1.5 BA1_exvivo 2852 1913 4753 2.418 0.620 0.104 0.024 19 2.7 BA2_exvivo 1089 740 1022 1.835 0.449 0.140 0.041 10 2.0 BA3a_exvivo 1822 1206 2637 1.934 0.672 0.117 0.032 20 2.4 BA3b_exvivo 1534 854 2457 2.483 0.512 0.105 0.039 17 2.1 BA4a_exvivo 1105 729 1815 2.486 0.517 0.100 0.023 6 1.0 BA4p_exvivo 6961 4598 17117 2.912 0.766 0.134 0.048 101 13.3 BA6_exvivo 2685 1850 6814 3.117 0.653 0.127 0.037 31 3.9 BA44_exvivo 3336 2325 9887 3.183 0.875 0.147 0.049 53 6.4 BA45_exvivo 3006 1934 3473 1.650 0.685 0.128 0.034 32 4.2 V1_exvivo 7101 4463 10274 2.101 0.696 0.142 0.044 108 11.8 V2_exvivo 1738 1191 3970 2.892 0.578 0.135 0.036 23 2.6 MT_exvivo 594 364 2019 3.589 0.803 0.118 0.046 6 1.1 perirhinal_exvivo 346 244 937 3.339 0.574 0.117 0.033 2 0.5 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 44538_T1_fs rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white... reading input pial surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test3/44538_T1_fs/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 255880 Total vertex volume 251876 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /cm/shared/apps/freesurfer/6.0.0/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) = 1565239 mm^3 (det: 1.244605 ) lhCtxGM: 246418.054 246126.000 diff= 292.1 pctdiff= 0.119 rhCtxGM: 250283.102 250399.000 diff= -115.9 pctdiff=-0.046 lhCtxWM: 199638.904 200177.000 diff= -538.1 pctdiff=-0.270 rhCtxWM: 198959.974 199531.000 diff= -571.0 pctdiff=-0.287 SubCortGMVol 58698.000 SupraTentVol 980279.034 (978426.000) diff=1853.034 pctdiff=0.189 SupraTentVolNotVent 956798.034 (954945.000) diff=1853.034 pctdiff=0.194 BrainSegVol 1136768.000 (1134094.000) diff=2674.000 pctdiff=0.235 BrainSegVolNotVent 1109214.000 (1108126.034) diff=1087.966 pctdiff=0.098 BrainSegVolNotVent 1109214.000 CerebellumVol 154114.000 VentChorVol 23481.000 3rd4th5thCSF 4073.000 CSFVol 1399.000, OptChiasmVol 155.000 MaskVol 1668967.000 610 331 1228 2.519 0.497 0.128 0.047 9 1.1 BA1_exvivo 1718 1114 3033 2.463 0.557 0.095 0.023 11 1.5 BA2_exvivo 963 656 836 1.810 0.404 0.141 0.041 8 1.8 BA3a_exvivo 1443 993 1797 1.717 0.476 0.108 0.026 11 1.6 BA3b_exvivo 993 536 1640 2.542 0.517 0.121 0.046 12 1.8 BA4a_exvivo 972 634 1542 2.520 0.509 0.096 0.027 5 0.9 BA4p_exvivo 4407 2902 10254 2.759 0.737 0.135 0.051 66 8.8 BA6_exvivo 724 504 2366 3.295 0.731 0.140 0.040 9 1.2 BA44_exvivo 731 504 2265 3.144 0.764 0.145 0.051 10 1.3 BA45_exvivo 2844 1834 2998 1.586 0.609 0.130 0.035 32 4.2 V1_exvivo 3885 2413 5635 2.063 0.731 0.145 0.046 64 7.0 V2_exvivo 293 187 691 2.783 0.660 0.134 0.038 5 0.5 MT_exvivo 343 216 1217 3.558 0.751 0.117 0.046 4 0.6 perirhinal_exvivo 247 168 598 3.242 0.462 0.125 0.041 2 0.5 entorhinal_exvivo Started at Sa 10. Mär 21:13:49 CET 2018 Ended at So 11. Mär 08:56:01 CET 2018 #@#%# recon-all-run-time-hours 11,703 recon-all -s 44538_T1_fs finished without error at So 11. Mär 08:56:01 CET 2018 New invocation of recon-all Mi 28. Mär 20:40:17 CEST 2018 /scratch/annadan1111/MABT1T2/reruncrosstest_cp2/44538_T1_fs_edit /cm/shared/apps/freesurfer/6.0.0/bin/recon-all -s 44538_T1_fs_edit -autorecon2 -autorecon3 subjid 44538_T1_fs_edit setenv SUBJECTS_DIR /scratch/annadan1111/MABT1T2/reruncrosstest_cp2 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 Actual FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux node098 2.6.32-696.20.1.el6.x86_64 #1 SMP Thu Jan 25 08:47:49 CST 2018 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 1310720 kbytes coredumpsize 0 kbytes memoryuse 2883584 kbytes vmemoryuse unlimited descriptors 8192 memorylocked unlimited maxproc 1024 total used free shared buffers cached Mem: 49551132 24499472 25051660 4039992 0 9375008 -/+ buffers/cache: 15124464 34426668 Swap: 0 0 0 ######################################## 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: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.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: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.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: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/28-18:40:18-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:19-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:19-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:19-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/28-18:40:19-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:19-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/28-18:40:19-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:19-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:19-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:19-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:19-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.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: 2018/03/28-18:40:19-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.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: 2018/03/28-18:40:19-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:19-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:19-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:19-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:19-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/28-18:40:19-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: annadan1111 Machine: node098 Platform: Linux PlatformVersion: 2.6.32-696.20.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /cm/shared/apps/freesurfer/6.0.0/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 /cm/shared/apps/freesurfer/6.0.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #------------------------------------- #@# EM Registration Mi 28. Mär 20:40:19 CEST 2018 /scratch/annadan1111/MABT1T2/reruncrosstest_cp2/44538_T1_fs_edit/mri mri_em_register -rusage /scratch/annadan1111/MABT1T2/reruncrosstest_cp2/44538_T1_fs_edit/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /cm/shared/apps/freesurfer/6.0.0/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 '/cm/shared/apps/freesurfer/6.0.0/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=25.0 skull bounding box = (62, 62, 37) --> (194, 184, 206) using (106, 103, 122) as brain centroid... mean wm in atlas = 107, using box (90,88,101) --> (122, 117,142) to find MRI wm before smoothing, mri peak at 109 robust fit to distribution - 109 +- 3.6 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 initial log_p = -4.131 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.828626 @ (-9.091, -9.091, -9.091) max log p = -3.747200 @ (4.545, 4.545, 4.545) max log p = -3.685573 @ (2.273, -2.273, -2.273) max log p = -3.652903 @ (-1.136, -1.136, -1.136) max log p = -3.650840 @ (0.568, -1.705, -0.568) max log p = -3.647266 @ (-2.557, 1.420, 0.284) Found translation: (-5.4, -8.2, -8.2): log p = -3.647 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.607, old_max_log_p =-3.647 (thresh=-3.6) 1.00000 0.00000 0.00000 -5.39773; 0.00000 1.07500 0.00000 -17.80329; 0.00000 0.00000 1.00000 -8.23864; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.607, old_max_log_p =-3.607 (thresh=-3.6) 1.00000 0.00000 0.00000 -5.39773; 0.00000 1.07500 0.00000 -17.80329; 0.00000 0.00000 1.00000 -8.23864; 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=-3.493, old_max_log_p =-3.607 (thresh=-3.6) 1.05582 0.03699 0.03341 -19.46851; -0.03456 1.09395 -0.03569 -9.71526; -0.03331 0.03450 1.01696 -12.08526; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.491, old_max_log_p =-3.493 (thresh=-3.5) 1.07626 0.00120 0.03299 -17.58301; -0.00206 1.07396 0.03137 -21.06540; -0.03098 -0.03713 1.01711 -3.39627; 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=-3.468, old_max_log_p =-3.491 (thresh=-3.5) 1.08005 0.00120 0.03311 -18.09078; -0.00206 1.07145 0.03130 -20.73644; -0.03105 -0.03721 1.01950 -3.65137; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.462, old_max_log_p =-3.468 (thresh=-3.5) 1.07879 0.00120 0.03307 -17.92106; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02308 -4.03521; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.462, old_max_log_p =-3.462 (thresh=-3.5) 1.07879 0.00120 0.03307 -17.92106; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02308 -4.03521; 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 1.07879 0.00120 0.03307 -17.92106; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02308 -4.03521; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.07879 0.00120 0.03307 -17.92106; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02308 -4.03521; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.07879 0.00120 0.03307 -17.92106; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02308 -4.03521; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.462 (old=-4.131) transform before final EM align: 1.07879 0.00120 0.03307 -17.92106; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02308 -4.03521; 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 1.07879 0.00120 0.03307 -17.92106; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02308 -4.03521; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.07879 0.00120 0.03307 -17.92106; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02308 -4.03521; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 3.9 tol 0.000000 final transform: 1.07879 0.00120 0.03307 -17.92106; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02308 -4.03521; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1285.087636 mri_em_register stimesec 2.244658 mri_em_register ru_maxrss 599032 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 159337 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 9152 mri_em_register ru_oublock 3 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 123 mri_em_register ru_nivcsw 3461 registration took 21 minutes and 30 seconds. #-------------------------------------- #@# CA Normalize Mi 28. Mär 21:01:50 CEST 2018 /scratch/annadan1111/MABT1T2/reruncrosstest_cp2/44538_T1_fs_edit/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /cm/shared/apps/freesurfer/6.0.0/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 '/cm/shared/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=26.0 skull bounding box = (62, 63, 37) --> (194, 183, 206) using (106, 103, 122) as brain centroid... mean wm in atlas = 107, using box (90,88,101) --> (122, 117,142) to find MRI wm before smoothing, mri peak at 109 robust fit to distribution - 109 +- 3.6 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 using 246344 sample points... INFO: compute sample coordinates transform 1.07879 0.00120 0.03307 -17.92106; -0.00205 1.06893 0.03122 -20.40825; -0.03116 -0.03734 1.02308 -4.03521; 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 (130, 65, 39) --> (191, 176, 203) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 7821 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (70, 65, 38) --> (131, 176, 202) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 9 of 7489 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (132, 146, 62) --> (177, 185, 114) Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 310 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (90, 146, 58) --> (131, 185, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 18 of 61 (29.5%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (115, 138, 95) --> (146, 203, 126) Brain_Stem: limiting intensities to 93.0 --> 132.0 0 of 529 (0.0%) samples deleted using 16210 total control points for intensity normalization... bias field = 0.976 +- 0.050 217 of 16183 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (130, 65, 39) --> (191, 176, 203) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 7 of 7944 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (70, 65, 38) --> (131, 176, 202) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 8 of 7650 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (132, 146, 62) --> (177, 185, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 330 (0.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (90, 146, 58) --> (131, 185, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 75 of 107 (70.1%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (115, 138, 95) --> (146, 203, 126) Brain_Stem: limiting intensities to 88.0 --> 132.0 1 of 587 (0.2%) samples deleted using 16618 total control points for intensity normalization... bias field = 1.009 +- 0.044 172 of 16450 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (130, 65, 39) --> (191, 176, 203) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 132.0 20 of 7941 (0.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (70, 65, 38) --> (131, 176, 202) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 10 of 7689 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (132, 146, 62) --> (177, 185, 114) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 104 of 419 (24.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (90, 146, 58) --> (131, 185, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 96 of 149 (64.4%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (115, 138, 95) --> (146, 203, 126) Brain_Stem: limiting intensities to 88.0 --> 132.0 7 of 587 (1.2%) samples deleted using 16785 total control points for intensity normalization... bias field = 1.006 +- 0.040 140 of 16434 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 39 seconds. #-------------------------------------- #@# CA Reg Mi 28. Mär 21:03:29 CEST 2018 /scratch/annadan1111/MABT1T2/reruncrosstest_cp2/44538_T1_fs_edit/mri mri_ca_register -rusage /scratch/annadan1111/MABT1T2/reruncrosstest_cp2/44538_T1_fs_edit/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /cm/shared/apps/freesurfer/6.0.0/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 '/cm/shared/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.18 (predicted orig area = 6.8) 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=0.834, neg=0, invalid=762 0001: dt=232.901758, rms=0.746 (10.555%), neg=0, invalid=762 0002: dt=139.994758, rms=0.718 (3.676%), neg=0, invalid=762 0003: dt=308.104289, rms=0.705 (1.829%), neg=0, invalid=762 0004: dt=129.472000, rms=0.700 (0.704%), neg=0, invalid=762 0005: dt=369.920000, rms=0.696 (0.555%), neg=0, invalid=762 0006: dt=129.472000, rms=0.694 (0.321%), neg=0, invalid=762 0007: dt=443.904000, rms=0.691 (0.388%), neg=0, invalid=762 0008: dt=129.472000, rms=0.689 (0.325%), neg=0, invalid=762 0009: dt=295.936000, rms=0.688 (0.226%), neg=0, invalid=762 0010: dt=295.936000, rms=0.688 (-0.011%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.688, neg=0, invalid=762 0011: dt=295.936000, rms=0.681 (1.056%), neg=0, invalid=762 0012: dt=110.976000, rms=0.679 (0.218%), neg=0, invalid=762 0013: dt=110.976000, rms=0.679 (0.064%), neg=0, invalid=762 0014: dt=110.976000, rms=0.678 (0.133%), neg=0, invalid=762 0015: dt=110.976000, rms=0.676 (0.204%), neg=0, invalid=762 0016: dt=110.976000, rms=0.675 (0.258%), neg=0, invalid=762 0017: dt=110.976000, rms=0.673 (0.274%), neg=0, invalid=762 0018: dt=110.976000, rms=0.671 (0.263%), neg=0, invalid=762 0019: dt=110.976000, rms=0.670 (0.225%), neg=0, invalid=762 0020: dt=110.976000, rms=0.668 (0.189%), neg=0, invalid=762 0021: dt=110.976000, rms=0.667 (0.160%), neg=0, invalid=762 0022: dt=110.976000, rms=0.666 (0.133%), neg=0, invalid=762 0023: dt=110.976000, rms=0.665 (0.136%), neg=0, invalid=762 0024: dt=110.976000, rms=0.664 (0.160%), neg=0, invalid=762 0025: dt=110.976000, rms=0.663 (0.159%), neg=0, invalid=762 0026: dt=110.976000, rms=0.662 (0.149%), neg=0, invalid=762 0027: dt=110.976000, rms=0.662 (0.126%), neg=0, invalid=762 0028: dt=110.976000, rms=0.661 (0.092%), neg=0, invalid=762 0029: dt=110.976000, rms=0.660 (0.078%), neg=0, invalid=762 0030: dt=887.808000, rms=0.659 (0.144%), neg=0, invalid=762 0031: dt=32.368000, rms=0.659 (0.005%), neg=0, invalid=762 0032: dt=32.368000, rms=0.659 (0.001%), neg=0, invalid=762 0033: dt=32.368000, rms=0.659 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.666, neg=0, invalid=762 0034: dt=36.288000, rms=0.664 (0.234%), neg=0, invalid=762 0035: dt=193.254902, rms=0.659 (0.794%), neg=0, invalid=762 0036: dt=167.312614, rms=0.645 (2.103%), neg=0, invalid=762 0037: dt=18.192420, rms=0.644 (0.254%), neg=0, invalid=762 0038: dt=6.480000, rms=0.644 (0.013%), neg=0, invalid=762 0039: dt=6.480000, rms=0.644 (-0.006%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.644, neg=0, invalid=762 0040: dt=103.680000, rms=0.641 (0.490%), neg=0, invalid=762 0041: dt=116.000000, rms=0.637 (0.676%), neg=0, invalid=762 0042: dt=31.104000, rms=0.636 (0.166%), neg=0, invalid=762 0043: dt=31.104000, rms=0.635 (0.066%), neg=0, invalid=762 0044: dt=31.104000, rms=0.634 (0.111%), neg=0, invalid=762 0045: dt=31.104000, rms=0.633 (0.202%), neg=0, invalid=762 0046: dt=31.104000, rms=0.631 (0.323%), neg=0, invalid=762 0047: dt=31.104000, rms=0.629 (0.367%), neg=0, invalid=762 0048: dt=31.104000, rms=0.627 (0.338%), neg=0, invalid=762 0049: dt=31.104000, rms=0.625 (0.290%), neg=0, invalid=762 0050: dt=31.104000, rms=0.623 (0.259%), neg=0, invalid=762 0051: dt=31.104000, rms=0.622 (0.270%), neg=0, invalid=762 0052: dt=31.104000, rms=0.620 (0.289%), neg=0, invalid=762 0053: dt=31.104000, rms=0.618 (0.297%), neg=0, invalid=762 0054: dt=31.104000, rms=0.618 (0.038%), neg=0, invalid=762 0055: dt=31.104000, rms=0.617 (0.044%), neg=0, invalid=762 0056: dt=31.104000, rms=0.617 (0.046%), neg=0, invalid=762 0057: dt=31.104000, rms=0.617 (0.056%), neg=0, invalid=762 0058: dt=31.104000, rms=0.616 (0.071%), neg=0, invalid=762 0059: dt=31.104000, rms=0.616 (0.076%), neg=0, invalid=762 0060: dt=31.104000, rms=0.615 (0.080%), neg=0, invalid=762 0061: dt=31.104000, rms=0.615 (0.101%), neg=0, invalid=762 0062: dt=31.104000, rms=0.614 (0.116%), neg=0, invalid=762 0063: dt=31.104000, rms=0.613 (0.123%), neg=0, invalid=762 0064: dt=31.104000, rms=0.612 (0.126%), neg=0, invalid=762 0065: dt=31.104000, rms=0.612 (0.129%), neg=0, invalid=762 0066: dt=31.104000, rms=0.611 (0.128%), neg=0, invalid=762 0067: dt=31.104000, rms=0.610 (0.129%), neg=0, invalid=762 0068: dt=31.104000, rms=0.609 (0.137%), neg=0, invalid=762 0069: dt=31.104000, rms=0.608 (0.136%), neg=0, invalid=762 0070: dt=31.104000, rms=0.608 (0.123%), neg=0, invalid=762 0071: dt=31.104000, rms=0.607 (0.108%), neg=0, invalid=762 0072: dt=145.152000, rms=0.607 (0.018%), neg=0, invalid=762 0073: dt=145.152000, rms=0.607 (0.047%), neg=0, invalid=762 0074: dt=145.152000, rms=0.607 (-0.022%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.633, neg=0, invalid=762 0075: dt=6.400000, rms=0.632 (0.151%), neg=0, invalid=762 0076: dt=2.800000, rms=0.632 (0.015%), neg=0, invalid=762 0077: dt=2.800000, rms=0.632 (0.007%), neg=0, invalid=762 0078: dt=2.800000, rms=0.632 (-0.008%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.633, neg=0, invalid=762 0079: dt=11.200000, rms=0.631 (0.194%), neg=0, invalid=762 0080: dt=9.600000, rms=0.631 (0.034%), neg=0, invalid=762 0081: dt=9.600000, rms=0.631 (0.015%), neg=0, invalid=762 0082: dt=9.600000, rms=0.631 (-0.033%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.684, neg=0, invalid=762 0083: dt=5.524590, rms=0.677 (1.121%), neg=0, invalid=762 0084: dt=6.842105, rms=0.675 (0.236%), neg=0, invalid=762 0085: dt=6.842105, rms=0.675 (0.025%), neg=0, invalid=762 0086: dt=6.842105, rms=0.675 (-0.167%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.675, neg=0, invalid=762 0087: dt=2.133333, rms=0.675 (0.096%), neg=0, invalid=762 0088: dt=1.008000, rms=0.675 (0.005%), neg=0, invalid=762 0089: dt=1.008000, rms=0.675 (0.003%), neg=0, invalid=762 0090: dt=1.008000, rms=0.675 (0.001%), neg=0, invalid=762 0091: dt=1.008000, rms=0.675 (-0.017%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.719, neg=0, invalid=762 0092: dt=0.000000, rms=0.718 (0.065%), neg=0, invalid=762 0093: dt=0.000000, rms=0.718 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.719, neg=0, invalid=762 0094: dt=0.000000, rms=0.718 (0.065%), neg=0, invalid=762 0095: dt=0.000000, rms=0.718 (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=0.644, neg=0, invalid=762 0096: dt=0.647297, rms=0.633 (1.715%), neg=0, invalid=762 0097: dt=0.064000, rms=0.633 (0.066%), neg=0, invalid=762 0098: dt=0.064000, rms=0.633 (-0.058%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.634, neg=0, invalid=762 0099: dt=0.028000, rms=0.633 (0.095%), neg=0, invalid=762 0100: dt=-0.000036, rms=0.633 (-0.001%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.11891 (29) Left_Lateral_Ventricle (4): linear fit = 1.51 x + 0.0 (1793 voxels, overlap=0.274) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (1793 voxels, peak = 30), gca=30.0 gca peak = 0.15565 (16) mri peak = 0.10626 (29) Right_Lateral_Ventricle (43): linear fit = 1.84 x + 0.0 (1606 voxels, overlap=0.098) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1606 voxels, peak = 29), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.09855 (98) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (1053 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (1053 voxels, peak = 99), gca=99.4 gca peak = 0.20183 (93) mri peak = 0.12897 (101) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (1037 voxels, overlap=0.870) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (1037 voxels, peak = 97), gca=97.2 gca peak = 0.21683 (55) mri peak = 0.12064 (74) Right_Hippocampus (53): linear fit = 1.34 x + 0.0 (1200 voxels, overlap=0.012) Right_Hippocampus (53): linear fit = 1.34 x + 0.0 (1200 voxels, peak = 73), gca=73.4 gca peak = 0.30730 (58) mri peak = 0.12403 (75) Left_Hippocampus (17): linear fit = 1.26 x + 0.0 (1179 voxels, overlap=0.012) Left_Hippocampus (17): linear fit = 1.26 x + 0.0 (1179 voxels, peak = 73), gca=73.4 gca peak = 0.11430 (101) mri peak = 0.14841 (105) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (70103 voxels, overlap=0.549) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (70103 voxels, peak = 105), gca=104.5 gca peak = 0.12076 (102) mri peak = 0.15941 (106) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (72682 voxels, overlap=0.353) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (72682 voxels, peak = 107), gca=106.6 gca peak = 0.14995 (59) mri peak = 0.04778 (74) Left_Cerebral_Cortex (3): linear fit = 1.26 x + 0.0 (40444 voxels, overlap=0.002) Left_Cerebral_Cortex (3): linear fit = 1.26 x + 0.0 (40444 voxels, peak = 75), gca=74.6 gca peak = 0.15082 (58) mri peak = 0.05439 (74) Right_Cerebral_Cortex (42): linear fit = 1.28 x + 0.0 (40448 voxels, overlap=0.001) Right_Cerebral_Cortex (42): linear fit = 1.28 x + 0.0 (40448 voxels, peak = 75), gca=74.5 gca peak = 0.14161 (67) mri peak = 0.16989 (86) Right_Caudate (50): linear fit = 1.27 x + 0.0 (517 voxels, overlap=0.013) Right_Caudate (50): linear fit = 1.27 x + 0.0 (517 voxels, peak = 85), gca=85.4 gca peak = 0.15243 (71) mri peak = 0.18042 (87) Left_Caudate (11): linear fit = 1.21 x + 0.0 (1106 voxels, overlap=0.005) Left_Caudate (11): linear fit = 1.21 x + 0.0 (1106 voxels, peak = 86), gca=85.6 gca peak = 0.13336 (57) mri peak = 0.05089 (75) Left_Cerebellum_Cortex (8): linear fit = 1.40 x + 0.0 (23523 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.40 x + 0.0 (23523 voxels, peak = 80), gca=80.1 gca peak = 0.13252 (56) mri peak = 0.04373 (75) Right_Cerebellum_Cortex (47): linear fit = 1.41 x + 0.0 (25084 voxels, overlap=0.002) Right_Cerebellum_Cortex (47): linear fit = 1.41 x + 0.0 (25084 voxels, peak = 79), gca=79.2 gca peak = 0.18181 (84) mri peak = 0.08522 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (9829 voxels, overlap=0.570) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (9829 voxels, peak = 94), gca=93.7 gca peak = 0.20573 (83) mri peak = 0.06878 (78) Right_Cerebellum_White_Matter (46): linear fit = 0.94 x + 0.0 (7336 voxels, overlap=0.867) Right_Cerebellum_White_Matter (46): linear fit = 0.94 x + 0.0 (7336 voxels, peak = 78), gca=77.6 gca peak = 0.21969 (57) mri peak = 0.16979 (74) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (556 voxels, overlap=0.040) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (556 voxels, peak = 74), gca=73.8 gca peak = 0.39313 (56) mri peak = 0.09843 (75) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (500 voxels, overlap=0.021) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (500 voxels, peak = 73), gca=72.5 gca peak = 0.14181 (85) mri peak = 0.08937 (97) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (5836 voxels, overlap=0.338) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (5836 voxels, peak = 96), gca=96.5 gca peak = 0.11978 (83) mri peak = 0.07506 (94) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4139 voxels, overlap=0.541) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4139 voxels, peak = 93), gca=92.5 gca peak = 0.13399 (79) mri peak = 0.13129 (92) Left_Putamen (12): linear fit = 1.15 x + 0.0 (2538 voxels, overlap=0.005) Left_Putamen (12): linear fit = 1.15 x + 0.0 (2538 voxels, peak = 91), gca=91.2 gca peak = 0.14159 (79) mri peak = 0.10043 (92) Right_Putamen (51): linear fit = 1.15 x + 0.0 (2764 voxels, overlap=0.019) Right_Putamen (51): linear fit = 1.15 x + 0.0 (2764 voxels, peak = 91), gca=91.2 gca peak = 0.10025 (80) mri peak = 0.14813 (91) Brain_Stem (16): linear fit = 1.14 x + 0.0 (10819 voxels, overlap=0.011) Brain_Stem (16): linear fit = 1.14 x + 0.0 (10819 voxels, peak = 92), gca=91.6 gca peak = 0.13281 (86) mri peak = 0.11288 (95) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1258 voxels, overlap=0.111) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1258 voxels, peak = 94), gca=94.2 gca peak = 0.12801 (89) mri peak = 0.12948 (97) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1435 voxels, overlap=0.084) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1435 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) mri peak = 1.00000 (29) gca peak = 0.15061 (21) mri peak = 0.33355 (28) Fourth_Ventricle (15): linear fit = 1.30 x + 0.0 (715 voxels, overlap=0.063) Fourth_Ventricle (15): linear fit = 1.30 x + 0.0 (715 voxels, peak = 27), gca=27.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.29 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 1.43 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.645, neg=0, invalid=762 0101: dt=98.225770, rms=0.618 (4.086%), neg=0, invalid=762 0102: dt=163.555556, rms=0.613 (0.839%), neg=0, invalid=762 0103: dt=517.888000, rms=0.605 (1.340%), neg=0, invalid=762 0104: dt=73.984000, rms=0.604 (0.062%), neg=0, invalid=762 0105: dt=295.936000, rms=0.603 (0.184%), neg=0, invalid=762 0106: dt=517.888000, rms=0.598 (0.864%), neg=0, invalid=762 0107: dt=18.496000, rms=0.598 (0.005%), neg=0, invalid=762 0108: dt=18.496000, rms=0.598 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.598, neg=0, invalid=762 0109: dt=110.976000, rms=0.598 (0.120%), neg=0, invalid=762 0110: dt=517.888000, rms=0.596 (0.258%), neg=0, invalid=762 0111: dt=369.920000, rms=0.595 (0.225%), neg=0, invalid=762 0112: dt=92.480000, rms=0.594 (0.097%), neg=0, invalid=762 0113: dt=443.904000, rms=0.594 (0.047%), neg=0, invalid=762 0114: dt=443.904000, rms=0.592 (0.303%), neg=0, invalid=762 0115: dt=443.904000, rms=0.592 (-0.156%), neg=0, invalid=762 0116: dt=32.368000, rms=0.592 (0.014%), neg=0, invalid=762 0117: dt=32.368000, rms=0.592 (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=0.592, neg=0, invalid=762 0118: dt=117.436893, rms=0.586 (1.006%), neg=0, invalid=762 0119: dt=190.020619, rms=0.574 (2.150%), neg=0, invalid=762 0120: dt=45.211009, rms=0.571 (0.545%), neg=0, invalid=762 0121: dt=145.152000, rms=0.569 (0.382%), neg=0, invalid=762 0122: dt=228.374101, rms=0.562 (1.143%), neg=0, invalid=762 0123: dt=36.288000, rms=0.560 (0.324%), neg=0, invalid=762 0124: dt=36.288000, rms=0.560 (0.066%), neg=0, invalid=762 0125: dt=145.152000, rms=0.559 (0.206%), neg=0, invalid=762 0126: dt=248.832000, rms=0.554 (0.750%), neg=0, invalid=762 0127: dt=36.288000, rms=0.554 (0.125%), neg=0, invalid=762 0128: dt=36.288000, rms=0.554 (0.035%), neg=0, invalid=762 0129: dt=36.288000, rms=0.553 (0.042%), neg=0, invalid=762 0130: dt=36.288000, rms=0.553 (0.084%), neg=0, invalid=762 0131: dt=36.288000, rms=0.552 (0.143%), neg=0, invalid=762 0132: dt=36.288000, rms=0.551 (0.206%), neg=0, invalid=762 0133: dt=36.288000, rms=0.550 (0.254%), neg=0, invalid=762 0134: dt=36.288000, rms=0.548 (0.260%), neg=0, invalid=762 0135: dt=36.288000, rms=0.547 (0.252%), neg=0, invalid=762 0136: dt=36.288000, rms=0.546 (0.226%), neg=0, invalid=762 0137: dt=36.288000, rms=0.544 (0.203%), neg=0, invalid=762 0138: dt=36.288000, rms=0.543 (0.187%), neg=0, invalid=762 0139: dt=36.288000, rms=0.543 (0.036%), neg=0, invalid=762 0140: dt=36.288000, rms=0.543 (0.057%), neg=0, invalid=762 0141: dt=36.288000, rms=0.543 (0.068%), neg=0, invalid=762 0142: dt=36.288000, rms=0.542 (0.071%), neg=0, invalid=762 0143: dt=36.288000, rms=0.542 (0.083%), neg=0, invalid=762 0144: dt=18.144000, rms=0.542 (0.014%), neg=0, invalid=762 0145: dt=9.072000, rms=0.542 (0.007%), neg=0, invalid=762 0146: dt=2.268000, rms=0.542 (0.002%), neg=0, invalid=762 0147: dt=2.268000, rms=0.542 (0.002%), neg=0, invalid=762 0148: dt=0.567000, rms=0.542 (0.000%), neg=0, invalid=762 0149: dt=0.017719, rms=0.542 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.542, neg=0, invalid=762 0150: dt=145.152000, rms=0.538 (0.616%), neg=0, invalid=762 0151: dt=82.944000, rms=0.538 (0.156%), neg=0, invalid=762 0152: dt=145.152000, rms=0.537 (0.150%), neg=0, invalid=762 0153: dt=62.208000, rms=0.536 (0.107%), neg=0, invalid=762 0154: dt=145.152000, rms=0.536 (0.111%), neg=0, invalid=762 0155: dt=36.288000, rms=0.535 (0.068%), neg=0, invalid=762 0156: dt=497.664000, rms=0.534 (0.227%), neg=0, invalid=762 0157: dt=36.288000, rms=0.533 (0.152%), neg=0, invalid=762 0158: dt=103.680000, rms=0.533 (0.075%), neg=0, invalid=762 0159: dt=62.208000, rms=0.533 (0.044%), neg=0, invalid=762 0160: dt=62.208000, rms=0.532 (0.044%), neg=0, invalid=762 0161: dt=62.208000, rms=0.532 (0.064%), neg=0, invalid=762 0162: dt=62.208000, rms=0.532 (0.096%), neg=0, invalid=762 0163: dt=62.208000, rms=0.531 (0.112%), neg=0, invalid=762 0164: dt=62.208000, rms=0.530 (0.132%), neg=0, invalid=762 0165: dt=62.208000, rms=0.530 (0.135%), neg=0, invalid=762 0166: dt=62.208000, rms=0.529 (0.147%), neg=0, invalid=762 0167: dt=62.208000, rms=0.528 (0.150%), neg=0, invalid=762 0168: dt=62.208000, rms=0.527 (0.148%), neg=0, invalid=762 0169: dt=62.208000, rms=0.526 (0.148%), neg=0, invalid=762 0170: dt=62.208000, rms=0.526 (0.142%), neg=0, invalid=762 0171: dt=62.208000, rms=0.525 (0.144%), neg=0, invalid=762 0172: dt=62.208000, rms=0.524 (0.129%), neg=0, invalid=762 0173: dt=62.208000, rms=0.524 (0.132%), neg=0, invalid=762 0174: dt=62.208000, rms=0.523 (0.124%), neg=0, invalid=762 0175: dt=62.208000, rms=0.522 (0.130%), neg=0, invalid=762 0176: dt=62.208000, rms=0.522 (0.132%), neg=0, invalid=762 0177: dt=62.208000, rms=0.521 (0.123%), neg=0, invalid=762 0178: dt=62.208000, rms=0.520 (0.119%), neg=0, invalid=762 0179: dt=62.208000, rms=0.520 (0.108%), neg=0, invalid=762 0180: dt=62.208000, rms=0.519 (0.110%), neg=0, invalid=762 0181: dt=62.208000, rms=0.519 (0.112%), neg=0, invalid=762 0182: dt=62.208000, rms=0.518 (0.109%), neg=0, invalid=762 0183: dt=62.208000, rms=0.517 (0.105%), neg=0, invalid=762 0184: dt=62.208000, rms=0.517 (0.095%), neg=0, invalid=762 0185: dt=62.208000, rms=0.516 (0.090%), neg=0, invalid=762 0186: dt=62.208000, rms=0.516 (0.082%), neg=0, invalid=762 0187: dt=62.208000, rms=0.516 (0.079%), neg=0, invalid=762 0188: dt=62.208000, rms=0.515 (0.075%), neg=0, invalid=762 0189: dt=62.208000, rms=0.515 (0.076%), neg=0, invalid=762 0190: dt=62.208000, rms=0.515 (0.069%), neg=0, invalid=762 0191: dt=62.208000, rms=0.514 (0.063%), neg=0, invalid=762 0192: dt=62.208000, rms=0.514 (0.060%), neg=0, invalid=762 0193: dt=62.208000, rms=0.514 (0.055%), neg=0, invalid=762 0194: dt=62.208000, rms=0.513 (0.054%), neg=0, invalid=762 0195: dt=62.208000, rms=0.513 (0.059%), neg=0, invalid=762 0196: dt=62.208000, rms=0.513 (0.060%), neg=0, invalid=762 0197: dt=62.208000, rms=0.512 (0.053%), neg=0, invalid=762 0198: dt=62.208000, rms=0.512 (0.056%), neg=0, invalid=762 0199: dt=62.208000, rms=0.512 (0.052%), neg=0, invalid=762 0200: dt=62.208000, rms=0.512 (0.050%), neg=0, invalid=762 0201: dt=62.208000, rms=0.511 (0.045%), neg=0, invalid=762 0202: dt=62.208000, rms=0.511 (0.044%), neg=0, invalid=762 0203: dt=62.208000, rms=0.511 (0.046%), neg=0, invalid=762 0204: dt=62.208000, rms=0.511 (0.044%), neg=0, invalid=762 0205: dt=62.208000, rms=0.510 (0.043%), neg=0, invalid=762 0206: dt=62.208000, rms=0.510 (0.039%), neg=0, invalid=762 0207: dt=62.208000, rms=0.510 (0.037%), neg=0, invalid=762 0208: dt=62.208000, rms=0.510 (0.036%), neg=0, invalid=762 0209: dt=62.208000, rms=0.510 (0.034%), neg=0, invalid=762 0210: dt=62.208000, rms=0.510 (0.034%), neg=0, invalid=762 0211: dt=62.208000, rms=0.509 (0.032%), neg=0, invalid=762 0212: dt=62.208000, rms=0.509 (0.030%), neg=0, invalid=762 0213: dt=62.208000, rms=0.509 (0.030%), neg=0, invalid=762 0214: dt=62.208000, rms=0.509 (0.031%), neg=0, invalid=762 0215: dt=62.208000, rms=0.509 (0.029%), neg=0, invalid=762 0216: dt=62.208000, rms=0.509 (0.030%), neg=0, invalid=762 0217: dt=62.208000, rms=0.509 (0.030%), neg=0, invalid=762 0218: dt=62.208000, rms=0.508 (0.026%), neg=0, invalid=762 0219: dt=62.208000, rms=0.508 (0.023%), neg=0, invalid=762 0220: dt=62.208000, rms=0.508 (0.024%), neg=0, invalid=762 0221: dt=62.208000, rms=0.508 (0.028%), neg=0, invalid=762 0222: dt=62.208000, rms=0.508 (0.031%), neg=0, invalid=762 0223: dt=62.208000, rms=0.508 (0.028%), neg=0, invalid=762 0224: dt=62.208000, rms=0.508 (0.023%), neg=0, invalid=762 0225: dt=62.208000, rms=0.507 (0.021%), neg=0, invalid=762 0226: dt=145.152000, rms=0.507 (0.007%), neg=0, invalid=762 0227: dt=145.152000, rms=0.507 (-0.016%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.517, neg=0, invalid=762 0228: dt=11.200000, rms=0.516 (0.119%), neg=0, invalid=762 0229: dt=11.200000, rms=0.516 (0.049%), neg=0, invalid=762 0230: dt=11.200000, rms=0.516 (0.044%), neg=0, invalid=762 0231: dt=11.200000, rms=0.516 (0.048%), neg=0, invalid=762 0232: dt=11.200000, rms=0.516 (0.027%), neg=0, invalid=762 0233: dt=11.200000, rms=0.515 (0.104%), neg=0, invalid=762 0234: dt=11.200000, rms=0.514 (0.175%), neg=0, invalid=762 0235: dt=11.200000, rms=0.514 (0.074%), neg=0, invalid=762 0236: dt=0.700000, rms=0.514 (0.005%), neg=0, invalid=762 0237: dt=0.350000, rms=0.514 (0.003%), neg=0, invalid=762 0238: dt=0.037500, rms=0.514 (0.000%), neg=0, invalid=762 0239: dt=0.002344, rms=0.514 (0.000%), neg=0, invalid=762 0240: dt=0.000146, rms=0.514 (0.000%), neg=0, invalid=762 0241: dt=0.000073, rms=0.514 (0.000%), neg=0, invalid=762 0242: dt=0.000037, rms=0.514 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.514, neg=0, invalid=762 0243: dt=85.170038, rms=0.507 (1.278%), neg=0, invalid=762 0244: dt=25.600000, rms=0.506 (0.254%), neg=0, invalid=762 0245: dt=102.400000, rms=0.504 (0.347%), neg=0, invalid=762 0246: dt=32.000000, rms=0.503 (0.283%), neg=0, invalid=762 0247: dt=44.800000, rms=0.502 (0.257%), neg=0, invalid=762 0248: dt=32.000000, rms=0.501 (0.142%), neg=0, invalid=762 0249: dt=44.800000, rms=0.500 (0.165%), neg=0, invalid=762 0250: dt=32.000000, rms=0.499 (0.132%), neg=0, invalid=762 0251: dt=38.400000, rms=0.499 (0.132%), neg=0, invalid=762 0252: dt=32.000000, rms=0.498 (0.108%), neg=0, invalid=762 0253: dt=38.400000, rms=0.498 (0.109%), neg=0, invalid=762 0254: dt=32.000000, rms=0.497 (0.100%), neg=0, invalid=762 0255: dt=32.000000, rms=0.497 (0.094%), neg=0, invalid=762 0256: dt=38.400000, rms=0.496 (0.092%), neg=0, invalid=762 0257: dt=32.000000, rms=0.496 (0.083%), neg=0, invalid=762 0258: dt=32.000000, rms=0.495 (0.090%), neg=0, invalid=762 0259: dt=38.400000, rms=0.495 (0.080%), neg=0, invalid=762 0260: dt=32.000000, rms=0.495 (0.074%), neg=0, invalid=762 0261: dt=32.000000, rms=0.494 (0.072%), neg=0, invalid=762 0262: dt=32.000000, rms=0.494 (0.069%), neg=0, invalid=762 0263: dt=32.000000, rms=0.494 (0.060%), neg=0, invalid=762 0264: dt=32.000000, rms=0.493 (0.063%), neg=0, invalid=762 0265: dt=38.400000, rms=0.493 (0.066%), neg=0, invalid=762 0266: dt=32.000000, rms=0.493 (0.055%), neg=0, invalid=762 0267: dt=32.000000, rms=0.492 (0.058%), neg=0, invalid=762 0268: dt=32.000000, rms=0.492 (0.057%), neg=0, invalid=762 0269: dt=32.000000, rms=0.492 (0.053%), neg=0, invalid=762 0270: dt=32.000000, rms=0.492 (0.047%), neg=0, invalid=762 0271: dt=32.000000, rms=0.491 (0.051%), neg=0, invalid=762 0272: dt=32.000000, rms=0.491 (0.095%), neg=0, invalid=762 0273: dt=32.000000, rms=0.490 (0.120%), neg=0, invalid=762 0274: dt=32.000000, rms=0.490 (0.161%), neg=0, invalid=762 0275: dt=32.000000, rms=0.489 (0.164%), neg=0, invalid=762 0276: dt=32.000000, rms=0.489 (0.029%), neg=0, invalid=762 0277: dt=32.000000, rms=0.488 (0.041%), neg=0, invalid=762 0278: dt=16.000000, rms=0.488 (0.029%), neg=0, invalid=762 0279: dt=4.000000, rms=0.488 (0.013%), neg=0, invalid=762 0280: dt=1.000000, rms=0.488 (0.000%), neg=0, invalid=762 0281: dt=0.700000, rms=0.488 (0.001%), neg=0, invalid=762 0282: dt=0.175000, rms=0.488 (0.000%), neg=0, invalid=762 0283: dt=0.087500, rms=0.488 (0.000%), neg=0, invalid=762 0284: dt=0.021875, rms=0.488 (0.000%), neg=0, invalid=762 0285: dt=0.005469, rms=0.488 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.507, neg=0, invalid=762 0286: dt=0.000000, rms=0.507 (0.056%), neg=0, invalid=762 0287: dt=0.000000, rms=0.507 (0.000%), neg=0, invalid=762 0288: dt=0.150000, rms=0.507 (-0.008%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.507, neg=0, invalid=762 0289: dt=0.000000, rms=0.507 (0.056%), neg=0, invalid=762 0290: dt=0.000000, rms=0.507 (0.000%), neg=0, invalid=762 0291: dt=0.150000, rms=0.507 (-0.005%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.544, neg=0, invalid=762 0292: dt=1.876712, rms=0.539 (0.888%), neg=0, invalid=762 0293: dt=0.768000, rms=0.539 (0.052%), neg=0, invalid=762 0294: dt=0.192000, rms=0.539 (0.003%), neg=0, invalid=762 0295: dt=0.192000, rms=0.539 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.539, neg=0, invalid=762 0296: dt=1.792000, rms=0.538 (0.260%), neg=0, invalid=762 0297: dt=0.448000, rms=0.538 (0.014%), neg=0, invalid=762 0298: dt=0.448000, rms=0.538 (0.005%), neg=0, invalid=762 0299: dt=0.448000, rms=0.538 (-0.015%), 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=0.504, neg=0, invalid=762 0300: dt=0.448000, rms=0.493 (2.243%), neg=0, invalid=762 0301: dt=1.280000, rms=0.486 (1.421%), neg=0, invalid=762 0302: dt=-0.000563, rms=0.486 (0.001%), neg=0, invalid=762 0303: dt=-0.000563, rms=0.486 (0.000%), neg=0, invalid=762 0304: dt=-0.000563, rms=0.486 (0.000%), neg=0, invalid=762 0305: dt=-0.000563, rms=0.486 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.486, neg=0, invalid=762 0306: dt=0.448000, rms=0.483 (0.722%), neg=0, invalid=762 0307: dt=0.448000, rms=0.482 (0.115%), neg=0, invalid=762 0308: dt=0.448000, rms=0.482 (0.085%), neg=0, invalid=762 0309: dt=0.448000, rms=0.481 (0.062%), neg=0, invalid=762 0310: dt=0.448000, rms=0.481 (0.051%), neg=0, invalid=762 0311: dt=0.448000, rms=0.481 (0.047%), neg=0, invalid=762 0312: dt=0.448000, rms=0.481 (0.041%), neg=0, invalid=762 0313: dt=0.448000, rms=0.480 (0.072%), neg=0, invalid=762 0314: dt=0.448000, rms=0.480 (0.090%), neg=0, invalid=762 0315: dt=0.448000, rms=0.479 (0.099%), neg=0, invalid=762 0316: dt=0.448000, rms=0.479 (0.095%), neg=0, invalid=762 0317: dt=0.448000, rms=0.479 (0.083%), neg=0, invalid=762 0318: dt=0.448000, rms=0.478 (0.065%), neg=0, invalid=762 0319: dt=0.448000, rms=0.478 (0.044%), neg=0, invalid=762 0320: dt=0.448000, rms=0.478 (0.025%), neg=0, invalid=762 0321: dt=0.448000, rms=0.478 (0.012%), neg=0, invalid=762 0322: dt=0.448000, rms=0.478 (-0.003%), neg=0, invalid=762 0323: dt=0.000000, rms=0.478 (0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.476, neg=0, invalid=762 0324: dt=0.000000, rms=0.475 (0.069%), neg=0, invalid=762 0325: dt=0.000000, rms=0.475 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.476, neg=0, invalid=762 0326: dt=110.976000, rms=0.475 (0.077%), neg=0, invalid=762 0327: dt=517.888000, rms=0.475 (0.066%), neg=0, invalid=762 0328: dt=517.888000, rms=0.475 (-0.761%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.475, neg=0, invalid=762 0329: dt=7.776000, rms=0.475 (0.074%), neg=0, invalid=762 0330: dt=3.888000, rms=0.475 (0.001%), neg=0, invalid=762 0331: dt=3.888000, rms=0.475 (0.000%), neg=0, invalid=762 0332: dt=3.888000, rms=0.475 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.475, neg=0, invalid=762 0333: dt=145.152000, rms=0.473 (0.418%), neg=0, invalid=762 0334: dt=36.288000, rms=0.473 (0.179%), neg=0, invalid=762 0335: dt=36.288000, rms=0.472 (0.065%), neg=0, invalid=762 0336: dt=36.288000, rms=0.472 (0.101%), neg=0, invalid=762 0337: dt=36.288000, rms=0.471 (0.137%), neg=0, invalid=762 0338: dt=36.288000, rms=0.470 (0.147%), neg=0, invalid=762 0339: dt=36.288000, rms=0.470 (0.148%), neg=0, invalid=762 0340: dt=36.288000, rms=0.469 (0.133%), neg=0, invalid=762 0341: dt=36.288000, rms=0.469 (0.129%), neg=0, invalid=762 0342: dt=36.288000, rms=0.468 (0.125%), neg=0, invalid=762 0343: dt=36.288000, rms=0.467 (0.112%), neg=0, invalid=762 0344: dt=36.288000, rms=0.467 (0.097%), neg=0, invalid=762 0345: dt=145.152000, rms=0.467 (0.049%), neg=0, invalid=762 0346: dt=145.152000, rms=0.467 (-0.025%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.468, neg=0, invalid=762 0347: dt=23.680000, rms=0.466 (0.322%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0348: dt=44.800000, rms=0.465 (0.320%), neg=0, invalid=762 0349: dt=44.800000, rms=0.464 (0.219%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0350: dt=44.800000, rms=0.463 (0.245%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 11 iterations, nbhd size=1, neg = 0 0351: dt=44.800000, rms=0.461 (0.350%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0352: dt=44.800000, rms=0.461 (0.013%), neg=0, invalid=762 iter 0, gcam->neg = 24 after 9 iterations, nbhd size=1, neg = 0 0353: dt=44.800000, rms=0.459 (0.452%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 13 iterations, nbhd size=1, neg = 0 0354: dt=44.800000, rms=0.458 (0.209%), neg=0, invalid=762 iter 0, gcam->neg = 26 after 11 iterations, nbhd size=1, neg = 0 0355: dt=44.800000, rms=0.457 (0.244%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 10 iterations, nbhd size=1, neg = 0 0356: dt=44.800000, rms=0.457 (-0.023%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0357: dt=25.600000, rms=0.456 (0.166%), neg=0, invalid=762 0358: dt=32.000000, rms=0.455 (0.097%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.456, neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0359: dt=74.384106, rms=0.450 (1.276%), neg=0, invalid=762 0360: dt=24.666667, rms=0.448 (0.405%), neg=0, invalid=762 0361: dt=44.800000, rms=0.447 (0.215%), neg=0, invalid=762 0362: dt=44.800000, rms=0.447 (0.111%), neg=0, invalid=762 0363: dt=44.800000, rms=0.445 (0.259%), neg=0, invalid=762 0364: dt=44.800000, rms=0.445 (0.134%), neg=0, invalid=762 0365: dt=44.800000, rms=0.445 (0.077%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0366: dt=44.800000, rms=0.444 (0.025%), neg=0, invalid=762 0367: dt=32.000000, rms=0.444 (0.098%), neg=0, invalid=762 0368: dt=25.600000, rms=0.444 (0.058%), neg=0, invalid=762 0369: dt=25.600000, rms=0.444 (0.045%), neg=0, invalid=762 0370: dt=25.600000, rms=0.443 (0.064%), neg=0, invalid=762 0371: dt=25.600000, rms=0.443 (0.061%), neg=0, invalid=762 0372: dt=25.600000, rms=0.443 (0.072%), neg=0, invalid=762 0373: dt=25.600000, rms=0.442 (0.056%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.450, neg=0, invalid=762 0374: dt=0.000000, rms=0.449 (0.059%), neg=0, invalid=762 0375: dt=0.000000, rms=0.449 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.450, neg=0, invalid=762 0376: dt=0.720000, rms=0.449 (0.061%), neg=0, invalid=762 0377: dt=0.252000, rms=0.449 (0.002%), neg=0, invalid=762 0378: dt=0.252000, rms=0.449 (0.001%), neg=0, invalid=762 0379: dt=0.252000, rms=0.449 (-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=0.463, neg=0, invalid=762 0380: dt=1.280000, rms=0.462 (0.319%), neg=0, invalid=762 0381: dt=0.384000, rms=0.462 (0.014%), neg=0, invalid=762 0382: dt=0.384000, rms=0.462 (-0.006%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.462, neg=0, invalid=762 0383: dt=1.792000, rms=0.461 (0.286%), neg=0, invalid=762 0384: dt=0.768000, rms=0.460 (0.020%), neg=0, invalid=762 0385: dt=0.768000, rms=0.460 (0.002%), neg=0, invalid=762 0386: dt=0.768000, rms=0.460 (-0.049%), 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=0.451, neg=0, invalid=762 iter 0, gcam->neg = 286 after 14 iterations, nbhd size=1, neg = 0 0387: dt=2.052090, rms=0.428 (5.036%), neg=0, invalid=762 0388: dt=0.080000, rms=0.428 (0.050%), neg=0, invalid=762 0389: dt=0.080000, rms=0.428 (-0.034%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.428, neg=0, invalid=762 0390: dt=0.080000, rms=0.428 (0.131%), neg=0, invalid=762 0391: dt=0.007000, rms=0.428 (0.001%), neg=0, invalid=762 0392: dt=0.007000, rms=0.428 (-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=0.417, neg=0, invalid=762 0393: dt=0.000000, rms=0.417 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.417, neg=0, invalid=762 0394: dt=18.496000, rms=0.417 (0.000%), neg=0, invalid=762 0395: dt=2.023000, rms=0.417 (0.000%), neg=0, invalid=762 0396: dt=2.023000, rms=0.417 (0.000%), neg=0, invalid=762 0397: dt=2.023000, rms=0.417 (-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=0.417, neg=0, invalid=762 0398: dt=0.000000, rms=0.417 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.417, neg=0, invalid=762 0399: dt=36.288000, rms=0.417 (0.027%), neg=0, invalid=762 0400: dt=145.152000, rms=0.416 (0.052%), neg=0, invalid=762 0401: dt=145.152000, rms=0.416 (0.094%), neg=0, invalid=762 0402: dt=25.920000, rms=0.416 (0.004%), neg=0, invalid=762 0403: dt=25.920000, rms=0.416 (0.004%), neg=0, invalid=762 0404: dt=25.920000, rms=0.416 (0.006%), neg=0, invalid=762 0405: dt=25.920000, rms=0.416 (0.011%), neg=0, invalid=762 0406: dt=25.920000, rms=0.416 (0.020%), neg=0, invalid=762 0407: dt=25.920000, rms=0.416 (0.027%), neg=0, invalid=762 0408: dt=25.920000, rms=0.416 (0.029%), neg=0, invalid=762 0409: dt=25.920000, rms=0.415 (0.026%), neg=0, invalid=762 0410: dt=25.920000, rms=0.415 (0.022%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.416, neg=0, invalid=762 0411: dt=6.400000, rms=0.416 (0.025%), neg=0, invalid=762 0412: dt=2.400000, rms=0.416 (0.003%), neg=0, invalid=762 0413: dt=2.400000, 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 0414: dt=116.363636, rms=0.412 (0.965%), neg=0, invalid=762 0415: dt=20.923077, rms=0.410 (0.332%), neg=0, invalid=762 0416: dt=44.800000, rms=0.410 (0.084%), neg=0, invalid=762 0417: dt=44.800000, rms=0.409 (0.145%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0418: dt=44.800000, rms=0.409 (0.238%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0419: dt=44.800000, rms=0.408 (0.229%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0420: dt=44.800000, rms=0.407 (0.245%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0421: dt=44.800000, rms=0.406 (0.245%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 9 iterations, nbhd size=1, neg = 0 0422: dt=44.800000, rms=0.405 (0.183%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 2 iterations, nbhd size=0, neg = 0 0423: dt=44.800000, rms=0.404 (0.174%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=0, neg = 0 0424: dt=44.800000, rms=0.404 (0.117%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0425: dt=44.800000, rms=0.403 (0.095%), neg=0, invalid=762 0426: dt=25.600000, rms=0.403 (0.022%), neg=0, invalid=762 0427: dt=25.600000, rms=0.403 (0.006%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0428: dt=25.600000, rms=0.403 (0.005%), neg=0, invalid=762 0429: dt=25.600000, rms=0.403 (0.006%), neg=0, invalid=762 0430: dt=25.600000, rms=0.403 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.409, neg=0, invalid=762 0431: dt=0.000000, rms=0.409 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.409, neg=0, invalid=762 0432: dt=3.666667, rms=0.408 (0.030%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0433: dt=1.728000, rms=0.408 (0.004%), neg=0, invalid=762 0434: dt=1.728000, rms=0.408 (0.001%), neg=0, invalid=762 0435: dt=1.728000, rms=0.408 (-0.012%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.418, neg=0, invalid=762 0436: dt=0.000000, rms=0.418 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.418, neg=0, invalid=762 0437: dt=0.192000, rms=0.418 (0.005%), neg=0, invalid=762 0438: dt=0.064000, rms=0.418 (0.000%), neg=0, invalid=762 0439: dt=0.064000, rms=0.418 (-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=0.403, neg=0, invalid=762 iter 0, gcam->neg = 242 after 13 iterations, nbhd size=1, neg = 0 0440: dt=1.280000, rms=0.396 (1.833%), neg=0, invalid=762 0441: dt=0.000023, rms=0.396 (0.000%), neg=0, invalid=762 0442: dt=0.000023, rms=0.396 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.396, neg=0, invalid=762 0443: dt=0.112000, rms=0.395 (0.059%), neg=0, invalid=762 0444: dt=0.080000, rms=0.395 (0.016%), neg=0, invalid=762 0445: dt=0.080000, rms=0.395 (0.007%), neg=0, invalid=762 0446: dt=0.080000, rms=0.395 (-0.024%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 3 hours, 20 minutes and 12 seconds. mri_ca_register utimesec 11994.059625 mri_ca_register stimesec 9.729520 mri_ca_register ru_maxrss 1333896 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4839486 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 5334 mri_ca_register ru_oublock 62728 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 215 mri_ca_register ru_nivcsw 19363 FSRUNTIME@ mri_ca_register 3.3368 hours 1 threads #-------------------------------------- #@# SubCort Seg Do 29. Mär 00:23:42 CEST 2018 mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.presurf.mgz --diff aseg.manedit.mgz $Id: mri_seg_diff.c,v 1.5 2011/03/02 00:04:24 nicks Exp $ cwd /scratch/annadan1111/MABT1T2/reruncrosstest_cp2/44538_T1_fs_edit/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.presurf.mgz --diff aseg.manedit.mgz sysname Linux hostname node098 machine x86_64 user annadan1111 Seg1 aseg.auto.mgz Seg2 aseg.presurf.mgz Diff aseg.manedit.mgz InDiff (null) Merged (null) ForceDiff 0 Computing difference between segmentations No difference found. mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /cm/shared/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname node098 machine x86_64 setenv SUBJECTS_DIR /scratch/annadan1111/MABT1T2/reruncrosstest_cp2 cd /scratch/annadan1111/MABT1T2/reruncrosstest_cp2/44538_T1_fs_edit/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /cm/shared/apps/freesurfer/6.0.0/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 /cm/shared/apps/freesurfer/6.0.0/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 6.77 Atlas used for the 3D morph was /cm/shared/apps/freesurfer/6.0.0/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 = 0.12253 (29) Left_Lateral_Ventricle (4): linear fit = 1.48 x + 0.0 (3662 voxels, overlap=0.186) Left_Lateral_Ventricle (4): linear fit = 1.48 x + 0.0 (3662 voxels, peak = 30), gca=29.5 gca peak = 0.17677 (13) mri peak = 0.12652 (29) Right_Lateral_Ventricle (43): linear fit = 2.08 x + 0.0 (3214 voxels, overlap=0.132) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (3214 voxels, peak = 27), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.16049 (98) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (729 voxels, overlap=0.953) Right_Pallidum (52): linear fit = 1.04 x + 0.0 (729 voxels, peak = 99), gca=99.3 gca peak = 0.16930 (96) mri peak = 0.24846 (101) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (648 voxels, overlap=0.353) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (648 voxels, peak = 100), gca=100.3 gca peak = 0.24553 (55) mri peak = 0.12510 (74) Right_Hippocampus (53): linear fit = 1.34 x + 0.0 (1223 voxels, overlap=0.017) Right_Hippocampus (53): linear fit = 1.34 x + 0.0 (1223 voxels, peak = 73), gca=73.4 gca peak = 0.30264 (59) mri peak = 0.13079 (75) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (1233 voxels, overlap=0.018) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (1233 voxels, peak = 76), gca=76.4 gca peak = 0.07580 (103) mri peak = 0.17130 (105) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (39685 voxels, overlap=0.495) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (39685 voxels, peak = 106), gca=105.6 gca peak = 0.07714 (104) mri peak = 0.17385 (106) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (41500 voxels, overlap=0.413) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (41500 voxels, peak = 107), gca=106.6 gca peak = 0.09712 (58) mri peak = 0.06464 (72) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (44777 voxels, overlap=0.022) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (44777 voxels, peak = 72), gca=72.2 gca peak = 0.11620 (58) mri peak = 0.06814 (72) Right_Cerebral_Cortex (42): linear fit = 1.25 x + 0.0 (44335 voxels, overlap=0.008) Right_Cerebral_Cortex (42): linear fit = 1.25 x + 0.0 (44335 voxels, peak = 72), gca=72.2 gca peak = 0.30970 (66) mri peak = 0.16020 (87) Right_Caudate (50): linear fit = 1.29 x + 0.0 (1392 voxels, overlap=0.015) Right_Caudate (50): linear fit = 1.29 x + 0.0 (1392 voxels, peak = 85), gca=85.5 gca peak = 0.15280 (69) mri peak = 0.16127 (87) Left_Caudate (11): linear fit = 1.23 x + 0.0 (1482 voxels, overlap=0.016) Left_Caudate (11): linear fit = 1.23 x + 0.0 (1482 voxels, peak = 85), gca=84.5 gca peak = 0.13902 (56) mri peak = 0.08431 (78) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (33464 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (33464 voxels, peak = 77), gca=77.0 gca peak = 0.14777 (55) mri peak = 0.09713 (75) Right_Cerebellum_Cortex (47): linear fit = 1.38 x + 0.0 (28018 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.38 x + 0.0 (28018 voxels, peak = 76), gca=75.6 gca peak = 0.16765 (84) mri peak = 0.21994 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (6530 voxels, overlap=0.002) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (6530 voxels, peak = 93), gca=92.8 gca peak = 0.18739 (84) mri peak = 0.11543 (94) Right_Cerebellum_White_Matter (46): linear fit = 1.11 x + 0.0 (12322 voxels, overlap=0.557) Right_Cerebellum_White_Matter (46): linear fit = 1.11 x + 0.0 (12322 voxels, peak = 93), gca=92.8 gca peak = 0.29869 (57) mri peak = 0.17170 (75) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (560 voxels, overlap=0.036) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (560 voxels, peak = 74), gca=73.8 gca peak = 0.33601 (57) mri peak = 0.13523 (75) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (562 voxels, overlap=0.046) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (562 voxels, peak = 74), gca=74.4 gca peak = 0.11131 (90) mri peak = 0.08753 (97) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (4753 voxels, overlap=0.528) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (4753 voxels, peak = 98), gca=97.7 gca peak = 0.11793 (83) mri peak = 0.08240 (95) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4216 voxels, overlap=0.426) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4216 voxels, peak = 93), gca=92.5 gca peak = 0.08324 (81) mri peak = 0.16558 (92) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1836 voxels, overlap=0.007) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1836 voxels, peak = 94), gca=93.6 gca peak = 0.10360 (77) mri peak = 0.12887 (92) Right_Putamen (51): linear fit = 1.16 x + 0.0 (2033 voxels, overlap=0.018) Right_Putamen (51): linear fit = 1.16 x + 0.0 (2033 voxels, peak = 90), gca=89.7 gca peak = 0.08424 (78) mri peak = 0.11968 (91) Brain_Stem (16): linear fit = 1.12 x + 0.0 (12631 voxels, overlap=0.159) Brain_Stem (16): linear fit = 1.12 x + 0.0 (12631 voxels, peak = 87), gca=87.0 gca peak = 0.12631 (89) mri peak = 0.10967 (98) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1469 voxels, overlap=0.205) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1469 voxels, peak = 97), gca=97.5 gca peak = 0.14500 (87) mri peak = 0.10440 (96) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1753 voxels, overlap=0.176) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1753 voxels, peak = 96), gca=96.1 gca peak = 0.14975 (24) mri peak = 0.12505 (30) Third_Ventricle (14): linear fit = 1.23 x + 0.0 (82 voxels, overlap=0.579) Third_Ventricle (14): linear fit = 1.23 x + 0.0 (82 voxels, peak = 29), gca=29.4 gca peak = 0.19357 (14) mri peak = 0.20721 (27) Fourth_Ventricle (15): linear fit = 1.76 x + 0.0 (260 voxels, overlap=0.172) Fourth_Ventricle (15): linear fit = 1.76 x + 0.0 (260 voxels, peak = 25), gca=24.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak 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 1.29 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.40 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15663 (27) mri peak = 0.12253 (29) Left_Lateral_Ventricle (4): linear fit = 0.99 x + 0.0 (3662 voxels, overlap=0.759) Left_Lateral_Ventricle (4): linear fit = 0.99 x + 0.0 (3662 voxels, peak = 27), gca=26.6 gca peak = 0.13981 (19) mri peak = 0.12652 (29) Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (3214 voxels, overlap=0.308) Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (3214 voxels, peak = 27), gca=26.7 gca peak = 0.29122 (100) mri peak = 0.16049 (98) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (729 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (729 voxels, peak = 100), gca=100.5 gca peak = 0.17230 (100) mri peak = 0.24846 (101) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (648 voxels, overlap=0.877) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (648 voxels, peak = 100), gca=99.5 gca peak = 0.22461 (74) mri peak = 0.12510 (74) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1223 voxels, overlap=0.943) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1223 voxels, peak = 73), gca=72.9 gca peak = 0.26484 (73) mri peak = 0.13079 (75) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (1233 voxels, overlap=1.001) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (1233 voxels, peak = 71), gca=71.2 gca peak = 0.07614 (105) mri peak = 0.17130 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (39685 voxels, overlap=0.612) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (39685 voxels, peak = 105), gca=105.0 gca peak = 0.07686 (107) mri peak = 0.17385 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (41500 voxels, overlap=0.539) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (41500 voxels, peak = 107), gca=107.0 gca peak = 0.07950 (72) mri peak = 0.06464 (72) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (44777 voxels, overlap=0.921) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (44777 voxels, peak = 72), gca=72.0 gca peak = 0.09549 (72) mri peak = 0.06814 (72) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (44335 voxels, overlap=0.917) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (44335 voxels, peak = 72), gca=72.0 gca peak = 0.21563 (85) mri peak = 0.16020 (87) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1392 voxels, overlap=0.998) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1392 voxels, peak = 85), gca=85.0 gca peak = 0.13452 (95) mri peak = 0.16127 (87) Left_Caudate (11): linear fit = 0.94 x + 0.0 (1482 voxels, overlap=0.630) Left_Caudate (11): linear fit = 0.94 x + 0.0 (1482 voxels, peak = 89), gca=88.8 gca peak = 0.10646 (76) mri peak = 0.08431 (78) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (33464 voxels, overlap=0.888) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (33464 voxels, peak = 76), gca=76.0 gca peak = 0.11437 (75) mri peak = 0.09713 (75) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (28018 voxels, overlap=0.873) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (28018 voxels, peak = 75), gca=75.0 gca peak = 0.14173 (93) mri peak = 0.21994 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6530 voxels, overlap=0.691) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6530 voxels, peak = 94), gca=94.4 gca peak = 0.16627 (93) mri peak = 0.11543 (94) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (12322 voxels, overlap=0.980) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (12322 voxels, peak = 93), gca=92.5 gca peak = 0.29270 (75) mri peak = 0.17170 (75) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (560 voxels, overlap=0.999) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (560 voxels, peak = 74), gca=73.9 gca peak = 0.29565 (74) mri peak = 0.13523 (75) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (562 voxels, overlap=1.004) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (562 voxels, peak = 75), gca=75.1 gca peak = 0.10206 (97) mri peak = 0.08753 (97) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4753 voxels, overlap=0.893) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4753 voxels, peak = 98), gca=98.5 gca peak = 0.10424 (90) mri peak = 0.08240 (95) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4216 voxels, overlap=0.937) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4216 voxels, peak = 90), gca=90.0 gca peak = 0.07366 (87) mri peak = 0.16558 (92) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1836 voxels, overlap=0.605) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1836 voxels, peak = 86), gca=85.7 gca peak = 0.08180 (87) mri peak = 0.12887 (92) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2033 voxels, overlap=0.733) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2033 voxels, peak = 87), gca=86.6 gca peak = 0.08176 (87) mri peak = 0.11968 (91) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12631 voxels, overlap=0.606) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12631 voxels, peak = 87), gca=86.6 gca peak = 0.12269 (92) mri peak = 0.10967 (98) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1469 voxels, overlap=0.742) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1469 voxels, peak = 93), gca=93.4 gca peak = 0.14981 (96) mri peak = 0.10440 (96) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1753 voxels, overlap=0.801) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1753 voxels, peak = 95), gca=94.6 gca peak = 0.12950 (31) mri peak = 0.12505 (30) Third_Ventricle (14): linear fit = 0.99 x + 0.0 (82 voxels, overlap=0.861) Third_Ventricle (14): linear fit = 0.99 x + 0.0 (82 voxels, peak = 31), gca=30.5 gca peak = 0.14735 (21) mri peak = 0.20721 (27) Fourth_Ventricle (15): linear fit = 1.23 x + 0.0 (260 voxels, overlap=0.351) Fourth_Ventricle (15): linear fit = 1.23 x + 0.0 (260 voxels, peak = 26), gca=25.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.17746 (35) gca peak Left_Thalamus = 0.36646 (105) gca peak CSF = 0.23763 (51) gca peak Left_Accumbens_area = 0.69378 (76) gca peak Left_undetermined = 0.96707 (34) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.11818 (35) gca peak Right_Inf_Lat_Vent = 0.24572 (31) gca peak Right_Accumbens_area = 0.29821 (84) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14504 (37) gca peak Fifth_Ventricle = 0.51669 (43) gca peak WM_hypointensities = 0.08625 (78) gca peak non_WM_hypointensities = 0.07502 (56) gca peak Optic_Chiasm = 0.68730 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.15 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 52286 voxels changed in iteration 0 of unlikely voxel relabeling 173 voxels changed in iteration 1 of unlikely voxel relabeling 34 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 46124 gm and wm labels changed (%42 to gray, %58 to white out of all changed labels) 445 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 63084 changed. image ll: -2.105, PF=0.500 pass 2: 17194 changed. image ll: -2.105, PF=0.500 pass 3: 5648 changed. pass 4: 2226 changed. 37636 voxels changed in iteration 0 of unlikely voxel relabeling 288 voxels changed in iteration 1 of unlikely voxel relabeling 7 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6318 voxels changed in iteration 0 of unlikely voxel relabeling 145 voxels changed in iteration 1 of unlikely voxel relabeling 11 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5350 voxels changed in iteration 0 of unlikely voxel relabeling 73 voxels changed in iteration 1 of unlikely voxel relabeling 15 voxels changed in iteration 2 of unlikely voxel relabeling 4 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 4798 voxels changed in iteration 0 of unlikely voxel relabeling 50 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 MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 3671.870790 mri_ca_label stimesec 1.778729 mri_ca_label ru_maxrss 2089776 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 996486 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 65483 mri_ca_label ru_oublock 405 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 460 mri_ca_label ru_nivcsw 4719 auto-labeling took 61 minutes and 15 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /scratch/annadan1111/MABT1T2/reruncrosstest_cp2/44538_T1_fs_edit/mri/transforms/cc_up.lta 44538_T1_fs_edit will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /scratch/annadan1111/MABT1T2/reruncrosstest_cp2/44538_T1_fs_edit/mri/transforms/cc_up.lta reading aseg from /scratch/annadan1111/MABT1T2/reruncrosstest_cp2/44538_T1_fs_edit/mri/aseg.auto_noCCseg.mgz reading norm from /scratch/annadan1111/MABT1T2/reruncrosstest_cp2/44538_T1_fs_edit/mri/norm.mgz 24009 voxels in left wm, 30404 in right wm, xrange [126, 132] searching rotation angles z=[-8 6], y=[-6 8] searching scale 1 Z rot -8.1 searching scale 1 Z rot -7.8 searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.3 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 global minimum found at slice 129.0, rotations (1.10, -0.81) final transformation (x=129.0, yr=1.095, zr=-0.806): 0.99972 0.01407 0.01911 -4.78580; -0.01407 0.99990 -0.00027 19.85735; -0.01912 0.00000 0.99982 11.48777; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 110 119 eigenvectors: -0.00018 -0.00234 1.00000; 0.14121 -0.98998 -0.00229; 0.98998 0.14121 0.00050; writing aseg with callosum to /scratch/annadan1111/MABT1T2/reruncrosstest_cp2/44538_T1_fs_edit/mri/aseg.auto.mgz... corpus callosum segmentation took 0.6 minutes #-------------------------------------- #@# Merge ASeg Do 29. Mär 01:25:35 CEST 2018 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Do 29. Mär 01:25:35 CEST 2018 /scratch/annadan1111/MABT1T2/reruncrosstest_cp2/44538_T1_fs_edit/mri mri_normalize -f /scratch/annadan1111/MABT1T2/reruncrosstest_cp2/44538_T1_fs_edit/tmp/control.dat -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz using control points from file /scratch/annadan1111/MABT1T2/reruncrosstest_cp2/44538_T1_fs_edit/tmp/control.dat... 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... Reading 48 control points... only using 48 control points from file, mean 80.8, scaling by 1.36... building Voronoi diagram... performing soap bubble smoothing, sigma = 8... processing with aseg removing outliers in the aseg WM... 535 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction HISTOalloc(-2147483648): could not allocate histogram building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 Cannot allocate memory Linux node098 2.6.32-696.20.1.el6.x86_64 #1 SMP Thu Jan 25 08:47:49 CST 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 44538_T1_fs_edit exited with ERRORS at Do 29. Mär 01:28:15 CEST 2018 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting