Do 22. Feb 23:20:15 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs /cm/shared/apps/freesurfer/6.0.0/bin/recon-all -i 15689_T1_MPRAGE.nii.gz -subject 15689_T1_fs -all subjid 15689_T1_fs setenv SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test 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 node016 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: 24729388 16053292 8676096 4134552 0 13471512 -/+ buffers/cache: 2581780 22147608 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: 2018/02/22-22:20:15-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: node016 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: 2018/02/22-22:20:15-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: node016 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: 2018/02/22-22:20:16-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: node016 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: 2018/02/22-22:20:16-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: node016 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: 2018/02/22-22:20:16-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: node016 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: 2018/02/22-22:20:16-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: node016 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: 2018/02/22-22:20:16-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: node016 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: 2018/02/22-22:20:16-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: node016 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: 2018/02/22-22:20:16-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: node016 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: 2018/02/22-22:20:16-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: node016 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: 2018/02/22-22:20:16-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: node016 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: 2018/02/22-22:20:16-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: node016 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: 2018/02/22-22:20:16-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: node016 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: 2018/02/22-22:20:16-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: node016 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: 2018/02/22-22:20:16-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: node016 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: 2018/02/22-22:20:16-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: node016 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: 2018/02/22-22:20:17-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: node016 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: 2018/02/22-22:20:17-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: node016 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: 2018/02/22-22:20:17-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: node016 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: 2018/02/22-22:20:17-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: node016 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: 2018/02/22-22:20:17-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: node016 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: 2018/02/22-22:20:17-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: node016 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: 2018/02/22-22:20:17-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: node016 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: 2018/02/22-22:20:17-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: node016 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: 2018/02/22-22:20:17-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: node016 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: 2018/02/22-22:20:17-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: node016 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: 2018/02/22-22:20:17-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: node016 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: 2018/02/22-22:20:17-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: node016 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: 2018/02/22-22:20:17-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: node016 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: 2018/02/22-22:20:17-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: node016 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: 2018/02/22-22:20:17-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: node016 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: 2018/02/22-22:20:18-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: node016 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: 2018/02/22-22:20:18-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: node016 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: 2018/02/22-22:20:18-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: node016 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: 2018/02/22-22:20:18-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: node016 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: 2018/02/22-22:20:18-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: node016 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: 2018/02/22-22:20:18-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: node016 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: 2018/02/22-22:20:18-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: node016 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: 2018/02/22-22:20:18-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: node016 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 ####################################### /scratch/annadan1111/MABT1T2/test/15689_T1_fs mri_convert /scratch/annadan1111/MABT1T2/test/15689_T1_MPRAGE.nii.gz /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/orig/001.mgz mri_convert.bin /scratch/annadan1111/MABT1T2/test/15689_T1_MPRAGE.nii.gz /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_T1_MPRAGE.nii.gz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.998087, -0.00566184, 0.0615673) j_ras = (-0.00718034, 0.978445, 0.206382) k_ras = (-0.0614088, -0.206429, 0.976533) writing to /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Do 22. Feb 23:20:25 CET 2018 Found 1 runs /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_T1_fs/mri/orig/001.mgz /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/rawavg.mgz /scratch/annadan1111/MABT1T2/test/15689_T1_fs mri_convert /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/rawavg.mgz /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/orig.mgz --conform mri_convert.bin /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/rawavg.mgz /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_T1_fs/mri/rawavg.mgz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.998087, -0.00566184, 0.0615673) j_ras = (-0.00718034, 0.978445, 0.206382) k_ras = (-0.0614088, -0.206429, 0.976533) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/orig.mgz... mri_add_xform_to_header -c /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/transforms/talairach.xfm /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/orig.mgz /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Do 22. Feb 23:20:37 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_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 node016 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 Do 22. Feb 23:20:37 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.17152 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17152/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.17152/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, 0, -3.72529e-09) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.17152/nu0.mnc... -------------------------------------------------------- Iteration 1 Do 22. Feb 23:20:40 CET 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.17152/nu0.mnc ./tmp.mri_nu_correct.mni.17152/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.17152/0/ -iterations 1000 -distance 50 [annadan1111@node016:/scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/] [2018-02-22 23:20:40] 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.17152/0/ ./tmp.mri_nu_correct.mni.17152/nu0.mnc ./tmp.mri_nu_correct.mni.17152/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 Number of iterations: 37 CV of field change: 0.000993404 mri_convert ./tmp.mri_nu_correct.mni.17152/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.17152/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.17152/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -3.72529e-09) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Do 22. Feb 23:22:04 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 Do 22. Feb 23:22:04 CET 2018 Ended at Do 22. Feb 23:23:02 CET 2018 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Do 22. Feb 23:23:04 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6112, pval=0.2817 >= threshold=0.0050) awk -f /cm/shared/apps/freesurfer/6.0.0/bin/extract_talairach_avi_QA.awk /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/transforms/talairach_avi.log tal_QC_AZS /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/transforms/talairach_avi.log TalAviQA: 0.97780 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Do 22. Feb 23:23:04 CET 2018 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /scratch/annadan1111/MABT1T2/test/15689_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 node016 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 Do 22. Feb 23:23:04 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.18335 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.18335/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.18335/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, 0, -3.72529e-09) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.18335/nu0.mnc... -------------------------------------------------------- Iteration 1 Do 22. Feb 23:23:08 CET 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.18335/nu0.mnc ./tmp.mri_nu_correct.mni.18335/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.18335/0/ [annadan1111@node016:/scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/] [2018-02-22 23:23:08] 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.18335/0/ ./tmp.mri_nu_correct.mni.18335/nu0.mnc ./tmp.mri_nu_correct.mni.18335/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 Number of iterations: 37 CV of field change: 0.000987233 -------------------------------------------------------- Iteration 2 Do 22. Feb 23:24:11 CET 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.18335/nu1.mnc ./tmp.mri_nu_correct.mni.18335/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.18335/1/ [annadan1111@node016:/scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/] [2018-02-22 23:24:11] 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.18335/1/ ./tmp.mri_nu_correct.mni.18335/nu1.mnc ./tmp.mri_nu_correct.mni.18335/nu2.imp 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: 11 CV of field change: 0.000970412 mri_binarize --i ./tmp.mri_nu_correct.mni.18335/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.18335/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.18335/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.18335/ones.mgz sysname Linux hostname node016 machine x86_64 user annadan1111 input ./tmp.mri_nu_correct.mni.18335/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.18335/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.18335/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.18335/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18335/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.18335/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.18335/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18335/input.mean.dat sysname Linux hostname node016 machine x86_64 user annadan1111 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.18335/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.18335/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.18335/ones.mgz --i ./tmp.mri_nu_correct.mni.18335/nu2.mnc --sum ./tmp.mri_nu_correct.mni.18335/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18335/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.18335/ones.mgz --i ./tmp.mri_nu_correct.mni.18335/nu2.mnc --sum ./tmp.mri_nu_correct.mni.18335/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18335/output.mean.dat sysname Linux hostname node016 machine x86_64 user annadan1111 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.18335/ones.mgz Loading ./tmp.mri_nu_correct.mni.18335/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.18335/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.18335/nu2.mnc ./tmp.mri_nu_correct.mni.18335/nu2.mnc mul 1.00808186681753665048 Saving result to './tmp.mri_nu_correct.mni.18335/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.18335/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.18335/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.18335/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -3.72529e-09) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 9 seconds. mapping ( 5, 103) to ( 3, 110) Do 22. Feb 23:25:43 CET 2018 mri_nu_correct.mni done mri_add_xform_to_header -c /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Do 22. Feb 23:25:45 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 1.06324 -0.01704 0.05228 4.18216; -0.00689 0.95498 0.30339 -43.69143; -0.03536 -0.31917 0.98249 -8.68593; 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 = 19 Starting OpenSpline(): npoints = 19 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 85 (85), valley at 51 (51) csf peak at 37, setting threshold to 69 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 88 (88), valley at 51 (51) csf peak at 38, setting threshold to 71 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 47 seconds. #-------------------------------------------- #@# Skull Stripping Do 22. Feb 23:28:34 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri mri_em_register -rusage /scratch/annadan1111/MABT1T2/test/15689_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=7.0 skull bounding box = (39, 33, 24) --> (219, 233, 255) using (99, 100, 140) as brain centroid... mean wm in atlas = 108, using box (77,75,111) --> (121, 124,168) to find MRI wm before smoothing, mri peak at 109 robust fit to distribution - 108 +- 4.6 after smoothing, mri peak at 108, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.620 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.460833 @ (-9.091, 9.091, -9.091) max log p = -4.386653 @ (4.545, -4.545, -4.545) max log p = -4.358040 @ (2.273, -2.273, -2.273) max log p = -4.323744 @ (-1.136, 1.136, -1.136) max log p = -4.321685 @ (0.568, -0.568, -0.568) max log p = -4.321685 @ (0.000, 0.000, 0.000) Found translation: (-2.8, 2.8, -17.6): log p = -4.322 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.195, old_max_log_p =-4.322 (thresh=-4.3) 1.06580 0.13553 0.03632 -34.79753; -0.14032 1.02949 0.27585 -11.30391; 0.00000 -0.23941 0.89348 29.43538; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.195, old_max_log_p =-4.195 (thresh=-4.2) 1.06580 0.13553 0.03632 -34.79753; -0.14032 1.02949 0.27585 -11.30391; 0.00000 -0.23941 0.89348 29.43538; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.127, old_max_log_p =-4.195 (thresh=-4.2) 1.03358 0.04079 -0.02156 -10.50348; -0.03451 1.01790 0.27166 -26.65924; 0.03378 -0.24611 0.92706 17.97531; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.127, old_max_log_p =-4.127 (thresh=-4.1) 1.03358 0.04079 -0.02156 -10.50348; -0.03451 1.01790 0.27166 -26.65924; 0.03378 -0.24611 0.92706 17.97531; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.118, old_max_log_p =-4.127 (thresh=-4.1) 1.03109 0.07013 0.00238 -17.29655; -0.06851 1.01686 0.26409 -21.62749; 0.01640 -0.23839 0.92833 18.99825; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.111, old_max_log_p =-4.118 (thresh=-4.1) 1.02942 0.07443 0.01970 -19.47505; -0.07669 1.01271 0.26301 -19.40396; -0.00048 -0.23979 0.92925 21.70050; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.111, old_max_log_p =-4.111 (thresh=-4.1) 1.02942 0.07443 0.01970 -19.47505; -0.07669 1.01271 0.26301 -19.40396; -0.00048 -0.23979 0.92925 21.70050; 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 1.02942 0.07443 0.01970 -19.47505; -0.07669 1.01271 0.26301 -19.40396; -0.00048 -0.23979 0.92925 21.70050; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.02942 0.07443 0.01970 -19.47505; -0.07669 1.01271 0.26301 -19.40396; -0.00048 -0.23979 0.92925 21.70050; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.02942 0.07443 0.01970 -19.47505; -0.07669 1.01271 0.26301 -19.40396; -0.00048 -0.23979 0.92925 21.70050; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.111 (old=-4.620) transform before final EM align: 1.02942 0.07443 0.01970 -19.47505; -0.07669 1.01271 0.26301 -19.40396; -0.00048 -0.23979 0.92925 21.70050; 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 1.02942 0.07443 0.01970 -19.47505; -0.07669 1.01271 0.26301 -19.40396; -0.00048 -0.23979 0.92925 21.70050; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.02942 0.07443 0.01970 -19.47505; -0.07669 1.01271 0.26301 -19.40396; -0.00048 -0.23979 0.92925 21.70050; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.5 tol 0.000000 final transform: 1.02942 0.07443 0.01970 -19.47505; -0.07669 1.01271 0.26301 -19.40396; -0.00048 -0.23979 0.92925 21.70050; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1523.128449 mri_em_register stimesec 3.757428 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 157446 mri_em_register ru_majflt 1 mri_em_register ru_nswap 0 mri_em_register ru_inblock 158402 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 110 mri_em_register ru_nivcsw 82531 registration took 25 minutes and 30 seconds. mri_watershed -rusage /scratch/annadan1111/MABT1T2/test/15689_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=116 z=126 r=87 first estimation of the main basin volume: 2826542 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=110, y=98, z=84, 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=9230328484 voxels, voxel volume =1.000 = 9230328484 mmm3 = 9230328.832 cm3 done. PostAnalyze...Basin Prior 58 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=129,y=120, z=120, r=10557 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=5, CSF_MAX=54 , nb = 42421 RIGHT_CER CSF_MIN=0, CSF_intensity=5, CSF_MAX=17 , nb = -1031592417 LEFT_CER CSF_MIN=0, CSF_intensity=6, CSF_MAX=18 , nb = 1100526356 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=75 , nb = -1061078936 LEFT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=63 , nb = 1079263664 OTHER CSF_MIN=0, CSF_intensity=4, CSF_MAX=12 , nb = 1081603304 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 54, 57, 60, 85 after analyzing : 54, 59, 60, 65 RIGHT_CER before analyzing : 17, 29, 59, 86 after analyzing : 17, 49, 59, 58 LEFT_CER before analyzing : 18, 30, 61, 92 after analyzing : 18, 50, 61, 60 RIGHT_BRAIN before analyzing : 75, 64, 61, 85 after analyzing : 42, 64, 64, 69 LEFT_BRAIN before analyzing : 63, 60, 60, 84 after analyzing : 38, 60, 60, 66 OTHER before analyzing : 12, 20, 27, 34 after analyzing : 12, 24, 27, 26 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...74 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.010 curvature mean = 72.676, std = 7.041 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 5.17, sigma = 7.38 after rotation: sse = 5.17, sigma = 7.38 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 6.45, its var is 8.51 before Erosion-Dilatation 3.98% of inacurate vertices after Erosion-Dilatation 5.61% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...42 iterations mri_strip_skull: done peeling brain Brain Size = 1844379 voxels, voxel volume = 1.000 mm3 = 1844379 mmm3 = 1844.379 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 30.601347 mri_watershed stimesec 0.538918 mri_watershed ru_maxrss 838880 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 215451 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 26110 mri_watershed ru_oublock 2683 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 180 mri_watershed ru_nivcsw 2865 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Do 22. Feb 23:54:36 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri mri_em_register -rusage /scratch/annadan1111/MABT1T2/test/15689_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=28.1 skull bounding box = (64, 47, 42) --> (193, 206, 209) using (107, 100, 126) as brain centroid... mean wm in atlas = 107, using box (91,80,105) --> (122, 119,146) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 107 +- 3.6 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.229 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.050279 @ (-9.091, 9.091, -9.091) max log p = -3.905276 @ (4.545, -4.545, -4.545) max log p = -3.880126 @ (2.273, -2.273, -2.273) max log p = -3.861774 @ (1.136, 3.409, -1.136) max log p = -3.846179 @ (-1.705, -1.705, 0.568) max log p = -3.840874 @ (0.852, 0.852, -0.852) Found translation: (-2.0, 4.8, -17.3): log p = -3.841 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.640, old_max_log_p =-3.841 (thresh=-3.8) 0.99144 0.12059 0.04995 -20.82280; -0.13053 0.91598 0.37941 -15.33249; 0.00000 -0.35398 0.85459 48.54015; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.640, old_max_log_p =-3.640 (thresh=-3.6) 0.99144 0.12059 0.04995 -20.82280; -0.13053 0.91598 0.37941 -15.33249; 0.00000 -0.35398 0.85459 48.54015; 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=-3.498, old_max_log_p =-3.640 (thresh=-3.6) 1.05440 0.07247 0.00014 -19.52762; -0.06396 0.92591 0.31526 -19.62059; 0.02413 -0.29238 0.89530 29.82175; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.498, old_max_log_p =-3.498 (thresh=-3.5) 1.05440 0.07247 0.00014 -19.52762; -0.06396 0.92591 0.31526 -19.62059; 0.02413 -0.29238 0.89530 29.82175; 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=-3.472, old_max_log_p =-3.498 (thresh=-3.5) 1.04950 0.08748 0.00513 -20.29430; -0.08096 0.92016 0.32133 -17.90592; 0.02489 -0.30045 0.89602 30.14474; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.470, old_max_log_p =-3.472 (thresh=-3.5) 1.04827 0.08738 0.00513 -20.12200; -0.08096 0.92016 0.32133 -17.90592; 0.02489 -0.30045 0.89602 30.14474; 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 1.04827 0.08738 0.00513 -20.12200; -0.08096 0.92016 0.32133 -17.90592; 0.02489 -0.30045 0.89602 30.14474; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.04827 0.08738 0.00513 -20.12200; -0.08096 0.92016 0.32133 -17.90592; 0.02489 -0.30045 0.89602 30.14474; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.04827 0.08738 0.00513 -20.12200; -0.08096 0.92016 0.32133 -17.90592; 0.02489 -0.30045 0.89602 30.14474; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.470 (old=-4.229) transform before final EM align: 1.04827 0.08738 0.00513 -20.12200; -0.08096 0.92016 0.32133 -17.90592; 0.02489 -0.30045 0.89602 30.14474; 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 1.04827 0.08738 0.00513 -20.12200; -0.08096 0.92016 0.32133 -17.90592; 0.02489 -0.30045 0.89602 30.14474; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.04827 0.08738 0.00513 -20.12200; -0.08096 0.92016 0.32133 -17.90592; 0.02489 -0.30045 0.89602 30.14474; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.0 tol 0.000000 final transform: 1.04827 0.08738 0.00513 -20.12200; -0.08096 0.92016 0.32133 -17.90592; 0.02489 -0.30045 0.89602 30.14474; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1140.425628 mri_em_register stimesec 2.931554 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 159337 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 151798 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 130 mri_em_register ru_nivcsw 67953 registration took 19 minutes and 6 seconds. #-------------------------------------- #@# CA Normalize Fr 23. Feb 00:13:43 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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=28.1 skull bounding box = (64, 47, 42) --> (193, 206, 209) using (107, 100, 126) as brain centroid... mean wm in atlas = 107, using box (91,80,105) --> (122, 119,146) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 107 +- 3.6 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 using 246344 sample points... INFO: compute sample coordinates transform 1.04827 0.08738 0.00513 -20.12200; -0.08096 0.92016 0.32133 -17.90592; 0.02489 -0.30045 0.89602 30.14474; 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 (125, 51, 42) --> (193, 177, 214) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 3 of 8847 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 49, 41) --> (133, 165, 214) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 5 of 8716 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (127, 148, 76) --> (172, 194, 133) Left_Cerebellum_White_Matter: limiting intensities to 105.0 --> 132.0 1 of 264 (0.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (82, 147, 73) --> (127, 188, 133) Right_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 292 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (110, 130, 111) --> (144, 202, 143) Brain_Stem: limiting intensities to 97.0 --> 132.0 2 of 888 (0.2%) samples deleted using 19007 total control points for intensity normalization... bias field = 0.951 +- 0.065 111 of 18996 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (125, 51, 42) --> (193, 177, 214) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 8 of 8989 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 49, 41) --> (133, 165, 214) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 15 of 9212 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (127, 148, 76) --> (172, 194, 133) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 175 of 381 (45.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (82, 147, 73) --> (127, 188, 133) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 92 of 341 (27.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (110, 130, 111) --> (144, 202, 143) Brain_Stem: limiting intensities to 88.0 --> 132.0 15 of 899 (1.7%) samples deleted using 19822 total control points for intensity normalization... bias field = 1.002 +- 0.043 136 of 19482 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (125, 51, 42) --> (193, 177, 214) Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 14 of 9016 (0.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 49, 41) --> (133, 165, 214) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 8 of 9191 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (127, 148, 76) --> (172, 194, 133) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 211 of 486 (43.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (82, 147, 73) --> (127, 188, 133) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 189 of 433 (43.6%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (110, 130, 111) --> (144, 202, 143) Brain_Stem: limiting intensities to 88.0 --> 132.0 167 of 888 (18.8%) samples deleted using 20014 total control points for intensity normalization... bias field = 1.000 +- 0.035 94 of 19352 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 Fr 23. Feb 00:15:23 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri mri_ca_register -rusage /scratch/annadan1111/MABT1T2/test/15689_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) = 0.97 (predicted orig area = 8.2) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.888, neg=0, invalid=762 0001: dt=295.936000, rms=0.786 (11.421%), neg=0, invalid=762 0002: dt=166.291755, rms=0.762 (3.087%), neg=0, invalid=762 0003: dt=295.936000, rms=0.751 (1.452%), neg=0, invalid=762 0004: dt=138.181818, rms=0.746 (0.724%), neg=0, invalid=762 0005: dt=443.904000, rms=0.741 (0.586%), neg=0, invalid=762 0006: dt=140.337349, rms=0.738 (0.481%), neg=0, invalid=762 0007: dt=369.920000, rms=0.736 (0.282%), neg=0, invalid=762 0008: dt=129.472000, rms=0.734 (0.272%), neg=0, invalid=762 0009: dt=517.888000, rms=0.732 (0.276%), neg=0, invalid=762 0010: dt=129.472000, rms=0.730 (0.255%), neg=0, invalid=762 0011: dt=443.904000, rms=0.728 (0.171%), neg=0, invalid=762 0012: dt=443.904000, rms=0.728 (-0.496%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.729, neg=0, invalid=762 0013: dt=129.472000, rms=0.725 (0.534%), neg=0, invalid=762 0014: dt=517.888000, rms=0.722 (0.349%), neg=0, invalid=762 0015: dt=295.936000, rms=0.721 (0.153%), neg=0, invalid=762 0016: dt=295.936000, rms=0.720 (0.150%), neg=0, invalid=762 0017: dt=295.936000, rms=0.719 (0.209%), neg=0, invalid=762 0018: dt=295.936000, rms=0.717 (0.245%), neg=0, invalid=762 0019: dt=295.936000, rms=0.715 (0.244%), neg=0, invalid=762 0020: dt=295.936000, rms=0.713 (0.314%), neg=0, invalid=762 0021: dt=295.936000, rms=0.712 (0.195%), neg=0, invalid=762 0022: dt=295.936000, rms=0.711 (0.135%), neg=0, invalid=762 0023: dt=295.936000, rms=0.709 (0.200%), neg=0, invalid=762 0024: dt=295.936000, rms=0.708 (0.166%), neg=0, invalid=762 0025: dt=295.936000, rms=0.708 (0.010%), neg=0, invalid=762 0026: dt=295.936000, rms=0.707 (0.098%), neg=0, invalid=762 0027: dt=295.936000, rms=0.705 (0.253%), neg=0, invalid=762 0028: dt=295.936000, rms=0.705 (0.109%), neg=0, invalid=762 0029: dt=295.936000, rms=0.705 (-0.033%), neg=0, invalid=762 0030: dt=0.000000, rms=0.705 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.716, neg=0, invalid=762 0031: dt=76.733420, rms=0.711 (0.612%), neg=0, invalid=762 0032: dt=218.402640, rms=0.698 (1.855%), neg=0, invalid=762 0033: dt=33.567347, rms=0.694 (0.557%), neg=0, invalid=762 0034: dt=115.854015, rms=0.692 (0.254%), neg=0, invalid=762 0035: dt=89.541284, rms=0.688 (0.685%), neg=0, invalid=762 0036: dt=27.711340, rms=0.686 (0.166%), neg=0, invalid=762 0037: dt=27.711340, rms=0.686 (0.064%), neg=0, invalid=762 0038: dt=27.711340, rms=0.685 (0.127%), neg=0, invalid=762 0039: dt=27.711340, rms=0.683 (0.236%), neg=0, invalid=762 0040: dt=27.711340, rms=0.681 (0.337%), neg=0, invalid=762 0041: dt=27.711340, rms=0.679 (0.370%), neg=0, invalid=762 0042: dt=27.711340, rms=0.676 (0.356%), neg=0, invalid=762 0043: dt=27.711340, rms=0.674 (0.311%), neg=0, invalid=762 0044: dt=27.711340, rms=0.672 (0.272%), neg=0, invalid=762 0045: dt=27.711340, rms=0.671 (0.262%), neg=0, invalid=762 0046: dt=27.711340, rms=0.669 (0.264%), neg=0, invalid=762 0047: dt=27.711340, rms=0.667 (0.264%), neg=0, invalid=762 0048: dt=27.711340, rms=0.665 (0.242%), neg=0, invalid=762 0049: dt=27.711340, rms=0.664 (0.216%), neg=0, invalid=762 0050: dt=27.711340, rms=0.663 (0.191%), neg=0, invalid=762 0051: dt=27.711340, rms=0.661 (0.181%), neg=0, invalid=762 0052: dt=27.711340, rms=0.660 (0.196%), neg=0, invalid=762 0053: dt=27.711340, rms=0.659 (0.185%), neg=0, invalid=762 0054: dt=27.711340, rms=0.658 (0.150%), neg=0, invalid=762 0055: dt=27.711340, rms=0.657 (0.122%), neg=0, invalid=762 0056: dt=27.711340, rms=0.656 (0.117%), neg=0, invalid=762 0057: dt=497.664000, rms=0.654 (0.311%), neg=0, invalid=762 0058: dt=9.072000, rms=0.654 (0.009%), neg=0, invalid=762 0059: dt=9.072000, rms=0.654 (0.006%), neg=0, invalid=762 0060: dt=9.072000, rms=0.654 (-0.014%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.655, neg=0, invalid=762 0061: dt=67.575419, rms=0.652 (0.377%), neg=0, invalid=762 0062: dt=103.680000, rms=0.651 (0.137%), neg=0, invalid=762 0063: dt=103.680000, rms=0.651 (0.023%), neg=0, invalid=762 0064: dt=103.680000, rms=0.649 (0.328%), neg=0, invalid=762 0065: dt=103.680000, rms=0.649 (0.053%), neg=0, invalid=762 0066: dt=103.680000, rms=0.648 (0.049%), neg=0, invalid=762 0067: dt=67.964602, rms=0.647 (0.219%), neg=0, invalid=762 0068: dt=15.552000, rms=0.647 (0.011%), neg=0, invalid=762 0069: dt=15.552000, rms=0.647 (0.005%), neg=0, invalid=762 0070: dt=15.552000, rms=0.647 (-0.004%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.681, neg=0, invalid=762 0071: dt=11.200000, rms=0.679 (0.261%), neg=0, invalid=762 0072: dt=9.600000, rms=0.679 (0.057%), neg=0, invalid=762 0073: dt=9.600000, rms=0.678 (0.045%), neg=0, invalid=762 0074: dt=9.600000, rms=0.678 (-0.011%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.679, neg=0, invalid=762 0075: dt=11.200000, rms=0.677 (0.210%), neg=0, invalid=762 0076: dt=11.200000, rms=0.677 (0.077%), neg=0, invalid=762 0077: dt=11.200000, rms=0.677 (0.041%), neg=0, invalid=762 0078: dt=11.200000, rms=0.676 (0.035%), neg=0, invalid=762 0079: dt=11.200000, rms=0.676 (-0.049%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.729, neg=0, invalid=762 0080: dt=3.458333, rms=0.726 (0.380%), neg=0, invalid=762 0081: dt=3.388889, rms=0.725 (0.105%), neg=0, invalid=762 0082: dt=3.388889, rms=0.725 (0.053%), neg=0, invalid=762 0083: dt=3.388889, rms=0.725 (-0.047%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.725, neg=0, invalid=762 0084: dt=0.252000, rms=0.725 (0.065%), neg=0, invalid=762 0085: dt=0.216000, rms=0.725 (-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=0.790, neg=0, invalid=762 0086: dt=0.448000, rms=0.789 (0.139%), neg=0, invalid=762 0087: dt=1.024000, rms=0.788 (0.118%), neg=0, invalid=762 0088: dt=1.024000, rms=0.785 (0.327%), neg=0, invalid=762 0089: dt=1.024000, rms=0.783 (0.323%), neg=0, invalid=762 0090: dt=1.024000, rms=0.782 (0.121%), neg=0, invalid=762 0091: dt=1.024000, rms=0.782 (0.006%), neg=0, invalid=762 0092: dt=7.663462, rms=0.770 (1.580%), neg=0, invalid=762 0093: dt=0.112000, rms=0.769 (0.006%), neg=0, invalid=762 0094: dt=0.112000, rms=0.769 (0.000%), neg=0, invalid=762 0095: dt=0.112000, rms=0.769 (-0.018%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.770, neg=0, invalid=762 0096: dt=0.256000, rms=0.769 (0.071%), neg=0, invalid=762 0097: dt=0.028000, rms=0.769 (-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=0.724, neg=0, invalid=762 0098: dt=0.751381, rms=0.710 (1.985%), neg=0, invalid=762 0099: dt=0.080000, rms=0.709 (0.098%), neg=0, invalid=762 0100: dt=0.080000, rms=0.709 (-0.069%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.710, neg=0, invalid=762 0101: dt=0.028000, rms=0.709 (0.077%), neg=0, invalid=762 0102: dt=0.001750, rms=0.709 (-0.001%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.23149 (34) Left_Lateral_Ventricle (4): linear fit = 1.91 x + 0.0 (2162 voxels, overlap=0.103) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (2162 voxels, peak = 38), gca=30.0 gca peak = 0.15565 (16) mri peak = 0.34980 (33) Right_Lateral_Ventricle (43): linear fit = 2.12 x + 0.0 (2682 voxels, overlap=0.019) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (2682 voxels, peak = 34), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.16214 (101) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (1187 voxels, overlap=0.354) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (1187 voxels, peak = 102), gca=102.2 gca peak = 0.20183 (93) mri peak = 0.12965 (103) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (1065 voxels, overlap=0.640) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (1065 voxels, peak = 100), gca=100.0 gca peak = 0.21683 (55) mri peak = 0.15870 (77) Right_Hippocampus (53): linear fit = 1.36 x + 0.0 (1488 voxels, overlap=0.011) Right_Hippocampus (53): linear fit = 1.36 x + 0.0 (1488 voxels, peak = 75), gca=74.5 gca peak = 0.30730 (58) mri peak = 0.07948 (76) Left_Hippocampus (17): linear fit = 1.33 x + 0.0 (1527 voxels, overlap=0.025) Left_Hippocampus (17): linear fit = 1.33 x + 0.0 (1527 voxels, peak = 77), gca=76.9 gca peak = 0.11430 (101) mri peak = 0.10225 (108) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (89985 voxels, overlap=0.473) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (89985 voxels, peak = 107), gca=106.6 gca peak = 0.12076 (102) mri peak = 0.13580 (107) Left_Cerebral_White_Matter (2): linear fit = 1.08 x + 0.0 (93349 voxels, overlap=0.353) Left_Cerebral_White_Matter (2): linear fit = 1.08 x + 0.0 (93349 voxels, peak = 110), gca=109.7 gca peak = 0.14995 (59) mri peak = 0.03777 (80) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (39989 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (39989 voxels, peak = 79), gca=79.4 gca peak = 0.15082 (58) mri peak = 0.04299 (80) Right_Cerebral_Cortex (42): linear fit = 1.40 x + 0.0 (46545 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.40 x + 0.0 (46545 voxels, peak = 81), gca=81.5 gca peak = 0.14161 (67) mri peak = 0.32383 (89) Right_Caudate (50): linear fit = 1.38 x + 0.0 (779 voxels, overlap=0.008) Right_Caudate (50): linear fit = 1.38 x + 0.0 (779 voxels, peak = 92), gca=92.1 gca peak = 0.15243 (71) mri peak = 0.17670 (90) Left_Caudate (11): linear fit = 1.23 x + 0.0 (1420 voxels, overlap=0.010) Left_Caudate (11): linear fit = 1.23 x + 0.0 (1420 voxels, peak = 87), gca=87.0 gca peak = 0.13336 (57) mri peak = 0.05352 (29) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (29056 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.38 x + 0.0 (29056 voxels, peak = 79), gca=78.9 gca peak = 0.13252 (56) mri peak = 0.04716 (72) Right_Cerebellum_Cortex (47): linear fit = 1.30 x + 0.0 (34985 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.30 x + 0.0 (34985 voxels, peak = 73), gca=73.1 gca peak = 0.18181 (84) mri peak = 0.06636 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (11287 voxels, overlap=0.462) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (11287 voxels, peak = 93), gca=92.8 gca peak = 0.20573 (83) mri peak = 0.07990 (89) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (9696 voxels, overlap=0.244) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (9696 voxels, peak = 89), gca=89.2 gca peak = 0.21969 (57) mri peak = 0.16993 (76) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (614 voxels, overlap=0.040) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (614 voxels, peak = 74), gca=73.8 gca peak = 0.39313 (56) mri peak = 0.14750 (75) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (736 voxels, overlap=0.025) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (736 voxels, peak = 73), gca=72.5 gca peak = 0.14181 (85) mri peak = 0.11598 (101) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (6793 voxels, overlap=0.116) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (6793 voxels, peak = 96), gca=96.5 gca peak = 0.11978 (83) mri peak = 0.08999 (95) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5585 voxels, overlap=0.183) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5585 voxels, peak = 93), gca=93.4 gca peak = 0.13399 (79) mri peak = 0.10525 (93) Left_Putamen (12): linear fit = 1.20 x + 0.0 (3149 voxels, overlap=0.007) Left_Putamen (12): linear fit = 1.20 x + 0.0 (3149 voxels, peak = 94), gca=94.4 gca peak = 0.14159 (79) mri peak = 0.08013 (91) Right_Putamen (51): linear fit = 1.20 x + 0.0 (3307 voxels, overlap=0.012) Right_Putamen (51): linear fit = 1.20 x + 0.0 (3307 voxels, peak = 94), gca=94.4 gca peak = 0.10025 (80) mri peak = 0.14537 (90) Brain_Stem (16): linear fit = 1.12 x + 0.0 (14242 voxels, overlap=0.166) Brain_Stem (16): linear fit = 1.12 x + 0.0 (14242 voxels, peak = 90), gca=90.0 gca peak = 0.13281 (86) mri peak = 0.24083 (97) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1585 voxels, overlap=0.009) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1585 voxels, peak = 96), gca=95.9 gca peak = 0.12801 (89) mri peak = 0.23085 (98) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1736 voxels, overlap=0.053) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1736 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) mri peak = 0.24000 (34) gca peak = 0.15061 (21) mri peak = 0.32523 (30) Fourth_Ventricle (15): linear fit = 1.37 x + 0.0 (604 voxels, overlap=0.072) Fourth_Ventricle (15): linear fit = 1.37 x + 0.0 (604 voxels, peak = 29), gca=28.7 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 1.34 x + 0.0 estimating mean wm scale to be 1.07 x + 0.0 estimating mean csf scale to be 1.45 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=0.737, neg=0, invalid=762 0103: dt=107.805825, rms=0.697 (5.350%), neg=0, invalid=762 0104: dt=188.800000, rms=0.690 (1.055%), neg=0, invalid=762 0105: dt=517.888000, rms=0.678 (1.660%), neg=0, invalid=762 0106: dt=92.480000, rms=0.677 (0.207%), neg=0, invalid=762 0107: dt=517.888000, rms=0.675 (0.296%), neg=0, invalid=762 0108: dt=517.888000, rms=0.666 (1.360%), neg=0, invalid=762 0109: dt=32.368000, rms=0.666 (0.053%), neg=0, invalid=762 0110: dt=2.023000, rms=0.666 (0.001%), neg=0, invalid=762 0111: dt=2.023000, rms=0.666 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.666, neg=0, invalid=762 0112: dt=32.368000, rms=0.665 (0.066%), neg=0, invalid=762 0113: dt=6.936000, rms=0.665 (0.001%), neg=0, invalid=762 0114: dt=6.936000, rms=0.665 (-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=0.666, neg=0, invalid=762 0115: dt=168.585366, rms=0.650 (2.436%), neg=0, invalid=762 0116: dt=111.027624, rms=0.633 (2.567%), neg=0, invalid=762 0117: dt=67.027027, rms=0.628 (0.734%), neg=0, invalid=762 0118: dt=248.832000, rms=0.619 (1.447%), neg=0, invalid=762 0119: dt=67.294118, rms=0.615 (0.673%), neg=0, invalid=762 0120: dt=145.152000, rms=0.611 (0.612%), neg=0, invalid=762 0121: dt=76.648968, rms=0.609 (0.319%), neg=0, invalid=762 0122: dt=145.152000, rms=0.607 (0.414%), neg=0, invalid=762 0123: dt=70.892308, rms=0.605 (0.290%), neg=0, invalid=762 0124: dt=145.152000, rms=0.603 (0.344%), neg=0, invalid=762 0125: dt=78.153846, rms=0.602 (0.219%), neg=0, invalid=762 0126: dt=145.152000, rms=0.600 (0.254%), neg=0, invalid=762 0127: dt=67.829060, rms=0.599 (0.215%), neg=0, invalid=762 0128: dt=145.152000, rms=0.597 (0.241%), neg=0, invalid=762 0129: dt=73.014085, rms=0.596 (0.162%), neg=0, invalid=762 0130: dt=145.152000, rms=0.595 (0.185%), neg=0, invalid=762 0131: dt=69.167702, rms=0.594 (0.170%), neg=0, invalid=762 0132: dt=145.152000, rms=0.593 (0.184%), neg=0, invalid=762 0133: dt=82.944000, rms=0.592 (0.140%), neg=0, invalid=762 0134: dt=103.680000, rms=0.592 (0.125%), neg=0, invalid=762 0135: dt=82.944000, rms=0.591 (0.136%), neg=0, invalid=762 0136: dt=103.680000, rms=0.590 (0.111%), neg=0, invalid=762 0137: dt=82.944000, rms=0.589 (0.129%), neg=0, invalid=762 0138: dt=103.680000, rms=0.589 (0.101%), neg=0, invalid=762 0139: dt=82.944000, rms=0.588 (0.125%), neg=0, invalid=762 0140: dt=103.680000, rms=0.588 (0.093%), neg=0, invalid=762 0141: dt=82.944000, rms=0.587 (0.117%), neg=0, invalid=762 0142: dt=36.288000, rms=0.587 (0.054%), neg=0, invalid=762 0143: dt=9.072000, rms=0.586 (0.016%), neg=0, invalid=762 0144: dt=4.536000, rms=0.586 (0.005%), neg=0, invalid=762 0145: dt=1.134000, rms=0.586 (0.002%), neg=0, invalid=762 0146: dt=0.283500, rms=0.586 (0.000%), neg=0, invalid=762 0147: dt=0.025312, rms=0.586 (0.000%), neg=0, invalid=762 0148: dt=0.000000, rms=0.586 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.587, neg=0, invalid=762 0149: dt=145.152000, rms=0.584 (0.463%), neg=0, invalid=762 0150: dt=145.152000, rms=0.583 (0.257%), neg=0, invalid=762 0151: dt=124.416000, rms=0.582 (0.103%), neg=0, invalid=762 0152: dt=103.680000, rms=0.581 (0.131%), neg=0, invalid=762 0153: dt=82.944000, rms=0.581 (0.097%), neg=0, invalid=762 0154: dt=124.416000, rms=0.580 (0.101%), neg=0, invalid=762 0155: dt=82.944000, rms=0.580 (0.090%), neg=0, invalid=762 0156: dt=103.680000, rms=0.579 (0.090%), neg=0, invalid=762 0157: dt=82.944000, rms=0.579 (0.073%), neg=0, invalid=762 0158: dt=103.680000, rms=0.578 (0.081%), neg=0, invalid=762 0159: dt=82.944000, rms=0.578 (0.063%), neg=0, invalid=762 0160: dt=103.680000, rms=0.577 (0.075%), neg=0, invalid=762 0161: dt=82.944000, rms=0.577 (0.060%), neg=0, invalid=762 0162: dt=103.680000, rms=0.577 (0.070%), neg=0, invalid=762 0163: dt=82.944000, rms=0.576 (0.057%), neg=0, invalid=762 0164: dt=103.680000, rms=0.576 (0.069%), neg=0, invalid=762 0165: dt=82.944000, rms=0.576 (0.054%), neg=0, invalid=762 0166: dt=103.680000, rms=0.575 (0.066%), neg=0, invalid=762 0167: dt=82.944000, rms=0.575 (0.054%), neg=0, invalid=762 0168: dt=103.680000, rms=0.574 (0.063%), neg=0, invalid=762 0169: dt=82.944000, rms=0.574 (0.056%), neg=0, invalid=762 0170: dt=103.680000, rms=0.574 (0.061%), neg=0, invalid=762 0171: dt=82.944000, rms=0.573 (0.055%), neg=0, invalid=762 0172: dt=103.680000, rms=0.573 (0.059%), neg=0, invalid=762 0173: dt=82.944000, rms=0.573 (0.052%), neg=0, invalid=762 0174: dt=82.944000, rms=0.573 (0.056%), neg=0, invalid=762 0175: dt=124.416000, rms=0.572 (0.057%), neg=0, invalid=762 0176: dt=7.776000, rms=0.572 (0.012%), neg=0, invalid=762 0177: dt=0.486000, rms=0.572 (0.001%), neg=0, invalid=762 0178: dt=0.121500, rms=0.572 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.579, neg=0, invalid=762 0179: dt=0.002734, rms=0.579 (0.061%), neg=0, invalid=762 0180: dt=0.001250, rms=0.579 (0.000%), neg=0, invalid=762 0181: dt=0.000156, rms=0.579 (0.000%), neg=0, invalid=762 0182: dt=0.000010, rms=0.579 (0.000%), neg=0, invalid=762 0183: dt=0.000005, rms=0.579 (0.000%), neg=0, invalid=762 0184: dt=0.000000, rms=0.579 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.579, neg=0, invalid=762 0185: dt=128.000000, rms=0.564 (2.624%), neg=0, invalid=762 0186: dt=32.000000, rms=0.558 (1.065%), neg=0, invalid=762 0187: dt=2.800000, rms=0.557 (0.073%), neg=0, invalid=762 0188: dt=2.800000, rms=0.557 (0.051%), neg=0, invalid=762 0189: dt=0.700000, rms=0.557 (0.015%), neg=0, invalid=762 0190: dt=0.175000, rms=0.557 (0.003%), neg=0, invalid=762 0191: dt=0.087500, rms=0.557 (0.002%), neg=0, invalid=762 0192: dt=0.021875, rms=0.557 (0.000%), neg=0, invalid=762 0193: dt=0.010937, rms=0.557 (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=0.575, neg=0, invalid=762 0194: dt=16.128000, rms=0.565 (1.787%), neg=0, invalid=762 0195: dt=16.128000, rms=0.559 (1.162%), neg=0, invalid=762 0196: dt=24.170213, rms=0.557 (0.297%), neg=0, invalid=762 0197: dt=16.128000, rms=0.555 (0.348%), neg=0, invalid=762 0198: dt=9.600000, rms=0.555 (0.065%), neg=0, invalid=762 0199: dt=11.520000, rms=0.554 (0.111%), neg=0, invalid=762 0200: dt=55.296000, rms=0.553 (0.088%), neg=0, invalid=762 0201: dt=12.512821, rms=0.553 (0.068%), neg=0, invalid=762 0202: dt=15.542857, rms=0.552 (0.133%), neg=0, invalid=762 0203: dt=7.563636, rms=0.552 (0.041%), neg=0, invalid=762 0204: dt=7.563636, rms=0.552 (0.023%), neg=0, invalid=762 0205: dt=7.563636, rms=0.552 (0.029%), neg=0, invalid=762 0206: dt=7.563636, rms=0.552 (0.045%), neg=0, invalid=762 0207: dt=7.563636, rms=0.551 (0.056%), neg=0, invalid=762 0208: dt=7.563636, rms=0.551 (0.068%), neg=0, invalid=762 0209: dt=7.563636, rms=0.551 (0.075%), neg=0, invalid=762 0210: dt=7.563636, rms=0.550 (0.076%), neg=0, invalid=762 0211: dt=7.563636, rms=0.550 (0.069%), neg=0, invalid=762 0212: dt=7.563636, rms=0.549 (0.067%), neg=0, invalid=762 0213: dt=7.563636, rms=0.549 (0.063%), neg=0, invalid=762 0214: dt=7.563636, rms=0.549 (0.052%), neg=0, invalid=762 0215: dt=7.563636, rms=0.548 (0.043%), neg=0, invalid=762 0216: dt=7.563636, rms=0.548 (0.046%), neg=0, invalid=762 0217: dt=7.563636, rms=0.548 (0.050%), neg=0, invalid=762 0218: dt=7.563636, rms=0.548 (0.047%), neg=0, invalid=762 0219: dt=7.563636, rms=0.548 (-0.000%), neg=0, invalid=762 0220: dt=2.880000, rms=0.548 (0.000%), neg=0, invalid=762 0221: dt=13.824000, rms=0.548 (0.004%), neg=0, invalid=762 0222: dt=16.128000, rms=0.548 (0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.548, neg=0, invalid=762 0223: dt=12.872180, rms=0.546 (0.299%), neg=0, invalid=762 0224: dt=16.128000, rms=0.546 (0.093%), neg=0, invalid=762 0225: dt=6.000000, rms=0.546 (-0.004%), neg=0, invalid=762 0226: dt=6.000000, rms=0.546 (0.009%), neg=0, invalid=762 0227: dt=6.000000, rms=0.546 (0.013%), neg=0, invalid=762 0228: dt=6.000000, rms=0.546 (0.042%), neg=0, invalid=762 0229: dt=6.000000, rms=0.545 (0.095%), neg=0, invalid=762 0230: dt=6.000000, rms=0.545 (0.101%), neg=0, invalid=762 0231: dt=6.000000, rms=0.544 (0.058%), neg=0, invalid=762 0232: dt=6.000000, rms=0.544 (0.036%), neg=0, invalid=762 0233: dt=6.000000, rms=0.544 (0.027%), neg=0, invalid=762 0234: dt=6.000000, rms=0.544 (0.033%), neg=0, invalid=762 0235: dt=6.000000, rms=0.543 (0.069%), neg=0, invalid=762 0236: dt=6.000000, rms=0.543 (0.081%), neg=0, invalid=762 0237: dt=6.000000, rms=0.543 (0.052%), neg=0, invalid=762 0238: dt=6.000000, rms=0.542 (0.029%), neg=0, invalid=762 0239: dt=6.000000, rms=0.542 (0.024%), neg=0, invalid=762 0240: dt=6.000000, rms=0.542 (0.029%), neg=0, invalid=762 0241: dt=6.000000, rms=0.542 (0.038%), neg=0, invalid=762 0242: dt=6.000000, rms=0.542 (0.048%), neg=0, invalid=762 0243: dt=6.000000, rms=0.541 (0.042%), neg=0, invalid=762 0244: dt=6.000000, rms=0.541 (0.031%), neg=0, invalid=762 0245: dt=6.000000, rms=0.541 (0.033%), neg=0, invalid=762 0246: dt=6.000000, rms=0.541 (0.026%), neg=0, invalid=762 0247: dt=6.000000, rms=0.541 (0.030%), neg=0, invalid=762 0248: dt=6.000000, rms=0.541 (0.031%), neg=0, invalid=762 0249: dt=6.000000, rms=0.541 (0.029%), neg=0, invalid=762 0250: dt=6.000000, rms=0.540 (0.028%), neg=0, invalid=762 0251: dt=6.000000, rms=0.540 (0.024%), neg=0, invalid=762 0252: dt=6.000000, rms=0.540 (0.018%), neg=0, invalid=762 0253: dt=9.216000, rms=0.540 (0.004%), neg=0, invalid=762 0254: dt=9.216000, rms=0.540 (0.009%), neg=0, invalid=762 0255: dt=9.216000, rms=0.540 (0.009%), neg=0, invalid=762 0256: dt=9.216000, rms=0.540 (0.007%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.559, neg=0, invalid=762 0257: dt=0.000000, rms=0.558 (0.060%), neg=0, invalid=762 0258: dt=0.000000, rms=0.558 (0.000%), neg=0, invalid=762 0259: dt=0.100000, rms=0.558 (-0.135%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.559, neg=0, invalid=762 0260: dt=0.000000, rms=0.558 (0.060%), neg=0, invalid=762 0261: dt=0.000000, rms=0.558 (0.000%), neg=0, invalid=762 0262: dt=0.100000, rms=0.558 (-0.124%), 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=0.528, neg=0, invalid=762 0263: dt=0.448000, rms=0.514 (2.532%), neg=0, invalid=762 0264: dt=0.448000, rms=0.511 (0.631%), neg=0, invalid=762 0265: dt=0.448000, rms=0.509 (0.350%), neg=0, invalid=762 0266: dt=0.448000, rms=0.508 (0.213%), neg=0, invalid=762 0267: dt=0.448000, rms=0.507 (0.161%), neg=0, invalid=762 0268: dt=0.448000, rms=0.507 (0.114%), neg=0, invalid=762 0269: dt=0.448000, rms=0.506 (0.100%), neg=0, invalid=762 0270: dt=0.448000, rms=0.506 (0.072%), neg=0, invalid=762 0271: dt=0.448000, rms=0.506 (0.067%), neg=0, invalid=762 0272: dt=0.448000, rms=0.505 (0.050%), neg=0, invalid=762 0273: dt=0.448000, rms=0.505 (0.049%), neg=0, invalid=762 0274: dt=0.448000, rms=0.505 (0.078%), neg=0, invalid=762 0275: dt=0.224000, rms=0.505 (0.017%), neg=0, invalid=762 0276: dt=0.224000, rms=0.504 (0.029%), neg=0, invalid=762 0277: dt=0.224000, rms=0.504 (0.012%), neg=0, invalid=762 0278: dt=0.224000, rms=0.504 (0.024%), neg=0, invalid=762 0279: dt=0.224000, rms=0.504 (0.028%), neg=0, invalid=762 0280: dt=0.224000, rms=0.504 (0.033%), neg=0, invalid=762 0281: dt=0.224000, rms=0.504 (0.036%), neg=0, invalid=762 0282: dt=0.224000, rms=0.504 (0.036%), neg=0, invalid=762 0283: dt=0.224000, rms=0.503 (0.032%), neg=0, invalid=762 0284: dt=0.224000, rms=0.503 (0.029%), neg=0, invalid=762 0285: dt=0.224000, rms=0.503 (0.024%), neg=0, invalid=762 0286: dt=0.224000, rms=0.503 (0.018%), neg=0, invalid=762 0287: dt=0.000000, rms=0.503 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.503, neg=0, invalid=762 0288: dt=0.448000, rms=0.499 (0.829%), neg=0, invalid=762 0289: dt=0.448000, rms=0.498 (0.165%), neg=0, invalid=762 0290: dt=0.448000, rms=0.498 (0.076%), neg=0, invalid=762 0291: dt=0.448000, rms=0.498 (0.030%), neg=0, invalid=762 0292: dt=0.448000, rms=0.498 (0.020%), neg=0, invalid=762 0293: dt=0.448000, rms=0.498 (0.020%), neg=0, invalid=762 0294: dt=0.448000, rms=0.498 (-0.007%), 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=0.495, neg=0, invalid=762 0295: dt=0.000000, rms=0.495 (0.079%), neg=0, invalid=762 0296: dt=0.000000, rms=0.495 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.495, neg=0, invalid=762 0297: dt=0.000000, rms=0.495 (0.079%), neg=0, invalid=762 0298: dt=0.000000, rms=0.495 (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=0.495, neg=0, invalid=762 0299: dt=0.000000, rms=0.495 (0.079%), neg=0, invalid=762 0300: dt=0.000000, rms=0.495 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.495, neg=0, invalid=762 0301: dt=25.920000, rms=0.495 (0.111%), neg=0, invalid=762 0302: dt=103.680000, rms=0.494 (0.172%), neg=0, invalid=762 0303: dt=248.832000, rms=0.490 (0.914%), neg=0, invalid=762 0304: dt=6.480000, rms=0.490 (0.005%), neg=0, invalid=762 0305: dt=6.480000, rms=0.490 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.490, neg=0, invalid=762 0306: dt=11.200000, rms=0.489 (0.296%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0307: dt=25.600000, rms=0.488 (0.224%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0308: dt=25.600000, rms=0.486 (0.331%), neg=0, invalid=762 iter 0, gcam->neg = 19 after 10 iterations, nbhd size=1, neg = 0 0309: dt=25.600000, rms=0.485 (0.277%), neg=0, invalid=762 iter 0, gcam->neg = 40 after 10 iterations, nbhd size=1, neg = 0 0310: dt=25.600000, rms=0.484 (0.091%), neg=0, invalid=762 iter 0, gcam->neg = 74 after 12 iterations, nbhd size=1, neg = 0 0311: dt=25.600000, rms=0.484 (0.058%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0312: dt=128.000000, rms=0.480 (0.860%), neg=0, invalid=762 0313: dt=11.200000, rms=0.480 (0.025%), neg=0, invalid=762 0314: dt=11.200000, rms=0.479 (0.053%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0315: dt=11.200000, rms=0.479 (-0.020%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.480, neg=0, invalid=762 0316: dt=44.800000, rms=0.475 (1.014%), neg=0, invalid=762 0317: dt=32.000000, rms=0.472 (0.494%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0318: dt=23.188406, rms=0.472 (0.127%), neg=0, invalid=762 0319: dt=23.188406, rms=0.471 (0.161%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0320: dt=23.188406, rms=0.470 (0.204%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0321: dt=23.188406, rms=0.469 (0.186%), neg=0, invalid=762 0322: dt=23.188406, rms=0.469 (0.130%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0323: dt=23.188406, rms=0.468 (0.095%), neg=0, invalid=762 0324: dt=23.188406, rms=0.468 (0.126%), neg=0, invalid=762 0325: dt=23.188406, rms=0.467 (0.129%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 0326: dt=23.188406, rms=0.467 (0.089%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0327: dt=23.188406, rms=0.466 (0.095%), neg=0, invalid=762 0328: dt=23.188406, rms=0.466 (0.135%), neg=0, invalid=762 0329: dt=23.188406, rms=0.465 (0.160%), neg=0, invalid=762 0330: dt=23.188406, rms=0.464 (0.130%), neg=0, invalid=762 0331: dt=23.188406, rms=0.464 (0.110%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0332: dt=23.188406, rms=0.463 (0.123%), neg=0, invalid=762 0333: dt=23.188406, rms=0.463 (0.130%), neg=0, invalid=762 0334: dt=23.188406, rms=0.462 (0.099%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0335: dt=23.188406, rms=0.462 (0.066%), neg=0, invalid=762 0336: dt=11.200000, rms=0.462 (0.005%), neg=0, invalid=762 0337: dt=11.200000, rms=0.462 (0.002%), neg=0, invalid=762 0338: dt=11.200000, rms=0.462 (0.003%), neg=0, invalid=762 0339: dt=11.200000, rms=0.462 (0.003%), neg=0, invalid=762 0340: dt=11.200000, rms=0.462 (-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=0.471, neg=0, invalid=762 0341: dt=0.000000, rms=0.470 (0.077%), neg=0, invalid=762 0342: dt=0.000000, rms=0.470 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.471, neg=0, invalid=762 0343: dt=0.576000, rms=0.470 (0.079%), neg=0, invalid=762 0344: dt=0.252000, rms=0.470 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.488, neg=0, invalid=762 0345: dt=1.536000, rms=0.486 (0.568%), neg=0, invalid=762 0346: dt=0.768000, rms=0.485 (0.058%), neg=0, invalid=762 0347: dt=0.768000, rms=0.485 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.486, neg=0, invalid=762 0348: dt=1.792000, rms=0.484 (0.393%), neg=0, invalid=762 0349: dt=1.792000, rms=0.483 (0.103%), neg=0, invalid=762 0350: dt=1.792000, rms=0.483 (0.047%), neg=0, invalid=762 0351: dt=1.792000, rms=0.483 (-0.048%), 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=0.474, neg=0, invalid=762 iter 0, gcam->neg = 465 after 17 iterations, nbhd size=1, neg = 0 0352: dt=1.938733, rms=0.450 (4.970%), neg=0, invalid=762 0353: dt=0.080000, rms=0.450 (0.054%), neg=0, invalid=762 0354: dt=0.080000, rms=0.450 (-0.033%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.450, neg=0, invalid=762 0355: dt=0.096000, rms=0.450 (0.148%), neg=0, invalid=762 0356: dt=0.000000, rms=0.450 (0.001%), neg=0, invalid=762 0357: dt=0.050000, rms=0.450 (-0.012%), 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=0.439, neg=0, invalid=762 0358: dt=2.023000, rms=0.439 (0.000%), neg=0, invalid=762 0359: dt=0.090313, rms=0.439 (0.000%), neg=0, invalid=762 0360: dt=0.090313, rms=0.439 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.439, neg=0, invalid=762 0361: dt=27.744000, rms=0.439 (0.002%), neg=0, invalid=762 0362: dt=23.120000, rms=0.439 (0.000%), neg=0, invalid=762 0363: dt=23.120000, rms=0.439 (0.000%), neg=0, invalid=762 0364: dt=23.120000, rms=0.439 (-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=0.439, neg=0, invalid=762 0365: dt=0.000000, rms=0.439 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.439, neg=0, invalid=762 0366: dt=62.208000, rms=0.439 (0.048%), neg=0, invalid=762 0367: dt=145.152000, rms=0.438 (0.073%), neg=0, invalid=762 0368: dt=82.944000, rms=0.438 (0.021%), neg=0, invalid=762 0369: dt=82.944000, rms=0.438 (0.033%), neg=0, invalid=762 0370: dt=82.944000, rms=0.438 (0.043%), neg=0, invalid=762 0371: dt=82.944000, rms=0.438 (0.020%), neg=0, invalid=762 0372: dt=82.944000, rms=0.438 (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=0.439, neg=0, invalid=762 0373: dt=9.600000, rms=0.438 (0.058%), neg=0, invalid=762 0374: dt=2.800000, rms=0.438 (0.006%), neg=0, invalid=762 0375: dt=2.800000, rms=0.438 (0.003%), neg=0, invalid=762 0376: dt=2.800000, rms=0.438 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.438, neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0377: dt=87.898734, rms=0.434 (0.866%), neg=0, invalid=762 0378: dt=22.794521, rms=0.433 (0.374%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0379: dt=44.800000, rms=0.432 (0.107%), neg=0, invalid=762 0380: dt=44.800000, rms=0.432 (0.126%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 8 iterations, nbhd size=1, neg = 0 0381: dt=44.800000, rms=0.431 (0.274%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 10 iterations, nbhd size=1, neg = 0 0382: dt=44.800000, rms=0.430 (0.192%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 11 iterations, nbhd size=1, neg = 0 0383: dt=44.800000, rms=0.429 (0.223%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 10 iterations, nbhd size=1, neg = 0 0384: dt=44.800000, rms=0.428 (0.220%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 2 iterations, nbhd size=0, neg = 0 0385: dt=44.800000, rms=0.427 (0.157%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 3 iterations, nbhd size=0, neg = 0 0386: dt=44.800000, rms=0.426 (0.169%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0387: dt=44.800000, rms=0.426 (0.086%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 3 iterations, nbhd size=0, neg = 0 0388: dt=44.800000, rms=0.426 (0.074%), neg=0, invalid=762 0389: dt=19.200000, rms=0.426 (0.034%), neg=0, invalid=762 0390: dt=19.200000, rms=0.426 (0.008%), neg=0, invalid=762 0391: dt=19.200000, rms=0.426 (0.010%), neg=0, invalid=762 0392: dt=19.200000, rms=0.426 (0.009%), neg=0, invalid=762 0393: dt=19.200000, rms=0.426 (0.006%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.432, neg=0, invalid=762 0394: dt=0.864000, rms=0.432 (0.005%), neg=0, invalid=762 0395: dt=0.144000, rms=0.432 (0.000%), neg=0, invalid=762 0396: dt=0.144000, rms=0.432 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.432, neg=0, invalid=762 0397: dt=6.909091, rms=0.432 (0.096%), neg=0, invalid=762 0398: dt=7.459459, rms=0.431 (0.057%), neg=0, invalid=762 0399: dt=7.459459, rms=0.431 (0.044%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0400: dt=7.459459, rms=0.431 (0.008%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0401: dt=7.459459, rms=0.431 (-0.046%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.438, neg=0, invalid=762 0402: dt=0.000050, rms=0.438 (0.000%), neg=0, invalid=762 0403: dt=0.000000, rms=0.438 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.438, neg=0, invalid=762 0404: dt=0.000000, rms=0.438 (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=0.427, neg=0, invalid=762 iter 0, gcam->neg = 293 after 12 iterations, nbhd size=1, neg = 0 0405: dt=1.280000, rms=0.418 (1.915%), neg=0, invalid=762 0406: dt=0.000023, rms=0.418 (0.000%), neg=0, invalid=762 0407: dt=0.000023, 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 0408: dt=0.112000, rms=0.418 (0.072%), neg=0, invalid=762 0409: dt=0.096000, rms=0.418 (0.024%), neg=0, invalid=762 0410: dt=0.096000, rms=0.418 (0.011%), neg=0, invalid=762 0411: dt=0.096000, rms=0.418 (-0.035%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 3 hours, 48 minutes and 52 seconds. mri_ca_register utimesec 13699.874302 mri_ca_register stimesec 13.066013 mri_ca_register ru_maxrss 1346936 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4630078 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 5577 mri_ca_register ru_oublock 63334 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 211 mri_ca_register ru_nivcsw 724612 FSRUNTIME@ mri_ca_register 3.8145 hours 1 threads #-------------------------------------- #@# SubCort Seg Fr 23. Feb 04:04:16 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 node016 machine x86_64 setenv SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test cd /scratch/annadan1111/MABT1T2/test/15689_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 8.23 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 = 0.29813 (33) Left_Lateral_Ventricle (4): linear fit = 1.59 x + 0.0 (5838 voxels, overlap=0.024) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (5838 voxels, peak = 32), gca=30.0 gca peak = 0.17677 (13) mri peak = 0.32887 (33) Right_Lateral_Ventricle (43): linear fit = 2.38 x + 0.0 (8085 voxels, overlap=0.012) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (8085 voxels, peak = 31), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.32892 (103) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (830 voxels, overlap=0.011) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (830 voxels, peak = 102), gca=102.1 gca peak = 0.16930 (96) mri peak = 0.31103 (104) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (807 voxels, overlap=0.014) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (807 voxels, peak = 103), gca=103.2 gca peak = 0.24553 (55) mri peak = 0.14740 (76) Right_Hippocampus (53): linear fit = 1.34 x + 0.0 (1523 voxels, overlap=0.015) Right_Hippocampus (53): linear fit = 1.34 x + 0.0 (1523 voxels, peak = 73), gca=73.4 gca peak = 0.30264 (59) mri peak = 0.18676 (76) Left_Hippocampus (17): linear fit = 1.35 x + 0.0 (1246 voxels, overlap=0.019) Left_Hippocampus (17): linear fit = 1.35 x + 0.0 (1246 voxels, peak = 79), gca=79.4 gca peak = 0.07580 (103) mri peak = 0.14600 (108) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (52173 voxels, overlap=0.437) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (52173 voxels, peak = 107), gca=106.6 gca peak = 0.07714 (104) mri peak = 0.15754 (107) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (51000 voxels, overlap=0.354) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (51000 voxels, peak = 109), gca=108.7 gca peak = 0.09712 (58) mri peak = 0.05116 (80) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (51564 voxels, overlap=0.001) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (51564 voxels, peak = 78), gca=78.0 gca peak = 0.11620 (58) mri peak = 0.05239 (80) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (51203 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (51203 voxels, peak = 78), gca=78.0 gca peak = 0.30970 (66) mri peak = 0.18765 (90) Right_Caudate (50): linear fit = 1.36 x + 0.0 (1653 voxels, overlap=0.013) Right_Caudate (50): linear fit = 1.36 x + 0.0 (1653 voxels, peak = 89), gca=89.4 gca peak = 0.15280 (69) mri peak = 0.14989 (90) Left_Caudate (11): linear fit = 1.25 x + 0.0 (1426 voxels, overlap=0.016) Left_Caudate (11): linear fit = 1.25 x + 0.0 (1426 voxels, peak = 87), gca=86.6 gca peak = 0.13902 (56) mri peak = 0.07075 (74) Left_Cerebellum_Cortex (8): linear fit = 1.34 x + 0.0 (34303 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.34 x + 0.0 (34303 voxels, peak = 75), gca=74.8 gca peak = 0.14777 (55) mri peak = 0.08057 (72) Right_Cerebellum_Cortex (47): linear fit = 1.29 x + 0.0 (37293 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.29 x + 0.0 (37293 voxels, peak = 71), gca=71.2 gca peak = 0.16765 (84) mri peak = 0.23676 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (5941 voxels, overlap=0.002) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (5941 voxels, peak = 93), gca=92.8 gca peak = 0.18739 (84) mri peak = 0.29821 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5771 voxels, overlap=0.037) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5771 voxels, peak = 89), gca=88.6 gca peak = 0.29869 (57) mri peak = 0.21717 (77) Left_Amygdala (18): linear fit = 1.32 x + 0.0 (788 voxels, overlap=0.040) Left_Amygdala (18): linear fit = 1.32 x + 0.0 (788 voxels, peak = 75), gca=75.0 gca peak = 0.33601 (57) mri peak = 0.21243 (75) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (885 voxels, overlap=0.032) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (885 voxels, peak = 74), gca=74.4 gca peak = 0.11131 (90) mri peak = 0.11247 (101) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (5730 voxels, overlap=0.308) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (5730 voxels, peak = 100), gca=100.3 gca peak = 0.11793 (83) mri peak = 0.10677 (98) Right_Thalamus_Proper (49): linear fit = 1.14 x + 0.0 (5510 voxels, overlap=0.186) Right_Thalamus_Proper (49): linear fit = 1.14 x + 0.0 (5510 voxels, peak = 95), gca=95.0 gca peak = 0.08324 (81) mri peak = 0.10475 (93) Left_Putamen (12): linear fit = 1.18 x + 0.0 (2062 voxels, overlap=0.011) Left_Putamen (12): linear fit = 1.18 x + 0.0 (2062 voxels, peak = 96), gca=96.0 gca peak = 0.10360 (77) mri peak = 0.12874 (91) Right_Putamen (51): linear fit = 1.17 x + 0.0 (2105 voxels, overlap=0.012) Right_Putamen (51): linear fit = 1.17 x + 0.0 (2105 voxels, peak = 90), gca=90.5 gca peak = 0.08424 (78) mri peak = 0.13326 (90) Brain_Stem (16): linear fit = 1.10 x + 0.0 (12920 voxels, overlap=0.359) Brain_Stem (16): linear fit = 1.10 x + 0.0 (12920 voxels, peak = 85), gca=85.4 gca peak = 0.12631 (89) mri peak = 0.19498 (97) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1846 voxels, overlap=0.007) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1846 voxels, peak = 97), gca=97.5 gca peak = 0.14500 (87) mri peak = 0.21872 (99) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1914 voxels, overlap=0.005) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1914 voxels, peak = 98), gca=97.9 gca peak = 0.14975 (24) mri peak = 0.28383 (34) Third_Ventricle (14): linear fit = 1.32 x + 0.0 (150 voxels, overlap=0.043) Third_Ventricle (14): linear fit = 1.32 x + 0.0 (150 voxels, peak = 32), gca=31.6 gca peak = 0.19357 (14) mri peak = 0.37152 (30) Fourth_Ventricle (15): linear fit = 1.97 x + 0.0 (782 voxels, overlap=0.074) Fourth_Ventricle (15): linear fit = 1.97 x + 0.0 (782 voxels, peak = 28), gca=27.5 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 1.33 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 1.44 x + 0.0 Left_Putamen too bright - rescaling by 1.009 (from 1.185) to 96.9 (was 96.0) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.12544 (31) mri peak = 0.29813 (33) Left_Lateral_Ventricle (4): linear fit = 1.08 x + 0.0 (5838 voxels, overlap=0.398) Left_Lateral_Ventricle (4): linear fit = 1.08 x + 0.0 (5838 voxels, peak = 33), gca=33.3 gca peak = 0.13981 (19) mri peak = 0.32887 (33) Right_Lateral_Ventricle (43): linear fit = 1.66 x + 0.0 (8085 voxels, overlap=0.140) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (8085 voxels, peak = 32), gca=28.5 gca peak = 0.21697 (102) mri peak = 0.32892 (103) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (830 voxels, overlap=0.885) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (830 voxels, peak = 101), gca=101.5 gca peak = 0.15811 (103) mri peak = 0.31103 (104) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (807 voxels, overlap=0.735) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (807 voxels, peak = 103), gca=103.0 gca peak = 0.21893 (74) mri peak = 0.14740 (76) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1523 voxels, overlap=0.999) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1523 voxels, peak = 74), gca=74.0 gca peak = 0.24207 (76) mri peak = 0.18676 (76) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1246 voxels, overlap=1.003) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1246 voxels, peak = 75), gca=74.9 gca peak = 0.07501 (106) mri peak = 0.14600 (108) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52173 voxels, overlap=0.592) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52173 voxels, peak = 106), gca=106.0 gca peak = 0.07788 (109) mri peak = 0.15754 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (51000 voxels, overlap=0.571) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (51000 voxels, peak = 109), gca=109.0 gca peak = 0.07319 (78) mri peak = 0.05116 (80) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (51564 voxels, overlap=0.946) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (51564 voxels, peak = 77), gca=76.8 gca peak = 0.08763 (78) mri peak = 0.05239 (80) Right_Cerebral_Cortex (42): linear fit = 1.01 x + 0.0 (51203 voxels, overlap=0.936) Right_Cerebral_Cortex (42): linear fit = 1.01 x + 0.0 (51203 voxels, peak = 79), gca=79.2 gca peak = 0.21168 (89) mri peak = 0.18765 (90) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1653 voxels, overlap=0.991) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1653 voxels, peak = 89), gca=89.0 gca peak = 0.14703 (97) mri peak = 0.14989 (90) Left_Caudate (11): linear fit = 1.01 x + 0.0 (1426 voxels, overlap=0.717) Left_Caudate (11): linear fit = 1.01 x + 0.0 (1426 voxels, peak = 98), gca=98.5 gca peak = 0.10706 (74) mri peak = 0.07075 (74) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (34303 voxels, overlap=0.943) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (34303 voxels, peak = 74), gca=74.0 gca peak = 0.11134 (71) mri peak = 0.08057 (72) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (37293 voxels, overlap=0.942) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (37293 voxels, peak = 71), gca=71.0 gca peak = 0.14173 (93) mri peak = 0.23676 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5941 voxels, overlap=0.759) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5941 voxels, peak = 93), gca=93.0 gca peak = 0.15721 (89) mri peak = 0.29821 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (5771 voxels, overlap=0.604) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (5771 voxels, peak = 90), gca=90.3 gca peak = 0.29106 (76) mri peak = 0.21717 (77) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (788 voxels, overlap=1.003) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (788 voxels, peak = 76), gca=76.0 gca peak = 0.31755 (74) mri peak = 0.21243 (75) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (885 voxels, overlap=0.979) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (885 voxels, peak = 74), gca=74.0 gca peak = 0.08945 (98) mri peak = 0.11247 (101) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5730 voxels, overlap=0.861) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5730 voxels, peak = 98), gca=98.0 gca peak = 0.10242 (95) mri peak = 0.10677 (98) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5510 voxels, overlap=0.900) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5510 voxels, peak = 95), gca=94.5 gca peak = 0.07880 (90) mri peak = 0.10475 (93) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2062 voxels, overlap=0.708) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2062 voxels, peak = 90), gca=89.6 gca peak = 0.08772 (92) mri peak = 0.12874 (91) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2105 voxels, overlap=0.756) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2105 voxels, peak = 93), gca=93.4 gca peak = 0.07891 (86) mri peak = 0.13326 (90) Brain_Stem (16): linear fit = 1.01 x + 0.0 (12920 voxels, overlap=0.682) Brain_Stem (16): linear fit = 1.01 x + 0.0 (12920 voxels, peak = 87), gca=87.3 gca peak = 0.12536 (92) mri peak = 0.19498 (97) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1846 voxels, overlap=0.681) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1846 voxels, peak = 92), gca=92.5 gca peak = 0.13928 (96) mri peak = 0.21872 (99) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1914 voxels, overlap=0.749) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1914 voxels, peak = 96), gca=95.5 gca peak = 0.16815 (34) mri peak = 0.28383 (34) Third_Ventricle (14): linear fit = 0.99 x + 0.0 (150 voxels, overlap=0.688) Third_Ventricle (14): linear fit = 0.99 x + 0.0 (150 voxels, peak = 33), gca=33.5 gca peak = 0.16541 (23) mri peak = 0.37152 (30) Fourth_Ventricle (15): linear fit = 1.33 x + 0.0 (782 voxels, overlap=0.104) Fourth_Ventricle (15): linear fit = 1.33 x + 0.0 (782 voxels, peak = 30), gca=30.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.14754 (37) gca peak Left_Thalamus = 0.36646 (107) gca peak CSF = 0.21337 (52) gca peak Left_Accumbens_area = 0.76113 (78) gca peak Left_undetermined = 0.95280 (34) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.12303 (35) gca peak Right_Inf_Lat_Vent = 0.24572 (31) gca peak Right_Accumbens_area = 0.28852 (89) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14504 (37) gca peak Fifth_Ventricle = 0.51780 (44) gca peak WM_hypointensities = 0.07821 (79) gca peak non_WM_hypointensities = 0.09744 (45) gca peak Optic_Chiasm = 0.68965 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.22 x + 0.0 Left_Pallidum too bright - rescaling by 1.012 (from 1.000) to 104.3 (was 103.0) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 63437 voxels changed in iteration 0 of unlikely voxel relabeling 337 voxels changed in iteration 1 of unlikely voxel relabeling 6 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 70545 gm and wm labels changed (%39 to gray, %61 to white out of all changed labels) 520 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 78425 changed. image ll: -2.157, PF=0.500 pass 2: 22260 changed. image ll: -2.156, PF=0.500 pass 3: 7646 changed. pass 4: 3076 changed. 54416 voxels changed in iteration 0 of unlikely voxel relabeling 871 voxels changed in iteration 1 of unlikely voxel relabeling 103 voxels changed in iteration 2 of unlikely voxel relabeling 3 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 7914 voxels changed in iteration 0 of unlikely voxel relabeling 124 voxels changed in iteration 1 of unlikely voxel relabeling 9 voxels changed in iteration 2 of unlikely voxel relabeling 5 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 6494 voxels changed in iteration 0 of unlikely voxel relabeling 104 voxels changed in iteration 1 of unlikely voxel relabeling 6 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6766 voxels changed in iteration 0 of unlikely voxel relabeling 56 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 5338.517421 mri_ca_label stimesec 3.927402 mri_ca_label ru_maxrss 2089540 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 1013958 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 66221 mri_ca_label ru_oublock 458 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 225 mri_ca_label ru_nivcsw 244885 auto-labeling took 89 minutes and 9 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/transforms/cc_up.lta 15689_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/test/15689_T1_fs/mri/transforms/cc_up.lta reading aseg from /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/aseg.auto_noCCseg.mgz reading norm from /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/norm.mgz 82049 voxels in left wm, 81195 in right wm, xrange [123, 138] searching rotation angles z=[-11 3], y=[-7 7] searching scale 1 Z rot -11.4 searching scale 1 Z rot -11.2 searching scale 1 Z rot -10.9 searching scale 1 Z rot -10.7 searching scale 1 Z rot -10.4 searching scale 1 Z rot -10.2 searching scale 1 Z rot -9.9 searching scale 1 Z rot -9.7 searching scale 1 Z rot -9.4 searching scale 1 Z rot -9.2 searching scale 1 Z rot -8.9 searching scale 1 Z rot -8.7 searching scale 1 Z rot -8.4 searching scale 1 Z rot -8.2 searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.2 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.2 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.2 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.2 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.2 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.6 global minimum found at slice 130.0, rotations (-0.23, -4.42) final transformation (x=130.0, yr=-0.225, zr=-4.418): 0.99702 0.07702 -0.00392 -8.64144; -0.07702 0.99703 0.00030 41.26711; 0.00393 0.00000 0.99999 14.48997; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 132] in xformed coordinates best xformed slice 129 cc center is found at 129 97 113 eigenvectors: -0.00206 0.00187 1.00000; -0.15473 -0.98796 0.00153; 0.98795 -0.15473 0.00232; error in mid anterior detected - correcting... writing aseg with callosum to /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/aseg.auto.mgz... corpus callosum segmentation took 1.4 minutes #-------------------------------------- #@# Merge ASeg Fr 23. Feb 05:34:51 CET 2018 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Fr 23. Feb 05:34:51 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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... 224 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 88 (88), valley at 56 (56) csf peak at 35, setting threshold to 70 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 88 (88), valley at 51 (51) csf peak at 37, setting threshold to 71 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 30 seconds. #-------------------------------------------- #@# Mask BFS Fr 23. Feb 05:38:23 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1818947 voxels in mask (pct= 10.84) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Fr 23. Feb 05:38:24 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): 104.4 +- 5.6 [79.0 --> 125.0] GM (74.0) : 70.7 +- 16.8 [30.0 --> 95.0] setting bottom of white matter range to 87.5 setting top of gray matter range to 104.3 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... 7541 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3205 filled 7311 bright non-wm voxels segmented. 4747 diagonally connected voxels added... white matter segmentation took 2.4 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 0.49 minutes reading wm segmentation from wm.seg.mgz... 131 voxels added to wm to prevent paths from MTL structures to cortex 3517 additional wm voxels added 0 additional wm voxels added SEG EDIT: 78375 voxels turned on, 91964 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+): 30 found - 30 modified | TOTAL: 30 pass 2 (xy+): 0 found - 30 modified | TOTAL: 30 pass 1 (xy-): 31 found - 31 modified | TOTAL: 61 pass 2 (xy-): 0 found - 31 modified | TOTAL: 61 pass 1 (yz+): 24 found - 24 modified | TOTAL: 85 pass 2 (yz+): 0 found - 24 modified | TOTAL: 85 pass 1 (yz-): 34 found - 34 modified | TOTAL: 119 pass 2 (yz-): 0 found - 34 modified | TOTAL: 119 pass 1 (xz+): 22 found - 22 modified | TOTAL: 141 pass 2 (xz+): 0 found - 22 modified | TOTAL: 141 pass 1 (xz-): 28 found - 28 modified | TOTAL: 169 pass 2 (xz-): 0 found - 28 modified | TOTAL: 169 Iteration Number : 1 pass 1 (+++): 29 found - 29 modified | TOTAL: 29 pass 2 (+++): 0 found - 29 modified | TOTAL: 29 pass 1 (+++): 29 found - 29 modified | TOTAL: 58 pass 2 (+++): 0 found - 29 modified | TOTAL: 58 pass 1 (+++): 29 found - 29 modified | TOTAL: 87 pass 2 (+++): 0 found - 29 modified | TOTAL: 87 pass 1 (+++): 44 found - 44 modified | TOTAL: 131 pass 2 (+++): 0 found - 44 modified | TOTAL: 131 Iteration Number : 1 pass 1 (++): 67 found - 67 modified | TOTAL: 67 pass 2 (++): 0 found - 67 modified | TOTAL: 67 pass 1 (+-): 53 found - 53 modified | TOTAL: 120 pass 2 (+-): 0 found - 53 modified | TOTAL: 120 pass 1 (--): 63 found - 63 modified | TOTAL: 183 pass 2 (--): 0 found - 63 modified | TOTAL: 183 pass 1 (-+): 71 found - 71 modified | TOTAL: 254 pass 2 (-+): 0 found - 71 modified | TOTAL: 254 Iteration Number : 2 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 7 found - 7 modified | TOTAL: 12 pass 2 (xy-): 0 found - 7 modified | TOTAL: 12 pass 1 (yz+): 7 found - 7 modified | TOTAL: 19 pass 2 (yz+): 0 found - 7 modified | TOTAL: 19 pass 1 (yz-): 9 found - 9 modified | TOTAL: 28 pass 2 (yz-): 0 found - 9 modified | TOTAL: 28 pass 1 (xz+): 6 found - 6 modified | TOTAL: 34 pass 2 (xz+): 0 found - 6 modified | TOTAL: 34 pass 1 (xz-): 6 found - 6 modified | TOTAL: 40 pass 2 (xz-): 0 found - 6 modified | TOTAL: 40 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 10 found - 10 modified | TOTAL: 12 pass 2 (+++): 0 found - 10 modified | TOTAL: 12 Iteration Number : 2 pass 1 (++): 9 found - 9 modified | TOTAL: 9 pass 2 (++): 0 found - 9 modified | TOTAL: 9 pass 1 (+-): 3 found - 3 modified | TOTAL: 12 pass 2 (+-): 0 found - 3 modified | TOTAL: 12 pass 1 (--): 7 found - 7 modified | TOTAL: 19 pass 2 (--): 0 found - 7 modified | TOTAL: 19 pass 1 (-+): 6 found - 6 modified | TOTAL: 25 pass 2 (-+): 0 found - 6 modified | TOTAL: 25 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 3 found - 3 modified | TOTAL: 3 pass 2 (xy-): 0 found - 3 modified | TOTAL: 3 pass 1 (yz+): 0 found - 0 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 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 (++): 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 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 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 : 4 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 : 4 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 = 636 (out of 705712: 0.090122) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Fr 23. Feb 05:41:24 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 1.04827 0.08738 0.00513 -20.12201; -0.08096 0.92016 0.32133 -17.90591; 0.02489 -0.30045 0.89602 30.14474; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.04827 0.08738 0.00513 -20.12201; -0.08096 0.92016 0.32133 -17.90591; 0.02489 -0.30045 0.89602 30.14474; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1308 (min = 350, max = 1400), aspect = 0.48 (min = 0.10, max = 0.75) no need to search using seed (126, 106, 91), TAL = (2.0, -37.0, 22.0) talairach voxel to voxel transform 0.94704 -0.08209 0.02402 16.86234; 0.08281 0.96567 -0.34679 29.41136; 0.00146 0.32609 0.99910 -24.24922; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 106, 91) --> (2.0, -37.0, 22.0) done. writing output to filled.mgz... filling took 0.6 minutes talairach cc position changed to (2.00, -37.00, 22.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -37.00, 22.00) SRC: (112.63, 109.16, 101.39) search lh wm seed point around talairach space (-16.00, -37.00, 22.00), SRC: (146.72, 112.14, 101.45) 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 Fr 23. Feb 05:42:02 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.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-): 6 found - 6 modified | TOTAL: 7 pass 2 (xy-): 0 found - 6 modified | TOTAL: 7 pass 1 (yz+): 4 found - 4 modified | TOTAL: 11 pass 2 (yz+): 0 found - 4 modified | TOTAL: 11 pass 1 (yz-): 2 found - 2 modified | TOTAL: 13 pass 2 (yz-): 0 found - 2 modified | TOTAL: 13 pass 1 (xz+): 2 found - 2 modified | TOTAL: 15 pass 2 (xz+): 0 found - 2 modified | TOTAL: 15 pass 1 (xz-): 3 found - 3 modified | TOTAL: 18 pass 2 (xz-): 0 found - 3 modified | TOTAL: 18 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 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 Iteration Number : 1 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 3 found - 3 modified | TOTAL: 6 pass 2 (+-): 0 found - 3 modified | TOTAL: 6 pass 1 (--): 2 found - 2 modified | TOTAL: 8 pass 2 (--): 0 found - 2 modified | TOTAL: 8 pass 1 (-+): 2 found - 2 modified | TOTAL: 10 pass 2 (-+): 0 found - 2 modified | TOTAL: 10 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 = 32 (out of 330425: 0.009684) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 1710 vertices, 1886 faces slice 60: 9261 vertices, 9598 faces slice 70: 20842 vertices, 21239 faces slice 80: 31848 vertices, 32212 faces slice 90: 42293 vertices, 42628 faces slice 100: 52744 vertices, 53102 faces slice 110: 64388 vertices, 64825 faces slice 120: 75846 vertices, 76271 faces slice 130: 87337 vertices, 87793 faces slice 140: 98904 vertices, 99364 faces slice 150: 110560 vertices, 111066 faces slice 160: 120463 vertices, 120855 faces slice 170: 128538 vertices, 128923 faces slice 180: 134873 vertices, 135154 faces slice 190: 140257 vertices, 140508 faces slice 200: 143542 vertices, 143743 faces slice 210: 145056 vertices, 145154 faces slice 220: 145056 vertices, 145154 faces slice 230: 145056 vertices, 145154 faces slice 240: 145056 vertices, 145154 faces slice 250: 145056 vertices, 145154 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... 145056 voxel in cpt #1: X=-98 [v=145056,e=435462,f=290308] located at (-27.939238, -11.066202, 16.397675) For the whole surface: X=-98 [v=145056,e=435462,f=290308] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Fr 23. Feb 05:42:08 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 3 found - 3 modified | TOTAL: 3 pass 2 (xy-): 0 found - 3 modified | TOTAL: 3 pass 1 (yz+): 1 found - 1 modified | TOTAL: 4 pass 2 (yz+): 0 found - 1 modified | TOTAL: 4 pass 1 (yz-): 1 found - 1 modified | TOTAL: 5 pass 2 (yz-): 0 found - 1 modified | TOTAL: 5 pass 1 (xz+): 0 found - 0 modified | TOTAL: 5 pass 1 (xz-): 2 found - 2 modified | TOTAL: 7 pass 2 (xz-): 0 found - 2 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 2 found - 2 modified | TOTAL: 3 pass 2 (+-): 0 found - 2 modified | TOTAL: 3 pass 1 (--): 0 found - 0 modified | TOTAL: 3 pass 1 (-+): 0 found - 0 modified | TOTAL: 3 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 = 10 (out of 350670: 0.002852) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 1471 vertices, 1595 faces slice 60: 8055 vertices, 8348 faces slice 70: 18113 vertices, 18474 faces slice 80: 28838 vertices, 29205 faces slice 90: 40425 vertices, 40834 faces slice 100: 51966 vertices, 52354 faces slice 110: 63784 vertices, 64189 faces slice 120: 76055 vertices, 76539 faces slice 130: 88808 vertices, 89281 faces slice 140: 100902 vertices, 101384 faces slice 150: 112817 vertices, 113330 faces slice 160: 122759 vertices, 123204 faces slice 170: 130318 vertices, 130697 faces slice 180: 136838 vertices, 137161 faces slice 190: 142341 vertices, 142630 faces slice 200: 146252 vertices, 146509 faces slice 210: 147798 vertices, 147928 faces slice 220: 147798 vertices, 147928 faces slice 230: 147798 vertices, 147928 faces slice 240: 147798 vertices, 147928 faces slice 250: 147798 vertices, 147928 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... 147798 voxel in cpt #1: X=-130 [v=147798,e=443784,f=295856] located at (26.050034, -9.952827, 19.771505) For the whole surface: X=-130 [v=147798,e=443784,f=295856] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Fr 23. Feb 05:42:14 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 Fr 23. Feb 05:42:19 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 Fr 23. Feb 05:42:25 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 = 50.4 mm, total surface area = 76854 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.6 minutes step 000: RMS=0.156 (target=0.015) step 005: RMS=0.118 (target=0.015) step 010: RMS=0.092 (target=0.015) step 015: RMS=0.080 (target=0.015) step 020: RMS=0.072 (target=0.015) step 025: RMS=0.067 (target=0.015) step 030: RMS=0.062 (target=0.015) step 035: RMS=0.059 (target=0.015) step 040: RMS=0.057 (target=0.015) step 045: RMS=0.056 (target=0.015) step 050: RMS=0.055 (target=0.015) step 055: RMS=0.055 (target=0.015) step 060: RMS=0.054 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 34.691726 mris_inflate stimesec 0.078987 mris_inflate ru_maxrss 186388 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 24516 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 11806 mris_inflate ru_oublock 10206 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 98 mris_inflate ru_nivcsw 178 #-------------------------------------------- #@# Inflation1 rh Fr 23. Feb 05:43:00 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 = 49.4 mm, total surface area = 78030 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.6 minutes step 000: RMS=0.160 (target=0.015) step 005: RMS=0.121 (target=0.015) step 010: RMS=0.097 (target=0.015) step 015: RMS=0.086 (target=0.015) step 020: RMS=0.078 (target=0.015) step 025: RMS=0.072 (target=0.015) step 030: RMS=0.067 (target=0.015) step 035: RMS=0.065 (target=0.015) step 040: RMS=0.062 (target=0.015) step 045: RMS=0.060 (target=0.015) step 050: RMS=0.060 (target=0.015) step 055: RMS=0.060 (target=0.015) step 060: RMS=0.059 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 35.367623 mris_inflate stimesec 0.068989 mris_inflate ru_maxrss 190144 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 24945 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 11424 mris_inflate ru_oublock 10400 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 104 mris_inflate ru_nivcsw 160 #-------------------------------------------- #@# QSphere lh Fr 23. Feb 05:43:35 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 0.96 +- 0.57 (0.00-->6.37) (max @ vno 62894 --> 62907) face area 0.03 +- 0.03 (-0.13-->0.59) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.321... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.312, avgs=0 005/300: dt: 0.9000, rms radial error=175.061, avgs=0 010/300: dt: 0.9000, rms radial error=174.522, avgs=0 015/300: dt: 0.9000, rms radial error=173.812, avgs=0 020/300: dt: 0.9000, rms radial error=173.003, avgs=0 025/300: dt: 0.9000, rms radial error=172.136, avgs=0 030/300: dt: 0.9000, rms radial error=171.238, avgs=0 035/300: dt: 0.9000, rms radial error=170.323, avgs=0 040/300: dt: 0.9000, rms radial error=169.399, avgs=0 045/300: dt: 0.9000, rms radial error=168.471, avgs=0 050/300: dt: 0.9000, rms radial error=167.543, avgs=0 055/300: dt: 0.9000, rms radial error=166.616, avgs=0 060/300: dt: 0.9000, rms radial error=165.690, avgs=0 065/300: dt: 0.9000, rms radial error=164.768, avgs=0 070/300: dt: 0.9000, rms radial error=163.849, avgs=0 075/300: dt: 0.9000, rms radial error=162.933, avgs=0 080/300: dt: 0.9000, rms radial error=162.021, avgs=0 085/300: dt: 0.9000, rms radial error=161.113, avgs=0 090/300: dt: 0.9000, rms radial error=160.212, avgs=0 095/300: dt: 0.9000, rms radial error=159.318, avgs=0 100/300: dt: 0.9000, rms radial error=158.428, avgs=0 105/300: dt: 0.9000, rms radial error=157.542, avgs=0 110/300: dt: 0.9000, rms radial error=156.660, avgs=0 115/300: dt: 0.9000, rms radial error=155.782, avgs=0 120/300: dt: 0.9000, rms radial error=154.908, avgs=0 125/300: dt: 0.9000, rms radial error=154.039, avgs=0 130/300: dt: 0.9000, rms radial error=153.174, avgs=0 135/300: dt: 0.9000, rms radial error=152.313, avgs=0 140/300: dt: 0.9000, rms radial error=151.456, avgs=0 145/300: dt: 0.9000, rms radial error=150.604, avgs=0 150/300: dt: 0.9000, rms radial error=149.758, avgs=0 155/300: dt: 0.9000, rms radial error=148.916, avgs=0 160/300: dt: 0.9000, rms radial error=148.078, avgs=0 165/300: dt: 0.9000, rms radial error=147.246, avgs=0 170/300: dt: 0.9000, rms radial error=146.419, avgs=0 175/300: dt: 0.9000, rms radial error=145.596, avgs=0 180/300: dt: 0.9000, rms radial error=144.777, avgs=0 185/300: dt: 0.9000, rms radial error=143.963, avgs=0 190/300: dt: 0.9000, rms radial error=143.154, avgs=0 195/300: dt: 0.9000, rms radial error=142.349, avgs=0 200/300: dt: 0.9000, rms radial error=141.548, avgs=0 205/300: dt: 0.9000, rms radial error=140.752, avgs=0 210/300: dt: 0.9000, rms radial error=139.961, avgs=0 215/300: dt: 0.9000, rms radial error=139.174, avgs=0 220/300: dt: 0.9000, rms radial error=138.391, avgs=0 225/300: dt: 0.9000, rms radial error=137.612, avgs=0 230/300: dt: 0.9000, rms radial error=136.838, avgs=0 235/300: dt: 0.9000, rms radial error=136.068, avgs=0 240/300: dt: 0.9000, rms radial error=135.302, avgs=0 245/300: dt: 0.9000, rms radial error=134.541, avgs=0 250/300: dt: 0.9000, rms radial error=133.783, avgs=0 255/300: dt: 0.9000, rms radial error=133.030, avgs=0 260/300: dt: 0.9000, rms radial error=132.281, avgs=0 265/300: dt: 0.9000, rms radial error=131.536, avgs=0 270/300: dt: 0.9000, rms radial error=130.795, avgs=0 275/300: dt: 0.9000, rms radial error=130.058, avgs=0 280/300: dt: 0.9000, rms radial error=129.325, avgs=0 285/300: dt: 0.9000, rms radial error=128.596, avgs=0 290/300: dt: 0.9000, rms radial error=127.871, avgs=0 295/300: dt: 0.9000, rms radial error=127.150, avgs=0 300/300: dt: 0.9000, rms radial error=126.434, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16812.58 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 2779.98 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 3 (K=160.0), pass 1, starting sse = 300.97 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00460 epoch 4 (K=640.0), pass 1, starting sse = 32.17 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/13 = 0.00560 final distance error %26.67 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.06 hours mris_sphere utimesec 223.510021 mris_sphere stimesec 0.103984 mris_sphere ru_maxrss 186584 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 24563 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 11230 mris_sphere ru_oublock 10207 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 107 mris_sphere ru_nivcsw 2289 FSRUNTIME@ mris_sphere 0.0621 hours 1 threads #-------------------------------------------- #@# QSphere rh Fr 23. Feb 05:47:19 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 0.95 +- 0.56 (0.00-->7.13) (max @ vno 64672 --> 65885) face area 0.03 +- 0.04 (-0.26-->0.80) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.323... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.455, avgs=0 005/300: dt: 0.9000, rms radial error=175.196, avgs=0 010/300: dt: 0.9000, rms radial error=174.640, avgs=0 015/300: dt: 0.9000, rms radial error=173.909, avgs=0 020/300: dt: 0.9000, rms radial error=173.076, avgs=0 025/300: dt: 0.9000, rms radial error=172.185, avgs=0 030/300: dt: 0.9000, rms radial error=171.261, avgs=0 035/300: dt: 0.9000, rms radial error=170.320, avgs=0 040/300: dt: 0.9000, rms radial error=169.370, avgs=0 045/300: dt: 0.9000, rms radial error=168.418, avgs=0 050/300: dt: 0.9000, rms radial error=167.473, avgs=0 055/300: dt: 0.9000, rms radial error=166.536, avgs=0 060/300: dt: 0.9000, rms radial error=165.602, avgs=0 065/300: dt: 0.9000, rms radial error=164.673, avgs=0 070/300: dt: 0.9000, rms radial error=163.749, avgs=0 075/300: dt: 0.9000, rms radial error=162.830, avgs=0 080/300: dt: 0.9000, rms radial error=161.915, avgs=0 085/300: dt: 0.9000, rms radial error=161.006, avgs=0 090/300: dt: 0.9000, rms radial error=160.102, avgs=0 095/300: dt: 0.9000, rms radial error=159.202, avgs=0 100/300: dt: 0.9000, rms radial error=158.308, avgs=0 105/300: dt: 0.9000, rms radial error=157.420, avgs=0 110/300: dt: 0.9000, rms radial error=156.539, avgs=0 115/300: dt: 0.9000, rms radial error=155.662, avgs=0 120/300: dt: 0.9000, rms radial error=154.790, avgs=0 125/300: dt: 0.9000, rms radial error=153.923, avgs=0 130/300: dt: 0.9000, rms radial error=153.060, avgs=0 135/300: dt: 0.9000, rms radial error=152.203, avgs=0 140/300: dt: 0.9000, rms radial error=151.349, avgs=0 145/300: dt: 0.9000, rms radial error=150.501, avgs=0 150/300: dt: 0.9000, rms radial error=149.657, avgs=0 155/300: dt: 0.9000, rms radial error=148.818, avgs=0 160/300: dt: 0.9000, rms radial error=147.982, avgs=0 165/300: dt: 0.9000, rms radial error=147.151, avgs=0 170/300: dt: 0.9000, rms radial error=146.325, avgs=0 175/300: dt: 0.9000, rms radial error=145.503, avgs=0 180/300: dt: 0.9000, rms radial error=144.686, avgs=0 185/300: dt: 0.9000, rms radial error=143.873, avgs=0 190/300: dt: 0.9000, rms radial error=143.064, avgs=0 195/300: dt: 0.9000, rms radial error=142.260, avgs=0 200/300: dt: 0.9000, rms radial error=141.460, avgs=0 205/300: dt: 0.9000, rms radial error=140.664, avgs=0 210/300: dt: 0.9000, rms radial error=139.873, avgs=0 215/300: dt: 0.9000, rms radial error=139.086, avgs=0 220/300: dt: 0.9000, rms radial error=138.303, avgs=0 225/300: dt: 0.9000, rms radial error=137.526, avgs=0 230/300: dt: 0.9000, rms radial error=136.753, avgs=0 235/300: dt: 0.9000, rms radial error=135.984, avgs=0 240/300: dt: 0.9000, rms radial error=135.220, avgs=0 245/300: dt: 0.9000, rms radial error=134.460, avgs=0 250/300: dt: 0.9000, rms radial error=133.705, avgs=0 255/300: dt: 0.9000, rms radial error=132.953, avgs=0 260/300: dt: 0.9000, rms radial error=132.206, avgs=0 265/300: dt: 0.9000, rms radial error=131.463, avgs=0 270/300: dt: 0.9000, rms radial error=130.724, avgs=0 275/300: dt: 0.9000, rms radial error=129.989, avgs=0 280/300: dt: 0.9000, rms radial error=129.258, avgs=0 285/300: dt: 0.9000, rms radial error=128.532, avgs=0 290/300: dt: 0.9000, rms radial error=127.809, avgs=0 295/300: dt: 0.9000, rms radial error=127.090, avgs=0 300/300: dt: 0.9000, rms radial error=126.375, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17102.41 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 2 (K=40.0), pass 1, starting sse = 2822.04 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 3 (K=160.0), pass 1, starting sse = 296.33 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00507 epoch 4 (K=640.0), pass 1, starting sse = 28.41 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/10 = 0.00554 final distance error %25.69 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.06 hours mris_sphere utimesec 217.452942 mris_sphere stimesec 0.077988 mris_sphere ru_maxrss 190340 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 24992 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 11425 mris_sphere ru_oublock 10401 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 112 mris_sphere ru_nivcsw 1969 FSRUNTIME@ mris_sphere 0.0604 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Fr 23. Feb 05:50:57 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Fr 23. Feb 05:50:57 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Fr 23. Feb 05:50:57 CET 2018 mris_fix_topology -rusage /scratch/annadan1111/MABT1T2/test/15689_T1_fs/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 15689_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=-98 (nv=145056, nf=290308, ne=435462, g=50) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 16927 ambiguous faces found in tessellation segmenting defects... 46 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 1 -merging segment 11 into 3 -merging segment 15 into 14 -merging segment 23 into 20 -merging segment 31 into 20 -merging segment 45 into 44 40 defects to be corrected 0 vertices coincident reading input surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.6180 (-4.3090) -vertex loglikelihood: -5.5781 (-2.7890) -normal dot loglikelihood: -3.6031 (-3.6031) -quad curv loglikelihood: -5.9275 (-2.9638) Total Loglikelihood : -23.7268 CORRECTING DEFECT 0 (vertices=46, convex hull=34, v0=1080) After retessellation of defect 0 (v0=1080), euler #=-39 (135523,404280,268718) : difference with theory (-37) = 2 CORRECTING DEFECT 1 (vertices=14, convex hull=29, v0=6895) After retessellation of defect 1 (v0=6895), euler #=-37 (135525,404295,268733) : difference with theory (-36) = 1 CORRECTING DEFECT 2 (vertices=1291, convex hull=408, v0=7340) After retessellation of defect 2 (v0=7340), euler #=-35 (135570,404645,269040) : difference with theory (-35) = 0 CORRECTING DEFECT 3 (vertices=12, convex hull=20, v0=8825) After retessellation of defect 3 (v0=8825), euler #=-34 (135572,404656,269050) : difference with theory (-34) = 0 CORRECTING DEFECT 4 (vertices=55, convex hull=93, v0=11035) After retessellation of defect 4 (v0=11035), euler #=-33 (135598,404771,269140) : difference with theory (-33) = 0 CORRECTING DEFECT 5 (vertices=102, convex hull=65, v0=11888) After retessellation of defect 5 (v0=11888), euler #=-32 (135620,404864,269212) : difference with theory (-32) = 0 CORRECTING DEFECT 6 (vertices=27, convex hull=28, v0=13171) After retessellation of defect 6 (v0=13171), euler #=-31 (135626,404890,269233) : difference with theory (-31) = 0 CORRECTING DEFECT 7 (vertices=56, convex hull=58, v0=13417) After retessellation of defect 7 (v0=13417), euler #=-30 (135635,404940,269275) : difference with theory (-30) = 0 CORRECTING DEFECT 8 (vertices=105, convex hull=72, v0=15645) After retessellation of defect 8 (v0=15645), euler #=-29 (135644,404998,269325) : difference with theory (-29) = 0 CORRECTING DEFECT 9 (vertices=299, convex hull=185, v0=16888) After retessellation of defect 9 (v0=16888), euler #=-28 (135680,405203,269495) : difference with theory (-28) = 0 CORRECTING DEFECT 10 (vertices=78, convex hull=72, v0=23723) After retessellation of defect 10 (v0=23723), euler #=-27 (135702,405301,269572) : difference with theory (-27) = 0 CORRECTING DEFECT 11 (vertices=2759, convex hull=733, v0=52029) XL defect detected... After retessellation of defect 11 (v0=52029), euler #=-27 (136061,406765,270677) : difference with theory (-26) = 1 CORRECTING DEFECT 12 (vertices=213, convex hull=226, v0=52452) After retessellation of defect 12 (v0=52452), euler #=-25 (136071,406907,270811) : difference with theory (-25) = 0 CORRECTING DEFECT 13 (vertices=36, convex hull=70, v0=56923) After retessellation of defect 13 (v0=56923), euler #=-24 (136090,406998,270884) : difference with theory (-24) = 0 CORRECTING DEFECT 14 (vertices=40, convex hull=39, v0=58032) After retessellation of defect 14 (v0=58032), euler #=-23 (136097,407031,270911) : difference with theory (-23) = 0 CORRECTING DEFECT 15 (vertices=42, convex hull=64, v0=63203) After retessellation of defect 15 (v0=63203), euler #=-22 (136121,407125,270982) : difference with theory (-22) = 0 CORRECTING DEFECT 16 (vertices=29, convex hull=66, v0=64281) After retessellation of defect 16 (v0=64281), euler #=-21 (136139,407208,271048) : difference with theory (-21) = 0 CORRECTING DEFECT 17 (vertices=2006, convex hull=975, v0=74400) XL defect detected... After retessellation of defect 17 (v0=74400), euler #=-20 (136333,408342,271989) : difference with theory (-20) = 0 CORRECTING DEFECT 18 (vertices=26, convex hull=60, v0=74647) After retessellation of defect 18 (v0=74647), euler #=-19 (136345,408400,272036) : difference with theory (-19) = 0 CORRECTING DEFECT 19 (vertices=23, convex hull=43, v0=81021) After retessellation of defect 19 (v0=81021), euler #=-18 (136358,408454,272078) : difference with theory (-18) = 0 CORRECTING DEFECT 20 (vertices=18, convex hull=64, v0=83628) After retessellation of defect 20 (v0=83628), euler #=-17 (136370,408512,272125) : difference with theory (-17) = 0 CORRECTING DEFECT 21 (vertices=22, convex hull=47, v0=93773) After retessellation of defect 21 (v0=93773), euler #=-16 (136379,408554,272159) : difference with theory (-16) = 0 CORRECTING DEFECT 22 (vertices=42, convex hull=72, v0=97674) After retessellation of defect 22 (v0=97674), euler #=-15 (136388,408615,272212) : difference with theory (-15) = 0 CORRECTING DEFECT 23 (vertices=6, convex hull=29, v0=98646) After retessellation of defect 23 (v0=98646), euler #=-14 (136390,408628,272224) : difference with theory (-14) = 0 CORRECTING DEFECT 24 (vertices=1111, convex hull=234, v0=100010) After retessellation of defect 24 (v0=100010), euler #=-13 (136463,408969,272493) : difference with theory (-13) = 0 CORRECTING DEFECT 25 (vertices=30, convex hull=67, v0=102108) After retessellation of defect 25 (v0=102108), euler #=-12 (136472,409021,272537) : difference with theory (-12) = 0 CORRECTING DEFECT 26 (vertices=75, convex hull=109, v0=102282) After retessellation of defect 26 (v0=102282), euler #=-11 (136496,409148,272641) : difference with theory (-11) = 0 CORRECTING DEFECT 27 (vertices=27, convex hull=52, v0=106357) After retessellation of defect 27 (v0=106357), euler #=-10 (136512,409215,272693) : difference with theory (-10) = 0 CORRECTING DEFECT 28 (vertices=33, convex hull=63, v0=106608) After retessellation of defect 28 (v0=106608), euler #=-9 (136533,409303,272761) : difference with theory (-9) = 0 CORRECTING DEFECT 29 (vertices=29, convex hull=27, v0=108081) After retessellation of defect 29 (v0=108081), euler #=-8 (136538,409326,272780) : difference with theory (-8) = 0 CORRECTING DEFECT 30 (vertices=52, convex hull=42, v0=110535) After retessellation of defect 30 (v0=110535), euler #=-7 (136543,409354,272804) : difference with theory (-7) = 0 CORRECTING DEFECT 31 (vertices=6, convex hull=18, v0=114582) After retessellation of defect 31 (v0=114582), euler #=-6 (136544,409362,272812) : difference with theory (-6) = 0 CORRECTING DEFECT 32 (vertices=12, convex hull=28, v0=115600) After retessellation of defect 32 (v0=115600), euler #=-5 (136545,409373,272823) : difference with theory (-5) = 0 CORRECTING DEFECT 33 (vertices=35, convex hull=60, v0=116546) After retessellation of defect 33 (v0=116546), euler #=-5 (136559,409447,272883) : difference with theory (-4) = 1 CORRECTING DEFECT 34 (vertices=244, convex hull=43, v0=118418) After retessellation of defect 34 (v0=118418), euler #=-4 (136569,409493,272920) : difference with theory (-3) = 1 CORRECTING DEFECT 35 (vertices=51, convex hull=94, v0=124323) After retessellation of defect 35 (v0=124323), euler #=-3 (136585,409577,272989) : difference with theory (-2) = 1 CORRECTING DEFECT 36 (vertices=155, convex hull=52, v0=124917) After retessellation of defect 36 (v0=124917), euler #=-2 (136595,409627,273030) : difference with theory (-1) = 1 CORRECTING DEFECT 37 (vertices=26, convex hull=35, v0=125056) After retessellation of defect 37 (v0=125056), euler #=-1 (136603,409663,273059) : difference with theory (0) = 1 CORRECTING DEFECT 38 (vertices=261, convex hull=237, v0=129984) After retessellation of defect 38 (v0=129984), euler #=0 (136697,410063,273366) : difference with theory (1) = 1 CORRECTING DEFECT 39 (vertices=36, convex hull=54, v0=136295) After retessellation of defect 39 (v0=136295), euler #=2 (136705,410109,273406) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.28 (0.06-->13.61) (max @ vno 95907 --> 99838) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.28 (0.06-->13.61) (max @ vno 95907 --> 99838) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 171 mutations (36.0%), 304 crossovers (64.0%), 1035 vertices were eliminated building final representation... 8351 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=136705, nf=273406, ne=410109, g=0) writing corrected surface to /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.orig... defective orientation at vertex 75440(75441) with faces 150460 and 269634 defective orientation at vertex 75440(76441) with faces 150460 and 270643 defective orientation at vertex 75441(75440) with faces 150460 and 269634 defective orientation at vertex 75441(76441) with faces 150460 and 269635 defective orientation at vertex 76441(75440) with faces 150460 and 270643 defective orientation at vertex 76441(75441) with faces 150460 and 269635 0.004 % of the vertices (6 vertices) exhibit an orientation change topology fixing took 52.5 minutes 0 defective edges removing intersecting faces 000: 804 intersecting 001: 127 intersecting 002: 88 intersecting 003: 47 intersecting expanding nbhd size to 2 004: 48 intersecting expanding nbhd size to 3 005: 51 intersecting 006: 48 intersecting expanding nbhd size to 4 007: 54 intersecting 008: 43 intersecting 009: 36 intersecting 010: 31 intersecting 011: 28 intersecting 012: 26 intersecting 013: 20 intersecting mris_fix_topology utimesec 3147.737471 mris_fix_topology stimesec 0.460929 mris_fix_topology ru_maxrss 485720 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 64629 mris_fix_topology ru_majflt 1 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 25594 mris_fix_topology ru_oublock 13012 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 339 mris_fix_topology ru_nivcsw 26477 FSRUNTIME@ mris_fix_topology lh 0.8748 hours 1 threads #@# Fix Topology rh Fr 23. Feb 06:43:26 CET 2018 mris_fix_topology -rusage /scratch/annadan1111/MABT1T2/test/15689_T1_fs/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 15689_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=-130 (nv=147798, nf=295856, ne=443784, g=66) 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... 14366 ambiguous faces found in tessellation segmenting defects... 44 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 32 into 26 -merging segment 35 into 26 42 defects to be corrected 0 vertices coincident reading input surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.2435 (-4.1217) -vertex loglikelihood: -5.6010 (-2.8005) -normal dot loglikelihood: -3.4856 (-3.4856) -quad curv loglikelihood: -5.9770 (-2.9885) Total Loglikelihood : -23.3071 CORRECTING DEFECT 0 (vertices=25, convex hull=25, v0=81) After retessellation of defect 0 (v0=81), euler #=-37 (139680,417139,277422) : difference with theory (-39) = -2 CORRECTING DEFECT 1 (vertices=42, convex hull=32, v0=996) After retessellation of defect 1 (v0=996), euler #=-36 (139685,417165,277444) : difference with theory (-38) = -2 CORRECTING DEFECT 2 (vertices=98, convex hull=64, v0=1190) After retessellation of defect 2 (v0=1190), euler #=-35 (139694,417219,277490) : difference with theory (-37) = -2 CORRECTING DEFECT 3 (vertices=13, convex hull=22, v0=1905) After retessellation of defect 3 (v0=1905), euler #=-34 (139694,417225,277497) : difference with theory (-36) = -2 CORRECTING DEFECT 4 (vertices=31, convex hull=35, v0=2103) After retessellation of defect 4 (v0=2103), euler #=-33 (139694,417238,277511) : difference with theory (-35) = -2 CORRECTING DEFECT 5 (vertices=35, convex hull=26, v0=2229) After retessellation of defect 5 (v0=2229), euler #=-32 (139697,417256,277527) : difference with theory (-34) = -2 CORRECTING DEFECT 6 (vertices=24, convex hull=33, v0=2913) After retessellation of defect 6 (v0=2913), euler #=-31 (139699,417272,277542) : difference with theory (-33) = -2 CORRECTING DEFECT 7 (vertices=17, convex hull=33, v0=4202) After retessellation of defect 7 (v0=4202), euler #=-30 (139700,417286,277556) : difference with theory (-32) = -2 CORRECTING DEFECT 8 (vertices=12, convex hull=20, v0=22136) After retessellation of defect 8 (v0=22136), euler #=-29 (139702,417298,277567) : difference with theory (-31) = -2 CORRECTING DEFECT 9 (vertices=10, convex hull=28, v0=22277) After retessellation of defect 9 (v0=22277), euler #=-28 (139704,417313,277581) : difference with theory (-30) = -2 CORRECTING DEFECT 10 (vertices=72, convex hull=78, v0=23092) After retessellation of defect 10 (v0=23092), euler #=-27 (139737,417447,277683) : difference with theory (-29) = -2 CORRECTING DEFECT 11 (vertices=19, convex hull=21, v0=29585) After retessellation of defect 11 (v0=29585), euler #=-26 (139739,417460,277695) : difference with theory (-28) = -2 CORRECTING DEFECT 12 (vertices=7, convex hull=26, v0=29731) After retessellation of defect 12 (v0=29731), euler #=-25 (139740,417470,277705) : difference with theory (-27) = -2 CORRECTING DEFECT 13 (vertices=90, convex hull=22, v0=38831) After retessellation of defect 13 (v0=38831), euler #=-24 (139743,417487,277720) : difference with theory (-26) = -2 CORRECTING DEFECT 14 (vertices=40, convex hull=77, v0=42651) After retessellation of defect 14 (v0=42651), euler #=-23 (139751,417543,277769) : difference with theory (-25) = -2 CORRECTING DEFECT 15 (vertices=7, convex hull=26, v0=49442) After retessellation of defect 15 (v0=49442), euler #=-22 (139753,417556,277781) : difference with theory (-24) = -2 CORRECTING DEFECT 16 (vertices=29, convex hull=61, v0=51488) After retessellation of defect 16 (v0=51488), euler #=-21 (139770,417629,277838) : difference with theory (-23) = -2 CORRECTING DEFECT 17 (vertices=10, convex hull=21, v0=57634) After retessellation of defect 17 (v0=57634), euler #=-20 (139773,417644,277851) : difference with theory (-22) = -2 CORRECTING DEFECT 18 (vertices=54, convex hull=50, v0=59227) After retessellation of defect 18 (v0=59227), euler #=-19 (139782,417689,277888) : difference with theory (-21) = -2 CORRECTING DEFECT 19 (vertices=22, convex hull=63, v0=59273) After retessellation of defect 19 (v0=59273), euler #=-18 (139791,417741,277932) : difference with theory (-20) = -2 CORRECTING DEFECT 20 (vertices=206, convex hull=179, v0=60111) After retessellation of defect 20 (v0=60111), euler #=-18 (139806,417873,278049) : difference with theory (-19) = -1 CORRECTING DEFECT 21 (vertices=2002, convex hull=611, v0=63862) XL defect detected... After retessellation of defect 21 (v0=63862), euler #=-18 (139926,418546,278602) : difference with theory (-18) = 0 CORRECTING DEFECT 22 (vertices=5, convex hull=26, v0=64631) After retessellation of defect 22 (v0=64631), euler #=-17 (139927,418554,278610) : difference with theory (-17) = 0 CORRECTING DEFECT 23 (vertices=80, convex hull=69, v0=65785) After retessellation of defect 23 (v0=65785), euler #=-16 (139944,418634,278674) : difference with theory (-16) = 0 CORRECTING DEFECT 24 (vertices=245, convex hull=62, v0=68686) After retessellation of defect 24 (v0=68686), euler #=-15 (139955,418696,278726) : difference with theory (-15) = 0 CORRECTING DEFECT 25 (vertices=37, convex hull=37, v0=73384) After retessellation of defect 25 (v0=73384), euler #=-14 (139959,418725,278752) : difference with theory (-14) = 0 CORRECTING DEFECT 26 (vertices=3502, convex hull=1095, v0=74535) XL defect detected... After retessellation of defect 26 (v0=74535), euler #=-13 (140127,419893,279753) : difference with theory (-13) = 0 CORRECTING DEFECT 27 (vertices=32, convex hull=61, v0=74855) After retessellation of defect 27 (v0=74855), euler #=-12 (140142,419961,279807) : difference with theory (-12) = 0 CORRECTING DEFECT 28 (vertices=31, convex hull=38, v0=76049) After retessellation of defect 28 (v0=76049), euler #=-11 (140144,419981,279826) : difference with theory (-11) = 0 CORRECTING DEFECT 29 (vertices=27, convex hull=82, v0=83712) After retessellation of defect 29 (v0=83712), euler #=-10 (140156,420048,279882) : difference with theory (-10) = 0 CORRECTING DEFECT 30 (vertices=36, convex hull=90, v0=86422) After retessellation of defect 30 (v0=86422), euler #=-9 (140165,420114,279940) : difference with theory (-9) = 0 CORRECTING DEFECT 31 (vertices=44, convex hull=22, v0=89948) After retessellation of defect 31 (v0=89948), euler #=-8 (140169,420135,279958) : difference with theory (-8) = 0 CORRECTING DEFECT 32 (vertices=702, convex hull=140, v0=100894) After retessellation of defect 32 (v0=100894), euler #=-7 (140189,420265,280069) : difference with theory (-7) = 0 CORRECTING DEFECT 33 (vertices=209, convex hull=272, v0=102788) After retessellation of defect 33 (v0=102788), euler #=-6 (140282,420671,280383) : difference with theory (-6) = 0 CORRECTING DEFECT 34 (vertices=14, convex hull=26, v0=112206) After retessellation of defect 34 (v0=112206), euler #=-5 (140284,420685,280396) : difference with theory (-5) = 0 CORRECTING DEFECT 35 (vertices=25, convex hull=58, v0=117040) After retessellation of defect 35 (v0=117040), euler #=-4 (140299,420755,280452) : difference with theory (-4) = 0 CORRECTING DEFECT 36 (vertices=35, convex hull=25, v0=127481) After retessellation of defect 36 (v0=127481), euler #=-3 (140301,420767,280463) : difference with theory (-3) = 0 CORRECTING DEFECT 37 (vertices=79, convex hull=46, v0=129546) After retessellation of defect 37 (v0=129546), euler #=-2 (140311,420815,280502) : difference with theory (-2) = 0 CORRECTING DEFECT 38 (vertices=60, convex hull=99, v0=130950) After retessellation of defect 38 (v0=130950), euler #=-1 (140336,420939,280602) : difference with theory (-1) = 0 CORRECTING DEFECT 39 (vertices=31, convex hull=46, v0=138051) After retessellation of defect 39 (v0=138051), euler #=0 (140353,421004,280651) : difference with theory (0) = 0 CORRECTING DEFECT 40 (vertices=27, convex hull=60, v0=139879) After retessellation of defect 40 (v0=139879), euler #=1 (140362,421053,280692) : difference with theory (1) = 0 CORRECTING DEFECT 41 (vertices=23, convex hull=65, v0=143957) After retessellation of defect 41 (v0=143957), euler #=2 (140374,421116,280744) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.28 (0.08-->20.22) (max @ vno 84054 --> 93646) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.28 (0.08-->20.22) (max @ vno 84054 --> 93646) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 210 mutations (38.0%), 342 crossovers (62.0%), 1249 vertices were eliminated building final representation... 7424 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=140374, nf=280744, ne=421116, g=0) writing corrected surface to /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 57.8 minutes 0 defective edges removing intersecting faces 000: 728 intersecting 001: 21 intersecting 002: 3 intersecting mris_fix_topology utimesec 3464.835264 mris_fix_topology stimesec 0.467928 mris_fix_topology ru_maxrss 492192 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 64720 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 25164 mris_fix_topology ru_oublock 13335 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 291 mris_fix_topology ru_nivcsw 29416 FSRUNTIME@ mris_fix_topology rh 0.9630 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 136705 - 410109 + 273406 = 2 --> 0 holes F =2V-4: 273406 = 273410-4 (0) 2E=3F: 820218 = 820218 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 140374 - 421116 + 280744 = 2 --> 0 holes F =2V-4: 280744 = 280748-4 (0) 2E=3F: 842232 = 842232 (0) total defect index = 0 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 303 intersecting 001: 119 intersecting 002: 84 intersecting 003: 40 intersecting 004: 37 intersecting expanding nbhd size to 2 005: 46 intersecting expanding nbhd size to 3 006: 46 intersecting 007: 43 intersecting 008: 33 intersecting 009: 30 intersecting 010: 29 intersecting 011: 28 intersecting 012: 26 intersecting 013: 25 intersecting 014: 20 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 207 intersecting 001: 6 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Fr 23. Feb 07:41:34 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 15689_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/test/15689_T1_fs/mri/filled.mgz... reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/brain.finalsurfs.mgz... reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/../mri/aseg.presurf.mgz... reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/wm.mgz... 20135 bright wm thresholded. 8403 bright non-wm voxels segmented. reading original surface position from /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.orig... computing class statistics... border white: 278935 voxels (1.66%) border gray 316246 voxels (1.88%) WM (102.0): 102.1 +- 5.4 [70.0 --> 110.0] GM (88.0) : 84.7 +- 12.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 74.4 (was 70) setting MAX_BORDER_WHITE to 110.4 (was 105) setting MIN_BORDER_WHITE to 87.0 (was 85) setting MAX_CSF to 61.9 (was 40) setting MAX_GRAY to 99.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 74.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 49.3 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.02-->6.88) (max @ vno 135802 --> 135900) face area 0.28 +- 0.13 (0.00-->5.63) mean absolute distance = 0.86 +- 1.19 4037 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-4.3, GM=87+-6.1 mean inside = 99.3, mean outside = 88.6 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group mean border=93.2, 170 (170) missing vertices, mean dist 0.1 [0.9 (%39.0)->0.8 (%61.0))] %52 local maxima, %43 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 0.90 +- 0.25 (0.07-->7.34) (max @ vno 135802 --> 135900) face area 0.28 +- 0.13 (0.00-->4.72) mean absolute distance = 0.52 +- 0.97 4707 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1580019.1, rms=6.122 001: dt: 0.5000, sse=994380.6, rms=4.114 (32.790%) 002: dt: 0.5000, sse=763004.2, rms=2.860 (30.488%) 003: dt: 0.5000, sse=674683.6, rms=2.177 (23.871%) 004: dt: 0.5000, sse=638101.3, rms=1.826 (16.147%) 005: dt: 0.5000, sse=625985.1, rms=1.655 (9.365%) 006: dt: 0.5000, sse=616649.6, rms=1.568 (5.214%) rms = 1.52, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=613160.7, rms=1.521 (3.033%) 008: dt: 0.2500, sse=594123.1, rms=1.194 (21.517%) rms = 1.15, time step reduction 2 of 3 to 0.125... 009: dt: 0.2500, sse=592282.2, rms=1.154 (3.339%) rms = 1.14, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=591167.2, rms=1.141 (1.122%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=94.6, 56 (21) missing vertices, mean dist -0.3 [0.7 (%61.6)->0.3 (%38.4))] %64 local maxima, %31 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 0.89 +- 0.25 (0.08-->7.24) (max @ vno 135802 --> 135900) face area 0.34 +- 0.16 (0.00-->5.63) mean absolute distance = 0.45 +- 0.68 4495 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=844040.9, rms=2.642 011: dt: 0.5000, sse=741519.1, rms=1.744 (33.992%) 012: dt: 0.5000, sse=711929.3, rms=1.396 (19.981%) 013: dt: 0.5000, sse=701593.9, rms=1.253 (10.224%) 014: dt: 0.5000, sse=703851.8, rms=1.178 (5.988%) rms = 1.19, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=691704.1, rms=1.055 (10.409%) 016: dt: 0.2500, sse=688821.4, rms=0.997 (5.523%) rms = 0.98, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=690360.4, rms=0.982 (1.499%) rms = 0.97, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=687081.9, rms=0.974 (0.786%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=96.1, 77 (13) missing vertices, mean dist -0.3 [0.5 (%66.6)->0.3 (%33.4))] %77 local maxima, %17 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 0.88 +- 0.25 (0.05-->7.15) (max @ vno 135802 --> 135900) face area 0.33 +- 0.16 (0.00-->5.40) mean absolute distance = 0.35 +- 0.50 4404 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=802227.6, rms=2.476 019: dt: 0.5000, sse=704805.2, rms=1.470 (40.605%) 020: dt: 0.5000, sse=679633.1, rms=1.141 (22.429%) 021: dt: 0.5000, sse=675069.1, rms=1.063 (6.800%) rms = 1.04, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=671859.0, rms=1.041 (2.113%) 023: dt: 0.2500, sse=667860.6, rms=0.899 (13.589%) rms = 0.89, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=665868.2, rms=0.890 (1.059%) rms = 0.88, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=668055.2, rms=0.884 (0.625%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=96.8, 70 (10) missing vertices, mean dist -0.1 [0.4 (%57.5)->0.3 (%42.5))] %83 local maxima, %11 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/test/15689_T1_fs/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=681844.5, rms=1.368 026: dt: 0.5000, sse=649510.3, rms=0.801 (41.448%) rms = 0.89, time step reduction 1 of 3 to 0.250... rms = 0.76, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=645181.9, rms=0.755 (5.681%) rms = 0.74, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=644591.5, rms=0.741 (1.936%) positioning took 0.3 minutes generating cortex label... 9 non-cortical segments detected only using segment with 8671 vertices erasing segment 1 (vno[0] = 78464) erasing segment 2 (vno[0] = 78541) erasing segment 3 (vno[0] = 83882) erasing segment 4 (vno[0] = 102564) erasing segment 5 (vno[0] = 102605) erasing segment 6 (vno[0] = 104421) erasing segment 7 (vno[0] = 106271) erasing segment 8 (vno[0] = 106305) writing cortex label to /scratch/annadan1111/MABT1T2/test/15689_T1_fs/label/lh.cortex.label... writing curvature file /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.curv writing smoothed area to lh.area writing curvature file /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.area vertex spacing 0.87 +- 0.26 (0.02-->7.09) (max @ vno 135802 --> 135900) face area 0.32 +- 0.16 (0.00-->5.30) refinement took 4.5 minutes #-------------------------------------------- #@# Make White Surf rh Fr 23. Feb 07:46:04 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 15689_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/test/15689_T1_fs/mri/filled.mgz... reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/brain.finalsurfs.mgz... reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/../mri/aseg.presurf.mgz... reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/wm.mgz... 20135 bright wm thresholded. 8403 bright non-wm voxels segmented. reading original surface position from /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.orig... computing class statistics... border white: 278935 voxels (1.66%) border gray 316246 voxels (1.88%) WM (102.0): 102.1 +- 5.4 [70.0 --> 110.0] GM (88.0) : 84.7 +- 12.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 77.4 (was 70) setting MAX_BORDER_WHITE to 109.4 (was 105) setting MIN_BORDER_WHITE to 90.0 (was 85) setting MAX_CSF to 64.9 (was 40) setting MAX_GRAY to 98.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 77.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 52.3 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.02-->6.57) (max @ vno 93253 --> 95293) face area 0.28 +- 0.13 (0.00-->8.37) mean absolute distance = 0.77 +- 1.09 4344 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=90+-7.0 mean inside = 99.0, mean outside = 89.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=95.0, 209 (209) missing vertices, mean dist -0.0 [0.9 (%45.0)->0.7 (%55.0))] %47 local maxima, %48 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 0.88 +- 0.25 (0.05-->9.16) (max @ vno 93253 --> 95293) face area 0.28 +- 0.14 (0.00-->10.37) mean absolute distance = 0.52 +- 0.93 5443 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1583717.1, rms=6.068 001: dt: 0.5000, sse=1014243.9, rms=4.102 (32.396%) 002: dt: 0.5000, sse=783309.9, rms=2.828 (31.070%) 003: dt: 0.5000, sse=687148.7, rms=2.117 (25.120%) 004: dt: 0.5000, sse=649319.0, rms=1.741 (17.755%) 005: dt: 0.5000, sse=645715.9, rms=1.619 (7.062%) 006: dt: 0.5000, sse=625984.5, rms=1.489 (8.009%) 007: dt: 0.5000, sse=621665.7, rms=1.420 (4.604%) 008: dt: 0.5000, sse=616647.5, rms=1.368 (3.711%) rms = 1.35, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=615553.7, rms=1.348 (1.413%) 010: dt: 0.2500, sse=603268.1, rms=1.098 (18.534%) rms = 1.06, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=601258.2, rms=1.060 (3.540%) rms = 1.06, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=599299.9, rms=1.057 (0.283%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=96.1, 120 (46) missing vertices, mean dist -0.3 [0.7 (%58.8)->0.3 (%41.2))] %60 local maxima, %34 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 0.87 +- 0.25 (0.05-->9.36) (max @ vno 93253 --> 95293) face area 0.33 +- 0.17 (0.00-->12.41) mean absolute distance = 0.45 +- 0.66 5014 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=802961.2, rms=2.349 013: dt: 0.5000, sse=733240.8, rms=1.625 (30.805%) 014: dt: 0.5000, sse=705537.4, rms=1.332 (18.038%) 015: dt: 0.5000, sse=706195.9, rms=1.224 (8.088%) 016: dt: 0.5000, sse=697618.0, rms=1.157 (5.517%) rms = 1.17, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=687861.9, rms=1.064 (8.053%) rms = 1.02, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=693543.4, rms=1.020 (4.124%) rms = 1.01, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=685947.1, rms=1.007 (1.207%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=97.4, 113 (30) missing vertices, mean dist -0.3 [0.6 (%64.4)->0.3 (%35.6))] %74 local maxima, %21 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 0.86 +- 0.25 (0.05-->9.35) (max @ vno 93253 --> 95293) face area 0.32 +- 0.17 (0.00-->12.19) mean absolute distance = 0.36 +- 0.49 4930 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=764203.7, rms=2.158 020: dt: 0.5000, sse=696823.9, rms=1.363 (36.818%) 021: dt: 0.5000, sse=675684.2, rms=1.107 (18.761%) 022: dt: 0.5000, sse=686674.6, rms=1.052 (4.997%) rms = 1.03, time step reduction 1 of 3 to 0.250... 023: dt: 0.5000, sse=675351.9, rms=1.030 (2.071%) 024: dt: 0.2500, sse=666524.1, rms=0.927 (10.005%) rms = 0.92, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=665529.7, rms=0.924 (0.356%) rms = 0.91, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=665472.3, rms=0.914 (1.031%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=98.0, 133 (21) missing vertices, mean dist -0.1 [0.4 (%56.6)->0.3 (%43.4))] %80 local maxima, %15 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/test/15689_T1_fs/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=673503.4, rms=1.301 027: dt: 0.5000, sse=653753.1, rms=0.833 (36.010%) rms = 0.90, time step reduction 1 of 3 to 0.250... rms = 0.80, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=646939.8, rms=0.798 (4.194%) rms = 0.79, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=646076.8, rms=0.786 (1.434%) positioning took 0.4 minutes generating cortex label... 6 non-cortical segments detected only using segment with 8318 vertices erasing segment 1 (vno[0] = 49822) erasing segment 2 (vno[0] = 104978) erasing segment 3 (vno[0] = 107990) erasing segment 4 (vno[0] = 108782) erasing segment 5 (vno[0] = 112036) writing cortex label to /scratch/annadan1111/MABT1T2/test/15689_T1_fs/label/rh.cortex.label... writing curvature file /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.curv writing smoothed area to rh.area writing curvature file /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.area vertex spacing 0.86 +- 0.26 (0.03-->9.34) (max @ vno 93253 --> 95293) face area 0.31 +- 0.17 (0.00-->11.92) refinement took 4.5 minutes #-------------------------------------------- #@# Smooth2 lh Fr 23. Feb 07:50:33 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 Fr 23. Feb 07:50:38 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 Fr 23. Feb 07:50:43 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts mris_inflate -rusage /scratch/annadan1111/MABT1T2/test/15689_T1_fs/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 50.0 mm, total surface area = 80587 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.167 (target=0.015) step 005: RMS=0.117 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.071 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. inflation took 0.5 minutes mris_inflate utimesec 32.560050 mris_inflate stimesec 0.065989 mris_inflate ru_maxrss 176032 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 23078 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 10639 mris_inflate ru_oublock 10684 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 110 mris_inflate ru_nivcsw 188 #-------------------------------------------- #@# Inflation2 rh Fr 23. Feb 07:51:16 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts mris_inflate -rusage /scratch/annadan1111/MABT1T2/test/15689_T1_fs/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 49.5 mm, total surface area = 79722 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.166 (target=0.015) step 005: RMS=0.118 (target=0.015) step 010: RMS=0.091 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.054 (target=0.015) step 030: RMS=0.046 (target=0.015) step 035: RMS=0.040 (target=0.015) step 040: RMS=0.034 (target=0.015) step 045: RMS=0.032 (target=0.015) step 050: RMS=0.029 (target=0.015) step 055: RMS=0.027 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. inflation took 0.6 minutes mris_inflate utimesec 33.472911 mris_inflate stimesec 0.060990 mris_inflate ru_maxrss 180712 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 23736 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 10897 mris_inflate ru_oublock 10971 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 101 mris_inflate ru_nivcsw 187 #-------------------------------------------- #@# Curv .H and .K lh Fr 23. Feb 07:51:49 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf mris_curvature -w lh.white.preaparc total integrated curvature = 0.064*4pi (0.805) --> 1 handles ICI = 154.6, FI = 1426.3, variation=23165.630 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 182 vertices thresholded to be in k1 ~ [-0.42 0.79], k2 ~ [-0.15 0.08] total integrated curvature = 0.551*4pi (6.921) --> 0 handles ICI = 1.4, FI = 9.5, variation=158.327 115 vertices thresholded to be in [-0.03 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 112 vertices thresholded to be in [-0.19 0.23] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.023 done. #-------------------------------------------- #@# Curv .H and .K rh Fr 23. Feb 07:53:12 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf mris_curvature -w rh.white.preaparc total integrated curvature = 8.697*4pi (109.285) --> -8 handles ICI = 177.9, FI = 1484.8, variation=24609.027 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 158 vertices thresholded to be in k1 ~ [-0.27 0.69], k2 ~ [-0.17 0.10] total integrated curvature = 0.484*4pi (6.086) --> 1 handles ICI = 1.4, FI = 9.6, variation=161.623 148 vertices thresholded to be in [-0.04 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 135 vertices thresholded to be in [-0.14 0.26] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.024 done. #----------------------------------------- #@# Curvature Stats lh Fr 23. Feb 07:54:37 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 15689_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 [ 15689_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 [ 233 ] Gb_filter = 0 WARN: S lookup min: -0.136033 WARN: S explicit min: 0.000000 vertex = 1189 #----------------------------------------- #@# Curvature Stats rh Fr 23. Feb 07:54:41 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 15689_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 [ 15689_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 [ 254 ] Gb_filter = 0 WARN: S lookup min: -0.426702 WARN: S explicit min: 0.000000 vertex = 102 #-------------------------------------------- #@# Sphere lh Fr 23. Feb 07:54:44 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts mris_sphere -rusage /scratch/annadan1111/MABT1T2/test/15689_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 0.310... 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 %18.06 pass 1: epoch 2 of 3 starting distance error %18.06 unfolding complete - removing small folds... starting distance error %17.99 removing remaining folds... final distance error %18.01 MRISunfold() return, current seed 1234 -01: dt=0.0000, 125 negative triangles 206: dt=0.9900, 125 negative triangles 207: dt=0.9900, 51 negative triangles 208: dt=0.9900, 32 negative triangles 209: dt=0.9900, 27 negative triangles 210: dt=0.9900, 19 negative triangles 211: dt=0.9900, 13 negative triangles 212: dt=0.9900, 16 negative triangles 213: dt=0.9900, 8 negative triangles 214: dt=0.9900, 12 negative triangles 215: dt=0.9900, 6 negative triangles 216: dt=0.9900, 7 negative triangles 217: dt=0.9900, 5 negative triangles 218: dt=0.9900, 5 negative triangles 219: dt=0.9900, 4 negative triangles 220: dt=0.9900, 8 negative triangles 221: dt=0.9900, 5 negative triangles 222: dt=0.9900, 3 negative triangles 223: dt=0.9900, 2 negative triangles 224: dt=0.9900, 3 negative triangles 225: dt=0.9900, 2 negative triangles 226: dt=0.9900, 1 negative triangles 227: dt=0.9900, 2 negative triangles 228: dt=0.9900, 1 negative triangles 229: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.76 hours mris_sphere utimesec 2746.868412 mris_sphere stimesec 0.491925 mris_sphere ru_maxrss 243124 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 39709 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 15760 mris_sphere ru_oublock 9617 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 97 mris_sphere ru_nivcsw 20455 FSRUNTIME@ mris_sphere 0.7634 hours 1 threads #-------------------------------------------- #@# Sphere rh Fr 23. Feb 08:40:33 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts mris_sphere -rusage /scratch/annadan1111/MABT1T2/test/15689_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 0.315... 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 %17.85 pass 1: epoch 2 of 3 starting distance error %17.81 unfolding complete - removing small folds... starting distance error %17.73 removing remaining folds... final distance error %17.74 MRISunfold() return, current seed 1234 -01: dt=0.0000, 390 negative triangles 197: dt=0.9900, 390 negative triangles 198: dt=0.9900, 229 negative triangles 199: dt=0.9900, 193 negative triangles 200: dt=0.9900, 165 negative triangles 201: dt=0.9900, 152 negative triangles 202: dt=0.9900, 139 negative triangles 203: dt=0.9900, 132 negative triangles 204: dt=0.9900, 128 negative triangles 205: dt=0.9900, 128 negative triangles 206: dt=0.9900, 114 negative triangles 207: dt=0.9900, 117 negative triangles 208: dt=0.9900, 101 negative triangles 209: dt=0.9900, 114 negative triangles 210: dt=0.9900, 99 negative triangles 211: dt=0.9900, 109 negative triangles 212: dt=0.9900, 83 negative triangles 213: dt=0.9900, 90 negative triangles 214: dt=0.9900, 77 negative triangles 215: dt=0.9900, 82 negative triangles 216: dt=0.9900, 76 negative triangles 217: dt=0.9900, 63 negative triangles 218: dt=0.9900, 51 negative triangles 219: dt=0.9900, 47 negative triangles 220: dt=0.9900, 40 negative triangles 221: dt=0.9900, 39 negative triangles 222: dt=0.9900, 29 negative triangles 223: dt=0.9900, 24 negative triangles 224: dt=0.9900, 24 negative triangles 225: dt=0.9900, 22 negative triangles 226: dt=0.9900, 18 negative triangles 227: dt=0.9900, 16 negative triangles 228: dt=0.9900, 13 negative triangles 229: dt=0.9900, 12 negative triangles 230: dt=0.9900, 14 negative triangles 231: dt=0.9900, 8 negative triangles 232: dt=0.9900, 3 negative triangles 233: dt=0.9900, 4 negative triangles 234: dt=0.9900, 3 negative triangles 235: dt=0.9900, 1 negative triangles 236: dt=0.9900, 1 negative triangles 237: dt=0.9900, 1 negative triangles 238: dt=0.9900, 1 negative triangles 239: dt=0.9900, 2 negative triangles 240: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.87 hours mris_sphere utimesec 3124.671977 mris_sphere stimesec 0.527919 mris_sphere ru_maxrss 248300 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 40762 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 16018 mris_sphere ru_oublock 9875 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 110 mris_sphere ru_nivcsw 23565 FSRUNTIME@ mris_sphere 0.8684 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Fr 23. Feb 09:32:39 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts mris_register -curv -rusage /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_T1_fs/scripts cmdline mris_register -curv -rusage /scratch/annadan1111/MABT1T2/test/15689_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 = 5.332 curvature mean = 0.035, std = 0.822 curvature mean = 0.022, std = 0.868 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 275393.2, tmin=1.0413 d=32.00 min @ (0.00, 0.00, -8.00) sse = 227695.9, tmin=2.1069 d=16.00 min @ (4.00, 4.00, 0.00) sse = 197186.2, tmin=3.1825 d=8.00 min @ (0.00, 0.00, 2.00) sse = 187786.3, tmin=4.2923 d=4.00 min @ (-1.00, -1.00, 0.00) sse = 186196.5, tmin=5.4133 d=2.00 min @ (0.50, 0.00, 0.00) sse = 185949.2, tmin=6.5393 d=1.00 min @ (0.00, 0.25, 0.00) sse = 185740.0, tmin=7.6547 d=0.50 min @ (0.00, 0.00, 0.12) sse = 185722.1, tmin=8.7652 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 8.77 min curvature mean = -0.004, std = 0.843 curvature mean = 0.008, std = 0.953 curvature mean = -0.008, std = 0.854 curvature mean = 0.003, std = 0.982 curvature mean = -0.009, std = 0.856 curvature mean = 0.001, std = 0.993 2 Reading smoothwm curvature mean = -0.031, std = 0.264 curvature mean = 0.035, std = 0.250 curvature mean = 0.060, std = 0.379 curvature mean = 0.030, std = 0.308 curvature mean = 0.029, std = 0.570 curvature mean = 0.029, std = 0.333 curvature mean = 0.016, std = 0.707 curvature mean = 0.028, std = 0.344 curvature mean = 0.005, std = 0.808 MRISregister() return, current seed 0 -01: dt=0.0000, 72 negative triangles 112: dt=0.9900, 72 negative triangles expanding nbhd size to 1 113: dt=0.9900, 87 negative triangles 114: dt=0.9900, 69 negative triangles 115: dt=0.9900, 68 negative triangles 116: dt=0.9900, 64 negative triangles 117: dt=0.9900, 63 negative triangles 118: dt=0.9900, 59 negative triangles 119: dt=0.9900, 55 negative triangles 120: dt=0.9900, 58 negative triangles 121: dt=0.9900, 53 negative triangles 122: dt=0.9900, 52 negative triangles 123: dt=0.9900, 52 negative triangles 124: dt=0.9900, 50 negative triangles 125: dt=0.9900, 48 negative triangles 126: dt=0.9900, 50 negative triangles 127: dt=0.9900, 50 negative triangles 128: dt=0.9900, 52 negative triangles 129: dt=0.9900, 52 negative triangles 130: dt=0.9900, 51 negative triangles 131: dt=0.9900, 51 negative triangles 132: dt=0.9900, 49 negative triangles 133: dt=0.9900, 48 negative triangles 134: dt=0.9900, 45 negative triangles 135: dt=0.9900, 43 negative triangles 136: dt=0.9900, 42 negative triangles 137: dt=0.9900, 44 negative triangles 138: dt=0.9900, 44 negative triangles 139: dt=0.9900, 49 negative triangles 140: dt=0.9900, 48 negative triangles 141: dt=0.9900, 47 negative triangles 142: dt=0.9900, 47 negative triangles 143: dt=0.9900, 46 negative triangles 144: dt=0.9900, 47 negative triangles 145: dt=0.9900, 44 negative triangles 146: dt=0.9405, 42 negative triangles 147: dt=0.9405, 41 negative triangles 148: dt=0.9405, 41 negative triangles 149: dt=0.9405, 39 negative triangles 150: dt=0.9405, 38 negative triangles 151: dt=0.9405, 38 negative triangles 152: dt=0.9405, 41 negative triangles 153: dt=0.9405, 37 negative triangles 154: dt=0.9405, 39 negative triangles 155: dt=0.9405, 38 negative triangles 156: dt=0.9405, 34 negative triangles 157: dt=0.9405, 33 negative triangles 158: dt=0.9405, 34 negative triangles 159: dt=0.9405, 31 negative triangles 160: dt=0.9405, 34 negative triangles 161: dt=0.9405, 31 negative triangles 162: dt=0.9405, 32 negative triangles 163: dt=0.9405, 29 negative triangles 164: dt=0.9405, 30 negative triangles 165: dt=0.9405, 26 negative triangles 166: dt=0.9405, 28 negative triangles 167: dt=0.9405, 26 negative triangles 168: dt=0.9405, 27 negative triangles 169: dt=0.9405, 26 negative triangles 170: dt=0.9405, 28 negative triangles 171: dt=0.9405, 28 negative triangles 172: dt=0.9405, 26 negative triangles 173: dt=0.9405, 25 negative triangles 174: dt=0.9405, 23 negative triangles 175: dt=0.9405, 22 negative triangles 176: dt=0.9405, 23 negative triangles 177: dt=0.9405, 23 negative triangles 178: dt=0.9405, 21 negative triangles 179: dt=0.9405, 21 negative triangles 180: dt=0.9405, 21 negative triangles 181: dt=0.9405, 20 negative triangles 182: dt=0.9405, 20 negative triangles 183: dt=0.9405, 19 negative triangles 184: dt=0.9405, 19 negative triangles 185: dt=0.9405, 18 negative triangles 186: dt=0.9405, 17 negative triangles 187: dt=0.9405, 17 negative triangles 188: dt=0.9405, 17 negative triangles 189: dt=0.9405, 17 negative triangles 190: dt=0.9405, 17 negative triangles 191: dt=0.9405, 17 negative triangles 192: dt=0.9405, 16 negative triangles 193: dt=0.9405, 14 negative triangles 194: dt=0.9405, 14 negative triangles 195: dt=0.9405, 13 negative triangles 196: dt=0.9405, 13 negative triangles 197: dt=0.9405, 13 negative triangles 198: dt=0.9405, 11 negative triangles 199: dt=0.9405, 11 negative triangles 200: dt=0.9405, 12 negative triangles 201: dt=0.9405, 10 negative triangles 202: dt=0.9405, 9 negative triangles 203: dt=0.9405, 9 negative triangles 204: dt=0.9405, 9 negative triangles 205: dt=0.9405, 11 negative triangles 206: dt=0.9405, 10 negative triangles 207: dt=0.9405, 10 negative triangles 208: dt=0.9405, 9 negative triangles 209: dt=0.9405, 5 negative triangles 210: dt=0.9405, 5 negative triangles 211: dt=0.9405, 5 negative triangles 212: dt=0.9405, 5 negative triangles 213: dt=0.9405, 6 negative triangles 214: dt=0.9405, 3 negative triangles 215: dt=0.9405, 2 negative triangles 216: dt=0.9405, 2 negative triangles 217: dt=0.9405, 2 negative triangles 218: dt=0.9405, 2 negative triangles 219: dt=0.9405, 3 negative triangles 220: dt=0.9405, 2 negative triangles 221: dt=0.9405, 2 negative triangles 222: dt=0.9405, 2 negative triangles 223: dt=0.9405, 2 negative triangles 224: dt=0.9405, 1 negative triangles 225: dt=0.9405, 1 negative triangles 226: dt=0.9405, 1 negative triangles 227: dt=0.9405, 1 negative triangles 228: dt=0.9405, 1 negative triangles 229: dt=0.9405, 1 negative triangles 230: dt=0.9405, 1 negative triangles 231: dt=0.9405, 1 negative triangles 232: dt=0.9405, 1 negative triangles 233: dt=0.9405, 1 negative triangles 234: dt=0.8935, 1 negative triangles 235: dt=0.8935, 1 negative triangles 236: dt=0.8935, 1 negative triangles 237: dt=0.8935, 1 negative triangles 238: dt=0.8935, 1 negative triangles 239: dt=0.8935, 1 negative triangles 240: dt=0.8935, 1 negative triangles 241: dt=0.8935, 1 negative triangles 242: dt=0.8935, 1 negative triangles 243: dt=0.8935, 1 negative triangles 244: dt=0.8488, 1 negative triangles 245: dt=0.8488, 1 negative triangles 246: dt=0.8488, 1 negative triangles 247: dt=0.8488, 1 negative triangles 248: dt=0.8488, 1 negative triangles 249: dt=0.8488, 1 negative triangles 250: dt=0.8488, 1 negative triangles 251: dt=0.8488, 1 negative triangles 252: dt=0.8488, 1 negative triangles 253: dt=0.8488, 1 negative triangles 254: dt=0.8064, 1 negative triangles 255: dt=0.8064, 1 negative triangles 256: dt=0.8064, 1 negative triangles 257: dt=0.8064, 1 negative triangles 258: dt=0.8064, 1 negative triangles 259: dt=0.8064, 1 negative triangles 260: dt=0.8064, 1 negative triangles 261: dt=0.8064, 1 negative triangles 262: dt=0.8064, 1 negative triangles 263: dt=0.8064, 1 negative triangles 264: dt=0.7660, 1 negative triangles 265: dt=0.7660, 1 negative triangles 266: dt=0.7660, 1 negative triangles 267: dt=0.7660, 1 negative triangles 268: dt=0.7660, 1 negative triangles 269: dt=0.7660, 1 negative triangles 270: dt=0.7660, 1 negative triangles 271: dt=0.7660, 1 negative triangles 272: dt=0.7660, 1 negative triangles 273: dt=0.7660, 1 negative triangles 274: dt=0.7277, 1 negative triangles 275: dt=0.7277, 1 negative triangles 276: dt=0.7277, 1 negative triangles 277: dt=0.7277, 1 negative triangles 278: dt=0.7277, 1 negative triangles 279: dt=0.7277, 1 negative triangles 280: dt=0.7277, 1 negative triangles 281: dt=0.7277, 1 negative triangles 282: dt=0.7277, 1 negative triangles 283: dt=0.7277, 1 negative triangles 284: dt=0.6914, 1 negative triangles 285: dt=0.6914, 1 negative triangles 286: dt=0.6914, 1 negative triangles 287: dt=0.6914, 1 negative triangles 288: dt=0.6914, 1 negative triangles 289: dt=0.6914, 1 negative triangles 290: dt=0.6914, 1 negative triangles 291: dt=0.6914, 1 negative triangles 292: dt=0.6914, 1 negative triangles 293: dt=0.6914, 1 negative triangles 294: dt=0.6568, 1 negative triangles 295: dt=0.6568, 1 negative triangles 296: dt=0.6568, 1 negative triangles 297: dt=0.6568, 1 negative triangles 298: dt=0.6568, 1 negative triangles 299: dt=0.6568, 1 negative triangles 300: dt=0.6568, 1 negative triangles 301: dt=0.6568, 1 negative triangles 302: dt=0.6568, 1 negative triangles 303: dt=0.6568, 1 negative triangles 304: dt=0.6239, 1 negative triangles 305: dt=0.6239, 1 negative triangles 306: dt=0.6239, 1 negative triangles 307: dt=0.6239, 1 negative triangles 308: dt=0.6239, 1 negative triangles 309: dt=0.6239, 1 negative triangles 310: dt=0.6239, 1 negative triangles 311: dt=0.6239, 1 negative triangles 312: dt=0.6239, 1 negative triangles 313: dt=0.6239, 1 negative triangles 314: dt=0.5927, 1 negative triangles 315: dt=0.5927, 1 negative triangles 316: dt=0.5927, 1 negative triangles 317: dt=0.5927, 1 negative triangles 318: dt=0.5927, 1 negative triangles 319: dt=0.5927, 1 negative triangles 320: dt=0.5927, 1 negative triangles 321: dt=0.5927, 1 negative triangles 322: dt=0.5927, 1 negative triangles 323: dt=0.5927, 1 negative triangles 324: dt=0.5631, 1 negative triangles 325: dt=0.5631, 1 negative triangles 326: dt=0.5631, 1 negative triangles 327: dt=0.5631, 1 negative triangles 328: dt=0.5631, 1 negative triangles 329: dt=0.5631, 1 negative triangles 330: dt=0.5631, 1 negative triangles 331: dt=0.5631, 1 negative triangles 332: dt=0.5631, 1 negative triangles 333: dt=0.5631, 1 negative triangles 334: dt=0.5350, 1 negative triangles 335: dt=0.5350, 1 negative triangles 336: dt=0.5350, 1 negative triangles 337: dt=0.5350, 1 negative triangles 338: dt=0.5350, 1 negative triangles 339: dt=0.5350, 1 negative triangles 340: dt=0.5350, 1 negative triangles 341: dt=0.5350, 1 negative triangles 342: dt=0.5350, 1 negative triangles 343: dt=0.5350, 1 negative triangles 344: dt=0.5082, 1 negative triangles 345: dt=0.5082, 1 negative triangles 346: dt=0.5082, 1 negative triangles 347: dt=0.5082, 1 negative triangles 348: dt=0.5082, 1 negative triangles 349: dt=0.5082, 1 negative triangles 350: dt=0.5082, 1 negative triangles 351: dt=0.5082, 1 negative triangles 352: dt=0.5082, 1 negative triangles 353: dt=0.5082, 1 negative triangles 354: dt=0.4828, 1 negative triangles 355: dt=0.4828, 1 negative triangles 356: dt=0.4828, 1 negative triangles 357: dt=0.4828, 1 negative triangles 358: dt=0.4828, 1 negative triangles 359: dt=0.4828, 1 negative triangles 360: dt=0.4828, 1 negative triangles 361: dt=0.4828, 1 negative triangles 362: dt=0.4828, 1 negative triangles 363: dt=0.4828, 1 negative triangles 364: dt=0.4587, 1 negative triangles 365: dt=0.4587, 1 negative triangles 366: dt=0.4587, 1 negative triangles 367: dt=0.4587, 1 negative triangles 368: dt=0.4587, 1 negative triangles 369: dt=0.4587, 1 negative triangles 370: dt=0.4587, 1 negative triangles 371: dt=0.4587, 1 negative triangles 372: dt=0.4587, 1 negative triangles 373: dt=0.4587, 1 negative triangles 374: dt=0.4357, 1 negative triangles 375: dt=0.4357, 1 negative triangles 376: dt=0.4357, 1 negative triangles 377: dt=0.4357, 1 negative triangles 378: dt=0.4357, 1 negative triangles 379: dt=0.4357, 1 negative triangles 380: dt=0.4357, 1 negative triangles 381: dt=0.4357, 1 negative triangles 382: dt=0.4357, 1 negative triangles 383: dt=0.4357, 1 negative triangles 384: dt=0.4139, 1 negative triangles 385: dt=0.4139, 1 negative triangles 386: dt=0.4139, 1 negative triangles 387: dt=0.4139, 1 negative triangles 388: dt=0.4139, 1 negative triangles 389: dt=0.4139, 1 negative triangles 390: dt=0.4139, 1 negative triangles 391: dt=0.4139, 1 negative triangles 392: dt=0.4139, 1 negative triangles 393: dt=0.4139, 1 negative triangles 394: dt=0.3932, 1 negative triangles 395: dt=0.3932, 1 negative triangles 396: dt=0.3932, 1 negative triangles 397: dt=0.3932, 1 negative triangles 398: dt=0.3932, 1 negative triangles 399: dt=0.3932, 1 negative triangles 400: dt=0.3932, 1 negative triangles 401: dt=0.3932, 1 negative triangles 402: dt=0.3932, 1 negative triangles 403: dt=0.3932, 1 negative triangles 404: dt=0.3736, 1 negative triangles 405: dt=0.3736, 1 negative triangles 406: dt=0.3736, 1 negative triangles 407: dt=0.3736, 1 negative triangles 408: dt=0.3736, 1 negative triangles 409: dt=0.3736, 1 negative triangles 410: dt=0.3736, 1 negative triangles 411: dt=0.3736, 1 negative triangles 412: dt=0.3736, 1 negative triangles 413: dt=0.3736, 1 negative triangles 414: dt=0.3549, 1 negative triangles 415: dt=0.3549, 1 negative triangles 416: dt=0.3549, 1 negative triangles 417: dt=0.3549, 1 negative triangles 418: dt=0.3549, 1 negative triangles 419: dt=0.3549, 1 negative triangles 420: dt=0.3549, 1 negative triangles 421: dt=0.3549, 1 negative triangles 422: dt=0.3549, 1 negative triangles 423: dt=0.3549, 1 negative triangles 424: dt=0.3372, 1 negative triangles 425: dt=0.3372, 1 negative triangles 426: dt=0.3372, 1 negative triangles 427: dt=0.3372, 1 negative triangles 428: dt=0.3372, 1 negative triangles 429: dt=0.3372, 1 negative triangles 430: dt=0.3372, 1 negative triangles 431: dt=0.3372, 1 negative triangles 432: dt=0.3372, 1 negative triangles 433: dt=0.3372, 1 negative triangles 434: dt=0.3203, 1 negative triangles 435: dt=0.3203, 1 negative triangles 436: dt=0.3203, 1 negative triangles 437: dt=0.3203, 1 negative triangles 438: dt=0.3203, 1 negative triangles 439: dt=0.3203, 1 negative triangles 440: dt=0.3203, 1 negative triangles 441: dt=0.3203, 1 negative triangles 442: dt=0.3203, 1 negative triangles 443: dt=0.3203, 1 negative triangles 444: dt=0.3043, 1 negative triangles 445: dt=0.3043, 1 negative triangles 446: dt=0.3043, 1 negative triangles 447: dt=0.3043, 1 negative triangles 448: dt=0.3043, 1 negative triangles 449: dt=0.3043, 1 negative triangles 450: dt=0.3043, 1 negative triangles 451: dt=0.3043, 1 negative triangles 452: dt=0.3043, 1 negative triangles 453: dt=0.3043, 1 negative triangles 454: dt=0.2891, 1 negative triangles 455: dt=0.2891, 1 negative triangles 456: dt=0.2891, 1 negative triangles 457: dt=0.2891, 1 negative triangles 458: dt=0.2891, 1 negative triangles 459: dt=0.2891, 1 negative triangles 460: dt=0.2891, 1 negative triangles 461: dt=0.2891, 1 negative triangles 462: dt=0.2891, 1 negative triangles 463: dt=0.2891, 1 negative triangles 464: dt=0.2746, 1 negative triangles 465: dt=0.2746, 1 negative triangles 466: dt=0.2746, 1 negative triangles 467: dt=0.2746, 1 negative triangles 468: dt=0.2746, 1 negative triangles 469: dt=0.2746, 1 negative triangles 470: dt=0.2746, 1 negative triangles 471: dt=0.2746, 1 negative triangles 472: dt=0.2746, 1 negative triangles 473: dt=0.2746, 1 negative triangles 474: dt=0.2609, 1 negative triangles 475: dt=0.2609, 1 negative triangles 476: dt=0.2609, 1 negative triangles 477: dt=0.2609, 1 negative triangles 478: dt=0.2609, 1 negative triangles 479: dt=0.2609, 1 negative triangles 480: dt=0.2609, 1 negative triangles 481: dt=0.2609, 1 negative triangles 482: dt=0.2609, 1 negative triangles 483: dt=0.2609, 1 negative triangles 484: dt=0.2478, 1 negative triangles 485: dt=0.2478, 1 negative triangles 486: dt=0.2478, 1 negative triangles 487: dt=0.2478, 1 negative triangles 488: dt=0.2478, 1 negative triangles 489: dt=0.2478, 1 negative triangles 490: dt=0.2478, 1 negative triangles 491: dt=0.2478, 1 negative triangles 492: dt=0.2478, 1 negative triangles 493: dt=0.2478, 1 negative triangles 494: dt=0.2354, 1 negative triangles 495: dt=0.2354, 1 negative triangles 496: dt=0.2354, 1 negative triangles 497: dt=0.2354, 1 negative triangles 498: dt=0.2354, 1 negative triangles 499: dt=0.2354, 1 negative triangles 500: dt=0.2354, 1 negative triangles 501: dt=0.2354, 1 negative triangles 502: dt=0.2354, 1 negative triangles 503: dt=0.2354, 1 negative triangles 504: dt=0.2237, 1 negative triangles 505: 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negative triangles 1018: dt=0.0164, 1 negative triangles 1019: dt=0.0164, 1 negative triangles 1020: dt=0.0164, 1 negative triangles 1021: dt=0.0164, 1 negative triangles 1022: dt=0.0164, 1 negative triangles 1023: dt=0.0164, 1 negative triangles 1024: dt=0.0155, 1 negative triangles 1025: dt=0.0155, 1 negative triangles 1026: dt=0.0155, 1 negative triangles 1027: dt=0.0155, 1 negative triangles 1028: dt=0.0155, 1 negative triangles 1029: dt=0.0155, 1 negative triangles 1030: dt=0.0155, 1 negative triangles 1031: dt=0.0155, 1 negative triangles 1032: dt=0.0155, 1 negative triangles 1033: dt=0.0155, 1 negative triangles 1034: dt=0.0148, 1 negative triangles 1035: dt=0.0148, 1 negative triangles 1036: dt=0.0148, 1 negative triangles 1037: dt=0.0148, 1 negative triangles 1038: dt=0.0148, 1 negative triangles 1039: dt=0.0148, 1 negative triangles 1040: dt=0.0148, 1 negative triangles 1041: dt=0.0148, 1 negative triangles 1042: dt=0.0148, 1 negative triangles 1043: dt=0.0148, 1 negative triangles 1044: dt=0.0140, 1 negative triangles 1045: dt=0.0140, 1 negative triangles 1046: dt=0.0140, 1 negative triangles 1047: dt=0.0140, 1 negative triangles 1048: dt=0.0140, 1 negative triangles 1049: dt=0.0140, 1 negative triangles 1050: dt=0.0140, 1 negative triangles 1051: dt=0.0140, 1 negative triangles 1052: dt=0.0140, 1 negative triangles 1053: dt=0.0140, 1 negative triangles 1054: dt=0.0133, 1 negative triangles 1055: dt=0.0133, 1 negative triangles 1056: dt=0.0133, 1 negative triangles 1057: dt=0.0133, 1 negative triangles 1058: dt=0.0133, 1 negative triangles 1059: dt=0.0133, 1 negative triangles 1060: dt=0.0133, 1 negative triangles 1061: dt=0.0133, 1 negative triangles 1062: dt=0.0133, 1 negative triangles 1063: dt=0.0133, 1 negative triangles 1064: dt=0.0127, 1 negative triangles 1065: dt=0.0127, 1 negative triangles 1066: dt=0.0127, 1 negative triangles 1067: dt=0.0127, 1 negative triangles 1068: dt=0.0127, 1 negative triangles 1069: dt=0.0127, 1 negative triangles 1070: dt=0.0127, 1 negative triangles 1071: dt=0.0127, 1 negative triangles 1072: dt=0.0127, 1 negative triangles 1073: dt=0.0127, 1 negative triangles 1074: dt=0.0120, 1 negative triangles 1075: dt=0.0120, 1 negative triangles 1076: dt=0.0120, 1 negative triangles 1077: dt=0.0120, 1 negative triangles 1078: dt=0.0120, 1 negative triangles 1079: dt=0.0120, 1 negative triangles 1080: dt=0.0120, 1 negative triangles 1081: dt=0.0120, 1 negative triangles 1082: dt=0.0120, 1 negative triangles 1083: dt=0.0120, 1 negative triangles 1084: dt=0.0114, 1 negative triangles 1085: dt=0.0114, 1 negative triangles 1086: dt=0.0114, 1 negative triangles 1087: dt=0.0114, 1 negative triangles 1088: dt=0.0114, 1 negative triangles 1089: dt=0.0114, 1 negative triangles 1090: dt=0.0114, 1 negative triangles 1091: dt=0.0114, 1 negative triangles 1092: dt=0.0114, 1 negative triangles 1093: dt=0.0114, 1 negative triangles 1094: dt=0.0108, 1 negative triangles 1095: dt=0.0108, 1 negative triangles 1096: dt=0.0108, 1 negative triangles 1097: dt=0.0108, 1 negative triangles 1098: dt=0.0108, 1 negative triangles 1099: dt=0.0108, 1 negative triangles 1100: dt=0.0108, 1 negative triangles 1101: dt=0.0108, 1 negative triangles 1102: dt=0.0108, 1 negative triangles 1103: dt=0.0108, 1 negative triangles 1104: dt=0.0103, 1 negative triangles 1105: dt=0.0103, 1 negative triangles 1106: dt=0.0103, 1 negative triangles 1107: dt=0.0103, 1 negative triangles 1108: dt=0.0103, 1 negative triangles 1109: dt=0.0103, 1 negative triangles 1110: dt=0.0103, 1 negative triangles 1111: dt=0.0103, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... 1112: dt=0.0103, 1 negative triangles 1113: 1 negative triangles registration took 1.02 hours mris_register utimesec 3682.231215 mris_register stimesec 0.827874 mris_register ru_maxrss 230876 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 30778 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 33677 mris_register ru_oublock 9618 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 211 mris_register ru_nivcsw 35762 FSRUNTIME@ mris_register 1.0235 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Fr 23. Feb 10:34:03 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts mris_register -curv -rusage /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_T1_fs/scripts cmdline mris_register -curv -rusage /scratch/annadan1111/MABT1T2/test/15689_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 = 5.328 curvature mean = 0.014, std = 0.817 curvature mean = 0.027, std = 0.872 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 357974.6, tmin=1.0679 d=32.00 min @ (-8.00, -8.00, 0.00) sse = 258415.3, tmin=2.1618 d=8.00 min @ (0.00, 0.00, -2.00) sse = 254968.2, tmin=4.3812 d=2.00 min @ (-0.50, 0.00, 0.50) sse = 254275.8, tmin=6.6086 d=1.00 min @ (0.00, -0.25, -0.25) sse = 254174.1, tmin=7.7384 d=0.50 min @ (0.00, 0.00, 0.12) sse = 254150.1, tmin=8.8914 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 8.89 min curvature mean = -0.032, std = 0.826 curvature mean = 0.010, std = 0.952 curvature mean = -0.038, std = 0.835 curvature mean = 0.003, std = 0.981 curvature mean = -0.040, std = 0.837 curvature mean = 0.001, std = 0.993 2 Reading smoothwm curvature mean = -0.040, std = 0.433 curvature mean = 0.021, std = 0.240 curvature mean = 0.056, std = 0.228 curvature mean = 0.018, std = 0.298 curvature mean = 0.031, std = 0.347 curvature mean = 0.017, std = 0.324 curvature mean = 0.019, std = 0.444 curvature mean = 0.017, std = 0.335 curvature mean = 0.008, std = 0.537 MRISregister() return, current seed 0 -01: dt=0.0000, 118 negative triangles 112: dt=0.9900, 118 negative triangles expanding nbhd size to 1 113: dt=0.9900, 148 negative triangles 114: dt=0.9900, 111 negative triangles 115: dt=0.9900, 108 negative triangles 116: dt=0.9900, 107 negative triangles 117: dt=0.9900, 105 negative triangles 118: dt=0.9900, 97 negative triangles 119: dt=0.9900, 94 negative triangles 120: dt=0.9900, 93 negative triangles 121: dt=0.9900, 88 negative triangles 122: dt=0.9900, 90 negative triangles 123: dt=0.9900, 82 negative triangles 124: dt=0.9900, 77 negative triangles 125: dt=0.9900, 72 negative triangles 126: dt=0.9900, 75 negative triangles 127: dt=0.9900, 68 negative triangles 128: dt=0.9900, 67 negative triangles 129: dt=0.9900, 62 negative triangles 130: dt=0.9900, 61 negative triangles 131: dt=0.9900, 57 negative triangles 132: dt=0.9900, 57 negative triangles 133: dt=0.9900, 54 negative triangles 134: dt=0.9900, 54 negative triangles 135: dt=0.9900, 51 negative triangles 136: dt=0.9900, 51 negative triangles 137: dt=0.9900, 49 negative triangles 138: dt=0.9900, 51 negative triangles 139: dt=0.9900, 49 negative triangles 140: dt=0.9900, 51 negative triangles 141: dt=0.9900, 53 negative triangles 142: dt=0.9900, 48 negative triangles 143: dt=0.9900, 47 negative triangles 144: dt=0.9900, 46 negative triangles 145: dt=0.9900, 46 negative triangles 146: dt=0.9900, 47 negative triangles 147: dt=0.9900, 48 negative triangles 148: dt=0.9900, 45 negative triangles 149: dt=0.9900, 46 negative triangles 150: dt=0.9900, 43 negative triangles 151: dt=0.9900, 44 negative triangles 152: dt=0.9900, 43 negative triangles 153: dt=0.9900, 45 negative triangles 154: dt=0.9900, 44 negative triangles 155: dt=0.9900, 42 negative triangles 156: dt=0.9900, 43 negative triangles 157: dt=0.9900, 43 negative triangles 158: dt=0.9900, 40 negative triangles 159: dt=0.9900, 38 negative triangles 160: dt=0.9900, 38 negative triangles 161: dt=0.9900, 39 negative triangles 162: dt=0.9900, 40 negative triangles 163: dt=0.9900, 39 negative triangles 164: dt=0.9900, 39 negative triangles 165: dt=0.9900, 38 negative triangles 166: dt=0.9900, 37 negative triangles 167: dt=0.9900, 38 negative triangles 168: dt=0.9900, 40 negative triangles 169: dt=0.9900, 40 negative triangles 170: dt=0.9900, 39 negative triangles 171: dt=0.9900, 38 negative triangles 172: dt=0.9900, 36 negative triangles 173: dt=0.9900, 36 negative triangles 174: dt=0.9900, 37 negative triangles 175: dt=0.9900, 39 negative triangles 176: dt=0.9900, 40 negative triangles 177: dt=0.9900, 41 negative triangles 178: dt=0.9900, 41 negative triangles 179: dt=0.9900, 38 negative triangles 180: dt=0.9900, 36 negative triangles 181: dt=0.9900, 35 negative triangles 182: dt=0.9900, 33 negative triangles 183: dt=0.9900, 34 negative triangles 184: dt=0.9900, 34 negative triangles 185: dt=0.9900, 36 negative triangles 186: dt=0.9900, 37 negative triangles 187: dt=0.9900, 36 negative triangles 188: dt=0.9900, 31 negative triangles 189: dt=0.9900, 29 negative triangles 190: dt=0.9900, 25 negative triangles 191: dt=0.9900, 24 negative triangles 192: dt=0.9900, 24 negative triangles 193: dt=0.9900, 25 negative triangles 194: dt=0.9900, 26 negative triangles 195: dt=0.9900, 27 negative triangles 196: dt=0.9900, 26 negative triangles 197: dt=0.9900, 27 negative triangles 198: dt=0.9900, 25 negative triangles 199: dt=0.9900, 25 negative triangles 200: dt=0.9900, 24 negative triangles 201: dt=0.9900, 23 negative triangles 202: dt=0.9900, 25 negative triangles 203: dt=0.9900, 26 negative triangles 204: dt=0.9900, 25 negative triangles 205: dt=0.9900, 25 negative triangles 206: dt=0.9900, 22 negative triangles 207: dt=0.9900, 22 negative triangles 208: dt=0.9900, 23 negative triangles 209: dt=0.9900, 25 negative triangles 210: dt=0.9900, 23 negative triangles 211: dt=0.9900, 23 negative triangles 212: dt=0.9900, 21 negative triangles 213: dt=0.9900, 20 negative triangles 214: dt=0.9900, 20 negative triangles 215: dt=0.9900, 20 negative triangles 216: dt=0.9900, 23 negative triangles 217: dt=0.9900, 23 negative triangles 218: dt=0.9900, 22 negative triangles 219: dt=0.9900, 20 negative triangles 220: dt=0.9900, 20 negative triangles 221: dt=0.9900, 19 negative triangles 222: dt=0.9900, 21 negative triangles 223: dt=0.9900, 22 negative triangles 224: dt=0.9900, 19 negative triangles 225: dt=0.9900, 19 negative triangles 226: dt=0.9900, 17 negative triangles 227: dt=0.9900, 18 negative triangles 228: dt=0.9900, 19 negative triangles 229: dt=0.9900, 16 negative triangles 230: dt=0.9900, 14 negative triangles 231: dt=0.9900, 14 negative triangles 232: dt=0.9900, 12 negative triangles 233: dt=0.9900, 14 negative triangles 234: dt=0.9900, 13 negative triangles 235: dt=0.9900, 11 negative triangles 236: dt=0.9900, 9 negative triangles 237: dt=0.9900, 8 negative triangles 238: dt=0.9900, 7 negative triangles 239: dt=0.9900, 9 negative triangles 240: dt=0.9900, 10 negative triangles 241: dt=0.9900, 8 negative triangles 242: dt=0.9900, 7 negative triangles 243: dt=0.9900, 7 negative triangles 244: dt=0.9900, 6 negative triangles 245: dt=0.9900, 7 negative triangles 246: dt=0.9900, 5 negative triangles 247: dt=0.9900, 6 negative triangles 248: dt=0.9900, 2 negative triangles 249: dt=0.9900, 4 negative triangles 250: dt=0.9900, 2 negative triangles 251: dt=0.9900, 5 negative triangles 252: dt=0.9900, 1 negative triangles 253: dt=0.9900, 2 negative triangles 254: dt=0.9900, 1 negative triangles 255: dt=0.9900, 2 negative triangles 256: dt=0.9900, 1 negative triangles 257: dt=0.9900, 1 negative triangles 258: dt=0.9900, 2 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.96 hours mris_register utimesec 3312.358444 mris_register stimesec 120.885622 mris_register ru_maxrss 233976 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 29774 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 33964 mris_register ru_oublock 9876 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 187 mris_register ru_nivcsw 1099795 FSRUNTIME@ mris_register 0.9556 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Fr 23. Feb 11:31:24 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 Fr 23. Feb 11:31:27 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 Fr 23. Feb 11:31:29 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 Fr 23. Feb 11:31:30 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 Fr 23. Feb 11:31:32 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 15689_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... 806 labels changed using aseg relabeling using gibbs priors... 000: 2985 changed, 136705 examined... 001: 714 changed, 12677 examined... 002: 152 changed, 3890 examined... 003: 48 changed, 905 examined... 004: 18 changed, 273 examined... 005: 5 changed, 103 examined... 006: 1 changed, 35 examined... 007: 0 changed, 7 examined... 182 labels changed using aseg 000: 92 total segments, 50 labels (192 vertices) changed 001: 43 total segments, 1 labels (1 vertices) changed 002: 42 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1675 vertices marked for relabeling... 1675 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 14 seconds. #----------------------------------------- #@# Cortical Parc rh Fr 23. Feb 11:31:46 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 15689_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... 790 labels changed using aseg relabeling using gibbs priors... 000: 2801 changed, 140374 examined... 001: 664 changed, 12205 examined... 002: 144 changed, 3699 examined... 003: 47 changed, 895 examined... 004: 13 changed, 286 examined... 005: 8 changed, 87 examined... 006: 3 changed, 41 examined... 007: 0 changed, 21 examined... 224 labels changed using aseg 000: 100 total segments, 55 labels (220 vertices) changed 001: 45 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1397 vertices marked for relabeling... 1397 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 13 seconds. #-------------------------------------------- #@# Make Pial Surf lh Fr 23. Feb 11:31:59 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 15689_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/test/15689_T1_fs/mri/filled.mgz... reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/brain.finalsurfs.mgz... reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/../mri/aseg.presurf.mgz... reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/wm.mgz... 20135 bright wm thresholded. 8403 bright non-wm voxels segmented. reading original surface position from /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.orig... computing class statistics... border white: 278935 voxels (1.66%) border gray 316246 voxels (1.88%) WM (102.0): 102.1 +- 5.4 [70.0 --> 110.0] GM (88.0) : 84.7 +- 12.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 74.4 (was 70) setting MAX_BORDER_WHITE to 110.4 (was 105) setting MIN_BORDER_WHITE to 87.0 (was 85) setting MAX_CSF to 61.9 (was 40) setting MAX_GRAY to 99.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 74.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 49.3 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-4.3, GM=87+-6.1 mean inside = 99.3, mean outside = 88.6 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.87 +- 0.26 (0.02-->7.09) (max @ vno 135802 --> 135900) face area 0.32 +- 0.16 (0.00-->5.28) mean absolute distance = 0.83 +- 1.17 3810 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 2 with 174 points - only 0.00% unknown deleting segment 3 with 12 points - only 0.00% unknown deleting segment 4 with 59 points - only 0.00% unknown removing 1 vertex label from ripped group mean border=93.2, 210 (210) missing vertices, mean dist 0.4 [1.5 (%16.2)->0.7 (%83.8))] %52 local maxima, %43 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 0.90 +- 0.26 (0.05-->7.06) (max @ vno 135802 --> 135900) face area 0.32 +- 0.16 (0.00-->5.09) mean absolute distance = 0.51 +- 0.96 4625 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1192241.0, rms=4.656 001: dt: 0.5000, sse=870435.4, rms=3.048 (34.527%) 002: dt: 0.5000, sse=750997.9, rms=2.172 (28.746%) 003: dt: 0.5000, sse=702728.3, rms=1.746 (19.605%) 004: dt: 0.5000, sse=683083.9, rms=1.508 (13.668%) 005: dt: 0.5000, sse=675858.2, rms=1.402 (7.018%) 006: dt: 0.5000, sse=671452.3, rms=1.347 (3.878%) rms = 1.34, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=670998.8, rms=1.343 (0.311%) 008: dt: 0.2500, sse=663292.3, rms=1.090 (18.823%) rms = 1.06, time step reduction 2 of 3 to 0.125... 009: dt: 0.2500, sse=658157.1, rms=1.064 (2.387%) rms = 1.06, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=657183.1, rms=1.058 (0.554%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 4 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown deleting segment 6 with 10 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown deleting segment 8 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 12 with 16 points - only 0.00% unknown mean border=94.5, 81 (26) missing vertices, mean dist -0.3 [0.7 (%60.2)->0.3 (%39.8))] %63 local maxima, %31 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 0.88 +- 0.25 (0.07-->6.90) (max @ vno 135802 --> 135900) face area 0.34 +- 0.17 (0.00-->5.45) mean absolute distance = 0.46 +- 0.68 4514 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=820450.1, rms=2.426 011: dt: 0.5000, sse=734123.7, rms=1.585 (34.652%) 012: dt: 0.5000, sse=711713.2, rms=1.275 (19.603%) 013: dt: 0.5000, sse=702073.0, rms=1.168 (8.359%) 014: dt: 0.5000, sse=702502.1, rms=1.110 (4.931%) rms = 1.14, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=693459.6, rms=0.988 (11.033%) rms = 0.94, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=691939.5, rms=0.941 (4.732%) rms = 0.93, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=690550.2, rms=0.933 (0.893%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 2 with 144 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 28 points - only 0.00% unknown mean border=96.1, 74 (14) missing vertices, mean dist -0.3 [0.6 (%66.8)->0.3 (%33.2))] %77 local maxima, %17 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 0.87 +- 0.26 (0.05-->6.74) (max @ vno 135802 --> 135900) face area 0.33 +- 0.17 (0.00-->5.20) mean absolute distance = 0.35 +- 0.50 4401 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=806756.9, rms=2.489 018: dt: 0.5000, sse=708683.9, rms=1.475 (40.718%) 019: dt: 0.5000, sse=686791.1, rms=1.129 (23.492%) 020: dt: 0.5000, sse=678531.6, rms=1.049 (7.107%) rms = 1.02, time step reduction 1 of 3 to 0.250... 021: dt: 0.5000, sse=675568.6, rms=1.020 (2.705%) 022: dt: 0.2500, sse=671375.2, rms=0.877 (14.041%) rms = 0.87, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=682950.1, rms=0.867 (1.125%) rms = 0.86, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=670671.8, rms=0.864 (0.326%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 2 with 178 points - only 0.00% unknown deleting segment 3 with 6 points - only 0.00% unknown deleting segment 4 with 49 points - only 0.00% unknown mean border=96.8, 87 (11) missing vertices, mean dist -0.1 [0.4 (%57.6)->0.3 (%42.4))] %83 local maxima, %11 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/test/15689_T1_fs/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=685243.0, rms=1.377 025: dt: 0.5000, sse=652152.6, rms=0.791 (42.534%) rms = 0.87, time step reduction 1 of 3 to 0.250... rms = 0.74, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=648067.8, rms=0.743 (6.135%) rms = 0.73, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=651582.6, rms=0.728 (1.974%) positioning took 0.4 minutes generating cortex label... 9 non-cortical segments detected only using segment with 8701 vertices erasing segment 1 (vno[0] = 78528) erasing segment 2 (vno[0] = 79524) erasing segment 3 (vno[0] = 82687) erasing segment 4 (vno[0] = 90875) erasing segment 5 (vno[0] = 102605) erasing segment 6 (vno[0] = 104421) erasing segment 7 (vno[0] = 106271) erasing segment 8 (vno[0] = 106305) writing cortex label to /scratch/annadan1111/MABT1T2/test/15689_T1_fs/label/lh.cortex.label... writing curvature file /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.curv writing smoothed area to lh.area writing curvature file /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.area vertex spacing 0.87 +- 0.26 (0.02-->6.71) (max @ vno 135802 --> 135900) face area 0.32 +- 0.17 (0.00-->5.13) 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 9 points - only 0.00% unknown removing 4 vertex label from ripped group removing 2 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=72.6, 230 (230) missing vertices, mean dist 1.8 [0.5 (%0.0)->3.3 (%100.0))] %19 local maxima, %34 large gradients and %41 min vals, 484 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=17020530.0, rms=25.186 001: dt: 0.0500, sse=15794547.0, rms=24.227 (3.809%) 002: dt: 0.0500, sse=14914012.0, rms=23.513 (2.945%) 003: dt: 0.0500, sse=14228865.0, rms=22.943 (2.427%) 004: dt: 0.0500, sse=13661807.0, rms=22.459 (2.107%) 005: dt: 0.0500, sse=13172209.0, rms=22.034 (1.896%) 006: dt: 0.0500, sse=12736199.0, rms=21.647 (1.754%) 007: dt: 0.0500, sse=12338905.0, rms=21.289 (1.655%) 008: dt: 0.0500, sse=11971115.0, rms=20.952 (1.584%) 009: dt: 0.0500, sse=11627044.0, rms=20.631 (1.529%) 010: dt: 0.0500, sse=11301904.0, rms=20.324 (1.490%) positioning took 0.9 minutes mean border=72.3, 171 (115) missing vertices, mean dist 1.6 [0.1 (%0.1)->2.7 (%99.9))] %20 local maxima, %34 large gradients and %40 min vals, 483 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=12462263.0, rms=21.390 011: dt: 0.0500, sse=12148285.0, rms=21.104 (1.337%) 012: dt: 0.0500, sse=11848022.0, rms=20.827 (1.314%) 013: dt: 0.0500, sse=11559581.0, rms=20.557 (1.296%) 014: dt: 0.0500, sse=11281857.0, rms=20.293 (1.281%) 015: dt: 0.0500, sse=11014154.0, rms=20.036 (1.267%) 016: dt: 0.0500, sse=10756117.0, rms=19.785 (1.253%) 017: dt: 0.0500, sse=10506698.0, rms=19.540 (1.242%) 018: dt: 0.0500, sse=10265847.0, rms=19.299 (1.230%) 019: dt: 0.0500, sse=10032970.0, rms=19.064 (1.219%) 020: dt: 0.0500, sse=9807692.0, rms=18.833 (1.209%) positioning took 0.9 minutes mean border=72.1, 165 (85) missing vertices, mean dist 1.4 [0.1 (%0.8)->2.4 (%99.2))] %20 local maxima, %35 large gradients and %40 min vals, 449 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=9941449.0, rms=18.970 021: dt: 0.0500, sse=9716645.0, rms=18.739 (1.218%) 022: dt: 0.0500, sse=9499372.0, rms=18.513 (1.207%) 023: dt: 0.0500, sse=9287604.0, rms=18.290 (1.206%) 024: dt: 0.0500, sse=9083457.0, rms=18.072 (1.191%) 025: dt: 0.0500, sse=8886522.0, rms=17.859 (1.177%) 026: dt: 0.0500, sse=8696021.0, rms=17.651 (1.166%) 027: dt: 0.0500, sse=8510494.0, rms=17.446 (1.163%) 028: dt: 0.0500, sse=8328099.5, rms=17.242 (1.171%) 029: dt: 0.0500, sse=8149067.0, rms=17.039 (1.177%) 030: dt: 0.0500, sse=7973567.0, rms=16.838 (1.181%) positioning took 0.9 minutes mean border=72.0, 198 (66) missing vertices, mean dist 1.2 [0.1 (%7.4)->2.2 (%92.6))] %20 local maxima, %35 large gradients and %39 min vals, 455 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=8106743.0, rms=16.986 031: dt: 0.5000, sse=6842128.0, rms=15.473 (8.906%) 032: dt: 0.5000, sse=5814684.0, rms=14.120 (8.743%) 033: dt: 0.5000, sse=4975391.5, rms=12.912 (8.557%) 034: dt: 0.5000, sse=4264408.0, rms=11.787 (8.716%) 035: dt: 0.5000, sse=3700218.8, rms=10.812 (8.272%) 036: dt: 0.5000, sse=3220136.5, rms=9.902 (8.410%) 037: dt: 0.5000, sse=2836660.5, rms=9.113 (7.968%) 038: dt: 0.5000, sse=2506061.5, rms=8.370 (8.152%) 039: dt: 0.5000, sse=2250691.0, rms=7.751 (7.405%) 040: dt: 0.5000, sse=2035651.9, rms=7.184 (7.312%) 041: dt: 0.5000, sse=1874295.8, rms=6.730 (6.323%) 042: dt: 0.5000, sse=1735640.1, rms=6.311 (6.218%) 043: dt: 0.5000, sse=1639003.1, rms=6.004 (4.868%) 044: dt: 0.5000, sse=1556094.6, rms=5.725 (4.650%) 045: dt: 0.5000, sse=1507695.9, rms=5.557 (2.924%) 046: dt: 0.5000, sse=1461263.6, rms=5.388 (3.044%) 047: dt: 0.5000, sse=1439214.2, rms=5.309 (1.474%) 048: dt: 0.5000, sse=1414285.0, rms=5.214 (1.792%) rms = 5.19, time step reduction 1 of 3 to 0.250... 049: dt: 0.5000, sse=1408395.2, rms=5.192 (0.418%) 050: dt: 0.2500, sse=1277730.1, rms=4.629 (10.850%) 051: dt: 0.2500, sse=1242977.1, rms=4.479 (3.228%) rms = 4.49, time step reduction 2 of 3 to 0.125... 052: dt: 0.1250, sse=1228018.8, rms=4.410 (1.536%) 053: dt: 0.1250, sse=1208265.4, rms=4.317 (2.122%) rms = 4.30, time step reduction 3 of 3 to 0.062... 054: dt: 0.1250, sse=1205328.2, rms=4.302 (0.347%) positioning took 2.9 minutes mean border=71.0, 2779 (21) missing vertices, mean dist 0.2 [0.2 (%42.1)->0.6 (%57.9))] %34 local maxima, %23 large gradients and %35 min vals, 386 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=1497540.0, rms=4.717 055: dt: 0.5000, sse=1460672.8, rms=4.575 (3.009%) 056: dt: 0.5000, sse=1382939.1, rms=4.256 (6.973%) rms = 4.47, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=1259167.4, rms=3.599 (15.426%) 058: dt: 0.2500, sse=1231774.4, rms=3.431 (4.661%) rms = 3.45, time step reduction 2 of 3 to 0.125... 059: dt: 0.1250, sse=1215607.4, rms=3.333 (2.880%) 060: dt: 0.1250, sse=1193578.0, rms=3.192 (4.211%) rms = 3.15, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=1186857.5, rms=3.150 (1.328%) positioning took 1.2 minutes mean border=70.4, 3492 (16) missing vertices, mean dist 0.1 [0.2 (%43.5)->0.4 (%56.5))] %43 local maxima, %15 large gradients and %34 min vals, 455 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=1219654.9, rms=3.379 rms = 3.89, time step reduction 1 of 3 to 0.250... 062: dt: 0.2500, sse=1185248.5, rms=3.170 (6.171%) rms = 3.15, time step reduction 2 of 3 to 0.125... 063: dt: 0.2500, sse=1180670.6, rms=3.150 (0.657%) 064: dt: 0.1250, sse=1166194.9, rms=3.055 (3.016%) rms = 3.02, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=1161048.2, rms=3.025 (0.983%) positioning took 0.8 minutes mean border=69.9, 6576 (15) missing vertices, mean dist 0.1 [0.2 (%46.6)->0.3 (%53.4))] %46 local maxima, %12 large gradients and %32 min vals, 487 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/test/15689_T1_fs/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1172528.8, rms=3.080 rms = 3.49, time step reduction 1 of 3 to 0.250... 066: dt: 0.2500, sse=1155469.1, rms=2.970 (3.571%) rms = 2.95, time step reduction 2 of 3 to 0.125... 067: dt: 0.2500, sse=1149718.9, rms=2.949 (0.677%) 068: dt: 0.1250, sse=1137170.9, rms=2.862 (2.970%) rms = 2.83, time step reduction 3 of 3 to 0.062... 069: dt: 0.1250, sse=1131857.8, rms=2.831 (1.093%) positioning took 0.8 minutes writing curvature file /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.area.pial vertex spacing 1.01 +- 0.45 (0.06-->9.01) (max @ vno 96800 --> 95950) face area 0.41 +- 0.34 (0.00-->10.04) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 136705 vertices processed 25000 of 136705 vertices processed 50000 of 136705 vertices processed 75000 of 136705 vertices processed 100000 of 136705 vertices processed 125000 of 136705 vertices processed 0 of 136705 vertices processed 25000 of 136705 vertices processed 50000 of 136705 vertices processed 75000 of 136705 vertices processed 100000 of 136705 vertices processed 125000 of 136705 vertices processed thickness calculation complete, 2115:5702 truncations. 32778 vertices at 0 distance 84136 vertices at 1 distance 73877 vertices at 2 distance 39432 vertices at 3 distance 17177 vertices at 4 distance 6704 vertices at 5 distance 2560 vertices at 6 distance 1002 vertices at 7 distance 418 vertices at 8 distance 198 vertices at 9 distance 118 vertices at 10 distance 83 vertices at 11 distance 60 vertices at 12 distance 57 vertices at 13 distance 52 vertices at 14 distance 40 vertices at 15 distance 36 vertices at 16 distance 40 vertices at 17 distance 29 vertices at 18 distance 27 vertices at 19 distance 48 vertices at 20 distance writing curvature file /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.thickness positioning took 15.1 minutes #-------------------------------------------- #@# Make Pial Surf rh Fr 23. Feb 11:47:03 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 15689_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/test/15689_T1_fs/mri/filled.mgz... reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/brain.finalsurfs.mgz... reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/../mri/aseg.presurf.mgz... reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/wm.mgz... 20135 bright wm thresholded. 8403 bright non-wm voxels segmented. reading original surface position from /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.orig... computing class statistics... border white: 278935 voxels (1.66%) border gray 316246 voxels (1.88%) WM (102.0): 102.1 +- 5.4 [70.0 --> 110.0] GM (88.0) : 84.7 +- 12.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 77.4 (was 70) setting MAX_BORDER_WHITE to 109.4 (was 105) setting MIN_BORDER_WHITE to 90.0 (was 85) setting MAX_CSF to 64.9 (was 40) setting MAX_GRAY to 98.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 77.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 52.3 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104+-4.3, GM=90+-7.0 mean inside = 99.0, mean outside = 89.1 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.86 +- 0.26 (0.03-->9.34) (max @ vno 93253 --> 95293) face area 0.31 +- 0.17 (0.00-->11.90) mean absolute distance = 0.79 +- 1.10 3899 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 3 with 175 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown deleting segment 6 with 36 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown deleting segment 9 with 23 points - only 0.00% unknown mean border=95.1, 414 (414) missing vertices, mean dist 0.3 [1.3 (%17.1)->0.7 (%82.9))] %47 local maxima, %48 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 0.88 +- 0.25 (0.06-->9.36) (max @ vno 93253 --> 95293) face area 0.31 +- 0.16 (0.00-->11.59) mean absolute distance = 0.50 +- 0.91 5365 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1052868.1, rms=3.983 001: dt: 0.5000, sse=821755.9, rms=2.689 (32.494%) 002: dt: 0.5000, sse=725144.1, rms=1.975 (26.539%) 003: dt: 0.5000, sse=704250.2, rms=1.637 (17.133%) 004: dt: 0.5000, sse=696467.9, rms=1.440 (12.026%) 005: dt: 0.5000, sse=667870.5, rms=1.350 (6.219%) 006: dt: 0.5000, sse=663343.4, rms=1.288 (4.615%) rms = 1.28, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=667935.4, rms=1.277 (0.847%) 008: dt: 0.2500, sse=652493.5, rms=1.081 (15.375%) rms = 1.06, time step reduction 2 of 3 to 0.125... 009: dt: 0.2500, sse=652727.8, rms=1.059 (1.978%) rms = 1.05, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=651022.6, rms=1.051 (0.807%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 2 with 69 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 4 with 14 points - only 0.00% unknown deleting segment 5 with 20 points - only 0.00% unknown mean border=96.2, 116 (58) missing vertices, mean dist -0.3 [0.7 (%57.3)->0.3 (%42.7))] %61 local maxima, %34 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 0.86 +- 0.25 (0.05-->9.32) (max @ vno 93253 --> 95293) face area 0.33 +- 0.17 (0.00-->12.31) mean absolute distance = 0.45 +- 0.65 5612 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=783250.1, rms=2.184 011: dt: 0.5000, sse=722126.1, rms=1.492 (31.713%) 012: dt: 0.5000, sse=696442.1, rms=1.223 (18.011%) 013: dt: 0.5000, sse=696027.9, rms=1.136 (7.096%) 014: dt: 0.5000, sse=688287.6, rms=1.083 (4.661%) rms = 1.10, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=682149.1, rms=0.989 (8.652%) rms = 0.96, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=687809.4, rms=0.955 (3.472%) rms = 0.94, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=685227.2, rms=0.945 (1.105%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 1 with 130 points - only 0.00% unknown deleting segment 2 with 39 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 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 20 points - only 0.00% unknown mean border=97.5, 115 (32) missing vertices, mean dist -0.3 [0.6 (%64.1)->0.3 (%35.9))] %74 local maxima, %21 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 0.86 +- 0.26 (0.04-->9.27) (max @ vno 93253 --> 95293) face area 0.32 +- 0.17 (0.00-->11.90) mean absolute distance = 0.36 +- 0.49 4951 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=760242.9, rms=2.110 018: dt: 0.5000, sse=692320.7, rms=1.324 (37.244%) 019: dt: 0.5000, sse=688027.8, rms=1.054 (20.381%) rms = 1.02, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=678972.9, rms=1.020 (3.293%) 021: dt: 0.2500, sse=665139.3, rms=0.900 (11.761%) rms = 0.89, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=665187.3, rms=0.887 (1.454%) rms = 0.88, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=661689.9, rms=0.879 (0.841%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 161 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 2 with 24 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 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 20 points - only 0.00% unknown mean border=98.1, 125 (24) missing vertices, mean dist -0.1 [0.4 (%56.7)->0.3 (%43.3))] %80 local maxima, %15 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/test/15689_T1_fs/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=672324.8, rms=1.286 024: dt: 0.5000, sse=651977.4, rms=0.798 (37.921%) rms = 0.87, time step reduction 1 of 3 to 0.250... rms = 0.76, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=644192.5, rms=0.758 (4.999%) rms = 0.75, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=645643.7, rms=0.745 (1.700%) positioning took 0.4 minutes generating cortex label... 7 non-cortical segments detected only using segment with 8282 vertices erasing segment 1 (vno[0] = 90047) erasing segment 2 (vno[0] = 93055) erasing segment 3 (vno[0] = 104030) erasing segment 4 (vno[0] = 107990) erasing segment 5 (vno[0] = 108782) erasing segment 6 (vno[0] = 112036) writing cortex label to /scratch/annadan1111/MABT1T2/test/15689_T1_fs/label/rh.cortex.label... writing curvature file /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.curv writing smoothed area to rh.area writing curvature file /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.area vertex spacing 0.86 +- 0.27 (0.03-->9.24) (max @ vno 93253 --> 95293) face area 0.31 +- 0.17 (0.00-->11.67) 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 8 points - only 0.00% unknown deleting segment 1 with 23 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 14 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=75.3, 447 (447) missing vertices, mean dist 1.9 [1.9 (%0.0)->3.3 (%100.0))] %21 local maxima, %34 large gradients and %40 min vals, 603 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=15907211.0, rms=23.977 001: dt: 0.0500, sse=14784921.0, rms=23.081 (3.736%) 002: dt: 0.0500, sse=13993908.0, rms=22.428 (2.830%) 003: dt: 0.0500, sse=13382193.0, rms=21.910 (2.312%) 004: dt: 0.0500, sse=12877237.0, rms=21.472 (1.997%) 005: dt: 0.0500, sse=12440697.0, rms=21.086 (1.796%) 006: dt: 0.0500, sse=12051054.0, rms=20.736 (1.662%) 007: dt: 0.0500, sse=11694975.0, rms=20.411 (1.570%) 008: dt: 0.0500, sse=11364173.0, rms=20.103 (1.505%) 009: dt: 0.0500, sse=11053432.0, rms=19.811 (1.457%) 010: dt: 0.0500, sse=10758760.0, rms=19.529 (1.423%) positioning took 0.9 minutes mean border=74.9, 259 (203) missing vertices, mean dist 1.6 [0.8 (%0.0)->2.8 (%100.0))] %22 local maxima, %34 large gradients and %39 min vals, 580 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=11992360.0, rms=20.661 011: dt: 0.0500, sse=11707577.0, rms=20.401 (1.261%) 012: dt: 0.0500, sse=11434394.0, rms=20.147 (1.241%) 013: dt: 0.0500, sse=11171610.0, rms=19.901 (1.224%) 014: dt: 0.0500, sse=10918427.0, rms=19.660 (1.209%) 015: dt: 0.0500, sse=10674737.0, rms=19.426 (1.192%) 016: dt: 0.0500, sse=10439945.0, rms=19.197 (1.177%) 017: dt: 0.0500, sse=10213649.0, rms=18.974 (1.161%) 018: dt: 0.0500, sse=9995538.0, rms=18.757 (1.146%) 019: dt: 0.0500, sse=9785168.0, rms=18.545 (1.131%) 020: dt: 0.0500, sse=9582086.0, rms=18.338 (1.117%) positioning took 0.9 minutes mean border=74.7, 224 (145) missing vertices, mean dist 1.4 [0.1 (%0.9)->2.4 (%99.1))] %22 local maxima, %34 large gradients and %38 min vals, 584 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=9764310.0, rms=18.520 021: dt: 0.0500, sse=9559637.0, rms=18.311 (1.129%) 022: dt: 0.0500, sse=9363220.0, rms=18.108 (1.108%) 023: dt: 0.0500, sse=9171451.0, rms=17.908 (1.107%) 024: dt: 0.0500, sse=8987729.0, rms=17.714 (1.084%) 025: dt: 0.0500, sse=8810949.0, rms=17.525 (1.067%) 026: dt: 0.0500, sse=8641075.0, rms=17.341 (1.047%) 027: dt: 0.0500, sse=8476763.0, rms=17.162 (1.035%) 028: dt: 0.0500, sse=8315489.0, rms=16.984 (1.037%) 029: dt: 0.0500, sse=8156969.5, rms=16.807 (1.042%) 030: dt: 0.0500, sse=8001734.0, rms=16.632 (1.042%) positioning took 0.9 minutes mean border=74.6, 217 (112) missing vertices, mean dist 1.2 [0.1 (%8.8)->2.3 (%91.2))] %22 local maxima, %34 large gradients and %38 min vals, 564 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=8125135.5, rms=16.764 031: dt: 0.5000, sse=6993266.0, rms=15.440 (7.897%) 032: dt: 0.5000, sse=6037858.5, rms=14.222 (7.889%) 033: dt: 0.5000, sse=5206779.0, rms=13.073 (8.083%) 034: dt: 0.5000, sse=4471872.5, rms=11.959 (8.520%) 035: dt: 0.5000, sse=3862309.0, rms=10.952 (8.421%) 036: dt: 0.5000, sse=3348707.0, rms=10.020 (8.512%) 037: dt: 0.5000, sse=2935064.5, rms=9.203 (8.146%) 038: dt: 0.5000, sse=2595715.5, rms=8.470 (7.964%) 039: dt: 0.5000, sse=2333822.0, rms=7.862 (7.187%) 040: dt: 0.5000, sse=2121304.0, rms=7.326 (6.813%) 041: dt: 0.5000, sse=1952718.1, rms=6.875 (6.150%) 042: dt: 0.5000, sse=1816483.2, rms=6.483 (5.710%) 043: dt: 0.5000, sse=1709690.1, rms=6.163 (4.938%) 044: dt: 0.5000, sse=1623656.4, rms=5.886 (4.484%) 045: dt: 0.5000, sse=1563900.6, rms=5.692 (3.304%) 046: dt: 0.5000, sse=1514191.9, rms=5.519 (3.034%) 047: dt: 0.5000, sse=1483172.1, rms=5.412 (1.934%) 048: dt: 0.5000, sse=1455278.2, rms=5.309 (1.915%) 049: dt: 0.5000, sse=1439100.9, rms=5.254 (1.033%) 050: dt: 0.5000, sse=1421968.0, rms=5.187 (1.277%) rms = 5.16, time step reduction 1 of 3 to 0.250... 051: dt: 0.5000, sse=1412793.9, rms=5.156 (0.591%) 052: dt: 0.2500, sse=1282884.2, rms=4.610 (10.591%) 053: dt: 0.2500, sse=1247063.9, rms=4.462 (3.222%) rms = 4.49, time step reduction 2 of 3 to 0.125... 054: dt: 0.1250, sse=1230153.8, rms=4.386 (1.689%) 055: dt: 0.1250, sse=1209391.5, rms=4.291 (2.176%) rms = 4.28, time step reduction 3 of 3 to 0.062... 056: dt: 0.1250, sse=1206245.9, rms=4.276 (0.356%) positioning took 3.3 minutes mean border=73.5, 3025 (29) missing vertices, mean dist 0.2 [0.2 (%40.2)->0.6 (%59.8))] %38 local maxima, %21 large gradients and %34 min vals, 463 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=1533962.2, rms=4.815 057: dt: 0.5000, sse=1492214.2, rms=4.659 (3.238%) 058: dt: 0.5000, sse=1380974.1, rms=4.206 (9.726%) rms = 4.48, time step reduction 1 of 3 to 0.250... 059: dt: 0.2500, sse=1252958.0, rms=3.542 (15.801%) 060: dt: 0.2500, sse=1225909.6, rms=3.377 (4.642%) rms = 3.42, time step reduction 2 of 3 to 0.125... 061: dt: 0.1250, sse=1207436.8, rms=3.267 (3.276%) 062: dt: 0.1250, sse=1183236.4, rms=3.115 (4.652%) rms = 3.07, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1175281.5, rms=3.066 (1.573%) positioning took 1.3 minutes mean border=72.8, 3639 (24) missing vertices, mean dist 0.1 [0.2 (%42.4)->0.4 (%57.6))] %46 local maxima, %13 large gradients and %33 min vals, 460 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=1202400.0, rms=3.275 rms = 3.84, time step reduction 1 of 3 to 0.250... 064: dt: 0.2500, sse=1165997.4, rms=3.055 (6.735%) rms = 3.03, time step reduction 2 of 3 to 0.125... 065: dt: 0.2500, sse=1161301.2, rms=3.031 (0.780%) 066: dt: 0.1250, sse=1145732.2, rms=2.928 (3.380%) rms = 2.89, time step reduction 3 of 3 to 0.062... 067: dt: 0.1250, sse=1139987.0, rms=2.894 (1.158%) positioning took 0.8 minutes mean border=72.4, 6351 (22) missing vertices, mean dist 0.1 [0.2 (%45.7)->0.3 (%54.3))] %48 local maxima, %11 large gradients and %32 min vals, 484 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/test/15689_T1_fs/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1145961.8, rms=2.916 rms = 3.42, time step reduction 1 of 3 to 0.250... 068: dt: 0.2500, sse=1128885.8, rms=2.804 (3.847%) rms = 2.79, time step reduction 2 of 3 to 0.125... 069: dt: 0.2500, sse=1124648.9, rms=2.792 (0.423%) 070: dt: 0.1250, sse=1112715.6, rms=2.707 (3.069%) rms = 2.67, time step reduction 3 of 3 to 0.062... 071: dt: 0.1250, sse=1106695.9, rms=2.671 (1.328%) positioning took 0.8 minutes writing curvature file /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.area.pial vertex spacing 0.99 +- 0.44 (0.06-->9.32) (max @ vno 105139 --> 102257) face area 0.39 +- 0.33 (0.00-->12.57) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 140374 vertices processed 25000 of 140374 vertices processed 50000 of 140374 vertices processed 75000 of 140374 vertices processed 100000 of 140374 vertices processed 125000 of 140374 vertices processed 0 of 140374 vertices processed 25000 of 140374 vertices processed 50000 of 140374 vertices processed 75000 of 140374 vertices processed 100000 of 140374 vertices processed 125000 of 140374 vertices processed thickness calculation complete, 2540:7687 truncations. 31999 vertices at 0 distance 81875 vertices at 1 distance 75439 vertices at 2 distance 42978 vertices at 3 distance 20023 vertices at 4 distance 8303 vertices at 5 distance 3406 vertices at 6 distance 1329 vertices at 7 distance 517 vertices at 8 distance 215 vertices at 9 distance 126 vertices at 10 distance 119 vertices at 11 distance 84 vertices at 12 distance 63 vertices at 13 distance 61 vertices at 14 distance 29 vertices at 15 distance 32 vertices at 16 distance 32 vertices at 17 distance 25 vertices at 18 distance 28 vertices at 19 distance 45 vertices at 20 distance writing curvature file /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.thickness positioning took 15.3 minutes #-------------------------------------------- #@# Surf Volume lh Fr 23. Feb 12:02:22 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf /scratch/annadan1111/MABT1T2/test/15689_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 15689_T1_fs lh /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.volume masking with /scratch/annadan1111/MABT1T2/test/15689_T1_fs/label/lh.cortex.label Total face volume 274300 Total vertex volume 270762 (mask=0) #@# 15689_T1_fs lh 270762 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Fr 23. Feb 12:02:26 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf /scratch/annadan1111/MABT1T2/test/15689_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 15689_T1_fs rh /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.volume masking with /scratch/annadan1111/MABT1T2/test/15689_T1_fs/label/rh.cortex.label Total face volume 277086 Total vertex volume 273287 (mask=0) #@# 15689_T1_fs rh 273287 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Fr 23. Feb 12:02:29 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 15689_T1_fs SUBJECTS_DIR is /scratch/annadan1111/MABT1T2/test 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 = 276 writing volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/ribbon.mgz mris_volmask took 8.51 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Fr 23. Feb 12:11:00 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 15689_T1_fs lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white... reading input pial surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test/15689_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 274300 Total vertex volume 270762 (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) = 1766996 mm^3 (det: 1.102495 ) lhCtxGM: 268173.730 267868.000 diff= 305.7 pctdiff= 0.114 rhCtxGM: 268287.733 268746.000 diff= -458.3 pctdiff=-0.171 lhCtxWM: 262563.790 263011.500 diff= -447.7 pctdiff=-0.171 rhCtxWM: 266031.420 267566.500 diff=-1535.1 pctdiff=-0.577 SubCortGMVol 67300.000 SupraTentVol 1185591.674 (1179005.000) diff=6586.674 pctdiff=0.556 SupraTentVolNotVent 1141081.674 (1134495.000) diff=6586.674 pctdiff=0.577 BrainSegVol 1352976.000 (1348423.000) diff=4553.000 pctdiff=0.337 BrainSegVolNotVent 1301808.000 (1299472.674) diff=2335.326 pctdiff=0.179 BrainSegVolNotVent 1301808.000 CerebellumVol 167113.000 VentChorVol 44510.000 3rd4th5thCSF 6658.000 CSFVol 2105.000, OptChiasmVol 200.000 MaskVol 1843183.000 1334 915 2167 2.456 0.546 0.103 0.026 9 1.4 bankssts 619 392 1341 3.203 0.693 0.083 0.011 3 0.3 caudalanteriorcingulate 3647 2119 6265 2.680 0.599 0.106 0.026 33 3.7 caudalmiddlefrontal 2042 1312 2219 1.622 0.534 0.131 0.030 25 2.4 cuneus 951 548 2859 3.422 0.939 0.108 0.039 9 1.7 entorhinal 4781 3186 12507 3.360 0.685 0.125 0.028 56 5.2 fusiform 6587 4428 14880 2.849 0.672 0.121 0.027 80 7.0 inferiorparietal 5195 3350 15220 3.389 0.818 0.127 0.037 69 7.3 inferiortemporal 1590 1048 3721 3.292 0.811 0.131 0.035 21 2.1 isthmuscingulate 7384 4669 12586 2.382 0.753 0.137 0.037 96 11.2 lateraloccipital 3730 2424 8432 3.206 0.891 0.127 0.037 44 5.6 lateralorbitofrontal 4390 2966 7821 2.287 0.948 0.133 0.029 52 5.2 lingual 2778 1793 6319 3.087 1.083 0.117 0.029 32 3.6 medialorbitofrontal 4904 3316 16114 3.502 0.799 0.131 0.034 70 6.9 middletemporal 1118 690 2286 2.855 0.753 0.076 0.014 6 0.7 parahippocampal 2294 1379 3343 2.300 0.624 0.084 0.014 11 1.3 paracentral 2460 1574 6060 3.120 0.688 0.118 0.023 28 2.5 parsopercularis 1082 655 3215 3.637 0.720 0.125 0.032 13 1.2 parsorbitalis 1910 1211 4517 3.042 0.733 0.125 0.030 21 2.3 parstriangularis 1680 1272 1495 1.341 0.314 0.154 0.036 24 2.4 pericalcarine 6788 4000 9589 2.100 0.785 0.103 0.023 54 6.4 postcentral 1477 1024 3825 3.269 0.722 0.112 0.022 17 1.3 posteriorcingulate 7448 4397 11536 2.397 0.657 0.098 0.023 62 6.9 precentral 6071 3890 11714 2.777 0.719 0.124 0.029 63 6.7 precuneus 1111 672 2728 3.751 0.969 0.110 0.029 13 1.2 rostralanteriorcingulate 7930 5185 18146 3.036 0.706 0.130 0.033 96 10.6 rostralmiddlefrontal 10530 6636 24040 3.079 0.750 0.108 0.024 88 10.0 superiorfrontal 8851 5420 13907 2.305 0.641 0.110 0.025 80 9.1 superiorparietal 5709 3771 15226 3.234 0.839 0.105 0.024 51 5.3 superiortemporal 5912 3961 13496 2.779 0.777 0.123 0.028 68 6.4 supramarginal 402 249 1334 3.582 0.747 0.164 0.054 7 0.9 frontalpole 631 386 2981 4.250 0.657 0.122 0.042 7 1.0 temporalpole 938 506 1480 2.846 0.400 0.131 0.031 12 1.1 transversetemporal 3263 2183 7323 3.319 0.894 0.092 0.020 17 2.6 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 15689_T1_fs lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.pial... reading input pial surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test/15689_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 274300 Total vertex volume 270762 (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) = 1766996 mm^3 (det: 1.102495 ) lhCtxGM: 268173.730 267868.000 diff= 305.7 pctdiff= 0.114 rhCtxGM: 268287.733 268746.000 diff= -458.3 pctdiff=-0.171 lhCtxWM: 262563.790 263011.500 diff= -447.7 pctdiff=-0.171 rhCtxWM: 266031.420 267566.500 diff=-1535.1 pctdiff=-0.577 SubCortGMVol 67300.000 SupraTentVol 1185591.674 (1179005.000) diff=6586.674 pctdiff=0.556 SupraTentVolNotVent 1141081.674 (1134495.000) diff=6586.674 pctdiff=0.577 BrainSegVol 1352976.000 (1348423.000) diff=4553.000 pctdiff=0.337 BrainSegVolNotVent 1301808.000 (1299472.674) diff=2335.326 pctdiff=0.179 BrainSegVolNotVent 1301808.000 CerebellumVol 167113.000 VentChorVol 44510.000 3rd4th5thCSF 6658.000 CSFVol 2105.000, OptChiasmVol 200.000 MaskVol 1843183.000 1334 872 2167 2.456 0.546 0.124 0.034 22 2.0 bankssts 619 499 1341 3.203 0.693 0.106 0.019 4 0.5 caudalanteriorcingulate 3647 2594 6265 2.680 0.599 0.105 0.023 38 3.7 caudalmiddlefrontal 2042 1549 2219 1.622 0.534 0.122 0.024 29 2.2 cuneus 951 1029 2859 3.422 0.939 0.150 0.033 9 1.5 entorhinal 4781 4091 12507 3.360 0.685 0.138 0.034 99 7.5 fusiform 6587 5731 14880 2.849 0.672 0.134 0.027 72 7.5 inferiorparietal 5195 5071 15220 3.389 0.818 0.156 0.035 83 8.6 inferiortemporal 1590 1232 3721 3.292 0.811 0.157 0.050 37 3.6 isthmuscingulate 7384 5900 12586 2.382 0.753 0.129 0.033 100 10.8 lateraloccipital 3730 2725 8432 3.206 0.891 0.125 0.030 56 5.1 lateralorbitofrontal 4390 3881 7821 2.287 0.948 0.148 0.037 76 7.9 lingual 2778 2305 6319 3.087 1.083 0.128 0.028 39 3.5 medialorbitofrontal 4904 5393 16114 3.502 0.799 0.179 0.035 6436 7.9 middletemporal 1118 938 2286 2.855 0.753 0.103 0.019 7 1.1 parahippocampal 2294 1584 3343 2.300 0.624 0.105 0.020 19 2.2 paracentral 2460 2215 6060 3.120 0.688 0.135 0.026 23 2.9 parsopercularis 1082 1062 3215 3.637 0.720 0.145 0.029 11 1.5 parsorbitalis 1910 1654 4517 3.042 0.733 0.134 0.030 20 2.5 parstriangularis 1680 1083 1495 1.341 0.314 0.114 0.033 26 2.3 pericalcarine 6788 5191 9589 2.100 0.785 0.110 0.021 48 6.2 postcentral 1477 1309 3825 3.269 0.722 0.121 0.032 23 2.0 posteriorcingulate 7448 5195 11536 2.397 0.657 0.102 0.023 76 7.1 precentral 6071 4406 11714 2.777 0.719 0.122 0.027 75 6.8 precuneus 1111 809 2728 3.751 0.969 0.140 0.037 27 1.4 rostralanteriorcingulate 7930 6407 18146 3.036 0.706 0.135 0.031 112 9.8 rostralmiddlefrontal 10530 8604 24040 3.079 0.750 0.128 0.026 129 11.7 superiorfrontal 8851 6471 13907 2.305 0.641 0.115 0.024 103 8.9 superiorparietal 5709 5182 15226 3.234 0.839 0.137 0.027 107 7.0 superiortemporal 5912 5224 13496 2.779 0.777 0.146 0.029 78 7.9 supramarginal 402 499 1334 3.582 0.747 0.204 0.037 4 0.8 frontalpole 631 885 2981 4.250 0.657 0.165 0.028 11 0.8 temporalpole 938 578 1480 2.846 0.400 0.099 0.020 6 0.8 transversetemporal 3263 2061 7323 3.319 0.894 0.110 0.024 39 3.4 insula #----------------------------------------- #@# Parcellation Stats rh Fr 23. Feb 12:12:03 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 15689_T1_fs rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white... reading input pial surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test/15689_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 277086 Total vertex volume 273287 (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) = 1766996 mm^3 (det: 1.102495 ) lhCtxGM: 268173.730 267868.000 diff= 305.7 pctdiff= 0.114 rhCtxGM: 268287.733 268746.000 diff= -458.3 pctdiff=-0.171 lhCtxWM: 262563.790 263011.500 diff= -447.7 pctdiff=-0.171 rhCtxWM: 266031.420 267566.500 diff=-1535.1 pctdiff=-0.577 SubCortGMVol 67300.000 SupraTentVol 1185591.674 (1179005.000) diff=6586.674 pctdiff=0.556 SupraTentVolNotVent 1141081.674 (1134495.000) diff=6586.674 pctdiff=0.577 BrainSegVol 1352976.000 (1348423.000) diff=4553.000 pctdiff=0.337 BrainSegVolNotVent 1301808.000 (1299472.674) diff=2335.326 pctdiff=0.179 BrainSegVolNotVent 1301808.000 CerebellumVol 167113.000 VentChorVol 44510.000 3rd4th5thCSF 6658.000 CSFVol 2105.000, OptChiasmVol 200.000 MaskVol 1843183.000 1393 959 3089 3.518 0.627 0.112 0.020 9 1.2 bankssts 800 488 2193 3.551 0.589 0.111 0.019 9 0.6 caudalanteriorcingulate 3828 2312 6763 2.681 0.591 0.118 0.038 40 5.8 caudalmiddlefrontal 1976 1221 2971 2.081 0.810 0.143 0.041 32 3.7 cuneus 628 358 2677 4.261 0.817 0.106 0.065 15 2.1 entorhinal 5176 3184 12809 3.294 0.771 0.122 0.040 64 8.3 fusiform 8538 5042 17149 3.003 0.703 0.110 0.027 81 9.0 inferiorparietal 5592 3335 14186 3.354 0.837 0.115 0.037 72 8.7 inferiortemporal 1375 840 2994 3.286 0.855 0.125 0.028 17 1.4 isthmuscingulate 7645 4352 14615 2.747 0.952 0.125 0.037 85 12.3 lateraloccipital 3286 2105 7961 3.313 0.919 0.131 0.045 45 6.5 lateralorbitofrontal 4977 2958 7723 2.368 0.854 0.128 0.036 57 7.5 lingual 2947 1859 6975 3.234 0.913 0.122 0.038 42 5.2 medialorbitofrontal 5152 3340 16645 3.640 0.752 0.125 0.034 65 7.0 middletemporal 923 600 1995 2.878 0.740 0.087 0.016 5 0.6 parahippocampal 2585 1529 4072 2.434 0.664 0.088 0.015 14 1.8 paracentral 1758 1114 4408 3.143 0.656 0.115 0.028 17 2.1 parsopercularis 1232 735 3995 3.537 0.903 0.132 0.056 21 2.6 parsorbitalis 1856 1202 4513 3.029 0.785 0.120 0.036 19 2.4 parstriangularis 1766 1156 1329 1.245 0.371 0.116 0.029 23 1.8 pericalcarine 6780 4161 9014 1.982 0.767 0.101 0.022 49 6.0 postcentral 1215 857 3303 3.269 0.831 0.121 0.025 14 1.2 posteriorcingulate 7140 4428 10728 2.276 0.620 0.108 0.026 60 7.9 precentral 6332 3981 12087 2.790 0.803 0.116 0.023 62 5.7 precuneus 927 560 2297 3.620 1.178 0.109 0.026 10 0.9 rostralanteriorcingulate 8597 5329 20342 2.920 0.891 0.126 0.044 113 16.0 rostralmiddlefrontal 9556 5845 21874 3.095 0.738 0.104 0.027 79 10.4 superiorfrontal 9970 5757 14104 2.235 0.609 0.106 0.023 87 9.4 superiorparietal 6109 3845 14533 3.117 0.744 0.108 0.029 59 7.0 superiortemporal 6679 3929 13077 2.841 0.743 0.115 0.030 75 7.8 supramarginal 453 274 1753 3.673 0.706 0.141 0.052 8 0.9 frontalpole 621 381 2740 4.183 0.896 0.130 0.048 9 1.1 temporalpole 576 309 778 2.507 0.539 0.111 0.030 5 0.7 transversetemporal 3224 2199 7510 3.260 1.023 0.101 0.022 18 3.0 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 15689_T1_fs rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.pial... reading input pial surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test/15689_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 277086 Total vertex volume 273287 (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) = 1766996 mm^3 (det: 1.102495 ) lhCtxGM: 268173.730 267868.000 diff= 305.7 pctdiff= 0.114 rhCtxGM: 268287.733 268746.000 diff= -458.3 pctdiff=-0.171 lhCtxWM: 262563.790 263011.500 diff= -447.7 pctdiff=-0.171 rhCtxWM: 266031.420 267566.500 diff=-1535.1 pctdiff=-0.577 SubCortGMVol 67300.000 SupraTentVol 1185591.674 (1179005.000) diff=6586.674 pctdiff=0.556 SupraTentVolNotVent 1141081.674 (1134495.000) diff=6586.674 pctdiff=0.577 BrainSegVol 1352976.000 (1348423.000) diff=4553.000 pctdiff=0.337 BrainSegVolNotVent 1301808.000 (1299472.674) diff=2335.326 pctdiff=0.179 BrainSegVolNotVent 1301808.000 CerebellumVol 167113.000 VentChorVol 44510.000 3rd4th5thCSF 6658.000 CSFVol 2105.000, OptChiasmVol 200.000 MaskVol 1843183.000 1393 738 3089 3.518 0.627 0.101 0.030 26 1.7 bankssts 800 743 2193 3.551 0.589 0.135 0.024 7 0.7 caudalanteriorcingulate 3828 2601 6763 2.681 0.591 0.110 0.025 47 3.8 caudalmiddlefrontal 1976 1598 2971 2.081 0.810 0.140 0.060 92 7.6 cuneus 628 751 2677 4.261 0.817 0.168 0.040 6 1.2 entorhinal 5176 4275 12809 3.294 0.771 0.138 0.038 92 9.2 fusiform 8538 6226 17149 3.003 0.703 0.114 0.027 134 10.0 inferiorparietal 5592 4822 14186 3.354 0.837 0.138 0.032 115 8.1 inferiortemporal 1375 1069 2994 3.286 0.855 0.133 0.037 23 2.0 isthmuscingulate 7645 6023 14615 2.747 0.952 0.123 0.033 139 11.6 lateraloccipital 3286 2494 7961 3.313 0.919 0.131 0.036 55 5.1 lateralorbitofrontal 4977 3731 7723 2.368 0.854 0.133 0.035 75 7.8 lingual 2947 2338 6975 3.234 0.913 0.125 0.030 38 3.8 medialorbitofrontal 5152 5369 16645 3.640 0.752 0.150 0.031 64 8.0 middletemporal 923 780 1995 2.878 0.740 0.108 0.021 6 1.0 parahippocampal 2585 1846 4072 2.434 0.664 0.105 0.020 20 2.3 paracentral 1758 1545 4408 3.143 0.656 0.131 0.025 23 1.9 parsopercularis 1232 1437 3995 3.537 0.903 0.198 0.049 21 2.7 parsorbitalis 1856 1560 4513 3.029 0.785 0.144 0.033 28 2.5 parstriangularis 1766 1121 1329 1.245 0.371 0.098 0.025 31 1.8 pericalcarine 6780 5037 9014 1.982 0.767 0.109 0.021 51 6.0 postcentral 1215 1121 3303 3.269 0.831 0.120 0.023 9 1.3 posteriorcingulate 7140 4968 10728 2.276 0.620 0.104 0.022 72 6.7 precentral 6332 4477 12087 2.790 0.803 0.116 0.026 84 6.7 precuneus 927 755 2297 3.620 1.178 0.153 0.043 25 1.8 rostralanteriorcingulate 8597 7827 20342 2.920 0.891 0.161 0.035 209 14.2 rostralmiddlefrontal 9556 7758 21874 3.095 0.738 0.126 0.025 111 10.3 superiorfrontal 9970 6976 14104 2.235 0.609 0.111 0.024 124 9.7 superiorparietal 6109 5174 14533 3.117 0.744 0.129 0.026 68 7.2 superiortemporal 6679 4958 13077 2.841 0.743 0.115 0.025 63 6.6 supramarginal 453 661 1753 3.673 0.706 0.245 0.047 7 1.2 frontalpole 621 768 2740 4.183 0.896 0.197 0.042 7 1.3 temporalpole 576 318 778 2.507 0.539 0.089 0.021 8 0.4 transversetemporal 3224 2014 7510 3.260 1.023 0.113 0.024 41 3.2 insula #----------------------------------------- #@# Cortical Parc 2 lh Fr 23. Feb 12:13:11 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 15689_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... 380 labels changed using aseg relabeling using gibbs priors... 000: 9119 changed, 136705 examined... 001: 2201 changed, 34806 examined... 002: 623 changed, 11302 examined... 003: 227 changed, 3525 examined... 004: 117 changed, 1327 examined... 005: 62 changed, 668 examined... 006: 34 changed, 342 examined... 007: 23 changed, 208 examined... 008: 9 changed, 108 examined... 009: 6 changed, 51 examined... 010: 3 changed, 29 examined... 011: 3 changed, 21 examined... 012: 1 changed, 11 examined... 013: 2 changed, 7 examined... 014: 0 changed, 10 examined... 177 labels changed using aseg 000: 268 total segments, 186 labels (2266 vertices) changed 001: 98 total segments, 16 labels (70 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 24 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 954 vertices marked for relabeling... 954 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 17 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Fr 23. Feb 12:13:28 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 15689_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... 112 labels changed using aseg relabeling using gibbs priors... 000: 8818 changed, 140374 examined... 001: 1988 changed, 34796 examined... 002: 572 changed, 10443 examined... 003: 233 changed, 3170 examined... 004: 121 changed, 1308 examined... 005: 56 changed, 683 examined... 006: 32 changed, 317 examined... 007: 17 changed, 183 examined... 008: 16 changed, 103 examined... 009: 4 changed, 77 examined... 010: 4 changed, 22 examined... 011: 1 changed, 17 examined... 012: 0 changed, 5 examined... 12 labels changed using aseg 000: 260 total segments, 177 labels (2787 vertices) changed 001: 93 total segments, 11 labels (64 vertices) changed 002: 83 total segments, 1 labels (1 vertices) changed 003: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 17 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 995 vertices marked for relabeling... 995 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 18 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Fr 23. Feb 12:13:46 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 15689_T1_fs lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white... reading input pial surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test/15689_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 274300 Total vertex volume 270762 (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) = 1766996 mm^3 (det: 1.102495 ) lhCtxGM: 268173.730 267868.000 diff= 305.7 pctdiff= 0.114 rhCtxGM: 268287.733 268746.000 diff= -458.3 pctdiff=-0.171 lhCtxWM: 262563.790 263011.500 diff= -447.7 pctdiff=-0.171 rhCtxWM: 266031.420 267566.500 diff=-1535.1 pctdiff=-0.577 SubCortGMVol 67300.000 SupraTentVol 1185591.674 (1179005.000) diff=6586.674 pctdiff=0.556 SupraTentVolNotVent 1141081.674 (1134495.000) diff=6586.674 pctdiff=0.577 BrainSegVol 1352976.000 (1348423.000) diff=4553.000 pctdiff=0.337 BrainSegVolNotVent 1301808.000 (1299472.674) diff=2335.326 pctdiff=0.179 BrainSegVolNotVent 1301808.000 CerebellumVol 167113.000 VentChorVol 44510.000 3rd4th5thCSF 6658.000 CSFVol 2105.000, OptChiasmVol 200.000 MaskVol 1843183.000 1250 845 3460 3.574 0.799 0.153 0.046 20 2.3 G&S_frontomargin 1597 1089 3272 2.648 0.719 0.150 0.045 24 3.0 G&S_occipital_inf 1881 1037 2442 2.010 0.537 0.091 0.017 12 1.3 G&S_paracentral 1530 949 3144 2.866 0.695 0.129 0.035 17 2.0 G&S_subcentral 695 453 1832 2.819 0.611 0.150 0.045 11 1.3 G&S_transv_frontopol 2044 1360 5671 3.807 0.704 0.121 0.029 24 2.2 G&S_cingul-Ant 1207 826 2522 3.267 0.614 0.098 0.014 6 0.8 G&S_cingul-Mid-Ant 1388 944 3063 3.085 0.622 0.096 0.017 10 1.0 G&S_cingul-Mid-Post 730 493 2473 3.736 0.539 0.147 0.037 12 1.0 G_cingul-Post-dorsal 281 194 757 3.691 0.832 0.149 0.036 4 0.3 G_cingul-Post-ventral 1951 1227 2192 1.568 0.557 0.131 0.028 22 2.4 G_cuneus 1488 878 4536 3.480 0.607 0.130 0.029 24 1.8 G_front_inf-Opercular 449 242 1325 3.568 0.598 0.130 0.035 6 0.6 G_front_inf-Orbital 1232 733 3439 3.181 0.690 0.128 0.033 17 1.7 G_front_inf-Triangul 5004 2887 11721 2.968 0.642 0.127 0.035 67 7.3 G_front_middle 7259 4292 17750 3.139 0.731 0.108 0.025 67 7.1 G_front_sup 674 440 1607 3.455 0.899 0.096 0.028 4 0.7 G_Ins_lg&S_cent_ins 661 394 2377 4.181 0.668 0.095 0.023 5 0.6 G_insular_short 2260 1417 5743 3.021 0.611 0.145 0.035 37 3.3 G_occipital_middle 1653 920 2580 2.349 0.758 0.117 0.040 23 2.7 G_occipital_sup 2081 1317 6940 3.697 0.674 0.142 0.035 34 2.6 G_oc-temp_lat-fusifor 3032 2010 5581 2.172 1.034 0.143 0.034 41 4.3 G_oc-temp_med-Lingual 1609 927 4143 3.155 0.943 0.095 0.028 13 1.9 G_oc-temp_med-Parahip 2425 1470 6882 3.413 1.054 0.137 0.043 39 4.1 G_orbital 2529 1626 7652 3.204 0.695 0.136 0.034 42 3.5 G_pariet_inf-Angular 2888 1904 8465 3.157 0.764 0.135 0.036 43 3.9 G_pariet_inf-Supramar 3293 1954 6088 2.457 0.631 0.106 0.024 29 3.1 G_parietal_sup 2712 1405 4069 2.204 0.730 0.105 0.024 25 2.7 G_postcentral 3020 1475 4872 2.471 0.698 0.090 0.028 29 3.6 G_precentral 3463 2082 7941 2.881 0.729 0.133 0.034 45 4.5 G_precuneus 852 493 2298 2.813 0.964 0.137 0.048 17 2.0 G_rectus 778 458 1335 2.822 1.341 0.075 0.024 5 0.8 G_subcallosal 678 362 1281 2.912 0.473 0.128 0.032 10 0.8 G_temp_sup-G_T_transv 2078 1307 8061 3.689 0.825 0.136 0.038 33 3.1 G_temp_sup-Lateral 694 449 2165 3.852 0.601 0.065 0.012 2 0.3 G_temp_sup-Plan_polar 851 573 1645 2.477 0.562 0.065 0.011 3 0.3 G_temp_sup-Plan_tempo 2794 1718 10062 3.593 0.837 0.136 0.050 52 5.2 G_temporal_inf 2964 1951 11760 3.680 0.770 0.144 0.044 60 5.4 G_temporal_middle 276 186 407 2.575 0.676 0.108 0.021 2 0.2 Lat_Fis-ant-Horizont 320 217 461 2.767 0.550 0.108 0.019 1 0.3 Lat_Fis-ant-Vertical 1099 737 1443 2.374 0.655 0.104 0.023 6 1.0 Lat_Fis-post 2302 1410 3089 1.954 0.623 0.130 0.035 28 3.5 Pole_occipital 1648 1070 6529 3.800 0.858 0.121 0.038 19 2.4 Pole_temporal 2033 1542 2490 1.940 0.931 0.145 0.033 25 2.7 S_calcarine 3125 2173 3526 1.777 0.553 0.103 0.020 21 2.6 S_central 1133 771 1622 2.318 0.438 0.096 0.013 6 0.6 S_cingul-Marginalis 463 325 966 3.613 0.434 0.098 0.023 2 0.4 S_circular_insula_ant 1347 964 2524 3.233 0.767 0.087 0.012 5 0.7 S_circular_insula_inf 1689 1173 2654 2.777 0.468 0.095 0.016 7 1.2 S_circular_insula_sup 902 634 1877 3.396 0.604 0.129 0.027 8 1.0 S_collat_transv_ant 517 350 618 2.083 0.649 0.143 0.031 6 0.7 S_collat_transv_post 2150 1502 3663 2.630 0.522 0.113 0.022 17 1.8 S_front_inf 1244 865 2011 2.682 0.562 0.115 0.024 9 1.2 S_front_middle 2861 1861 4899 2.680 0.574 0.098 0.019 18 2.0 S_front_sup 311 235 525 2.463 0.376 0.116 0.013 2 0.2 S_interm_prim-Jensen 3355 2235 4682 2.262 0.546 0.102 0.017 22 2.4 S_intrapariet&P_trans 739 485 1041 2.284 0.682 0.126 0.029 7 0.8 S_oc_middle&Lunatus 1381 964 1899 2.205 0.546 0.107 0.019 10 1.1 S_oc_sup&transversal 745 498 1224 2.767 0.621 0.126 0.033 7 0.9 S_occipital_ant 1122 761 1999 2.970 0.443 0.106 0.019 7 0.8 S_oc-temp_lat 2196 1526 3783 2.721 0.592 0.102 0.018 15 1.6 S_oc-temp_med&Lingual 302 216 563 2.916 0.587 0.124 0.028 2 0.3 S_orbital_lateral 612 458 914 2.624 0.729 0.131 0.023 6 0.5 S_orbital_med-olfact 1436 970 3179 3.348 0.714 0.119 0.032 12 1.9 S_orbital-H_Shaped 1796 1195 2394 2.282 0.641 0.114 0.024 16 1.6 S_parieto_occipital 748 459 1006 2.978 0.746 0.112 0.036 11 1.0 S_pericallosal 3274 2139 4216 2.030 0.550 0.109 0.021 25 2.7 S_postcentral 1307 868 1886 2.405 0.549 0.094 0.015 6 0.8 S_precentral-inf-part 1374 935 1984 2.514 0.503 0.090 0.016 7 0.8 S_precentral-sup-part 755 509 1760 3.663 0.853 0.114 0.018 5 0.6 S_suborbital 1128 792 1890 2.935 0.548 0.122 0.026 8 1.2 S_subparietal 1683 1165 3083 3.012 0.592 0.112 0.018 11 1.3 S_temporal_inf 5752 3918 10229 2.752 0.663 0.106 0.022 42 4.8 S_temporal_sup 388 260 582 2.703 0.429 0.109 0.018 3 0.2 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Fr 23. Feb 12:14:18 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 15689_T1_fs rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white... reading input pial surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test/15689_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 277086 Total vertex volume 273287 (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) = 1766996 mm^3 (det: 1.102495 ) lhCtxGM: 268173.730 267868.000 diff= 305.7 pctdiff= 0.114 rhCtxGM: 268287.733 268746.000 diff= -458.3 pctdiff=-0.171 lhCtxWM: 262563.790 263011.500 diff= -447.7 pctdiff=-0.171 rhCtxWM: 266031.420 267566.500 diff=-1535.1 pctdiff=-0.577 SubCortGMVol 67300.000 SupraTentVol 1185591.674 (1179005.000) diff=6586.674 pctdiff=0.556 SupraTentVolNotVent 1141081.674 (1134495.000) diff=6586.674 pctdiff=0.577 BrainSegVol 1352976.000 (1348423.000) diff=4553.000 pctdiff=0.337 BrainSegVolNotVent 1301808.000 (1299472.674) diff=2335.326 pctdiff=0.179 BrainSegVolNotVent 1301808.000 CerebellumVol 167113.000 VentChorVol 44510.000 3rd4th5thCSF 6658.000 CSFVol 2105.000, OptChiasmVol 200.000 MaskVol 1843183.000 902 523 2607 3.510 0.823 0.121 0.042 12 1.4 G&S_frontomargin 1660 903 3883 3.084 0.903 0.128 0.040 19 3.0 G&S_occipital_inf 1639 927 2227 2.050 0.582 0.090 0.018 10 1.3 G&S_paracentral 1419 887 2910 2.864 0.610 0.128 0.032 16 1.7 G&S_subcentral 1181 700 3561 3.455 0.714 0.136 0.050 17 2.3 G&S_transv_frontopol 3023 1967 7578 3.535 0.744 0.106 0.026 25 3.0 G&S_cingul-Ant 1095 726 2665 3.185 0.602 0.097 0.018 7 0.9 G&S_cingul-Mid-Ant 1111 756 2424 2.933 0.712 0.100 0.016 8 0.8 G&S_cingul-Mid-Post 653 400 1881 3.701 0.601 0.138 0.035 10 0.9 G_cingul-Post-dorsal 295 171 730 3.451 1.094 0.114 0.027 3 0.2 G_cingul-Post-ventral 1829 1110 2858 2.105 0.847 0.138 0.041 28 3.6 G_cuneus 1310 785 3932 3.362 0.596 0.128 0.037 19 2.0 G_front_inf-Opercular 373 228 1568 3.735 0.588 0.154 0.047 7 0.7 G_front_inf-Orbital 819 493 2601 3.469 0.661 0.128 0.054 12 1.6 G_front_inf-Triangul 4614 2612 11307 3.000 0.786 0.131 0.058 80 11.5 G_front_middle 6591 3755 16484 3.216 0.759 0.107 0.029 63 8.0 G_front_sup 540 364 1681 3.958 0.721 0.105 0.025 4 0.5 G_Ins_lg&S_cent_ins 833 506 2438 3.334 1.168 0.100 0.031 7 1.1 G_insular_short 2455 1199 4870 3.097 0.765 0.112 0.033 29 3.3 G_occipital_middle 1495 790 2389 2.667 0.609 0.104 0.030 13 2.0 G_occipital_sup 2627 1458 7564 3.472 0.821 0.130 0.055 45 5.9 G_oc-temp_lat-fusifor 3368 1901 5154 2.362 0.934 0.131 0.038 44 5.4 G_oc-temp_med-Lingual 1317 764 4583 3.794 0.937 0.101 0.041 20 2.6 G_oc-temp_med-Parahip 2654 1550 8338 3.459 1.040 0.138 0.064 51 7.3 G_orbital 3863 1991 9175 3.221 0.671 0.117 0.032 51 4.9 G_pariet_inf-Angular 3211 1764 7361 3.115 0.722 0.115 0.032 44 4.0 G_pariet_inf-Supramar 4075 2197 5797 2.202 0.581 0.104 0.022 37 3.8 G_parietal_sup 2586 1390 3274 1.918 0.626 0.104 0.024 21 2.7 G_postcentral 2880 1531 4384 2.286 0.640 0.100 0.030 26 3.7 G_precentral 3360 1928 7754 2.990 0.740 0.125 0.028 44 3.5 G_precuneus 894 528 2326 2.857 0.902 0.146 0.047 21 1.9 G_rectus 450 278 728 2.734 1.041 0.106 0.075 8 1.7 G_subcallosal 449 240 841 2.664 0.601 0.096 0.027 4 0.4 G_temp_sup-G_T_transv 2158 1288 6270 3.263 0.612 0.125 0.041 32 3.6 G_temp_sup-Lateral 896 599 2377 3.520 1.109 0.083 0.019 3 0.7 G_temp_sup-Plan_polar 1191 696 2226 2.550 0.640 0.107 0.027 13 1.3 G_temp_sup-Plan_tempo 3152 1706 9395 3.512 0.897 0.117 0.049 53 6.4 G_temporal_inf 2907 1804 11328 3.810 0.697 0.133 0.044 47 5.0 G_temporal_middle 360 251 527 2.449 0.529 0.102 0.019 2 0.3 Lat_Fis-ant-Horizont 69 48 116 3.095 0.537 0.145 0.028 1 0.1 Lat_Fis-ant-Vertical 1363 927 1920 2.445 0.701 0.110 0.024 8 1.3 Lat_Fis-post 3486 2055 6973 2.452 1.083 0.122 0.035 38 5.1 Pole_occipital 1828 1176 7877 3.947 0.798 0.135 0.047 27 3.2 Pole_temporal 1946 1293 2041 1.781 0.855 0.119 0.028 24 1.8 S_calcarine 3012 2151 3184 1.675 0.586 0.099 0.018 16 2.3 S_central 1179 841 1815 2.236 0.615 0.085 0.012 5 0.6 S_cingul-Marginalis 439 311 1016 3.797 0.512 0.112 0.027 2 0.5 S_circular_insula_ant 1143 795 1918 2.922 0.844 0.085 0.014 4 0.7 S_circular_insula_inf 1302 906 2116 2.807 0.508 0.100 0.019 5 1.1 S_circular_insula_sup 933 613 1786 3.324 0.638 0.094 0.019 5 0.6 S_collat_transv_ant 378 261 501 2.390 0.718 0.155 0.051 4 0.9 S_collat_transv_post 1942 1318 3300 2.395 0.565 0.113 0.023 13 1.9 S_front_inf 2210 1448 4240 2.573 0.768 0.124 0.034 22 3.0 S_front_middle 2600 1734 4539 2.619 0.591 0.107 0.024 19 2.3 S_front_sup 532 362 713 2.368 0.470 0.108 0.020 4 0.4 S_interm_prim-Jensen 3725 2365 5275 2.407 0.628 0.107 0.020 27 2.9 S_intrapariet&P_trans 839 469 1133 2.782 0.772 0.123 0.038 9 1.5 S_oc_middle&Lunatus 1435 967 1812 2.180 0.596 0.128 0.036 16 2.0 S_oc_sup&transversal 798 550 1339 2.608 0.658 0.118 0.024 6 0.8 S_occipital_ant 1465 984 2151 2.798 0.433 0.106 0.023 8 1.4 S_oc-temp_lat 1875 1301 2947 2.582 0.546 0.100 0.018 10 1.3 S_oc-temp_med&Lingual 526 368 780 2.242 0.546 0.115 0.021 3 0.5 S_orbital_lateral 688 489 1177 2.926 0.672 0.117 0.018 5 0.5 S_orbital_med-olfact 1055 725 2365 3.473 0.793 0.114 0.021 7 1.0 S_orbital-H_Shaped 2091 1310 2441 2.132 0.709 0.110 0.021 19 1.8 S_parieto_occipital 890 529 1306 3.221 1.154 0.128 0.027 14 0.7 S_pericallosal 2953 1935 3699 2.064 0.633 0.105 0.020 20 2.3 S_postcentral 1725 1174 2546 2.456 0.509 0.110 0.022 11 1.6 S_precentral-inf-part 1106 735 1631 2.498 0.539 0.117 0.025 10 1.1 S_precentral-sup-part 322 207 711 3.840 0.581 0.126 0.023 3 0.3 S_suborbital 1387 961 2661 2.966 0.590 0.115 0.022 10 1.1 S_subparietal 1468 989 2475 3.181 0.587 0.117 0.020 11 1.3 S_temporal_inf 6425 4437 12450 3.140 0.734 0.109 0.021 42 5.5 S_temporal_sup 275 168 336 2.633 0.443 0.121 0.024 2 0.3 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Fr 23. Feb 12:14:51 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 15689_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... 1578 labels changed using aseg relabeling using gibbs priors... 000: 2005 changed, 136705 examined... 001: 432 changed, 9100 examined... 002: 118 changed, 2464 examined... 003: 57 changed, 683 examined... 004: 37 changed, 328 examined... 005: 23 changed, 193 examined... 006: 14 changed, 136 examined... 007: 10 changed, 80 examined... 008: 3 changed, 52 examined... 009: 4 changed, 17 examined... 010: 3 changed, 17 examined... 011: 1 changed, 13 examined... 012: 1 changed, 7 examined... 013: 2 changed, 4 examined... 014: 2 changed, 14 examined... 015: 1 changed, 8 examined... 016: 2 changed, 11 examined... 017: 2 changed, 10 examined... 018: 2 changed, 12 examined... 019: 1 changed, 10 examined... 020: 1 changed, 7 examined... 021: 1 changed, 7 examined... 022: 1 changed, 7 examined... 023: 0 changed, 5 examined... 302 labels changed using aseg 000: 58 total segments, 25 labels (214 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 5 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 514 vertices marked for relabeling... 514 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 13 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Fr 23. Feb 12:15:04 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 15689_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... 1154 labels changed using aseg relabeling using gibbs priors... 000: 2022 changed, 140374 examined... 001: 494 changed, 9324 examined... 002: 154 changed, 2753 examined... 003: 57 changed, 874 examined... 004: 34 changed, 310 examined... 005: 27 changed, 207 examined... 006: 20 changed, 141 examined... 007: 17 changed, 106 examined... 008: 16 changed, 91 examined... 009: 4 changed, 84 examined... 010: 3 changed, 25 examined... 011: 4 changed, 21 examined... 012: 4 changed, 30 examined... 013: 5 changed, 26 examined... 014: 2 changed, 26 examined... 015: 2 changed, 12 examined... 016: 3 changed, 12 examined... 017: 2 changed, 13 examined... 018: 3 changed, 8 examined... 019: 1 changed, 15 examined... 020: 1 changed, 8 examined... 021: 1 changed, 7 examined... 022: 1 changed, 7 examined... 023: 1 changed, 6 examined... 024: 1 changed, 6 examined... 025: 0 changed, 7 examined... 295 labels changed using aseg 000: 58 total segments, 25 labels (428 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 515 vertices marked for relabeling... 515 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 14 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Fr 23. Feb 12:15:18 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 15689_T1_fs lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white... reading input pial surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test/15689_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 274300 Total vertex volume 270762 (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) = 1766996 mm^3 (det: 1.102495 ) lhCtxGM: 268173.730 267868.000 diff= 305.7 pctdiff= 0.114 rhCtxGM: 268287.733 268746.000 diff= -458.3 pctdiff=-0.171 lhCtxWM: 262563.790 263011.500 diff= -447.7 pctdiff=-0.171 rhCtxWM: 266031.420 267566.500 diff=-1535.1 pctdiff=-0.577 SubCortGMVol 67300.000 SupraTentVol 1185591.674 (1179005.000) diff=6586.674 pctdiff=0.556 SupraTentVolNotVent 1141081.674 (1134495.000) diff=6586.674 pctdiff=0.577 BrainSegVol 1352976.000 (1348423.000) diff=4553.000 pctdiff=0.337 BrainSegVolNotVent 1301808.000 (1299472.674) diff=2335.326 pctdiff=0.179 BrainSegVolNotVent 1301808.000 CerebellumVol 167113.000 VentChorVol 44510.000 3rd4th5thCSF 6658.000 CSFVol 2105.000, OptChiasmVol 200.000 MaskVol 1843183.000 1385 921 3358 3.296 0.655 0.102 0.015 11 0.9 caudalanteriorcingulate 3852 2247 6589 2.676 0.590 0.104 0.025 34 3.8 caudalmiddlefrontal 2781 1771 3157 1.709 0.559 0.128 0.029 33 3.5 cuneus 911 514 2724 3.418 0.921 0.107 0.041 9 1.6 entorhinal 4417 2929 11506 3.357 0.709 0.130 0.029 54 4.9 fusiform 6600 4457 14935 2.831 0.671 0.123 0.026 78 7.0 inferiorparietal 5202 3374 15285 3.370 0.788 0.124 0.037 69 7.4 inferiortemporal 1572 1039 3706 3.314 0.757 0.133 0.036 21 2.1 isthmuscingulate 7419 4664 12353 2.359 0.748 0.135 0.038 99 11.7 lateraloccipital 4043 2629 9885 3.262 0.983 0.131 0.039 50 6.5 lateralorbitofrontal 4477 3036 7935 2.273 0.948 0.132 0.028 52 5.2 lingual 2283 1445 5281 3.027 1.092 0.121 0.033 30 3.4 medialorbitofrontal 6506 4388 19649 3.385 0.799 0.129 0.033 90 8.6 middletemporal 1153 720 2361 2.817 0.794 0.077 0.014 6 0.7 parahippocampal 2631 1607 4221 2.381 0.643 0.082 0.013 12 1.5 paracentral 2269 1450 5614 3.138 0.690 0.120 0.024 27 2.3 parsopercularis 1101 657 2897 3.666 0.666 0.124 0.029 11 1.2 parsorbitalis 2291 1470 5188 3.005 0.680 0.120 0.028 23 2.4 parstriangularis 1653 1245 1446 1.325 0.302 0.154 0.036 23 2.3 pericalcarine 7757 4627 11043 2.120 0.766 0.104 0.023 61 7.4 postcentral 1668 1145 4011 3.219 0.724 0.113 0.023 18 1.5 posteriorcingulate 7413 4377 11481 2.410 0.662 0.099 0.023 62 7.0 precentral 6050 3837 11952 2.822 0.696 0.127 0.030 66 6.8 precuneus 1604 1009 4427 3.788 0.898 0.117 0.031 20 1.7 rostralanteriorcingulate 5878 3791 13793 3.074 0.661 0.130 0.033 72 7.8 rostralmiddlefrontal 11094 6980 24588 3.014 0.746 0.113 0.026 100 11.7 superiorfrontal 7109 4388 11218 2.310 0.625 0.105 0.022 57 6.3 superiorparietal 7249 4778 19604 3.224 0.926 0.104 0.025 61 7.1 superiortemporal 5407 3615 12446 2.803 0.783 0.123 0.028 62 6.0 supramarginal 914 486 1425 2.845 0.401 0.132 0.031 12 1.1 transversetemporal 2799 1873 6682 3.444 0.819 0.086 0.017 14 1.9 insula #----------------------------------------- #@# Parcellation Stats 3 rh Fr 23. Feb 12:15:49 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 15689_T1_fs rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white... reading input pial surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test/15689_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 277086 Total vertex volume 273287 (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) = 1766996 mm^3 (det: 1.102495 ) lhCtxGM: 268173.730 267868.000 diff= 305.7 pctdiff= 0.114 rhCtxGM: 268287.733 268746.000 diff= -458.3 pctdiff=-0.171 lhCtxWM: 262563.790 263011.500 diff= -447.7 pctdiff=-0.171 rhCtxWM: 266031.420 267566.500 diff=-1535.1 pctdiff=-0.577 SubCortGMVol 67300.000 SupraTentVol 1185591.674 (1179005.000) diff=6586.674 pctdiff=0.556 SupraTentVolNotVent 1141081.674 (1134495.000) diff=6586.674 pctdiff=0.577 BrainSegVol 1352976.000 (1348423.000) diff=4553.000 pctdiff=0.337 BrainSegVolNotVent 1301808.000 (1299472.674) diff=2335.326 pctdiff=0.179 BrainSegVolNotVent 1301808.000 CerebellumVol 167113.000 VentChorVol 44510.000 3rd4th5thCSF 6658.000 CSFVol 2105.000, OptChiasmVol 200.000 MaskVol 1843183.000 876 543 2372 3.546 0.585 0.115 0.020 10 0.8 caudalanteriorcingulate 4025 2443 7085 2.687 0.582 0.117 0.038 42 6.0 caudalmiddlefrontal 2474 1510 3699 2.099 0.826 0.137 0.038 38 4.3 cuneus 615 344 2571 4.246 0.819 0.107 0.066 15 2.2 entorhinal 4673 2849 11256 3.269 0.765 0.121 0.041 58 7.5 fusiform 8685 5052 17283 2.995 0.697 0.110 0.028 84 9.5 inferiorparietal 5967 3584 15511 3.371 0.842 0.116 0.038 76 9.2 inferiortemporal 1358 830 2964 3.268 0.857 0.126 0.029 17 1.4 isthmuscingulate 7638 4334 14450 2.725 0.947 0.124 0.037 86 12.1 lateraloccipital 3802 2389 9358 3.300 0.989 0.129 0.045 52 7.6 lateralorbitofrontal 4965 2952 7741 2.371 0.859 0.128 0.035 57 7.5 lingual 2306 1440 5500 3.203 0.944 0.127 0.038 36 3.5 medialorbitofrontal 6280 4121 19154 3.621 0.748 0.125 0.032 74 8.1 middletemporal 1014 656 2187 2.883 0.775 0.088 0.018 6 0.6 parahippocampal 2699 1605 4314 2.435 0.666 0.087 0.015 14 1.8 paracentral 1903 1216 4697 3.100 0.666 0.117 0.029 19 2.4 parsopercularis 1085 676 3237 3.254 0.801 0.126 0.042 14 1.8 parsorbitalis 1858 1206 4414 2.966 0.825 0.117 0.035 18 2.4 parstriangularis 1729 1138 1291 1.231 0.348 0.117 0.028 23 1.8 pericalcarine 7494 4617 10010 1.995 0.780 0.103 0.022 56 6.9 postcentral 1262 890 3284 3.250 0.823 0.122 0.025 15 1.2 posteriorcingulate 7040 4369 10541 2.269 0.627 0.109 0.026 60 7.9 precentral 6577 4053 12616 2.797 0.779 0.115 0.024 65 6.0 precuneus 1295 789 3469 3.581 1.156 0.117 0.042 19 2.8 rostralanteriorcingulate 6179 3825 14794 2.912 0.940 0.130 0.048 90 12.6 rostralmiddlefrontal 12266 7531 28608 3.091 0.745 0.107 0.029 107 14.3 superiorfrontal 8357 4876 11961 2.241 0.603 0.105 0.022 70 7.4 superiorparietal 7893 4990 19945 3.264 0.804 0.111 0.030 77 9.4 superiortemporal 6107 3634 11598 2.788 0.731 0.113 0.029 68 6.9 supramarginal 542 286 742 2.495 0.526 0.105 0.029 5 0.6 transversetemporal 2681 1824 6635 3.410 0.876 0.100 0.021 15 2.4 insula #----------------------------------------- #@# WM/GM Contrast lh Fr 23. Feb 12:16:21 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts pctsurfcon --s 15689_T1_fs --lh-only Log file is /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts/pctsurfcon.log Fr 23. Feb 12:16:21 CET 2018 setenv SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test cd /scratch/annadan1111/MABT1T2/test/15689_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 node016 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 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 mri_vol2surf --mov /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/tmp.pctsurfcon.29660/lh.wm.mgh --regheader 15689_T1_fs --cortex srcvol = /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_T1_fs/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99809 0.00566 -0.06157 -0.00002; -0.06141 -0.20643 0.97653 0.00000; 0.00718 -0.97845 -0.20638 0.00001; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /scratch/annadan1111/MABT1T2/test/15689_T1_fs/label/lh.cortex.label Reading surface /scratch/annadan1111/MABT1T2/test/15689_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 = 75350 Masking with /scratch/annadan1111/MABT1T2/test/15689_T1_fs/label/lh.cortex.label Writing to /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/tmp.pctsurfcon.29660/lh.wm.mgh Dim: 136705 1 1 mri_vol2surf --mov /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/tmp.pctsurfcon.29660/lh.gm.mgh --projfrac 0.3 --regheader 15689_T1_fs --cortex srcvol = /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_T1_fs/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99809 0.00566 -0.06157 -0.00002; -0.06141 -0.20643 0.97653 0.00000; 0.00718 -0.97845 -0.20638 0.00001; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /scratch/annadan1111/MABT1T2/test/15689_T1_fs/label/lh.cortex.label Reading surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Done reading source surface Reading thickness /scratch/annadan1111/MABT1T2/test/15689_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 = 86873 Masking with /scratch/annadan1111/MABT1T2/test/15689_T1_fs/label/lh.cortex.label Writing to /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/tmp.pctsurfcon.29660/lh.gm.mgh Dim: 136705 1 1 mri_concat /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/tmp.pctsurfcon.29660/lh.wm.mgh /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/tmp.pctsurfcon.29660/lh.gm.mgh --paired-diff-norm --mul 100 --o /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_T1_fs/surf/lh.w-g.pct.mgh mri_segstats --in /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.w-g.pct.mgh --annot 15689_T1_fs lh aparc --sum /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_T1_fs/surf/lh.w-g.pct.mgh --annot 15689_T1_fs lh aparc --sum /scratch/annadan1111/MABT1T2/test/15689_T1_fs/stats/lh.w-g.pct.stats --snr sysname Linux hostname node016 machine x86_64 user annadan1111 UseRobust 0 Constructing seg from annotation Reading annotation /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_T1_fs/surf/lh.w-g.pct.mgh Vertex Area is 0.641638 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 Fr 23. Feb 12:16:28 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts pctsurfcon --s 15689_T1_fs --rh-only Log file is /scratch/annadan1111/MABT1T2/test/15689_T1_fs/scripts/pctsurfcon.log Fr 23. Feb 12:16:28 CET 2018 setenv SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test cd /scratch/annadan1111/MABT1T2/test/15689_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 node016 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 FREESURFER_HOME /cm/shared/apps/freesurfer/6.0.0 mri_vol2surf --mov /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/tmp.pctsurfcon.29713/rh.wm.mgh --regheader 15689_T1_fs --cortex srcvol = /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_T1_fs/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99809 0.00566 -0.06157 -0.00002; -0.06141 -0.20643 0.97653 0.00000; 0.00718 -0.97845 -0.20638 0.00001; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /scratch/annadan1111/MABT1T2/test/15689_T1_fs/label/rh.cortex.label Reading surface /scratch/annadan1111/MABT1T2/test/15689_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 = 74926 Masking with /scratch/annadan1111/MABT1T2/test/15689_T1_fs/label/rh.cortex.label Writing to /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/tmp.pctsurfcon.29713/rh.wm.mgh Dim: 140374 1 1 mri_vol2surf --mov /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/tmp.pctsurfcon.29713/rh.gm.mgh --projfrac 0.3 --regheader 15689_T1_fs --cortex srcvol = /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_T1_fs/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99809 0.00566 -0.06157 -0.00002; -0.06141 -0.20643 0.97653 0.00000; 0.00718 -0.97845 -0.20638 0.00001; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /scratch/annadan1111/MABT1T2/test/15689_T1_fs/label/rh.cortex.label Reading surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Done reading source surface Reading thickness /scratch/annadan1111/MABT1T2/test/15689_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 = 86856 Masking with /scratch/annadan1111/MABT1T2/test/15689_T1_fs/label/rh.cortex.label Writing to /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/tmp.pctsurfcon.29713/rh.gm.mgh Dim: 140374 1 1 mri_concat /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/tmp.pctsurfcon.29713/rh.wm.mgh /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/tmp.pctsurfcon.29713/rh.gm.mgh --paired-diff-norm --mul 100 --o /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_T1_fs/surf/rh.w-g.pct.mgh mri_segstats --in /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.w-g.pct.mgh --annot 15689_T1_fs rh aparc --sum /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_T1_fs/surf/rh.w-g.pct.mgh --annot 15689_T1_fs rh aparc --sum /scratch/annadan1111/MABT1T2/test/15689_T1_fs/stats/rh.w-g.pct.stats --snr sysname Linux hostname node016 machine x86_64 user annadan1111 UseRobust 0 Constructing seg from annotation Reading annotation /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_T1_fs/surf/rh.w-g.pct.mgh Vertex Area is 0.616966 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 Fr 23. Feb 12:16:33 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 5955 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 8077 voxels changed to hypointensity... 13423 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Fr 23. Feb 12:16:56 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs mri_aparc2aseg --s 15689_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/test subject 15689_T1_fs outvol /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading lh pial surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.pial Loading lh annotations from /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_T1_fs/surf/rh.white Reading rh pial surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.pial Loading rh annotations from /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_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/test/15689_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 8.23 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 109 rescaling Left_Cerebral_Cortex from 61 --> 77 rescaling Left_Lateral_Ventricle from 13 --> 33 rescaling Left_Inf_Lat_Vent from 34 --> 36 rescaling Left_Cerebellum_White_Matter from 86 --> 93 rescaling Left_Cerebellum_Cortex from 60 --> 74 rescaling Left_Thalamus from 94 --> 107 rescaling Left_Thalamus_Proper from 84 --> 98 rescaling Left_Caudate from 75 --> 98 rescaling Left_Putamen from 80 --> 90 rescaling Left_Pallidum from 98 --> 104 rescaling Third_Ventricle from 25 --> 33 rescaling Fourth_Ventricle from 22 --> 30 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 75 rescaling Left_Amygdala from 56 --> 76 rescaling CSF from 32 --> 64 rescaling Left_Accumbens_area from 62 --> 79 rescaling Left_VentralDC from 87 --> 96 rescaling Right_Cerebral_White_Matter from 105 --> 106 rescaling Right_Cerebral_Cortex from 58 --> 79 rescaling Right_Lateral_Ventricle from 13 --> 28 rescaling Right_Inf_Lat_Vent from 25 --> 31 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 71 rescaling Right_Thalamus_Proper from 85 --> 95 rescaling Right_Caudate from 62 --> 89 rescaling Right_Putamen from 80 --> 93 rescaling Right_Pallidum from 97 --> 101 rescaling Right_Hippocampus from 53 --> 74 rescaling Right_Amygdala from 55 --> 74 rescaling Right_Accumbens_area from 65 --> 89 rescaling Right_VentralDC from 86 --> 92 rescaling Fifth_Ventricle from 40 --> 54 rescaling WM_hypointensities from 78 --> 79 rescaling non_WM_hypointensities from 40 --> 45 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 539547 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 257 changed. pass 2: 14 changed. pass 3: 3 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Fr 23. Feb 12:21:43 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs mri_aparc2aseg --s 15689_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/test subject 15689_T1_fs outvol /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading lh pial surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.pial Loading lh annotations from /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_T1_fs/surf/rh.white Reading rh pial surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.pial Loading rh annotations from /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_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/test/15689_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 8.23 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 109 rescaling Left_Cerebral_Cortex from 61 --> 77 rescaling Left_Lateral_Ventricle from 13 --> 33 rescaling Left_Inf_Lat_Vent from 34 --> 36 rescaling Left_Cerebellum_White_Matter from 86 --> 93 rescaling Left_Cerebellum_Cortex from 60 --> 74 rescaling Left_Thalamus from 94 --> 107 rescaling Left_Thalamus_Proper from 84 --> 98 rescaling Left_Caudate from 75 --> 98 rescaling Left_Putamen from 80 --> 90 rescaling Left_Pallidum from 98 --> 104 rescaling Third_Ventricle from 25 --> 33 rescaling Fourth_Ventricle from 22 --> 30 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 75 rescaling Left_Amygdala from 56 --> 76 rescaling CSF from 32 --> 64 rescaling Left_Accumbens_area from 62 --> 79 rescaling Left_VentralDC from 87 --> 96 rescaling Right_Cerebral_White_Matter from 105 --> 106 rescaling Right_Cerebral_Cortex from 58 --> 79 rescaling Right_Lateral_Ventricle from 13 --> 28 rescaling Right_Inf_Lat_Vent from 25 --> 31 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 71 rescaling Right_Thalamus_Proper from 85 --> 95 rescaling Right_Caudate from 62 --> 89 rescaling Right_Putamen from 80 --> 93 rescaling Right_Pallidum from 97 --> 101 rescaling Right_Hippocampus from 53 --> 74 rescaling Right_Amygdala from 55 --> 74 rescaling Right_Accumbens_area from 65 --> 89 rescaling Right_VentralDC from 86 --> 92 rescaling Fifth_Ventricle from 40 --> 54 rescaling WM_hypointensities from 78 --> 79 rescaling non_WM_hypointensities from 40 --> 45 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 539556 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 257 changed. pass 2: 14 changed. pass 3: 3 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Fr 23. Feb 12:26:20 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs mri_aparc2aseg --s 15689_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/test subject 15689_T1_fs outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading lh pial surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.pial Loading lh annotations from /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_T1_fs/surf/rh.white Reading rh pial surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.pial Loading rh annotations from /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_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/test/15689_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 8.23 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 109 rescaling Left_Cerebral_Cortex from 61 --> 77 rescaling Left_Lateral_Ventricle from 13 --> 33 rescaling Left_Inf_Lat_Vent from 34 --> 36 rescaling Left_Cerebellum_White_Matter from 86 --> 93 rescaling Left_Cerebellum_Cortex from 60 --> 74 rescaling Left_Thalamus from 94 --> 107 rescaling Left_Thalamus_Proper from 84 --> 98 rescaling Left_Caudate from 75 --> 98 rescaling Left_Putamen from 80 --> 90 rescaling Left_Pallidum from 98 --> 104 rescaling Third_Ventricle from 25 --> 33 rescaling Fourth_Ventricle from 22 --> 30 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 75 rescaling Left_Amygdala from 56 --> 76 rescaling CSF from 32 --> 64 rescaling Left_Accumbens_area from 62 --> 79 rescaling Left_VentralDC from 87 --> 96 rescaling Right_Cerebral_White_Matter from 105 --> 106 rescaling Right_Cerebral_Cortex from 58 --> 79 rescaling Right_Lateral_Ventricle from 13 --> 28 rescaling Right_Inf_Lat_Vent from 25 --> 31 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 71 rescaling Right_Thalamus_Proper from 85 --> 95 rescaling Right_Caudate from 62 --> 89 rescaling Right_Putamen from 80 --> 93 rescaling Right_Pallidum from 97 --> 101 rescaling Right_Hippocampus from 53 --> 74 rescaling Right_Amygdala from 55 --> 74 rescaling Right_Accumbens_area from 65 --> 89 rescaling Right_VentralDC from 86 --> 92 rescaling Fifth_Ventricle from 40 --> 54 rescaling WM_hypointensities from 78 --> 79 rescaling non_WM_hypointensities from 40 --> 45 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 539556 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 257 changed. pass 2: 14 changed. pass 3: 3 changed. pass 4: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Fr 23. Feb 12:30:59 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Fr 23. Feb 12:30:59 CET 2018 setenv SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test cd /scratch/annadan1111/MABT1T2/test/15689_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 node016 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 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/test/15689_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 node016 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 Fr 23. Feb 12:30:59 CET 2018 Ended at Fr 23. Feb 12:31:05 CET 2018 Apas2aseg-Run-Time-Sec 6 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Fr 23. Feb 12:31:05 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_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 15689_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 15689_T1_fs sysname Linux hostname node016 machine x86_64 user annadan1111 UseRobust 0 atlas_icv (eTIV) = 1766996 mm^3 (det: 1.102495 ) Computing euler number orig.nofix lheno = -98, rheno = -130 orig.nofix lhholes = 50, rhholes = 66 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 268173.730 267868.000 diff= 305.7 pctdiff= 0.114 rhCtxGM: 268287.733 268746.000 diff= -458.3 pctdiff=-0.171 lhCtxWM: 262563.790 263011.500 diff= -447.7 pctdiff=-0.171 rhCtxWM: 266031.420 267566.500 diff=-1535.1 pctdiff=-0.577 SubCortGMVol 67300.000 SupraTentVol 1185591.674 (1179005.000) diff=6586.674 pctdiff=0.556 SupraTentVolNotVent 1141081.674 (1134495.000) diff=6586.674 pctdiff=0.577 BrainSegVol 1352976.000 (1348423.000) diff=4553.000 pctdiff=0.337 BrainSegVolNotVent 1301808.000 (1299472.674) diff=2335.326 pctdiff=0.179 BrainSegVolNotVent 1301808.000 CerebellumVol 167113.000 VentChorVol 44510.000 3rd4th5thCSF 6658.000 CSFVol 2105.000, OptChiasmVol 200.000 MaskVol 1843183.000 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 Fr 23. Feb 12:33:32 CET 2018 /scratch/annadan1111/MABT1T2/test/15689_T1_fs mri_aparc2aseg --s 15689_T1_fs --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test subject 15689_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/test/15689_T1_fs/mri/aparc+aseg.mgz Reading lh white surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading lh pial surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.pial Loading lh annotations from /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_T1_fs/surf/rh.white Reading rh pial surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.pial Loading rh annotations from /scratch/annadan1111/MABT1T2/test/15689_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/test/15689_T1_fs/mri/ribbon.mgz Loading filled from /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 9168 vertices from left hemi Ripped 8762 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/test/15689_T1_fs/mri/aseg.mgz Loading Ctx Seg File /scratch/annadan1111/MABT1T2/test/15689_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 = 1067717 Used brute-force search on 756 voxels Fixing Parahip LH WM Found 10 clusters 0 k 2.000000 1 k 5.000000 2 k 4.000000 3 k 2.000000 4 k 1391.000000 5 k 1.000000 6 k 1.000000 7 k 7.000000 8 k 24.000000 9 k 1.000000 Fixing Parahip RH WM Found 14 clusters 0 k 2.000000 1 k 1.000000 2 k 2.000000 3 k 10.000000 4 k 1253.000000 5 k 1.000000 6 k 1.000000 7 k 1.000000 8 k 7.000000 9 k 2.000000 10 k 2.000000 11 k 1.000000 12 k 1.000000 13 k 1.000000 Writing output aseg to mri/wmparc.mgz mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 15689_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 15689_T1_fs --surf-wm-vol --ctab /cm/shared/apps/freesurfer/6.0.0/WMParcStatsLUT.txt --etiv sysname Linux hostname node016 machine x86_64 user annadan1111 UseRobust 0 atlas_icv (eTIV) = 1766996 mm^3 (det: 1.102495 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 268173.730 267868.000 diff= 305.7 pctdiff= 0.114 rhCtxGM: 268287.733 268746.000 diff= -458.3 pctdiff=-0.171 lhCtxWM: 262563.790 263011.500 diff= -447.7 pctdiff=-0.171 rhCtxWM: 266031.420 267566.500 diff=-1535.1 pctdiff=-0.577 SubCortGMVol 67300.000 SupraTentVol 1185591.674 (1179005.000) diff=6586.674 pctdiff=0.556 SupraTentVolNotVent 1141081.674 (1134495.000) diff=6586.674 pctdiff=0.577 BrainSegVol 1352976.000 (1348423.000) diff=4553.000 pctdiff=0.337 BrainSegVolNotVent 1301808.000 (1299472.674) diff=2335.326 pctdiff=0.179 BrainSegVolNotVent 1301808.000 CerebellumVol 167113.000 VentChorVol 44510.000 3rd4th5thCSF 6658.000 CSFVol 2105.000, OptChiasmVol 200.000 MaskVol 1843183.000 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/test/15689_T1_fs/label INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /scratch/annadan1111/MABT1T2/test; ln -s /cm/shared/apps/freesurfer/6.0.0/subjects/fsaverage; cd - #-------------------------------------------- #@# BA_exvivo Labels lh Fr 23. Feb 12:42:54 CET 2018 mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA1_exvivo.label --trgsubject 15689_T1_fs --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 469 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4598 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA2_exvivo.label --trgsubject 15689_T1_fs --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 617 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8526 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA3a_exvivo.label --trgsubject 15689_T1_fs --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 195 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4272 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA3b_exvivo.label --trgsubject 15689_T1_fs --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 414 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6397 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA4a_exvivo.label --trgsubject 15689_T1_fs --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 375 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6159 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA4p_exvivo.label --trgsubject 15689_T1_fs --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 294 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4364 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA6_exvivo.label --trgsubject 15689_T1_fs --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 1329 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14918 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA44_exvivo.label --trgsubject 15689_T1_fs --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 283 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4464 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA45_exvivo.label --trgsubject 15689_T1_fs --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 684 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4106 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.V1_exvivo.label --trgsubject 15689_T1_fs --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 1198 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5839 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.V2_exvivo.label --trgsubject 15689_T1_fs --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 2513 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 10627 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.MT_exvivo.label --trgsubject 15689_T1_fs --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 394 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2412 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject 15689_T1_fs --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 270 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1560 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject 15689_T1_fs --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 171 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1370 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 117 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1131 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 238 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2330 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 59 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1563 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 140 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2136 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 189 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2508 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 131 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1680 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 441 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7476 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 112 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2024 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 349 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1500 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 852 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4257 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 1168 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4502 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 133 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 646 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 137 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 607 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 136705 Number of reverse mapping hits = 57 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 507 mri_label2label: Done mris_label2annot --s 15689_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/test/15689_T1_fs/label cmdline mris_label2annot --s 15689_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 node016 machine x86_64 user annadan1111 subject 15689_T1_fs hemi lh SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test 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/test/15689_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 95030 unhit vertices Writing annot to /scratch/annadan1111/MABT1T2/test/15689_T1_fs/label/lh.BA_exvivo.annot mris_label2annot --s 15689_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/test/15689_T1_fs/label cmdline mris_label2annot --s 15689_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 node016 machine x86_64 user annadan1111 subject 15689_T1_fs hemi lh SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test 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/test/15689_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 112054 unhit vertices Writing annot to /scratch/annadan1111/MABT1T2/test/15689_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 15689_T1_fs lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white... reading input pial surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 274300 Total vertex volume 270762 (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) = 1766996 mm^3 (det: 1.102495 ) lhCtxGM: 268173.730 267868.000 diff= 305.7 pctdiff= 0.114 rhCtxGM: 268287.733 268746.000 diff= -458.3 pctdiff=-0.171 lhCtxWM: 262563.790 263011.500 diff= -447.7 pctdiff=-0.171 rhCtxWM: 266031.420 267566.500 diff=-1535.1 pctdiff=-0.577 SubCortGMVol 67300.000 SupraTentVol 1185591.674 (1179005.000) diff=6586.674 pctdiff=0.556 SupraTentVolNotVent 1141081.674 (1134495.000) diff=6586.674 pctdiff=0.577 BrainSegVol 1352976.000 (1348423.000) diff=4553.000 pctdiff=0.337 BrainSegVolNotVent 1301808.000 (1299472.674) diff=2335.326 pctdiff=0.179 BrainSegVolNotVent 1301808.000 CerebellumVol 167113.000 VentChorVol 44510.000 3rd4th5thCSF 6658.000 CSFVol 2105.000, OptChiasmVol 200.000 MaskVol 1843183.000 1314 656 2186 2.305 0.818 0.102 0.024 12 1.2 BA1_exvivo 4200 2581 6364 2.214 0.637 0.111 0.024 36 4.0 BA2_exvivo 1048 773 1016 1.630 0.407 0.147 0.033 12 1.4 BA3a_exvivo 2479 1547 3238 1.858 0.753 0.100 0.021 18 2.2 BA3b_exvivo 1827 998 2570 2.253 0.584 0.078 0.013 8 1.0 BA4a_exvivo 1376 867 1937 2.228 0.563 0.086 0.018 14 1.1 BA4p_exvivo 9566 5458 18070 2.792 0.698 0.098 0.023 76 9.0 BA6_exvivo 2138 1335 5159 3.061 0.759 0.115 0.024 25 2.1 BA44_exvivo 3031 1942 6815 2.962 0.655 0.122 0.029 33 3.5 BA45_exvivo 3284 2322 3398 1.471 0.479 0.136 0.031 38 4.0 V1_exvivo 7895 5062 11684 2.069 0.781 0.138 0.036 108 11.8 V2_exvivo 1955 1323 4970 3.005 0.646 0.140 0.038 28 2.7 MT_exvivo 815 447 2337 3.395 0.924 0.108 0.042 9 1.7 perirhinal_exvivo 747 493 1835 3.252 0.756 0.088 0.024 4 0.9 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 15689_T1_fs lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white... reading input pial surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 274300 Total vertex volume 270762 (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) = 1766996 mm^3 (det: 1.102495 ) lhCtxGM: 268173.730 267868.000 diff= 305.7 pctdiff= 0.114 rhCtxGM: 268287.733 268746.000 diff= -458.3 pctdiff=-0.171 lhCtxWM: 262563.790 263011.500 diff= -447.7 pctdiff=-0.171 rhCtxWM: 266031.420 267566.500 diff=-1535.1 pctdiff=-0.577 SubCortGMVol 67300.000 SupraTentVol 1185591.674 (1179005.000) diff=6586.674 pctdiff=0.556 SupraTentVolNotVent 1141081.674 (1134495.000) diff=6586.674 pctdiff=0.577 BrainSegVol 1352976.000 (1348423.000) diff=4553.000 pctdiff=0.337 BrainSegVolNotVent 1301808.000 (1299472.674) diff=2335.326 pctdiff=0.179 BrainSegVolNotVent 1301808.000 CerebellumVol 167113.000 VentChorVol 44510.000 3rd4th5thCSF 6658.000 CSFVol 2105.000, OptChiasmVol 200.000 MaskVol 1843183.000 831 389 1384 2.312 0.794 0.104 0.025 8 0.8 BA1_exvivo 1803 1074 2582 2.141 0.653 0.101 0.021 14 1.6 BA2_exvivo 908 661 845 1.625 0.417 0.149 0.033 10 1.3 BA3a_exvivo 1528 964 1436 1.458 0.326 0.083 0.015 8 1.0 BA3b_exvivo 1740 966 2439 2.238 0.589 0.073 0.012 7 1.0 BA4a_exvivo 1159 743 1627 2.228 0.566 0.092 0.019 13 1.1 BA4p_exvivo 5049 2872 9278 2.696 0.705 0.093 0.023 36 4.6 BA6_exvivo 1354 863 3609 3.188 0.780 0.119 0.023 16 1.3 BA44_exvivo 1342 797 3400 3.069 0.744 0.125 0.029 16 1.6 BA45_exvivo 3484 2471 3797 1.523 0.549 0.133 0.029 38 4.1 V1_exvivo 4049 2597 5555 1.934 0.725 0.143 0.037 59 6.1 V2_exvivo 550 360 1079 2.605 0.648 0.140 0.034 8 0.8 MT_exvivo 441 224 1221 3.268 0.992 0.109 0.039 6 0.8 perirhinal_exvivo 413 251 1078 3.385 0.701 0.074 0.021 1 0.4 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Fr 23. Feb 12:47:30 CET 2018 mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA1_exvivo.label --trgsubject 15689_T1_fs --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 492 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4454 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA2_exvivo.label --trgsubject 15689_T1_fs --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 680 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7367 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA3a_exvivo.label --trgsubject 15689_T1_fs --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 170 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4150 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA3b_exvivo.label --trgsubject 15689_T1_fs --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 340 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4862 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA4a_exvivo.label --trgsubject 15689_T1_fs --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 398 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6145 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA4p_exvivo.label --trgsubject 15689_T1_fs --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 182 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4655 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA6_exvivo.label --trgsubject 15689_T1_fs --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 928 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13184 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA44_exvivo.label --trgsubject 15689_T1_fs --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 543 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7455 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA45_exvivo.label --trgsubject 15689_T1_fs --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 724 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6079 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.V1_exvivo.label --trgsubject 15689_T1_fs --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 1211 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5938 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.V2_exvivo.label --trgsubject 15689_T1_fs --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 2571 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10587 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.MT_exvivo.label --trgsubject 15689_T1_fs --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 664 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2596 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject 15689_T1_fs --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 211 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1249 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject 15689_T1_fs --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 135 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 887 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 158 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 1034 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 307 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2995 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 66 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1764 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 164 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2347 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 103 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1491 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 52 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1541 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 553 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7512 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 101 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1113 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 82 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1260 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 720 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 3952 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 1173 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4610 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 66 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 334 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 177 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 871 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject 15689_T1_fs --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /scratch/annadan1111/MABT1T2/test/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 15689_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/test 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/test/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white Reading target registration /scratch/annadan1111/MABT1T2/test/15689_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 140374 Number of reverse mapping hits = 59 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 350 mri_label2label: Done mris_label2annot --s 15689_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/test/15689_T1_fs/label cmdline mris_label2annot --s 15689_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 node016 machine x86_64 user annadan1111 subject 15689_T1_fs hemi rh SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test 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/test/15689_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 100438 unhit vertices Writing annot to /scratch/annadan1111/MABT1T2/test/15689_T1_fs/label/rh.BA_exvivo.annot mris_label2annot --s 15689_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/test/15689_T1_fs/label cmdline mris_label2annot --s 15689_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 node016 machine x86_64 user annadan1111 subject 15689_T1_fs hemi rh SUBJECTS_DIR /scratch/annadan1111/MABT1T2/test 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/test/15689_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 117907 unhit vertices Writing annot to /scratch/annadan1111/MABT1T2/test/15689_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 15689_T1_fs rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white... reading input pial surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 277086 Total vertex volume 273287 (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) = 1766996 mm^3 (det: 1.102495 ) lhCtxGM: 268173.730 267868.000 diff= 305.7 pctdiff= 0.114 rhCtxGM: 268287.733 268746.000 diff= -458.3 pctdiff=-0.171 lhCtxWM: 262563.790 263011.500 diff= -447.7 pctdiff=-0.171 rhCtxWM: 266031.420 267566.500 diff=-1535.1 pctdiff=-0.577 SubCortGMVol 67300.000 SupraTentVol 1185591.674 (1179005.000) diff=6586.674 pctdiff=0.556 SupraTentVolNotVent 1141081.674 (1134495.000) diff=6586.674 pctdiff=0.577 BrainSegVol 1352976.000 (1348423.000) diff=4553.000 pctdiff=0.337 BrainSegVolNotVent 1301808.000 (1299472.674) diff=2335.326 pctdiff=0.179 BrainSegVolNotVent 1301808.000 CerebellumVol 167113.000 VentChorVol 44510.000 3rd4th5thCSF 6658.000 CSFVol 2105.000, OptChiasmVol 200.000 MaskVol 1843183.000 1063 617 1511 1.886 0.667 0.119 0.030 10 1.4 BA1_exvivo 3785 2269 4876 2.074 0.632 0.097 0.020 24 3.0 BA2_exvivo 1090 794 1002 1.580 0.504 0.138 0.031 10 1.4 BA3a_exvivo 2065 1327 2262 1.572 0.555 0.097 0.019 14 1.8 BA3b_exvivo 1548 913 2385 2.245 0.709 0.086 0.016 8 1.1 BA4a_exvivo 1244 815 1785 2.208 0.598 0.084 0.014 5 0.7 BA4p_exvivo 7556 4288 13770 2.748 0.716 0.102 0.027 63 8.6 BA6_exvivo 3371 2186 7265 2.863 0.656 0.115 0.027 33 3.7 BA44_exvivo 3747 2408 9904 2.993 0.842 0.125 0.040 43 6.0 BA45_exvivo 3423 2191 5136 1.814 1.047 0.126 0.030 45 4.0 V1_exvivo 7748 4542 12311 2.440 0.872 0.128 0.038 91 12.9 V2_exvivo 2240 1300 4277 2.913 0.740 0.119 0.035 22 3.5 MT_exvivo 694 381 2627 4.117 0.804 0.105 0.063 16 2.2 perirhinal_exvivo 362 236 1327 3.914 0.718 0.094 0.015 2 0.3 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 15689_T1_fs rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /scratch/annadan1111/MABT1T2/test/15689_T1_fs/mri/wm.mgz... reading input surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white... reading input pial surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.pial... reading input white surface /scratch/annadan1111/MABT1T2/test/15689_T1_fs/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 277086 Total vertex volume 273287 (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) = 1766996 mm^3 (det: 1.102495 ) lhCtxGM: 268173.730 267868.000 diff= 305.7 pctdiff= 0.114 rhCtxGM: 268287.733 268746.000 diff= -458.3 pctdiff=-0.171 lhCtxWM: 262563.790 263011.500 diff= -447.7 pctdiff=-0.171 rhCtxWM: 266031.420 267566.500 diff=-1535.1 pctdiff=-0.577 SubCortGMVol 67300.000 SupraTentVol 1185591.674 (1179005.000) diff=6586.674 pctdiff=0.556 SupraTentVolNotVent 1141081.674 (1134495.000) diff=6586.674 pctdiff=0.577 BrainSegVol 1352976.000 (1348423.000) diff=4553.000 pctdiff=0.337 BrainSegVolNotVent 1301808.000 (1299472.674) diff=2335.326 pctdiff=0.179 BrainSegVolNotVent 1301808.000 CerebellumVol 167113.000 VentChorVol 44510.000 3rd4th5thCSF 6658.000 CSFVol 2105.000, OptChiasmVol 200.000 MaskVol 1843183.000 769 423 1076 1.875 0.625 0.115 0.029 6 1.0 BA1_exvivo 2206 1276 2812 2.044 0.575 0.088 0.017 12 1.5 BA2_exvivo 962 706 810 1.557 0.419 0.141 0.030 9 1.2 BA3a_exvivo 1614 1097 1521 1.371 0.334 0.089 0.016 9 1.1 BA3b_exvivo 1002 568 1538 2.274 0.674 0.091 0.017 6 0.8 BA4a_exvivo 991 664 1480 2.277 0.655 0.088 0.014 4 0.6 BA4p_exvivo 4904 2755 8466 2.615 0.711 0.106 0.030 46 6.4 BA6_exvivo 847 506 2250 3.280 0.693 0.116 0.035 10 1.2 BA44_exvivo 805 508 2505 3.442 0.655 0.130 0.047 10 1.4 BA45_exvivo 3250 2067 4529 1.755 1.013 0.125 0.029 43 3.7 V1_exvivo 4090 2465 6877 2.297 0.831 0.132 0.037 48 6.5 V2_exvivo 289 195 458 2.410 0.559 0.125 0.034 2 0.4 MT_exvivo 446 244 1636 3.991 0.874 0.110 0.081 14 2.0 perirhinal_exvivo 292 169 1225 4.346 0.615 0.092 0.017 2 0.2 entorhinal_exvivo Started at Do 22. Feb 23:20:15 CET 2018 Ended at Fr 23. Feb 12:52:11 CET 2018 #@#%# recon-all-run-time-hours 13,532 recon-all -s 15689_T1_fs finished without error at Fr 23. Feb 12:52:11 CET 2018 New invocation of recon-all Mon Mar 5 03:47:08 PST 2018 /home/mindful/Desktop/MABT1T2_cross/15689_T1_fs /home/mindful/Desktop/freesurfer/bin/recon-all -skullstrip -clean-bm -gcut -subjid 15689_T1_fs subjid 15689_T1_fs setenv SUBJECTS_DIR /home/mindful/Desktop/MABT1T2_cross FREESURFER_HOME /home/mindful/Desktop/freesurfer Actual FREESURFER_HOME /home/mindful/Desktop/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux ubuntu 4.13.0-36-generic #40~16.04.1-Ubuntu SMP Fri Feb 16 23:25:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 15483 maxlocks unlimited maxsignal 15483 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 4016400 1487728 2240000 75824 288672 2200796 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: 2018/03/05-11:47:08-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:08-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:09-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/05-11:47:09-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:09-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:09-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/05-11:47:10-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/05-11:47:10-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/05-11:47:10-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/05-11:47:10-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/05-11:47:10-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/05-11:47:10-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:11-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:11-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/05-11:47:11-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:11-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:11-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:11-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:11-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:11-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:12-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/05-11:47:12-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:12-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:12-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:12-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/05-11:47:12-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:12-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/05-11:47:12-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:13-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:13-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:13-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:13-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:13-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:13-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:13-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:13-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:14-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:14-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/05-11:47:14-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: mindful Machine: ubuntu Platform: Linux PlatformVersion: 4.13.0-36-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/mindful/Desktop/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /home/mindful/Desktop/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### mv -f /home/mindful/Desktop/MABT1T2_cross/15689_T1_fs/mri/brainmask.mgz /home/mindful/Desktop/MABT1T2_cross/15689_T1_fs/trash #-------------------------------------------- #@# Skull Stripping Mon Mar 5 03:47:14 PST 2018 /home/mindful/Desktop/MABT1T2_cross/15689_T1_fs/mri mri_watershed -rusage /home/mindful/Desktop/MABT1T2_cross/15689_T1_fs/touch/rusage.mri_watershed.dat -T1 -brain_atlas /home/mindful/Desktop/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=129 y=116 z=126 r=87 first estimation of the main basin volume: 2826542 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=110, y=98, z=84, 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=355857124 voxels, voxel volume =1.000 = 355857124 mmm3 = 355857.120 cm3 done. PostAnalyze...Basin Prior 58 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=129,y=120, z=120, r=10557 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=5, CSF_MAX=54 , nb = 42421 RIGHT_CER CSF_MIN=0, CSF_intensity=5, CSF_MAX=17 , nb = -1031592417 LEFT_CER CSF_MIN=0, CSF_intensity=6, CSF_MAX=18 , nb = 1100526356 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=75 , nb = -1061078936 LEFT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=63 , nb = 1079263664 OTHER CSF_MIN=0, CSF_intensity=4, CSF_MAX=12 , nb = 1081603304 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 54, 57, 60, 85 after analyzing : 54, 59, 60, 65 RIGHT_CER before analyzing : 17, 29, 59, 86 after analyzing : 17, 49, 59, 58 LEFT_CER before analyzing : 18, 30, 61, 92 after analyzing : 18, 50, 61, 60 RIGHT_BRAIN before analyzing : 75, 64, 61, 85 after analyzing : 42, 64, 64, 69 LEFT_BRAIN before analyzing : 63, 60, 60, 84 after analyzing : 38, 60, 60, 66 OTHER before analyzing : 12, 20, 27, 34 after analyzing : 12, 24, 27, 26 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...74 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.010 curvature mean = 72.676, std = 7.041 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 5.17, sigma = 7.38 after rotation: sse = 5.17, sigma = 7.38 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 6.45, its var is 8.51 before Erosion-Dilatation 3.98% of inacurate vertices after Erosion-Dilatation 5.61% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...42 iterations mri_strip_skull: done peeling brain Brain Size = 1844379 voxels, voxel volume = 1.000 mm3 = 1844379 mmm3 = 1844.379 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 16.412661 mri_watershed stimesec 0.863405 mri_watershed ru_maxrss 843312 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 214306 mri_watershed ru_majflt 9 mri_watershed ru_nswap 0 mri_watershed ru_inblock 167232 mri_watershed ru_oublock 2688 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 58 mri_watershed ru_nivcsw 1585 mri_watershed done rm -f brainmask.gcuts.mgz mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz brainmask.gcuts.mgz INFO: Care must be taken to thoroughly inspect your data when using mri_gcut. In particular, inspect the edges of gm and cerebellum for over-aggressive cutting. Add -segmentation brainmask.gcuts.mgz to the tkmedit command string to view the voxels which gcut has removed. Killed Linux ubuntu 4.13.0-36-generic #40~16.04.1-Ubuntu SMP Fri Feb 16 23:25:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 15689_T1_fs exited with ERRORS at Mon Mar 5 03:47:39 PST 2018 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting