Sat Oct 7 16:10:09 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all -subjid 0050660 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/CMU_a_2/0050660/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2 subjid 0050660 setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Actual FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux tars-542 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse 10485760 kbytes vmemoryuse unlimited descriptors 65536 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 65993388 54952940 11040448 1752720 0 51971412 -/+ buffers/cache: 2981528 63011860 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: 2017/10/07-14:10:09-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/10/07-14:10:10-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: ntraut Machine: tars-542 Platform: Linux PlatformVersion: 2.6.32-696.3.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /pasteur/homes/ntraut/bin/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 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/CMU_a_2/0050660/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/orig/001.mgz mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/CMU_a_2/0050660/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/CMU_a_2/0050660/session_1/anat_1/mprage.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sat Oct 7 16:10:13 CEST 2017 Found 1 runs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/orig.mgz --conform mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/orig.mgz... mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Sat Oct 7 16:10:21 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri /pasteur/homes/ntraut/bin/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 tars-542 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sat Oct 7 16:10:21 CEST 2017 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.1777 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1777/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.1777/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.1777/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 16:10:23 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.1777/nu0.mnc ./tmp.mri_nu_correct.mni.1777/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1777/0/ -iterations 1000 -distance 50 [ntraut@tars-542:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/] [2017-10-07 16:10:24] running: /pasteur/homes/ntraut/bin/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.1777/0/ ./tmp.mri_nu_correct.mni.1777/nu0.mnc ./tmp.mri_nu_correct.mni.1777/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 39 CV of field change: 0.00099166 mri_convert ./tmp.mri_nu_correct.mni.1777/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.1777/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.1777/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) 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... Sat Oct 7 16:11:25 CEST 2017 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Sat Oct 7 16:11:26 CEST 2017 Ended at Sat Oct 7 16:11:58 CEST 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sat Oct 7 16:12:00 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.3137, pval=0.0254 >= threshold=0.0050) awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/transforms/talairach_avi.log tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/transforms/talairach_avi.log TalAviQA: 0.97325 z-score: -1 #-------------------------------------------- #@# Nu Intensity Correction Sat Oct 7 16:12:00 CEST 2017 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri /pasteur/homes/ntraut/bin/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 tars-542 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Sat Oct 7 16:12:00 CEST 2017 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.2541 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2541/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.2541/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.2541/nu0.mnc... -------------------------------------------------------- Iteration 1 Sat Oct 7 16:12:02 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.2541/nu0.mnc ./tmp.mri_nu_correct.mni.2541/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.2541/0/ [ntraut@tars-542:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/] [2017-10-07 16:12:02] running: /pasteur/homes/ntraut/bin/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.2541/0/ ./tmp.mri_nu_correct.mni.2541/nu0.mnc ./tmp.mri_nu_correct.mni.2541/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 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Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 39 CV of field change: 0.000952228 -------------------------------------------------------- Iteration 2 Sat Oct 7 16:12:49 CEST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.2541/nu1.mnc ./tmp.mri_nu_correct.mni.2541/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.2541/1/ [ntraut@tars-542:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/] [2017-10-07 16:12:49] running: /pasteur/homes/ntraut/bin/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.2541/1/ ./tmp.mri_nu_correct.mni.2541/nu1.mnc ./tmp.mri_nu_correct.mni.2541/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 8 CV of field change: 0.00093359 mri_binarize --i ./tmp.mri_nu_correct.mni.2541/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.2541/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.2541/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.2541/ones.mgz sysname Linux hostname tars-542 machine x86_64 user ntraut input ./tmp.mri_nu_correct.mni.2541/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.2541/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.2541/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2541/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2541/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.2541/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2541/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2541/input.mean.dat sysname Linux hostname tars-542 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.2541/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.2541/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2541/ones.mgz --i ./tmp.mri_nu_correct.mni.2541/nu2.mnc --sum ./tmp.mri_nu_correct.mni.2541/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2541/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.2541/ones.mgz --i ./tmp.mri_nu_correct.mni.2541/nu2.mnc --sum ./tmp.mri_nu_correct.mni.2541/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2541/output.mean.dat sysname Linux hostname tars-542 machine x86_64 user ntraut UseRobust 0 Loading ./tmp.mri_nu_correct.mni.2541/ones.mgz Loading ./tmp.mri_nu_correct.mni.2541/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.2541/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.2541/nu2.mnc ./tmp.mri_nu_correct.mni.2541/nu2.mnc mul .97354204708638120492 Saving result to './tmp.mri_nu_correct.mni.2541/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.2541/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.2541/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.2541/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) 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 7 seconds. mapping ( 9, 129) to ( 3, 110) Sat Oct 7 16:13:50 CEST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Sat Oct 7 16:13:51 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 1.03450 0.05910 -0.05801 6.31035; -0.02976 0.83984 0.56017 -36.56604; 0.09372 -0.60837 1.10812 -64.27377; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 18 Starting OpenSpline(): npoints = 18 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 81 (81), valley at 39 (39) csf peak at 41, setting threshold to 67 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 81 (81), valley at 39 (39) csf peak at 41, setting threshold to 67 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 0 seconds. #-------------------------------------------- #@# Skull Stripping Sat Oct 7 16:15:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /pasteur/homes/ntraut/bin/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 = 2 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/pasteur/homes/ntraut/bin/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=19.0 skull bounding box = (39, 27, 14) --> (207, 172, 214) using (95, 75, 114) as brain centroid... mean wm in atlas = 108, using box (74,57,89) --> (115, 92,138) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 106 +- 5.1 after smoothing, mri peak at 106, scaling input intensities by 1.019 scaling channel 0 by 1.01887 initial log_p = -4.568 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.575286 @ (9.091, 27.273, -9.091) max log p = -4.504565 @ (-4.545, -13.636, 4.545) max log p = -4.485532 @ (-2.273, 2.273, -2.273) max log p = -4.466875 @ (1.136, -1.136, 1.136) max log p = -4.447379 @ (-0.568, 1.705, -0.568) max log p = -4.447379 @ (0.000, 0.000, 0.000) Found translation: (2.8, 16.5, -6.3): log p = -4.447 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.272, old_max_log_p =-4.447 (thresh=-4.4) 1.06375 0.00000 0.00000 -4.93878; 0.00000 1.07062 0.61813 -53.42551; 0.00000 -0.57500 0.99593 55.63156; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.186, old_max_log_p =-4.272 (thresh=-4.3) 1.06375 0.00000 0.00000 -4.93878; 0.00000 1.18814 0.54970 -58.44056; 0.00000 -0.32386 0.93208 42.46684; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.186, old_max_log_p =-4.186 (thresh=-4.2) 1.06375 0.00000 0.00000 -4.93878; 0.00000 1.18814 0.54970 -58.44056; 0.00000 -0.32386 0.93208 42.46684; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.137, old_max_log_p =-4.186 (thresh=-4.2) 1.06113 -0.01141 -0.07578 3.45823; 0.04251 1.20165 0.69975 -80.27608; 0.06471 -0.47812 0.84930 60.03991; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.135, old_max_log_p =-4.137 (thresh=-4.1) 1.04325 -0.03931 -0.01826 2.25901; 0.04113 1.23946 0.68418 -82.62960; -0.00354 -0.44506 0.89123 59.91553; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.112, old_max_log_p =-4.135 (thresh=-4.1) 1.04532 -0.04954 -0.02397 4.29910; 0.04962 1.22924 0.70650 -83.66947; -0.00469 -0.47589 0.87520 64.93446; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.110, old_max_log_p =-4.112 (thresh=-4.1) 1.04532 -0.04954 -0.02397 4.29910; 0.04962 1.22924 0.70650 -83.66947; -0.00469 -0.47533 0.87417 64.98835; 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 1.04532 -0.04954 -0.02397 4.29910; 0.04962 1.22924 0.70650 -83.66947; -0.00469 -0.47533 0.87417 64.98835; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.04532 -0.04954 -0.02397 4.29910; 0.04962 1.22924 0.70650 -83.66947; -0.00469 -0.47533 0.87417 64.98835; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.04532 -0.04954 -0.02397 4.29910; 0.04962 1.22924 0.70650 -83.66947; -0.00469 -0.47533 0.87417 64.98835; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.110 (old=-4.568) transform before final EM align: 1.04532 -0.04954 -0.02397 4.29910; 0.04962 1.22924 0.70650 -83.66947; -0.00469 -0.47533 0.87417 64.98835; 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 1.04532 -0.04954 -0.02397 4.29910; 0.04962 1.22924 0.70650 -83.66947; -0.00469 -0.47533 0.87417 64.98835; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.04532 -0.04954 -0.02397 4.29910; 0.04962 1.22924 0.70650 -83.66947; -0.00469 -0.47533 0.87417 64.98835; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.5 tol 0.000000 final transform: 1.04532 -0.04954 -0.02397 4.29910; 0.04962 1.22924 0.70650 -83.66947; -0.00469 -0.47533 0.87417 64.98835; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1176.780102 mri_em_register stimesec 1.087834 mri_em_register ru_maxrss 609824 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157601 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 174 mri_em_register ru_nivcsw 5745 registration took 10 minutes and 13 seconds. mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mri_watershed.dat -T1 -brain_atlas /pasteur/homes/ntraut/bin/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=123 y=95 z=106 r=69 first estimation of the main basin volume: 1410028 voxels Looking for seedpoints 2 found in the cerebellum 14 found in the rest of the brain global maximum in x=144, y=92, z=76, Imax=255 CSF=18, 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=7541118642 voxels, voxel volume =1.000 = 7541118642 mmm3 = 7541118.464 cm3 done. PostAnalyze...Basin Prior 51 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=123,y=105, z=106, r=10367 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 39104 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1050308968 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1046739996 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=56 , nb = -1077193073 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=43 , nb = 1065464322 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1078504670 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 5, 10, 53, 76 after analyzing : 5, 38, 53, 47 RIGHT_CER before analyzing : 4, 9, 60, 79 after analyzing : 4, 43, 60, 52 LEFT_CER before analyzing : 4, 8, 56, 76 after analyzing : 4, 40, 56, 49 RIGHT_BRAIN before analyzing : 56, 53, 53, 77 after analyzing : 32, 53, 53, 59 LEFT_BRAIN before analyzing : 43, 48, 52, 76 after analyzing : 43, 50, 52, 56 OTHER before analyzing : 4, 12, 76, 91 after analyzing : 4, 54, 76, 63 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...66 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 70.412, std = 8.191 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 5.83, sigma = 10.94 after rotation: sse = 5.83, sigma = 10.94 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 8.95, its var is 16.76 before Erosion-Dilatation 9.16% of inacurate vertices after Erosion-Dilatation 11.74% 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...43 iterations mri_strip_skull: done peeling brain Brain Size = 1688594 voxels, voxel volume = 1.000 mm3 = 1688594 mmm3 = 1688.594 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 23.246466 mri_watershed stimesec 0.378942 mri_watershed ru_maxrss 819116 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 212123 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 2672 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 1299 mri_watershed ru_nivcsw 87 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sat Oct 7 16:26:28 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/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 = 2 == reading 1 input volumes... logging results to talairach.log reading '/pasteur/homes/ntraut/bin/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=28.0 skull bounding box = (53, 41, 29) --> (192, 172, 191) using (99, 85, 110) as brain centroid... mean wm in atlas = 107, using box (82,69,90) --> (116, 101,129) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 106 +- 4.7 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 initial log_p = -4.223 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.234888 @ (0.000, 0.000, 0.000) max log p = -4.040623 @ (4.545, 13.636, -4.545) max log p = -4.013413 @ (-2.273, 2.273, -2.273) max log p = -3.997553 @ (1.136, 1.136, 1.136) max log p = -3.957727 @ (-0.568, 0.568, -1.705) max log p = -3.957727 @ (0.000, 0.000, 0.000) Found translation: (2.8, 17.6, -7.4): log p = -3.958 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.684, old_max_log_p =-3.958 (thresh=-4.0) 0.99144 -0.13262 -0.06526 24.74865; 0.13053 1.00733 0.49572 -55.23638; 0.00000 -0.53750 0.76973 80.74652; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.684, old_max_log_p =-3.684 (thresh=-3.7) 0.99144 -0.13262 -0.06526 24.74865; 0.13053 1.00733 0.49572 -55.23638; 0.00000 -0.53750 0.76973 80.74652; 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=-3.599, old_max_log_p =-3.684 (thresh=-3.7) 1.05319 -0.05904 -0.06662 9.36601; 0.06143 1.00903 0.46828 -42.19876; 0.03837 -0.52483 0.81343 68.17387; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.594, old_max_log_p =-3.599 (thresh=-3.6) 1.03344 -0.05793 -0.06537 11.56671; 0.06383 1.00991 0.50392 -46.38089; 0.03634 -0.55756 0.79768 73.47760; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.590, old_max_log_p =-3.594 (thresh=-3.6) 1.02903 -0.07435 -0.10754 18.29556; 0.09633 1.02573 0.47428 -50.75941; 0.07084 -0.51598 0.79595 63.22182; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.590, old_max_log_p =-3.590 (thresh=-3.6) 1.02903 -0.07435 -0.10754 18.29556; 0.09633 1.02573 0.47428 -50.75941; 0.07084 -0.51598 0.79595 63.22182; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.564, old_max_log_p =-3.590 (thresh=-3.6) 1.02854 -0.09137 -0.11521 20.95689; 0.11237 1.03631 0.46099 -51.46078; 0.07233 -0.49854 0.80266 60.49803; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.563, old_max_log_p =-3.564 (thresh=-3.6) 1.03064 -0.08302 -0.11151 19.43493; 0.10442 1.03170 0.46792 -50.75214; 0.07140 -0.50700 0.79886 62.36522; 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 1.03064 -0.08302 -0.11151 19.43493; 0.10442 1.03170 0.46792 -50.75214; 0.07140 -0.50700 0.79886 62.36522; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.03064 -0.08302 -0.11151 19.43493; 0.10442 1.03170 0.46792 -50.75214; 0.07140 -0.50700 0.79886 62.36522; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.03064 -0.08302 -0.11151 19.43493; 0.10442 1.03170 0.46792 -50.75214; 0.07140 -0.50700 0.79886 62.36522; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.563 (old=-4.223) transform before final EM align: 1.03064 -0.08302 -0.11151 19.43493; 0.10442 1.03170 0.46792 -50.75214; 0.07140 -0.50700 0.79886 62.36522; 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 1.03064 -0.08302 -0.11151 19.43493; 0.10442 1.03170 0.46792 -50.75214; 0.07140 -0.50700 0.79886 62.36522; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.03064 -0.08302 -0.11151 19.43493; 0.10442 1.03170 0.46792 -50.75214; 0.07140 -0.50700 0.79886 62.36522; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.0 tol 0.000000 final transform: 1.03064 -0.08302 -0.11151 19.43493; 0.10442 1.03170 0.46792 -50.75214; 0.07140 -0.50700 0.79886 62.36522; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1186.531619 mri_em_register stimesec 1.230812 mri_em_register ru_maxrss 599052 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 158954 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 189 mri_em_register ru_nivcsw 3631 registration took 10 minutes and 15 seconds. #-------------------------------------- #@# CA Normalize Sat Oct 7 16:36:43 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/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 '/pasteur/homes/ntraut/bin/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=24.0 skull bounding box = (53, 40, 28) --> (192, 172, 192) using (99, 84, 110) as brain centroid... mean wm in atlas = 107, using box (82,68,90) --> (116, 100,130) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 106 +- 4.7 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 using 246344 sample points... INFO: compute sample coordinates transform 1.03064 -0.08302 -0.11151 19.43493; 0.10442 1.03170 0.46792 -50.75214; 0.07140 -0.50700 0.79886 62.36522; 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 (118, 43, 29) --> (189, 159, 202) Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0 0 of 228 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (60, 45, 34) --> (129, 154, 203) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 124 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (125, 130, 69) --> (175, 168, 127) Left_Cerebellum_White_Matter: limiting intensities to 99.0 --> 132.0 0 of 12 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 131, 70) --> (126, 169, 130) Right_Cerebellum_White_Matter: limiting intensities to 105.0 --> 132.0 0 of 13 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (110, 112, 101) --> (146, 170, 139) Brain_Stem: limiting intensities to 92.0 --> 132.0 0 of 13 (0.0%) samples deleted using 390 total control points for intensity normalization... bias field = 0.935 +- 0.065 0 of 390 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (118, 43, 29) --> (189, 159, 202) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 383 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (60, 45, 34) --> (129, 154, 203) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0 18 of 229 (7.9%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (125, 130, 69) --> (175, 168, 127) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 9 of 91 (9.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 131, 70) --> (126, 169, 130) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 4 of 79 (5.1%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (110, 112, 101) --> (146, 170, 139) Brain_Stem: limiting intensities to 88.0 --> 132.0 19 of 93 (20.4%) samples deleted using 875 total control points for intensity normalization... bias field = 0.993 +- 0.073 1 of 811 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (118, 43, 29) --> (189, 159, 202) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 390 (0.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (60, 45, 34) --> (129, 154, 203) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 1 of 292 (0.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (125, 130, 69) --> (175, 168, 127) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 56 of 117 (47.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 131, 70) --> (126, 169, 130) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 69 of 146 (47.3%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (110, 112, 101) --> (146, 170, 139) Brain_Stem: limiting intensities to 88.0 --> 132.0 72 of 154 (46.8%) samples deleted using 1099 total control points for intensity normalization... bias field = 0.996 +- 0.060 4 of 893 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 46 seconds. #-------------------------------------- #@# CA Reg Sat Oct 7 16:38:28 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /pasteur/homes/ntraut/bin/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 = 2 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.11 (predicted orig area = 7.2) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.899, neg=0, invalid=762 0001: dt=275.147192, rms=0.827 (7.999%), neg=0, invalid=762 0002: dt=242.955950, rms=0.802 (3.077%), neg=0, invalid=762 0003: dt=231.836735, rms=0.791 (1.282%), neg=0, invalid=762 0004: dt=140.698413, rms=0.786 (0.668%), neg=0, invalid=762 0005: dt=517.888000, rms=0.778 (1.067%), neg=0, invalid=762 0006: dt=129.472000, rms=0.776 (0.182%), neg=0, invalid=762 0007: dt=129.472000, rms=0.775 (0.147%), neg=0, invalid=762 0008: dt=129.472000, rms=0.773 (0.244%), neg=0, invalid=762 0009: dt=129.472000, rms=0.771 (0.325%), neg=0, invalid=762 0010: dt=129.472000, rms=0.768 (0.349%), neg=0, invalid=762 0011: dt=129.472000, rms=0.765 (0.351%), neg=0, invalid=762 0012: dt=129.472000, rms=0.763 (0.294%), neg=0, invalid=762 0013: dt=129.472000, rms=0.761 (0.231%), neg=0, invalid=762 0014: dt=129.472000, rms=0.760 (0.197%), neg=0, invalid=762 0015: dt=129.472000, rms=0.759 (0.172%), neg=0, invalid=762 0016: dt=129.472000, rms=0.758 (0.133%), neg=0, invalid=762 0017: dt=129.472000, rms=0.757 (0.090%), neg=0, invalid=762 0018: dt=129.472000, rms=0.756 (0.077%), neg=0, invalid=762 0019: dt=517.888000, rms=0.755 (0.113%), neg=0, invalid=762 0020: dt=129.472000, rms=0.755 (0.059%), neg=0, invalid=762 0021: dt=129.472000, rms=0.755 (0.041%), neg=0, invalid=762 0022: dt=129.472000, rms=0.754 (0.047%), neg=0, invalid=762 0023: dt=129.472000, rms=0.754 (0.054%), neg=0, invalid=762 0024: dt=129.472000, rms=0.753 (0.060%), neg=0, invalid=762 0025: dt=129.472000, rms=0.753 (0.052%), neg=0, invalid=762 0026: dt=129.472000, rms=0.753 (0.062%), neg=0, invalid=762 0027: dt=129.472000, rms=0.752 (0.056%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.753, neg=0, invalid=762 0028: dt=129.472000, rms=0.751 (0.265%), neg=0, invalid=762 0029: dt=32.368000, rms=0.751 (-0.002%), neg=0, invalid=762 0030: dt=32.368000, rms=0.751 (0.002%), neg=0, invalid=762 0031: dt=32.368000, rms=0.751 (0.003%), neg=0, invalid=762 0032: dt=32.368000, rms=0.751 (-0.005%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.758, neg=0, invalid=762 0033: dt=77.623762, rms=0.753 (0.689%), neg=0, invalid=762 0034: dt=248.163265, rms=0.737 (2.160%), neg=0, invalid=762 0035: dt=29.312336, rms=0.732 (0.623%), neg=0, invalid=762 0036: dt=9.072000, rms=0.732 (0.024%), neg=0, invalid=762 0037: dt=9.072000, rms=0.732 (0.017%), neg=0, invalid=762 0038: dt=9.072000, rms=0.732 (0.010%), neg=0, invalid=762 0039: dt=9.072000, rms=0.732 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.732, neg=0, invalid=762 0040: dt=62.208000, rms=0.729 (0.415%), neg=0, invalid=762 0041: dt=82.944000, rms=0.728 (0.097%), neg=0, invalid=762 0042: dt=82.944000, rms=0.726 (0.310%), neg=0, invalid=762 0043: dt=82.944000, rms=0.724 (0.357%), neg=0, invalid=762 0044: dt=82.944000, rms=0.721 (0.368%), neg=0, invalid=762 0045: dt=82.944000, rms=0.717 (0.548%), neg=0, invalid=762 0046: dt=82.944000, rms=0.712 (0.662%), neg=0, invalid=762 0047: dt=82.944000, rms=0.708 (0.591%), neg=0, invalid=762 0048: dt=82.944000, rms=0.705 (0.454%), neg=0, invalid=762 0049: dt=82.944000, rms=0.702 (0.383%), neg=0, invalid=762 0050: dt=82.944000, rms=0.700 (0.371%), neg=0, invalid=762 0051: dt=82.944000, rms=0.698 (0.291%), neg=0, invalid=762 0052: dt=82.944000, rms=0.696 (0.200%), neg=0, invalid=762 0053: dt=82.944000, rms=0.695 (0.166%), neg=0, invalid=762 0054: dt=82.944000, rms=0.694 (0.184%), neg=0, invalid=762 0055: dt=82.944000, rms=0.693 (0.137%), neg=0, invalid=762 0056: dt=82.944000, rms=0.692 (0.066%), neg=0, invalid=762 0057: dt=82.944000, rms=0.691 (0.112%), neg=0, invalid=762 0058: dt=82.944000, rms=0.690 (0.225%), neg=0, invalid=762 0059: dt=82.944000, rms=0.688 (0.280%), neg=0, invalid=762 0060: dt=82.944000, rms=0.687 (0.193%), neg=0, invalid=762 0061: dt=82.944000, rms=0.686 (0.092%), neg=0, invalid=762 0062: dt=82.944000, rms=0.685 (0.125%), neg=0, invalid=762 0063: dt=82.944000, rms=0.684 (0.134%), neg=0, invalid=762 0064: dt=82.944000, rms=0.684 (0.095%), neg=0, invalid=762 0065: dt=82.944000, rms=0.683 (0.066%), neg=0, invalid=762 0066: dt=145.152000, rms=0.683 (0.093%), neg=0, invalid=762 0067: dt=6.480000, rms=0.683 (0.001%), neg=0, invalid=762 0068: dt=6.480000, rms=0.683 (0.001%), neg=0, invalid=762 0069: dt=6.480000, rms=0.683 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.708, neg=0, invalid=762 0070: dt=6.400000, rms=0.707 (0.138%), neg=0, invalid=762 0071: dt=2.800000, rms=0.707 (0.017%), neg=0, invalid=762 0072: dt=2.800000, rms=0.707 (0.006%), neg=0, invalid=762 0073: dt=2.800000, rms=0.707 (-0.015%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.708, neg=0, invalid=762 0074: dt=0.000000, rms=0.707 (0.069%), neg=0, invalid=762 0075: dt=0.000000, rms=0.707 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.776, neg=0, invalid=762 0076: dt=6.000000, rms=0.756 (2.530%), neg=0, invalid=762 0077: dt=8.098940, rms=0.752 (0.541%), neg=0, invalid=762 0078: dt=2.880000, rms=0.752 (0.018%), neg=0, invalid=762 0079: dt=2.880000, rms=0.752 (0.034%), neg=0, invalid=762 0080: dt=2.880000, rms=0.751 (0.038%), neg=0, invalid=762 0081: dt=2.880000, rms=0.751 (0.013%), neg=0, invalid=762 0082: dt=2.880000, rms=0.751 (-0.061%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.752, neg=0, invalid=762 0083: dt=0.000000, rms=0.751 (0.057%), neg=0, invalid=762 0084: dt=0.000000, rms=0.751 (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=0.792, neg=0, invalid=762 0085: dt=0.000000, rms=0.792 (0.051%), neg=0, invalid=762 0086: dt=0.000000, rms=0.792 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.792, neg=0, invalid=762 0087: dt=0.000000, rms=0.792 (0.051%), neg=0, invalid=762 0088: dt=0.000000, rms=0.792 (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=0.723, neg=0, invalid=762 0089: dt=0.922014, rms=0.703 (2.817%), neg=0, invalid=762 0090: dt=0.096000, rms=0.702 (0.175%), neg=0, invalid=762 0091: dt=0.096000, rms=0.702 (-0.102%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.702, neg=0, invalid=762 0092: dt=0.028000, rms=0.702 (0.093%), neg=0, invalid=762 0093: dt=0.020000, rms=0.702 (0.003%), neg=0, invalid=762 0094: dt=0.020000, rms=0.702 (-0.005%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.09504 (30) Left_Lateral_Ventricle (4): linear fit = 1.68 x + 0.0 (1149 voxels, overlap=0.298) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (1149 voxels, peak = 34), gca=30.0 gca peak = 0.15565 (16) mri peak = 0.10881 (31) Right_Lateral_Ventricle (43): linear fit = 1.90 x + 0.0 (1263 voxels, overlap=0.129) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1263 voxels, peak = 30), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.06444 (96) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (901 voxels, overlap=0.955) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (901 voxels, peak = 96), gca=95.5 gca peak = 0.20183 (93) mri peak = 0.07652 (84) Left_Pallidum (13): linear fit = 0.90 x + 0.0 (763 voxels, overlap=0.559) Left_Pallidum (13): linear fit = 0.90 x + 0.0 (763 voxels, peak = 84), gca=84.2 gca peak = 0.21683 (55) mri peak = 0.08275 (72) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (1012 voxels, overlap=0.020) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (1012 voxels, peak = 70), gca=69.6 gca peak = 0.30730 (58) mri peak = 0.08023 (69) Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (704 voxels, overlap=0.044) Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (704 voxels, peak = 69), gca=68.7 gca peak = 0.11430 (101) mri peak = 0.09011 (106) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (65574 voxels, overlap=0.687) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (65574 voxels, peak = 107), gca=106.6 gca peak = 0.12076 (102) mri peak = 0.08743 (107) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (68714 voxels, overlap=0.656) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (68714 voxels, peak = 107), gca=106.6 gca peak = 0.14995 (59) mri peak = 0.04539 (74) Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (23446 voxels, overlap=0.002) Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (23446 voxels, peak = 76), gca=76.4 gca peak = 0.15082 (58) mri peak = 0.05316 (76) Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (24764 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (24764 voxels, peak = 77), gca=76.9 gca peak = 0.14161 (67) mri peak = 0.10185 (84) Right_Caudate (50): linear fit = 1.25 x + 0.0 (679 voxels, overlap=0.011) Right_Caudate (50): linear fit = 1.25 x + 0.0 (679 voxels, peak = 84), gca=84.1 gca peak = 0.15243 (71) mri peak = 0.06370 (83) Left_Caudate (11): linear fit = 1.18 x + 0.0 (946 voxels, overlap=0.032) Left_Caudate (11): linear fit = 1.18 x + 0.0 (946 voxels, peak = 84), gca=84.1 gca peak = 0.13336 (57) mri peak = 0.05901 (72) Left_Cerebellum_Cortex (8): linear fit = 1.29 x + 0.0 (22716 voxels, overlap=0.010) Left_Cerebellum_Cortex (8): linear fit = 1.29 x + 0.0 (22716 voxels, peak = 74), gca=73.8 gca peak = 0.13252 (56) mri peak = 0.05907 (72) Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (23782 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (23782 voxels, peak = 74), gca=74.2 gca peak = 0.18181 (84) mri peak = 0.08760 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (9161 voxels, overlap=0.784) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (9161 voxels, peak = 89), gca=89.5 gca peak = 0.20573 (83) mri peak = 0.07913 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (7754 voxels, overlap=0.807) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (7754 voxels, peak = 88), gca=87.6 gca peak = 0.21969 (57) mri peak = 0.08505 (72) Left_Amygdala (18): linear fit = 1.23 x + 0.0 (389 voxels, overlap=0.053) Left_Amygdala (18): linear fit = 1.23 x + 0.0 (389 voxels, peak = 70), gca=69.8 gca peak = 0.39313 (56) mri peak = 0.08578 (71) Right_Amygdala (54): linear fit = 1.23 x + 0.0 (446 voxels, overlap=0.018) Right_Amygdala (54): linear fit = 1.23 x + 0.0 (446 voxels, peak = 69), gca=68.6 gca peak = 0.14181 (85) mri peak = 0.07514 (96) Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (5827 voxels, overlap=0.415) Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (5827 voxels, peak = 93), gca=93.1 gca peak = 0.11978 (83) mri peak = 0.07075 (94) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4482 voxels, overlap=0.540) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4482 voxels, peak = 93), gca=92.5 gca peak = 0.13399 (79) mri peak = 0.07103 (88) Left_Putamen (12): linear fit = 1.14 x + 0.0 (2307 voxels, overlap=0.257) Left_Putamen (12): linear fit = 1.14 x + 0.0 (2307 voxels, peak = 90), gca=90.5 gca peak = 0.14159 (79) mri peak = 0.07604 (88) Right_Putamen (51): linear fit = 1.14 x + 0.0 (2412 voxels, overlap=0.454) Right_Putamen (51): linear fit = 1.14 x + 0.0 (2412 voxels, peak = 90), gca=90.5 gca peak = 0.10025 (80) mri peak = 0.09053 (87) Brain_Stem (16): linear fit = 1.10 x + 0.0 (11580 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (11580 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.07812 (90) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1015 voxels, overlap=0.648) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1015 voxels, peak = 93), gca=93.3 gca peak = 0.12801 (89) mri peak = 0.09083 (90) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1288 voxels, overlap=0.667) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1288 voxels, peak = 92), gca=92.1 gca peak = 0.20494 (23) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15061 (21) mri peak = 0.14865 (29) Fourth_Ventricle (15): linear fit = 1.36 x + 0.0 (532 voxels, overlap=0.280) Fourth_Ventricle (15): linear fit = 1.36 x + 0.0 (532 voxels, peak = 28), gca=28.5 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 1.25 x + 0.0 estimating mean wm scale to be 1.05 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=0.687, neg=0, invalid=762 0095: dt=64.861759, rms=0.673 (2.143%), neg=0, invalid=762 0096: dt=32.368000, rms=0.672 (0.133%), neg=0, invalid=762 0097: dt=32.368000, rms=0.671 (0.057%), neg=0, invalid=762 0098: dt=32.368000, rms=0.671 (0.041%), neg=0, invalid=762 0099: dt=32.368000, rms=0.671 (0.036%), neg=0, invalid=762 0100: dt=32.368000, rms=0.671 (0.022%), neg=0, invalid=762 0101: dt=32.368000, rms=0.671 (-0.028%), neg=0, invalid=762 0102: dt=129.472000, rms=0.670 (0.135%), neg=0, invalid=762 0103: dt=517.888000, rms=0.666 (0.617%), neg=0, invalid=762 0104: dt=517.888000, rms=0.661 (0.696%), neg=0, invalid=762 0105: dt=129.472000, rms=0.660 (0.205%), neg=0, invalid=762 0106: dt=73.984000, rms=0.660 (0.001%), neg=0, invalid=762 0107: dt=73.984000, rms=0.659 (0.032%), neg=0, invalid=762 0108: dt=73.984000, rms=0.659 (0.062%), neg=0, invalid=762 0109: dt=73.984000, rms=0.658 (0.093%), neg=0, invalid=762 0110: dt=73.984000, rms=0.657 (0.129%), neg=0, invalid=762 0111: dt=73.984000, rms=0.656 (0.152%), neg=0, invalid=762 0112: dt=73.984000, rms=0.655 (0.162%), neg=0, invalid=762 0113: dt=73.984000, rms=0.654 (0.148%), neg=0, invalid=762 0114: dt=73.984000, rms=0.654 (0.130%), neg=0, invalid=762 0115: dt=73.984000, rms=0.653 (0.111%), neg=0, invalid=762 0116: dt=73.984000, rms=0.652 (0.095%), neg=0, invalid=762 0117: dt=73.984000, rms=0.652 (0.083%), neg=0, invalid=762 0118: dt=73.984000, rms=0.651 (0.078%), neg=0, invalid=762 0119: dt=73.984000, rms=0.651 (0.077%), neg=0, invalid=762 0120: dt=73.984000, rms=0.650 (0.076%), neg=0, invalid=762 0121: dt=73.984000, rms=0.650 (0.073%), neg=0, invalid=762 0122: dt=73.984000, rms=0.649 (0.076%), neg=0, invalid=762 0123: dt=73.984000, rms=0.649 (0.075%), neg=0, invalid=762 0124: dt=73.984000, rms=0.648 (0.071%), neg=0, invalid=762 0125: dt=73.984000, rms=0.648 (0.070%), neg=0, invalid=762 0126: dt=73.984000, rms=0.647 (0.070%), neg=0, invalid=762 0127: dt=73.984000, rms=0.647 (0.063%), neg=0, invalid=762 0128: dt=73.984000, rms=0.647 (0.060%), neg=0, invalid=762 0129: dt=73.984000, rms=0.646 (0.051%), neg=0, invalid=762 0130: dt=73.984000, rms=0.646 (0.050%), neg=0, invalid=762 0131: dt=73.984000, rms=0.646 (0.052%), neg=0, invalid=762 0132: dt=73.984000, rms=0.645 (0.056%), neg=0, invalid=762 0133: dt=73.984000, rms=0.645 (0.059%), neg=0, invalid=762 0134: dt=73.984000, rms=0.644 (0.057%), neg=0, invalid=762 0135: dt=73.984000, rms=0.644 (0.049%), neg=0, invalid=762 0136: dt=73.984000, rms=0.644 (0.047%), neg=0, invalid=762 0137: dt=73.984000, rms=0.644 (0.046%), neg=0, invalid=762 0138: dt=73.984000, rms=0.643 (0.055%), neg=0, invalid=762 0139: dt=73.984000, rms=0.643 (0.059%), neg=0, invalid=762 0140: dt=73.984000, rms=0.642 (0.061%), neg=0, invalid=762 0141: dt=73.984000, rms=0.642 (0.058%), neg=0, invalid=762 0142: dt=73.984000, rms=0.642 (0.051%), neg=0, invalid=762 0143: dt=73.984000, rms=0.641 (0.046%), neg=0, invalid=762 0144: dt=73.984000, rms=0.641 (0.047%), neg=0, invalid=762 0145: dt=73.984000, rms=0.641 (0.048%), neg=0, invalid=762 0146: dt=73.984000, rms=0.640 (0.051%), neg=0, invalid=762 0147: dt=73.984000, rms=0.640 (0.048%), neg=0, invalid=762 0148: dt=73.984000, rms=0.640 (0.044%), neg=0, invalid=762 0149: dt=73.984000, rms=0.640 (0.038%), neg=0, invalid=762 0150: dt=73.984000, rms=0.639 (0.034%), neg=0, invalid=762 0151: dt=73.984000, rms=0.639 (0.033%), neg=0, invalid=762 0152: dt=73.984000, rms=0.639 (0.034%), neg=0, invalid=762 0153: dt=73.984000, rms=0.639 (0.034%), neg=0, invalid=762 0154: dt=73.984000, rms=0.639 (0.033%), neg=0, invalid=762 0155: dt=73.984000, rms=0.638 (0.030%), neg=0, invalid=762 0156: dt=73.984000, rms=0.638 (0.028%), neg=0, invalid=762 0157: dt=73.984000, rms=0.638 (0.025%), neg=0, invalid=762 0158: dt=73.984000, rms=0.638 (0.021%), neg=0, invalid=762 0159: dt=5918.720000, rms=0.637 (0.079%), neg=0, invalid=762 0160: dt=110.976000, rms=0.637 (0.077%), neg=0, invalid=762 0161: dt=73.984000, rms=0.637 (0.002%), neg=0, invalid=762 0162: dt=73.984000, rms=0.637 (0.005%), neg=0, invalid=762 0163: dt=73.984000, rms=0.637 (0.008%), neg=0, invalid=762 0164: dt=73.984000, rms=0.637 (0.009%), neg=0, invalid=762 0165: dt=73.984000, rms=0.637 (0.012%), neg=0, invalid=762 0166: dt=73.984000, rms=0.637 (0.013%), neg=0, invalid=762 0167: dt=73.984000, rms=0.637 (0.016%), neg=0, invalid=762 0168: dt=73.984000, rms=0.636 (0.013%), neg=0, invalid=762 0169: dt=73.984000, rms=0.636 (0.011%), neg=0, invalid=762 0170: dt=129.472000, rms=0.636 (0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.637, neg=0, invalid=762 0171: dt=0.000000, rms=0.636 (0.051%), neg=0, invalid=762 0172: dt=0.000000, rms=0.636 (0.000%), neg=0, invalid=762 0173: dt=0.850000, rms=0.636 (-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=0.638, neg=0, invalid=762 0174: dt=497.664000, rms=0.623 (2.285%), neg=0, invalid=762 0175: dt=80.718802, rms=0.619 (0.596%), neg=0, invalid=762 0176: dt=145.152000, rms=0.616 (0.470%), neg=0, invalid=762 0177: dt=36.288000, rms=0.615 (0.191%), neg=0, invalid=762 0178: dt=145.152000, rms=0.614 (0.261%), neg=0, invalid=762 0179: dt=124.416000, rms=0.612 (0.235%), neg=0, invalid=762 0180: dt=36.288000, rms=0.611 (0.130%), neg=0, invalid=762 0181: dt=145.152000, rms=0.610 (0.191%), neg=0, invalid=762 0182: dt=124.416000, rms=0.609 (0.202%), neg=0, invalid=762 0183: dt=36.288000, rms=0.608 (0.088%), neg=0, invalid=762 0184: dt=145.152000, rms=0.608 (0.142%), neg=0, invalid=762 0185: dt=124.416000, rms=0.606 (0.182%), neg=0, invalid=762 0186: dt=36.288000, rms=0.606 (0.072%), neg=0, invalid=762 0187: dt=145.152000, rms=0.605 (0.121%), neg=0, invalid=762 0188: dt=124.416000, rms=0.604 (0.156%), neg=0, invalid=762 0189: dt=36.288000, rms=0.604 (0.053%), neg=0, invalid=762 0190: dt=248.832000, rms=0.603 (0.129%), neg=0, invalid=762 0191: dt=73.142857, rms=0.602 (0.166%), neg=0, invalid=762 0192: dt=36.288000, rms=0.602 (0.032%), neg=0, invalid=762 0193: dt=36.288000, rms=0.602 (0.027%), neg=0, invalid=762 0194: dt=36.288000, rms=0.602 (0.050%), neg=0, invalid=762 0195: dt=36.288000, rms=0.601 (0.072%), neg=0, invalid=762 0196: dt=36.288000, rms=0.601 (0.093%), neg=0, invalid=762 0197: dt=36.288000, rms=0.600 (0.104%), neg=0, invalid=762 0198: dt=36.288000, rms=0.599 (0.109%), neg=0, invalid=762 0199: dt=36.288000, rms=0.599 (0.118%), neg=0, invalid=762 0200: dt=36.288000, rms=0.599 (0.017%), neg=0, invalid=762 0201: dt=36.288000, rms=0.598 (0.035%), neg=0, invalid=762 0202: dt=36.288000, rms=0.598 (0.048%), neg=0, invalid=762 0203: dt=2.268000, rms=0.598 (0.001%), neg=0, invalid=762 0204: dt=0.283500, rms=0.598 (0.000%), neg=0, invalid=762 0205: dt=0.008859, rms=0.598 (0.000%), neg=0, invalid=762 0206: dt=0.004430, rms=0.598 (0.000%), neg=0, invalid=762 0207: dt=0.001107, rms=0.598 (0.000%), neg=0, invalid=762 0208: dt=0.000035, rms=0.598 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.598, neg=0, invalid=762 0209: dt=36.288000, rms=0.597 (0.165%), neg=0, invalid=762 0210: dt=82.944000, rms=0.597 (0.088%), neg=0, invalid=762 0211: dt=497.664000, rms=0.593 (0.631%), neg=0, invalid=762 0212: dt=25.920000, rms=0.593 (0.033%), neg=0, invalid=762 0213: dt=25.920000, rms=0.593 (0.020%), neg=0, invalid=762 0214: dt=25.920000, rms=0.593 (-0.009%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.598, neg=0, invalid=762 0215: dt=48.273245, rms=0.589 (1.620%), neg=0, invalid=762 0216: dt=11.200000, rms=0.586 (0.520%), neg=0, invalid=762 0217: dt=11.200000, rms=0.583 (0.371%), neg=0, invalid=762 0218: dt=11.200000, rms=0.582 (0.300%), neg=0, invalid=762 0219: dt=8.000000, rms=0.581 (0.184%), neg=0, invalid=762 0220: dt=0.700000, rms=0.581 (0.014%), neg=0, invalid=762 0221: dt=0.700000, rms=0.580 (0.015%), neg=0, invalid=762 0222: dt=0.087500, rms=0.580 (0.001%), neg=0, invalid=762 0223: dt=0.043750, rms=0.580 (0.001%), neg=0, invalid=762 0224: dt=0.010937, rms=0.580 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.581, neg=0, invalid=762 0225: dt=32.000000, rms=0.576 (0.762%), neg=0, invalid=762 0226: dt=72.615385, rms=0.569 (1.250%), neg=0, invalid=762 0227: dt=11.200000, rms=0.567 (0.384%), neg=0, invalid=762 0228: dt=11.200000, rms=0.566 (0.170%), neg=0, invalid=762 0229: dt=44.800000, rms=0.564 (0.295%), neg=0, invalid=762 0230: dt=52.528302, rms=0.561 (0.593%), neg=0, invalid=762 0231: dt=11.200000, rms=0.560 (0.231%), neg=0, invalid=762 0232: dt=24.387665, rms=0.559 (0.134%), neg=0, invalid=762 0233: dt=11.200000, rms=0.558 (0.141%), neg=0, invalid=762 0234: dt=9.600000, rms=0.558 (0.087%), neg=0, invalid=762 0235: dt=0.700000, rms=0.558 (0.007%), neg=0, invalid=762 0236: dt=0.175000, rms=0.558 (0.001%), neg=0, invalid=762 0237: dt=0.087500, rms=0.558 (0.001%), neg=0, invalid=762 0238: dt=0.043750, rms=0.558 (0.000%), neg=0, invalid=762 0239: dt=0.010937, rms=0.558 (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=0.572, neg=0, invalid=762 0240: dt=12.106339, rms=0.568 (0.813%), neg=0, invalid=762 0241: dt=0.003938, rms=0.568 (-0.000%), neg=0, invalid=762 0242: dt=0.003938, rms=0.568 (0.000%), neg=0, invalid=762 0243: dt=0.003938, rms=0.568 (0.000%), neg=0, invalid=762 0244: dt=0.001969, rms=0.568 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.568, neg=0, invalid=762 0245: dt=0.000984, rms=0.568 (0.066%), neg=0, invalid=762 0246: dt=0.000000, rms=0.568 (0.000%), neg=0, invalid=762 0247: dt=0.000073, rms=0.568 (0.000%), neg=0, invalid=762 0248: dt=0.000002, rms=0.568 (0.000%), neg=0, invalid=762 0249: dt=0.000001, rms=0.568 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.594, neg=0, invalid=762 0250: dt=1.280000, rms=0.593 (0.203%), neg=0, invalid=762 0251: dt=1.024000, rms=0.592 (0.045%), neg=0, invalid=762 0252: dt=1.024000, rms=0.592 (0.019%), neg=0, invalid=762 0253: dt=1.024000, rms=0.592 (-0.054%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.593, neg=0, invalid=762 0254: dt=4.096000, rms=0.588 (0.748%), neg=0, invalid=762 0255: dt=6.144000, rms=0.584 (0.629%), neg=0, invalid=762 0256: dt=0.112000, rms=0.584 (-0.003%), neg=0, invalid=762 0257: dt=0.112000, rms=0.584 (0.000%), neg=0, invalid=762 0258: dt=0.112000, rms=0.584 (-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=0.562, neg=0, invalid=762 0259: dt=0.448000, rms=0.545 (3.082%), neg=0, invalid=762 0260: dt=0.448000, rms=0.540 (0.949%), neg=0, invalid=762 0261: dt=0.448000, rms=0.537 (0.542%), neg=0, invalid=762 0262: dt=0.448000, rms=0.535 (0.276%), neg=0, invalid=762 0263: dt=0.448000, rms=0.534 (0.230%), neg=0, invalid=762 0264: dt=0.448000, rms=0.533 (0.130%), neg=0, invalid=762 0265: dt=0.448000, rms=0.533 (0.143%), neg=0, invalid=762 0266: dt=0.448000, rms=0.532 (0.073%), neg=0, invalid=762 0267: dt=0.448000, rms=0.532 (0.101%), neg=0, invalid=762 0268: dt=0.448000, rms=0.531 (0.042%), neg=0, invalid=762 0269: dt=0.448000, rms=0.531 (0.076%), neg=0, invalid=762 0270: dt=0.448000, rms=0.530 (0.093%), neg=0, invalid=762 0271: dt=0.448000, rms=0.530 (0.027%), neg=0, invalid=762 0272: dt=0.448000, rms=0.530 (0.073%), neg=0, invalid=762 0273: dt=0.448000, rms=0.530 (0.028%), neg=0, invalid=762 0274: dt=0.448000, rms=0.530 (0.027%), neg=0, invalid=762 0275: dt=0.448000, rms=0.530 (0.026%), neg=0, invalid=762 0276: dt=0.448000, rms=0.529 (0.003%), neg=0, invalid=762 0277: dt=0.448000, rms=0.529 (0.019%), neg=0, invalid=762 0278: dt=0.448000, rms=0.529 (0.026%), neg=0, invalid=762 0279: dt=0.448000, rms=0.529 (0.026%), neg=0, invalid=762 0280: dt=0.448000, rms=0.529 (-0.008%), neg=0, invalid=762 0281: dt=0.112000, rms=0.529 (0.001%), neg=0, invalid=762 0282: dt=0.320000, rms=0.529 (0.005%), neg=0, invalid=762 0283: dt=0.448000, rms=0.529 (0.006%), neg=0, invalid=762 0284: dt=0.256000, rms=0.529 (0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.529, neg=0, invalid=762 0285: dt=0.448000, rms=0.522 (1.366%), neg=0, invalid=762 0286: dt=0.112000, rms=0.522 (0.072%), neg=0, invalid=762 0287: dt=0.448000, rms=0.520 (0.258%), neg=0, invalid=762 0288: dt=0.448000, rms=0.520 (0.100%), neg=0, invalid=762 0289: dt=0.448000, rms=0.520 (0.047%), neg=0, invalid=762 0290: dt=0.448000, rms=0.520 (0.010%), neg=0, invalid=762 0291: dt=0.448000, rms=0.520 (0.008%), neg=0, invalid=762 0292: dt=0.448000, rms=0.520 (0.010%), neg=0, invalid=762 0293: dt=0.448000, rms=0.520 (-0.003%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.517, neg=0, invalid=762 0294: dt=0.000000, rms=0.517 (0.080%), neg=0, invalid=762 0295: dt=0.000000, rms=0.517 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.517, neg=0, invalid=762 0296: dt=0.000000, rms=0.517 (0.080%), neg=0, invalid=762 0297: dt=0.000000, rms=0.517 (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=0.517, neg=0, invalid=762 0298: dt=0.567000, rms=0.517 (0.080%), neg=0, invalid=762 0299: dt=0.357143, rms=0.517 (0.000%), neg=0, invalid=762 0300: dt=0.357143, rms=0.517 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.517, neg=0, invalid=762 0301: dt=9.072000, rms=0.517 (0.091%), neg=0, invalid=762 0302: dt=20.736000, rms=0.517 (0.017%), neg=0, invalid=762 0303: dt=20.736000, rms=0.517 (0.050%), neg=0, invalid=762 0304: dt=20.736000, rms=0.516 (0.076%), neg=0, invalid=762 0305: dt=20.736000, rms=0.516 (0.091%), neg=0, invalid=762 0306: dt=20.736000, rms=0.515 (0.103%), neg=0, invalid=762 0307: dt=20.736000, rms=0.515 (0.117%), neg=0, invalid=762 0308: dt=20.736000, rms=0.514 (0.120%), neg=0, invalid=762 0309: dt=20.736000, rms=0.513 (0.107%), neg=0, invalid=762 0310: dt=20.736000, rms=0.513 (0.091%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.514, neg=0, invalid=762 0311: dt=22.936709, rms=0.510 (0.636%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 9 iterations, nbhd size=1, neg = 0 0312: dt=32.000000, rms=0.508 (0.388%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0313: dt=11.200000, rms=0.508 (0.138%), neg=0, invalid=762 0314: dt=11.200000, rms=0.507 (0.096%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0315: dt=11.200000, rms=0.507 (0.129%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 0316: dt=11.200000, rms=0.506 (0.093%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0317: dt=11.200000, rms=0.506 (0.071%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 0 iterations, nbhd size=0, neg = 0 0318: dt=153.600000, rms=0.504 (0.375%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0319: dt=11.200000, rms=0.504 (0.025%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0320: dt=11.200000, rms=0.504 (0.021%), neg=0, invalid=762 0321: dt=11.200000, rms=0.503 (0.022%), neg=0, invalid=762 0322: dt=11.200000, rms=0.503 (0.019%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0323: dt=11.200000, rms=0.503 (0.020%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0324: dt=11.200000, rms=0.503 (0.025%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 9 iterations, nbhd size=1, neg = 0 0325: dt=11.200000, rms=0.503 (0.047%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0326: dt=11.200000, rms=0.503 (0.038%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0327: dt=44.800000, rms=0.502 (0.059%), neg=0, invalid=762 0328: dt=19.200000, rms=0.502 (0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.503, neg=0, invalid=762 0329: dt=27.886163, rms=0.497 (1.171%), neg=0, invalid=762 0330: dt=22.974359, rms=0.493 (0.706%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0331: dt=11.200000, rms=0.492 (0.282%), neg=0, invalid=762 0332: dt=102.400000, rms=0.488 (0.743%), neg=0, invalid=762 0333: dt=22.857143, rms=0.487 (0.295%), neg=0, invalid=762 0334: dt=9.600000, rms=0.487 (0.046%), neg=0, invalid=762 0335: dt=9.600000, rms=0.486 (0.024%), neg=0, invalid=762 0336: dt=9.600000, rms=0.486 (0.041%), neg=0, invalid=762 0337: dt=9.600000, rms=0.486 (0.066%), neg=0, invalid=762 0338: dt=9.600000, rms=0.486 (0.089%), neg=0, invalid=762 0339: dt=9.600000, rms=0.485 (0.094%), neg=0, invalid=762 0340: dt=9.600000, rms=0.485 (0.087%), neg=0, invalid=762 0341: dt=9.600000, rms=0.484 (0.081%), neg=0, invalid=762 0342: dt=44.800000, rms=0.484 (0.044%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.491, neg=0, invalid=762 0343: dt=2.000000, rms=0.490 (0.112%), neg=0, invalid=762 0344: dt=0.000000, rms=0.490 (0.003%), neg=0, invalid=762 0345: dt=0.150000, rms=0.490 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.491, neg=0, invalid=762 0346: dt=6.095238, rms=0.490 (0.221%), neg=0, invalid=762 0347: dt=10.084034, rms=0.489 (0.139%), neg=0, invalid=762 0348: dt=10.084034, rms=0.488 (0.191%), neg=0, invalid=762 0349: dt=10.084034, rms=0.487 (0.257%), neg=0, invalid=762 0350: dt=10.084034, rms=0.485 (0.262%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0351: dt=10.084034, rms=0.484 (0.388%), neg=0, invalid=762 0352: dt=10.084034, rms=0.481 (0.580%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 8 iterations, nbhd size=1, neg = 0 0353: dt=10.084034, rms=0.478 (0.617%), neg=0, invalid=762 0354: dt=10.084034, rms=0.476 (0.440%), neg=0, invalid=762 0355: dt=10.084034, rms=0.475 (0.168%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 12 iterations, nbhd size=1, neg = 0 0356: dt=10.084034, rms=0.475 (-0.018%), neg=0, invalid=762 0357: dt=0.000000, rms=0.475 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.483, neg=0, invalid=762 0358: dt=0.000000, rms=0.482 (0.095%), neg=0, invalid=762 0359: dt=0.000000, rms=0.482 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.483, neg=0, invalid=762 0360: dt=0.000000, rms=0.482 (0.095%), neg=0, invalid=762 0361: dt=0.000000, rms=0.482 (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=0.470, neg=0, invalid=762 iter 0, gcam->neg = 565 after 16 iterations, nbhd size=1, neg = 0 0362: dt=1.688703, rms=0.452 (3.866%), neg=0, invalid=762 0363: dt=0.028000, rms=0.452 (0.020%), neg=0, invalid=762 0364: dt=0.028000, rms=0.452 (-0.004%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.453, neg=0, invalid=762 0365: dt=0.112000, rms=0.451 (0.248%), neg=0, invalid=762 0366: dt=0.064000, rms=0.451 (0.026%), neg=0, invalid=762 0367: dt=0.064000, rms=0.451 (-0.004%), 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=0.444, neg=0, invalid=762 0368: dt=0.000000, rms=0.444 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.444, neg=0, invalid=762 0369: dt=0.000000, rms=0.444 (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=0.444, neg=0, invalid=762 0370: dt=0.000000, rms=0.444 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.444, neg=0, invalid=762 0371: dt=4.888889, rms=0.444 (0.002%), neg=0, invalid=762 0372: dt=1.620000, rms=0.444 (0.000%), neg=0, invalid=762 0373: dt=1.620000, rms=0.444 (0.000%), neg=0, invalid=762 0374: dt=1.620000, rms=0.444 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.444, neg=0, invalid=762 0375: dt=6.400000, rms=0.444 (0.072%), neg=0, invalid=762 0376: dt=2.800000, rms=0.444 (0.007%), neg=0, invalid=762 0377: dt=2.800000, rms=0.444 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.444, neg=0, invalid=762 0378: dt=25.600000, rms=0.443 (0.342%), neg=0, invalid=762 0379: dt=25.600000, rms=0.441 (0.294%), neg=0, invalid=762 0380: dt=11.200000, rms=0.441 (0.103%), neg=0, invalid=762 0381: dt=11.200000, rms=0.440 (0.073%), neg=0, invalid=762 0382: dt=11.200000, rms=0.440 (0.113%), neg=0, invalid=762 0383: dt=11.200000, rms=0.439 (0.134%), neg=0, invalid=762 0384: dt=11.200000, rms=0.439 (0.131%), neg=0, invalid=762 0385: dt=11.200000, rms=0.438 (0.127%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0386: dt=11.200000, rms=0.438 (0.108%), neg=0, invalid=762 0387: dt=11.200000, rms=0.437 (0.110%), neg=0, invalid=762 0388: dt=11.200000, rms=0.437 (0.100%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0389: dt=44.800000, rms=0.437 (0.062%), neg=0, invalid=762 0390: dt=44.800000, rms=0.437 (-0.062%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.439, neg=0, invalid=762 0391: dt=2.285714, rms=0.439 (0.037%), neg=0, invalid=762 0392: dt=0.000563, rms=0.439 (0.000%), neg=0, invalid=762 0393: dt=0.000563, 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 0394: dt=15.337931, rms=0.437 (0.452%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 9 iterations, nbhd size=1, neg = 0 0395: dt=15.117647, rms=0.435 (0.391%), neg=0, invalid=762 0396: dt=5.130435, rms=0.435 (0.122%), neg=0, invalid=762 0397: dt=5.130435, rms=0.435 (0.059%), neg=0, invalid=762 0398: dt=5.130435, rms=0.434 (0.100%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0399: dt=5.130435, rms=0.433 (0.141%), neg=0, invalid=762 0400: dt=5.130435, rms=0.433 (0.160%), neg=0, invalid=762 0401: dt=5.130435, rms=0.432 (0.159%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0402: dt=5.130435, rms=0.431 (0.144%), neg=0, invalid=762 0403: dt=5.130435, rms=0.431 (0.128%), neg=0, invalid=762 0404: dt=5.130435, rms=0.430 (0.111%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0405: dt=5.130435, rms=0.430 (0.085%), neg=0, invalid=762 0406: dt=2.880000, rms=0.430 (0.001%), neg=0, invalid=762 0407: dt=2.880000, rms=0.430 (0.000%), neg=0, invalid=762 0408: dt=2.880000, rms=0.430 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.435, neg=0, invalid=762 0409: dt=0.000000, rms=0.435 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.435, neg=0, invalid=762 0410: dt=0.000000, rms=0.435 (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 = 309 after 13 iterations, nbhd size=1, neg = 0 0411: dt=1.280000, rms=0.420 (1.726%), neg=0, invalid=762 0412: dt=0.000023, rms=0.420 (0.000%), neg=0, invalid=762 0413: dt=0.000023, rms=0.420 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.420, neg=0, invalid=762 0414: dt=0.192000, rms=0.419 (0.226%), neg=0, invalid=762 0415: dt=0.256000, rms=0.418 (0.141%), neg=0, invalid=762 0416: dt=0.256000, rms=0.417 (0.190%), neg=0, invalid=762 0417: dt=0.256000, rms=0.416 (0.228%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 9 iterations, nbhd size=1, neg = 0 0418: dt=0.256000, rms=0.416 (0.153%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 11 iterations, nbhd size=1, neg = 0 0419: dt=0.256000, rms=0.415 (0.186%), neg=0, invalid=762 iter 0, gcam->neg = 20 after 9 iterations, nbhd size=1, neg = 0 0420: dt=0.256000, rms=0.414 (0.208%), neg=0, invalid=762 iter 0, gcam->neg = 24 after 10 iterations, nbhd size=1, neg = 0 0421: dt=0.256000, rms=0.414 (0.107%), neg=0, invalid=762 iter 0, gcam->neg = 24 after 10 iterations, nbhd size=1, neg = 0 0422: dt=0.256000, rms=0.414 (-0.051%), neg=0, invalid=762 0423: dt=0.048000, rms=0.414 (0.002%), neg=0, invalid=762 0424: dt=0.028000, rms=0.414 (0.001%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 49 minutes and 18 seconds. mri_ca_register utimesec 7253.512298 mri_ca_register stimesec 8.396723 mri_ca_register ru_maxrss 1350436 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4541415 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 67888 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 3730 mri_ca_register ru_nivcsw 32511 FSRUNTIME@ mri_ca_register 1.8217 hours 2 threads #-------------------------------------- #@# SubCort Seg Sat Oct 7 18:27:47 CEST 2017 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname tars-542 machine x86_64 setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/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 = 2 == 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 /pasteur/homes/ntraut/bin/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 7.19 Atlas used for the 3D morph was /pasteur/homes/ntraut/bin/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 = 0.10476 (29) Left_Lateral_Ventricle (4): linear fit = 1.53 x + 0.0 (406 voxels, overlap=0.189) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (406 voxels, peak = 31), gca=30.0 gca peak = 0.17677 (13) mri peak = 0.11901 (31) Right_Lateral_Ventricle (43): linear fit = 2.15 x + 0.0 (1977 voxels, overlap=0.110) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1977 voxels, peak = 28), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.11811 (100) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (882 voxels, overlap=0.959) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (882 voxels, peak = 101), gca=101.2 gca peak = 0.16930 (96) mri peak = 0.08976 (97) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (989 voxels, overlap=0.987) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (989 voxels, peak = 100), gca=100.3 gca peak = 0.24553 (55) mri peak = 0.08358 (72) Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (1047 voxels, overlap=0.025) Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (1047 voxels, peak = 70), gca=70.1 gca peak = 0.30264 (59) mri peak = 0.07350 (71) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1034 voxels, overlap=0.024) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1034 voxels, peak = 72), gca=72.3 gca peak = 0.07580 (103) mri peak = 0.09607 (106) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (52018 voxels, overlap=0.643) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (52018 voxels, peak = 107), gca=106.6 gca peak = 0.07714 (104) mri peak = 0.09706 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (51783 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (51783 voxels, peak = 107), gca=106.6 gca peak = 0.09712 (58) mri peak = 0.04854 (74) Left_Cerebral_Cortex (3): linear fit = 1.26 x + 0.0 (32835 voxels, overlap=0.052) Left_Cerebral_Cortex (3): linear fit = 1.26 x + 0.0 (32835 voxels, peak = 73), gca=73.4 gca peak = 0.11620 (58) mri peak = 0.05644 (77) Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (30959 voxels, overlap=0.001) Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (30959 voxels, peak = 75), gca=75.1 gca peak = 0.30970 (66) mri peak = 0.10463 (87) Right_Caudate (50): linear fit = 1.26 x + 0.0 (1167 voxels, overlap=0.020) Right_Caudate (50): linear fit = 1.26 x + 0.0 (1167 voxels, peak = 83), gca=83.5 gca peak = 0.15280 (69) mri peak = 0.11535 (84) Left_Caudate (11): linear fit = 1.12 x + 0.0 (971 voxels, overlap=0.214) Left_Caudate (11): linear fit = 1.12 x + 0.0 (971 voxels, peak = 78), gca=77.6 gca peak = 0.13902 (56) mri peak = 0.06272 (72) Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (23514 voxels, overlap=0.014) Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (23514 voxels, peak = 71), gca=70.8 gca peak = 0.14777 (55) mri peak = 0.06852 (72) Right_Cerebellum_Cortex (47): linear fit = 1.29 x + 0.0 (25164 voxels, overlap=0.003) Right_Cerebellum_Cortex (47): linear fit = 1.29 x + 0.0 (25164 voxels, peak = 71), gca=71.2 gca peak = 0.16765 (84) mri peak = 0.10701 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (7540 voxels, overlap=0.810) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (7540 voxels, peak = 88), gca=87.8 gca peak = 0.18739 (84) mri peak = 0.10575 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (7302 voxels, overlap=0.742) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (7302 voxels, peak = 89), gca=89.5 gca peak = 0.29869 (57) mri peak = 0.08661 (71) Left_Amygdala (18): linear fit = 1.22 x + 0.0 (629 voxels, overlap=0.061) Left_Amygdala (18): linear fit = 1.22 x + 0.0 (629 voxels, peak = 69), gca=69.3 gca peak = 0.33601 (57) mri peak = 0.08442 (74) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (652 voxels, overlap=0.049) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (652 voxels, peak = 74), gca=74.4 gca peak = 0.11131 (90) mri peak = 0.07244 (93) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5147 voxels, overlap=0.720) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5147 voxels, peak = 95), gca=94.9 gca peak = 0.11793 (83) mri peak = 0.07083 (94) Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (4989 voxels, overlap=0.497) Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (4989 voxels, peak = 92), gca=91.7 gca peak = 0.08324 (81) mri peak = 0.08802 (90) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1950 voxels, overlap=0.355) Left_Putamen (12): linear fit = 1.12 x + 0.0 (1950 voxels, peak = 90), gca=90.3 gca peak = 0.10360 (77) mri peak = 0.08380 (90) Right_Putamen (51): linear fit = 1.16 x + 0.0 (2502 voxels, overlap=0.323) Right_Putamen (51): linear fit = 1.16 x + 0.0 (2502 voxels, peak = 90), gca=89.7 gca peak = 0.08424 (78) mri peak = 0.09690 (84) Brain_Stem (16): linear fit = 1.07 x + 0.0 (13507 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.07 x + 0.0 (13507 voxels, peak = 83), gca=83.1 gca peak = 0.12631 (89) mri peak = 0.08881 (92) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1643 voxels, overlap=0.738) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1643 voxels, peak = 94), gca=93.9 gca peak = 0.14500 (87) mri peak = 0.08964 (90) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1871 voxels, overlap=0.843) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1871 voxels, peak = 90), gca=90.0 gca peak = 0.14975 (24) mri peak = 0.20005 (36) gca peak = 0.19357 (14) mri peak = 0.12725 (29) Fourth_Ventricle (15): linear fit = 1.84 x + 0.0 (302 voxels, overlap=0.172) Fourth_Ventricle (15): linear fit = 1.84 x + 0.0 (302 voxels, peak = 26), gca=25.7 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.26 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.50 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.12544 (31) mri peak = 0.10476 (29) Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (406 voxels, overlap=0.834) Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (406 voxels, peak = 32), gca=32.4 gca peak = 0.13981 (19) mri peak = 0.11901 (31) Right_Lateral_Ventricle (43): linear fit = 1.46 x + 0.0 (1977 voxels, overlap=0.329) Right_Lateral_Ventricle (43): linear fit = 1.46 x + 0.0 (1977 voxels, peak = 28), gca=27.6 gca peak = 0.25726 (102) mri peak = 0.11811 (100) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (882 voxels, overlap=1.011) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (882 voxels, peak = 103), gca=102.5 gca peak = 0.17215 (100) mri peak = 0.08976 (97) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (989 voxels, overlap=1.005) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (989 voxels, peak = 100), gca=100.5 gca peak = 0.24040 (71) mri peak = 0.08358 (72) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1047 voxels, overlap=1.003) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1047 voxels, peak = 71), gca=71.0 gca peak = 0.30146 (69) mri peak = 0.07350 (71) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (1034 voxels, overlap=1.007) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (1034 voxels, peak = 70), gca=70.0 gca peak = 0.07496 (106) mri peak = 0.09607 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52018 voxels, overlap=0.787) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52018 voxels, peak = 105), gca=105.5 gca peak = 0.07686 (107) mri peak = 0.09706 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (51783 voxels, overlap=0.722) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (51783 voxels, peak = 107), gca=107.0 gca peak = 0.07826 (73) mri peak = 0.04854 (74) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (32835 voxels, overlap=0.960) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (32835 voxels, peak = 73), gca=73.0 gca peak = 0.09095 (75) mri peak = 0.05644 (77) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (30959 voxels, overlap=0.939) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (30959 voxels, peak = 75), gca=75.0 gca peak = 0.21463 (83) mri peak = 0.10463 (87) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1167 voxels, overlap=1.001) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1167 voxels, peak = 83), gca=83.0 gca peak = 0.16640 (87) mri peak = 0.11535 (84) Left_Caudate (11): linear fit = 1.01 x + 0.0 (971 voxels, overlap=0.977) Left_Caudate (11): linear fit = 1.01 x + 0.0 (971 voxels, peak = 88), gca=88.3 gca peak = 0.11270 (70) mri peak = 0.06272 (72) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (23514 voxels, overlap=0.972) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (23514 voxels, peak = 70), gca=70.0 gca peak = 0.11145 (71) mri peak = 0.06852 (72) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (25164 voxels, overlap=0.975) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (25164 voxels, peak = 71), gca=71.0 gca peak = 0.15145 (88) mri peak = 0.10701 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7540 voxels, overlap=0.949) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7540 voxels, peak = 88), gca=88.0 gca peak = 0.15153 (90) mri peak = 0.10575 (88) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (7302 voxels, overlap=0.966) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (7302 voxels, peak = 89), gca=88.7 gca peak = 0.28119 (69) mri peak = 0.08661 (71) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (629 voxels, overlap=1.016) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (629 voxels, peak = 69), gca=69.0 gca peak = 0.33194 (74) mri peak = 0.08442 (74) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (652 voxels, overlap=1.001) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (652 voxels, peak = 73), gca=72.9 gca peak = 0.10670 (93) mri peak = 0.07244 (93) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5147 voxels, overlap=0.917) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5147 voxels, peak = 93), gca=92.5 gca peak = 0.10075 (89) mri peak = 0.07083 (94) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (4989 voxels, overlap=0.925) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (4989 voxels, peak = 88), gca=87.7 gca peak = 0.07946 (92) mri peak = 0.08802 (90) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1950 voxels, overlap=0.807) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1950 voxels, peak = 92), gca=91.5 gca peak = 0.08151 (87) mri peak = 0.08380 (90) Right_Putamen (51): linear fit = 0.99 x + 0.0 (2502 voxels, overlap=0.845) Right_Putamen (51): linear fit = 0.99 x + 0.0 (2502 voxels, peak = 86), gca=85.7 gca peak = 0.07297 (83) mri peak = 0.09690 (84) Brain_Stem (16): linear fit = 0.99 x + 0.0 (13507 voxels, overlap=0.704) Brain_Stem (16): linear fit = 0.99 x + 0.0 (13507 voxels, peak = 82), gca=81.8 gca peak = 0.12764 (94) mri peak = 0.08881 (92) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1643 voxels, overlap=0.827) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1643 voxels, peak = 95), gca=95.4 gca peak = 0.15712 (90) mri peak = 0.08964 (90) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1871 voxels, overlap=0.892) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1871 voxels, peak = 90), gca=89.6 gca peak = 0.12656 (38) mri peak = 0.20005 (36) gca peak = 0.16542 (24) mri peak = 0.12725 (29) Fourth_Ventricle (15): linear fit = 1.32 x + 0.0 (302 voxels, overlap=0.530) Fourth_Ventricle (15): linear fit = 1.32 x + 0.0 (302 voxels, peak = 32), gca=31.6 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16283 (33) gca peak Left_Thalamus = 0.36646 (105) gca peak Third_Ventricle = 0.12656 (38) gca peak CSF = 0.15446 (55) gca peak Left_Accumbens_area = 0.61405 (70) 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 = 0.19636 (29) gca peak Right_Accumbens_area = 0.29938 (82) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14504 (37) gca peak Fifth_Ventricle = 0.51780 (46) gca peak WM_hypointensities = 0.08077 (80) gca peak non_WM_hypointensities = 0.11678 (56) gca peak Optic_Chiasm = 0.70876 (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 1.27 x + 0.0 Right_Pallidum too bright - rescaling by 1.005 (from 1.005) to 103.0 (was 102.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 91743 voxels changed in iteration 0 of unlikely voxel relabeling 453 voxels changed in iteration 1 of unlikely voxel relabeling 107 voxels changed in iteration 2 of unlikely voxel relabeling 2 voxels changed in iteration 3 of unlikely voxel relabeling 103 voxels changed in iteration 4 of unlikely voxel relabeling 80431 gm and wm labels changed (%35 to gray, %65 to white out of all changed labels) 634 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 87140 changed. image ll: -2.154, PF=0.500 pass 2: 22126 changed. image ll: -2.153, PF=0.500 pass 3: 6230 changed. pass 4: 2220 changed. 65766 voxels changed in iteration 0 of unlikely voxel relabeling 579 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 13 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 9228 voxels changed in iteration 0 of unlikely voxel relabeling 166 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 7603 voxels changed in iteration 0 of unlikely voxel relabeling 134 voxels changed in iteration 1 of unlikely voxel relabeling 8 voxels changed in iteration 2 of unlikely voxel relabeling 4 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 6625 voxels changed in iteration 0 of unlikely voxel relabeling 30 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 4547.352697 mri_ca_label stimesec 2.758580 mri_ca_label ru_maxrss 2126616 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 700517 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 67880 mri_ca_label ru_oublock 488 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 320 mri_ca_label ru_nivcsw 20246 auto-labeling took 74 minutes and 59 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/transforms/cc_up.lta 0050660 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/transforms/cc_up.lta reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/aseg.auto_noCCseg.mgz reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/norm.mgz 64144 voxels in left wm, 90156 in right wm, xrange [114, 129] searching rotation angles z=[-5 9], y=[-11 3] 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 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.6 searching scale 1 Z rot 6.8 searching scale 1 Z rot 7.1 searching scale 1 Z rot 7.3 searching scale 1 Z rot 7.6 searching scale 1 Z rot 7.8 searching scale 1 Z rot 8.1 searching scale 1 Z rot 8.3 searching scale 1 Z rot 8.6 global minimum found at slice 122.2, rotations (-3.65, 1.81) final transformation (x=122.2, yr=-3.652, zr=1.813): 0.99747 -0.03163 -0.06366 15.38184; 0.03157 0.99950 -0.00201 35.39107; 0.06370 0.00000 0.99797 18.42117; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 89 102 eigenvectors: -0.00056 0.00389 0.99999; -0.34416 -0.93891 0.00347; 0.93891 -0.34415 0.00186; writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/aseg.auto.mgz... corpus callosum segmentation took 1.7 minutes #-------------------------------------- #@# Merge ASeg Sat Oct 7 19:44:26 CEST 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Sat Oct 7 19:44:26 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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... 1315 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 82 (82), valley at 37 (37) csf peak at 42, setting threshold to 68 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 81 (81), valley at 17 (17) csf peak at 41, setting threshold to 67 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 8 seconds. #-------------------------------------------- #@# Mask BFS Sat Oct 7 19:47:35 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1640741 voxels in mask (pct= 9.78) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sat Oct 7 19:47:37 CEST 2017 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 104.2 +- 6.5 [79.0 --> 125.0] GM (76.0) : 72.5 +- 13.6 [30.0 --> 95.0] setting bottom of white matter range to 86.0 setting top of gray matter range to 99.6 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 18472 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5422 filled 9866 bright non-wm voxels segmented. 9926 diagonally connected voxels added... white matter segmentation took 2.1 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.53 minutes reading wm segmentation from wm.seg.mgz... 690 voxels added to wm to prevent paths from MTL structures to cortex 4326 additional wm voxels added 0 additional wm voxels added SEG EDIT: 52618 voxels turned on, 57472 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 36 found - 36 modified | TOTAL: 36 pass 2 (xy+): 0 found - 36 modified | TOTAL: 36 pass 1 (xy-): 36 found - 36 modified | TOTAL: 72 pass 2 (xy-): 0 found - 36 modified | TOTAL: 72 pass 1 (yz+): 39 found - 39 modified | TOTAL: 111 pass 2 (yz+): 0 found - 39 modified | TOTAL: 111 pass 1 (yz-): 34 found - 34 modified | TOTAL: 145 pass 2 (yz-): 0 found - 34 modified | TOTAL: 145 pass 1 (xz+): 37 found - 37 modified | TOTAL: 182 pass 2 (xz+): 0 found - 37 modified | TOTAL: 182 pass 1 (xz-): 45 found - 45 modified | TOTAL: 227 pass 2 (xz-): 0 found - 45 modified | TOTAL: 227 Iteration Number : 1 pass 1 (+++): 68 found - 68 modified | TOTAL: 68 pass 2 (+++): 0 found - 68 modified | TOTAL: 68 pass 1 (+++): 65 found - 65 modified | TOTAL: 133 pass 2 (+++): 0 found - 65 modified | TOTAL: 133 pass 1 (+++): 104 found - 104 modified | TOTAL: 237 pass 2 (+++): 0 found - 104 modified | TOTAL: 237 pass 1 (+++): 92 found - 92 modified | TOTAL: 329 pass 2 (+++): 0 found - 92 modified | TOTAL: 329 Iteration Number : 1 pass 1 (++): 238 found - 238 modified | TOTAL: 238 pass 2 (++): 0 found - 238 modified | TOTAL: 238 pass 1 (+-): 253 found - 253 modified | TOTAL: 491 pass 2 (+-): 2 found - 255 modified | TOTAL: 493 pass 3 (+-): 0 found - 255 modified | TOTAL: 493 pass 1 (--): 268 found - 268 modified | TOTAL: 761 pass 2 (--): 1 found - 269 modified | TOTAL: 762 pass 3 (--): 0 found - 269 modified | TOTAL: 762 pass 1 (-+): 231 found - 231 modified | TOTAL: 993 pass 2 (-+): 0 found - 231 modified | TOTAL: 993 Iteration Number : 2 pass 1 (xy+): 18 found - 18 modified | TOTAL: 18 pass 2 (xy+): 0 found - 18 modified | TOTAL: 18 pass 1 (xy-): 23 found - 23 modified | TOTAL: 41 pass 2 (xy-): 0 found - 23 modified | TOTAL: 41 pass 1 (yz+): 24 found - 24 modified | TOTAL: 65 pass 2 (yz+): 0 found - 24 modified | TOTAL: 65 pass 1 (yz-): 19 found - 19 modified | TOTAL: 84 pass 2 (yz-): 0 found - 19 modified | TOTAL: 84 pass 1 (xz+): 18 found - 18 modified | TOTAL: 102 pass 2 (xz+): 0 found - 18 modified | TOTAL: 102 pass 1 (xz-): 12 found - 12 modified | TOTAL: 114 pass 2 (xz-): 0 found - 12 modified | TOTAL: 114 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 pass 1 (+++): 6 found - 6 modified | TOTAL: 10 pass 2 (+++): 0 found - 6 modified | TOTAL: 10 pass 1 (+++): 2 found - 2 modified | TOTAL: 12 pass 2 (+++): 0 found - 2 modified | TOTAL: 12 Iteration Number : 2 pass 1 (++): 8 found - 8 modified | TOTAL: 8 pass 2 (++): 0 found - 8 modified | TOTAL: 8 pass 1 (+-): 10 found - 10 modified | TOTAL: 18 pass 2 (+-): 0 found - 10 modified | TOTAL: 18 pass 1 (--): 6 found - 6 modified | TOTAL: 24 pass 2 (--): 0 found - 6 modified | TOTAL: 24 pass 1 (-+): 7 found - 7 modified | TOTAL: 31 pass 2 (-+): 0 found - 7 modified | TOTAL: 31 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 1 found - 1 modified | TOTAL: 3 pass 2 (yz-): 0 found - 1 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 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 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 0 found - 0 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 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 Iteration Number : 5 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 : 5 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 : 5 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 = 1712 (out of 584603: 0.292848) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sat Oct 7 19:50:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 1.03064 -0.08302 -0.11151 19.43493; 0.10442 1.03170 0.46792 -50.75214; 0.07140 -0.50700 0.79886 62.36523; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.03064 -0.08302 -0.11151 19.43493; 0.10442 1.03170 0.46792 -50.75214; 0.07140 -0.50700 0.79886 62.36523; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 3007 (min = 350, max = 1400), aspect = 1.19 (min = 0.10, max = 0.75) need search nearby using seed (127, 116, 89), TAL = (1.0, -39.0, 12.0) talairach voxel to voxel transform 0.95434 0.11046 0.06851 -17.21404; -0.04496 0.74743 -0.44407 66.50200; -0.11384 0.46448 0.96382 -34.32321; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (127, 116, 89) --> (1.0, -39.0, 12.0) done. writing output to filled.mgz... filling took 0.7 minutes talairach cc position changed to (1.00, -39.00, 12.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, -39.00, 12.00) SRC: (105.72, 108.78, 92.93) search lh wm seed point around talairach space (-17.00, -39.00, 12.00), SRC: (140.08, 107.16, 88.83) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Sat Oct 7 19:50:59 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 6 found - 6 modified | TOTAL: 8 pass 2 (xy-): 0 found - 6 modified | TOTAL: 8 pass 1 (yz+): 2 found - 2 modified | TOTAL: 10 pass 2 (yz+): 0 found - 2 modified | TOTAL: 10 pass 1 (yz-): 2 found - 2 modified | TOTAL: 12 pass 2 (yz-): 0 found - 2 modified | TOTAL: 12 pass 1 (xz+): 3 found - 3 modified | TOTAL: 15 pass 2 (xz+): 0 found - 3 modified | TOTAL: 15 pass 1 (xz-): 1 found - 1 modified | TOTAL: 16 pass 2 (xz-): 0 found - 1 modified | TOTAL: 16 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 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 2 found - 2 modified | TOTAL: 4 pass 2 (--): 0 found - 2 modified | TOTAL: 4 pass 1 (-+): 1 found - 1 modified | TOTAL: 5 pass 2 (-+): 0 found - 1 modified | TOTAL: 5 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-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 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 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 22 (out of 270992: 0.008118) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 3002 vertices, 3259 faces slice 50: 12198 vertices, 12610 faces slice 60: 24806 vertices, 25273 faces slice 70: 38576 vertices, 39102 faces slice 80: 52130 vertices, 52631 faces slice 90: 64138 vertices, 64592 faces slice 100: 75789 vertices, 76248 faces slice 110: 86714 vertices, 87208 faces slice 120: 96907 vertices, 97392 faces slice 130: 106880 vertices, 107339 faces slice 140: 116764 vertices, 117195 faces slice 150: 125173 vertices, 125599 faces slice 160: 132940 vertices, 133293 faces slice 170: 138663 vertices, 138987 faces slice 180: 143709 vertices, 144019 faces slice 190: 146441 vertices, 146653 faces slice 200: 146666 vertices, 146830 faces slice 210: 146666 vertices, 146830 faces slice 220: 146666 vertices, 146830 faces slice 230: 146666 vertices, 146830 faces slice 240: 146666 vertices, 146830 faces slice 250: 146666 vertices, 146830 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... 146666 voxel in cpt #1: X=-164 [v=146666,e=440490,f=293660] located at (-22.299660, -27.050495, 30.157221) For the whole surface: X=-164 [v=146666,e=440490,f=293660] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Sat Oct 7 19:51:05 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 1 found - 1 modified | TOTAL: 3 pass 2 (yz-): 0 found - 1 modified | TOTAL: 3 pass 1 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 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 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 Iteration Number : 1 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 : 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 = 7 (out of 283071: 0.002473) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 1268 vertices, 1403 faces slice 50: 7850 vertices, 8170 faces slice 60: 18936 vertices, 19358 faces slice 70: 31614 vertices, 32111 faces slice 80: 44991 vertices, 45472 faces slice 90: 57135 vertices, 57571 faces slice 100: 69227 vertices, 69693 faces slice 110: 81116 vertices, 81596 faces slice 120: 92933 vertices, 93421 faces slice 130: 103836 vertices, 104350 faces slice 140: 115093 vertices, 115608 faces slice 150: 125588 vertices, 126074 faces slice 160: 134583 vertices, 135045 faces slice 170: 142013 vertices, 142395 faces slice 180: 147794 vertices, 148130 faces slice 190: 151706 vertices, 151981 faces slice 200: 152648 vertices, 152834 faces slice 210: 152648 vertices, 152834 faces slice 220: 152648 vertices, 152834 faces slice 230: 152648 vertices, 152834 faces slice 240: 152648 vertices, 152834 faces slice 250: 152648 vertices, 152834 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... 152648 voxel in cpt #1: X=-186 [v=152648,e=458502,f=305668] located at (33.261925, -20.849012, 29.512178) For the whole surface: X=-186 [v=152648,e=458502,f=305668] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sat Oct 7 19:51:10 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Sat Oct 7 19:51:10 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 15802 of (15802 15805) to complete... Waiting for PID 15805 of (15802 15805) to complete... 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... 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... PIDs (15802 15805) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Sat Oct 7 19:51:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Sat Oct 7 19:51:17 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 15849 of (15849 15852) to complete... Waiting for PID 15852 of (15849 15852) to complete... mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 49.1 mm, total surface area = 75555 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.8 minutes step 000: RMS=0.166 (target=0.015) step 005: RMS=0.127 (target=0.015) step 010: RMS=0.097 (target=0.015) step 015: RMS=0.084 (target=0.015) step 020: RMS=0.074 (target=0.015) step 025: RMS=0.067 (target=0.015) step 030: RMS=0.061 (target=0.015) step 035: RMS=0.057 (target=0.015) step 040: RMS=0.054 (target=0.015) step 045: RMS=0.052 (target=0.015) step 050: RMS=0.051 (target=0.015) step 055: RMS=0.051 (target=0.015) step 060: RMS=0.050 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 45.048151 mris_inflate stimesec 0.127980 mris_inflate ru_maxrss 214712 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 31135 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 10328 mris_inflate ru_oublock 10344 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 5233 mris_inflate ru_nivcsw 5882 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 48.1 mm, total surface area = 77919 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.8 minutes step 000: RMS=0.169 (target=0.015) step 005: RMS=0.130 (target=0.015) step 010: RMS=0.102 (target=0.015) step 015: RMS=0.090 (target=0.015) step 020: RMS=0.079 (target=0.015) step 025: RMS=0.073 (target=0.015) step 030: RMS=0.067 (target=0.015) step 035: RMS=0.062 (target=0.015) step 040: RMS=0.060 (target=0.015) step 045: RMS=0.059 (target=0.015) step 050: RMS=0.058 (target=0.015) step 055: RMS=0.057 (target=0.015) step 060: RMS=0.056 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 47.242818 mris_inflate stimesec 0.140978 mris_inflate ru_maxrss 223856 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 32394 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 10744 mris_inflate ru_oublock 10768 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 5997 mris_inflate ru_nivcsw 5284 PIDs (15849 15852) completed and logs appended. #-------------------------------------------- #@# QSphere lh Sat Oct 7 19:52:04 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Sat Oct 7 19:52:04 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 15951 of (15951 15954) to complete... Waiting for PID 15954 of (15951 15954) to complete... 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 0.95 +- 0.62 (0.00-->11.65) (max @ vno 107643 --> 107644) face area 0.03 +- 0.03 (-0.43-->0.96) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.318... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.394, avgs=0 005/300: dt: 0.9000, rms radial error=175.142, avgs=0 010/300: dt: 0.9000, rms radial error=174.602, avgs=0 015/300: dt: 0.9000, rms radial error=173.893, avgs=0 020/300: dt: 0.9000, rms radial error=173.084, avgs=0 025/300: dt: 0.9000, rms radial error=172.219, avgs=0 030/300: dt: 0.9000, rms radial error=171.321, avgs=0 035/300: dt: 0.9000, rms radial error=170.407, avgs=0 040/300: dt: 0.9000, rms radial error=169.484, avgs=0 045/300: dt: 0.9000, rms radial error=168.557, avgs=0 050/300: dt: 0.9000, rms radial error=167.630, avgs=0 055/300: dt: 0.9000, rms radial error=166.705, avgs=0 060/300: dt: 0.9000, rms radial error=165.782, avgs=0 065/300: dt: 0.9000, rms radial error=164.862, avgs=0 070/300: dt: 0.9000, rms radial error=163.946, avgs=0 075/300: dt: 0.9000, rms radial error=163.034, avgs=0 080/300: dt: 0.9000, rms radial error=162.125, avgs=0 085/300: dt: 0.9000, rms radial error=161.221, avgs=0 090/300: dt: 0.9000, rms radial error=160.321, avgs=0 095/300: dt: 0.9000, rms radial error=159.426, avgs=0 100/300: dt: 0.9000, rms radial error=158.535, avgs=0 105/300: dt: 0.9000, rms radial error=157.649, avgs=0 110/300: dt: 0.9000, rms radial error=156.767, avgs=0 115/300: dt: 0.9000, rms radial error=155.890, avgs=0 120/300: dt: 0.9000, rms radial error=155.016, avgs=0 125/300: dt: 0.9000, rms radial error=154.147, avgs=0 130/300: dt: 0.9000, rms radial error=153.281, avgs=0 135/300: dt: 0.9000, rms radial error=152.420, avgs=0 140/300: dt: 0.9000, rms radial error=151.563, avgs=0 145/300: dt: 0.9000, rms radial error=150.711, avgs=0 150/300: dt: 0.9000, rms radial error=149.863, avgs=0 155/300: dt: 0.9000, rms radial error=149.021, avgs=0 160/300: dt: 0.9000, rms radial error=148.183, avgs=0 165/300: dt: 0.9000, rms radial error=147.350, avgs=0 170/300: dt: 0.9000, rms radial error=146.521, avgs=0 175/300: dt: 0.9000, rms radial error=145.697, avgs=0 180/300: dt: 0.9000, rms radial error=144.877, avgs=0 185/300: dt: 0.9000, rms radial error=144.062, avgs=0 190/300: dt: 0.9000, rms radial error=143.251, avgs=0 195/300: dt: 0.9000, rms radial error=142.445, avgs=0 200/300: dt: 0.9000, rms radial error=141.643, avgs=0 205/300: dt: 0.9000, rms radial error=140.845, avgs=0 210/300: dt: 0.9000, rms radial error=140.052, avgs=0 215/300: dt: 0.9000, rms radial error=139.263, avgs=0 220/300: dt: 0.9000, rms radial error=138.479, avgs=0 225/300: dt: 0.9000, rms radial error=137.699, avgs=0 230/300: dt: 0.9000, rms radial error=136.923, avgs=0 235/300: dt: 0.9000, rms radial error=136.151, avgs=0 240/300: dt: 0.9000, rms radial error=135.384, avgs=0 245/300: dt: 0.9000, rms radial error=134.620, avgs=0 250/300: dt: 0.9000, rms radial error=133.862, avgs=0 255/300: dt: 0.9000, rms radial error=133.107, avgs=0 260/300: dt: 0.9000, rms radial error=132.356, avgs=0 265/300: dt: 0.9000, rms radial error=131.610, avgs=0 270/300: dt: 0.9000, rms radial error=130.868, avgs=0 275/300: dt: 0.9000, rms radial error=130.130, avgs=0 280/300: dt: 0.9000, rms radial error=129.396, avgs=0 285/300: dt: 0.9000, rms radial error=128.667, avgs=0 290/300: dt: 0.9000, rms radial error=127.941, avgs=0 295/300: dt: 0.9000, rms radial error=127.220, avgs=0 300/300: dt: 0.9000, rms radial error=126.502, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17159.51 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00008 epoch 2 (K=40.0), pass 1, starting sse = 2938.88 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 333.43 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/10 = 0.00153 epoch 4 (K=640.0), pass 1, starting sse = 29.90 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00469 final distance error %29.86 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 263.761902 mris_sphere stimesec 0.200969 mris_sphere ru_maxrss 214908 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 31180 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10368 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 8212 mris_sphere ru_nivcsw 19294 FSRUNTIME@ mris_sphere 0.0733 hours 1 threads 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 0.94 +- 0.58 (0.00-->10.49) (max @ vno 113661 --> 113662) face area 0.03 +- 0.03 (-0.27-->0.50) == Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.316... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.498, avgs=0 005/300: dt: 0.9000, rms radial error=175.242, avgs=0 010/300: dt: 0.9000, rms radial error=174.691, avgs=0 015/300: dt: 0.9000, rms radial error=173.966, avgs=0 020/300: dt: 0.9000, rms radial error=173.141, avgs=0 025/300: dt: 0.9000, rms radial error=172.259, avgs=0 030/300: dt: 0.9000, rms radial error=171.346, avgs=0 035/300: dt: 0.9000, rms radial error=170.415, avgs=0 040/300: dt: 0.9000, rms radial error=169.478, avgs=0 045/300: dt: 0.9000, rms radial error=168.543, avgs=0 050/300: dt: 0.9000, rms radial error=167.608, avgs=0 055/300: dt: 0.9000, rms radial error=166.675, avgs=0 060/300: dt: 0.9000, rms radial error=165.744, avgs=0 065/300: dt: 0.9000, rms radial error=164.817, avgs=0 070/300: dt: 0.9000, rms radial error=163.893, avgs=0 075/300: dt: 0.9000, rms radial error=162.974, avgs=0 080/300: dt: 0.9000, rms radial error=162.058, avgs=0 085/300: dt: 0.9000, rms radial error=161.146, avgs=0 090/300: dt: 0.9000, rms radial error=160.240, avgs=0 095/300: dt: 0.9000, rms radial error=159.338, avgs=0 100/300: dt: 0.9000, rms radial error=158.440, avgs=0 105/300: dt: 0.9000, rms radial error=157.547, avgs=0 110/300: dt: 0.9000, rms radial error=156.659, avgs=0 115/300: dt: 0.9000, rms radial error=155.780, avgs=0 120/300: dt: 0.9000, rms radial error=154.905, avgs=0 125/300: dt: 0.9000, rms radial error=154.035, avgs=0 130/300: dt: 0.9000, rms radial error=153.169, avgs=0 135/300: dt: 0.9000, rms radial error=152.309, avgs=0 140/300: dt: 0.9000, rms radial error=151.453, avgs=0 145/300: dt: 0.9000, rms radial error=150.602, avgs=0 150/300: dt: 0.9000, rms radial error=149.755, avgs=0 155/300: dt: 0.9000, rms radial error=148.914, avgs=0 160/300: dt: 0.9000, rms radial error=148.077, avgs=0 165/300: dt: 0.9000, rms radial error=147.245, avgs=0 170/300: dt: 0.9000, rms radial error=146.417, avgs=0 175/300: dt: 0.9000, rms radial error=145.594, avgs=0 180/300: dt: 0.9000, rms radial error=144.776, avgs=0 185/300: dt: 0.9000, rms radial error=143.962, avgs=0 190/300: dt: 0.9000, rms radial error=143.152, avgs=0 195/300: dt: 0.9000, rms radial error=142.347, avgs=0 200/300: dt: 0.9000, rms radial error=141.546, avgs=0 205/300: dt: 0.9000, rms radial error=140.750, avgs=0 210/300: dt: 0.9000, rms radial error=139.958, avgs=0 215/300: dt: 0.9000, rms radial error=139.171, avgs=0 220/300: dt: 0.9000, rms radial error=138.388, avgs=0 225/300: dt: 0.9000, rms radial error=137.609, avgs=0 230/300: dt: 0.9000, rms radial error=136.834, avgs=0 235/300: dt: 0.9000, rms radial error=136.064, avgs=0 240/300: dt: 0.9000, rms radial error=135.298, avgs=0 245/300: dt: 0.9000, rms radial error=134.537, avgs=0 250/300: dt: 0.9000, rms radial error=133.780, avgs=0 255/300: dt: 0.9000, rms radial error=133.028, avgs=0 260/300: dt: 0.9000, rms radial error=132.280, avgs=0 265/300: dt: 0.9000, rms radial error=131.536, avgs=0 270/300: dt: 0.9000, rms radial error=130.797, avgs=0 275/300: dt: 0.9000, rms radial error=130.062, avgs=0 280/300: dt: 0.9000, rms radial error=129.331, avgs=0 285/300: dt: 0.9000, rms radial error=128.604, avgs=0 290/300: dt: 0.9000, rms radial error=127.881, avgs=0 295/300: dt: 0.9000, rms radial error=127.162, avgs=0 300/300: dt: 0.9000, rms radial error=126.446, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17896.21 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 2 (K=40.0), pass 1, starting sse = 3041.67 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00018 epoch 3 (K=160.0), pass 1, starting sse = 337.71 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/10 = 0.00223 epoch 4 (K=640.0), pass 1, starting sse = 33.54 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00416 final distance error %27.59 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 272.089636 mris_sphere stimesec 0.153976 mris_sphere ru_maxrss 224052 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 32441 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10792 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 8146 mris_sphere ru_nivcsw 18974 FSRUNTIME@ mris_sphere 0.0747 hours 1 threads PIDs (15951 15954) completed and logs appended. #-------------------------------------------- #@# Fix Topology Copy lh Sat Oct 7 19:56:33 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Sat Oct 7 19:56:33 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Sat Oct 7 19:56:33 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050660 lh #@# Fix Topology rh Sat Oct 7 19:56:34 CEST 2017 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050660 rh Waiting for PID 16152 of (16152 16155) to complete... Waiting for PID 16155 of (16152 16155) to complete... mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050660 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=-164 (nv=146666, nf=293660, ne=440490, g=83) 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... 8579 ambiguous faces found in tessellation segmenting defects... 91 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 57 into 52 -merging segment 79 into 73 -merging segment 86 into 85 88 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1234 (-4.5617) -vertex loglikelihood: -5.9425 (-2.9713) -normal dot loglikelihood: -3.5911 (-3.5911) -quad curv loglikelihood: -6.1749 (-3.0875) Total Loglikelihood : -24.8320 CORRECTING DEFECT 0 (vertices=23, convex hull=45, v0=17) After retessellation of defect 0 (v0=17), euler #=-84 (141308,421372,279980) : difference with theory (-85) = -1 CORRECTING DEFECT 1 (vertices=26, convex hull=63, v0=1685) After retessellation of defect 1 (v0=1685), euler #=-83 (141319,421429,280027) : difference with theory (-84) = -1 CORRECTING DEFECT 2 (vertices=17, convex hull=46, v0=6122) After retessellation of defect 2 (v0=6122), euler #=-82 (141327,421466,280057) : difference with theory (-83) = -1 CORRECTING DEFECT 3 (vertices=71, convex hull=88, v0=6942) After retessellation of defect 3 (v0=6942), euler #=-81 (141359,421602,280162) : difference with theory (-82) = -1 CORRECTING DEFECT 4 (vertices=178, convex hull=145, v0=10128) After retessellation of defect 4 (v0=10128), euler #=-82 (141406,421847,280359) : difference with theory (-81) = 1 CORRECTING DEFECT 5 (vertices=19, convex hull=22, v0=10178) After retessellation of defect 5 (v0=10178), euler #=-81 (141408,421861,280372) : difference with theory (-80) = 1 CORRECTING DEFECT 6 (vertices=48, convex hull=66, v0=13323) After retessellation of defect 6 (v0=13323), euler #=-80 (141426,421940,280434) : difference with theory (-79) = 1 CORRECTING DEFECT 7 (vertices=35, convex hull=68, v0=14449) After retessellation of defect 7 (v0=14449), euler #=-79 (141438,422005,280488) : difference with theory (-78) = 1 CORRECTING DEFECT 8 (vertices=33, convex hull=66, v0=14646) After retessellation of defect 8 (v0=14646), euler #=-78 (141458,422092,280556) : difference with theory (-77) = 1 CORRECTING DEFECT 9 (vertices=52, convex hull=97, v0=24211) After retessellation of defect 9 (v0=24211), euler #=-77 (141484,422219,280658) : difference with theory (-76) = 1 CORRECTING DEFECT 10 (vertices=73, convex hull=28, v0=25033) After retessellation of defect 10 (v0=25033), euler #=-76 (141488,422242,280678) : difference with theory (-75) = 1 CORRECTING DEFECT 11 (vertices=68, convex hull=86, v0=26771) After retessellation of defect 11 (v0=26771), euler #=-76 (141502,422330,280752) : difference with theory (-74) = 2 CORRECTING DEFECT 12 (vertices=18, convex hull=55, v0=27271) After retessellation of defect 12 (v0=27271), euler #=-75 (141511,422377,280791) : difference with theory (-73) = 2 CORRECTING DEFECT 13 (vertices=27, convex hull=57, v0=28558) After retessellation of defect 13 (v0=28558), euler #=-74 (141522,422431,280835) : difference with theory (-72) = 2 CORRECTING DEFECT 14 (vertices=180, convex hull=153, v0=34278) After retessellation of defect 14 (v0=34278), euler #=-74 (141595,422728,281059) : difference with theory (-71) = 3 CORRECTING DEFECT 15 (vertices=70, convex hull=78, v0=39550) After retessellation of defect 15 (v0=39550), euler #=-73 (141619,422832,281140) : difference with theory (-70) = 3 CORRECTING DEFECT 16 (vertices=39, convex hull=60, v0=39649) After retessellation of defect 16 (v0=39649), euler #=-72 (141637,422909,281200) : difference with theory (-69) = 3 CORRECTING DEFECT 17 (vertices=6, convex hull=24, v0=41241) After retessellation of defect 17 (v0=41241), euler #=-71 (141638,422919,281210) : difference with theory (-68) = 3 CORRECTING DEFECT 18 (vertices=78, convex hull=105, v0=42535) After retessellation of defect 18 (v0=42535), euler #=-70 (141654,423012,281288) : difference with theory (-67) = 3 CORRECTING DEFECT 19 (vertices=44, convex hull=82, v0=42850) After retessellation of defect 19 (v0=42850), euler #=-69 (141678,423118,281371) : difference with theory (-66) = 3 CORRECTING DEFECT 20 (vertices=6, convex hull=23, v0=42962) After retessellation of defect 20 (v0=42962), euler #=-68 (141680,423130,281382) : difference with theory (-65) = 3 CORRECTING DEFECT 21 (vertices=18, convex hull=47, v0=43252) After retessellation of defect 21 (v0=43252), euler #=-67 (141689,423172,281416) : difference with theory (-64) = 3 CORRECTING DEFECT 22 (vertices=43, convex hull=72, v0=43874) After retessellation of defect 22 (v0=43874), euler #=-66 (141710,423268,281492) : difference with theory (-63) = 3 CORRECTING DEFECT 23 (vertices=90, convex hull=147, v0=44052) After retessellation of defect 23 (v0=44052), euler #=-65 (141757,423472,281650) : difference with theory (-62) = 3 CORRECTING DEFECT 24 (vertices=53, convex hull=36, v0=45177) After retessellation of defect 24 (v0=45177), euler #=-64 (141767,423514,281683) : difference with theory (-61) = 3 CORRECTING DEFECT 25 (vertices=63, convex hull=28, v0=47909) After retessellation of defect 25 (v0=47909), euler #=-63 (141772,423537,281702) : difference with theory (-60) = 3 CORRECTING DEFECT 26 (vertices=13, convex hull=9, v0=48597) After retessellation of defect 26 (v0=48597), euler #=-62 (141773,423541,281706) : difference with theory (-59) = 3 CORRECTING DEFECT 27 (vertices=35, convex hull=71, v0=50832) After retessellation of defect 27 (v0=50832), euler #=-61 (141788,423616,281767) : difference with theory (-58) = 3 CORRECTING DEFECT 28 (vertices=112, convex hull=36, v0=52165) After retessellation of defect 28 (v0=52165), euler #=-60 (141796,423656,281800) : difference with theory (-57) = 3 CORRECTING DEFECT 29 (vertices=27, convex hull=60, v0=53452) After retessellation of defect 29 (v0=53452), euler #=-59 (141809,423717,281849) : difference with theory (-56) = 3 CORRECTING DEFECT 30 (vertices=21, convex hull=52, v0=59242) After retessellation of defect 30 (v0=59242), euler #=-58 (141818,423764,281888) : difference with theory (-55) = 3 CORRECTING DEFECT 31 (vertices=26, convex hull=61, v0=61418) After retessellation of defect 31 (v0=61418), euler #=-57 (141833,423831,281941) : difference with theory (-54) = 3 CORRECTING DEFECT 32 (vertices=14, convex hull=18, v0=66690) After retessellation of defect 32 (v0=66690), euler #=-56 (141836,423844,281952) : difference with theory (-53) = 3 CORRECTING DEFECT 33 (vertices=575, convex hull=220, v0=68481) After retessellation of defect 33 (v0=68481), euler #=-55 (141990,424407,282362) : difference with theory (-52) = 3 CORRECTING DEFECT 34 (vertices=21, convex hull=23, v0=69531) After retessellation of defect 34 (v0=69531), euler #=-54 (141996,424435,282385) : difference with theory (-51) = 3 CORRECTING DEFECT 35 (vertices=23, convex hull=35, v0=71638) After retessellation of defect 35 (v0=71638), euler #=-53 (142001,424462,282408) : difference with theory (-50) = 3 CORRECTING DEFECT 36 (vertices=6, convex hull=14, v0=72692) After retessellation of defect 36 (v0=72692), euler #=-52 (142002,424470,282416) : difference with theory (-49) = 3 CORRECTING DEFECT 37 (vertices=13, convex hull=21, v0=74327) After retessellation of defect 37 (v0=74327), euler #=-51 (142005,424485,282429) : difference with theory (-48) = 3 CORRECTING DEFECT 38 (vertices=80, convex hull=71, v0=75826) After retessellation of defect 38 (v0=75826), euler #=-50 (142014,424541,282477) : difference with theory (-47) = 3 CORRECTING DEFECT 39 (vertices=26, convex hull=71, v0=78286) After retessellation of defect 39 (v0=78286), euler #=-49 (142030,424618,282539) : difference with theory (-46) = 3 CORRECTING DEFECT 40 (vertices=51, convex hull=78, v0=86176) After retessellation of defect 40 (v0=86176), euler #=-48 (142063,424755,282644) : difference with theory (-45) = 3 CORRECTING DEFECT 41 (vertices=64, convex hull=23, v0=87861) After retessellation of defect 41 (v0=87861), euler #=-47 (142068,424776,282661) : difference with theory (-44) = 3 CORRECTING DEFECT 42 (vertices=48, convex hull=21, v0=95847) After retessellation of defect 42 (v0=95847), euler #=-46 (142071,424793,282676) : difference with theory (-43) = 3 CORRECTING DEFECT 43 (vertices=29, convex hull=54, v0=97158) After retessellation of defect 43 (v0=97158), euler #=-45 (142085,424855,282725) : difference with theory (-42) = 3 CORRECTING DEFECT 44 (vertices=34, convex hull=66, v0=98484) After retessellation of defect 44 (v0=98484), euler #=-44 (142103,424938,282791) : difference with theory (-41) = 3 CORRECTING DEFECT 45 (vertices=11, convex hull=30, v0=100649) After retessellation of defect 45 (v0=100649), euler #=-43 (142105,424954,282806) : difference with theory (-40) = 3 CORRECTING DEFECT 46 (vertices=10, convex hull=22, v0=103118) After retessellation of defect 46 (v0=103118), euler #=-42 (142106,424965,282817) : difference with theory (-39) = 3 CORRECTING DEFECT 47 (vertices=162, convex hull=143, v0=104539) After retessellation of defect 47 (v0=104539), euler #=-41 (142164,425199,282994) : difference with theory (-38) = 3 CORRECTING DEFECT 48 (vertices=64, convex hull=36, v0=105232) After retessellation of defect 48 (v0=105232), euler #=-40 (142174,425239,283025) : difference with theory (-37) = 3 CORRECTING DEFECT 49 (vertices=21, convex hull=29, v0=106628) After retessellation of defect 49 (v0=106628), euler #=-39 (142179,425265,283047) : difference with theory (-36) = 3 CORRECTING DEFECT 50 (vertices=16, convex hull=37, v0=106689) After retessellation of defect 50 (v0=106689), euler #=-38 (142185,425298,283075) : difference with theory (-35) = 3 CORRECTING DEFECT 51 (vertices=50, convex hull=47, v0=106853) After retessellation of defect 51 (v0=106853), euler #=-37 (142208,425386,283141) : difference with theory (-34) = 3 CORRECTING DEFECT 52 (vertices=71, convex hull=120, v0=107428) After retessellation of defect 52 (v0=107428), euler #=-35 (142230,425507,283242) : difference with theory (-33) = 2 CORRECTING DEFECT 53 (vertices=382, convex hull=289, v0=107445) After retessellation of defect 53 (v0=107445), euler #=-34 (142338,425997,283625) : difference with theory (-32) = 2 CORRECTING DEFECT 54 (vertices=33, convex hull=62, v0=109421) After retessellation of defect 54 (v0=109421), euler #=-33 (142359,426083,283691) : difference with theory (-31) = 2 CORRECTING DEFECT 55 (vertices=25, convex hull=55, v0=109545) After retessellation of defect 55 (v0=109545), euler #=-32 (142370,426133,283731) : difference with theory (-30) = 2 CORRECTING DEFECT 56 (vertices=20, convex hull=26, v0=111727) After retessellation of defect 56 (v0=111727), euler #=-31 (142373,426148,283744) : difference with theory (-29) = 2 CORRECTING DEFECT 57 (vertices=20, convex hull=33, v0=112706) After retessellation of defect 57 (v0=112706), euler #=-30 (142378,426176,283768) : difference with theory (-28) = 2 CORRECTING DEFECT 58 (vertices=24, convex hull=55, v0=114799) After retessellation of defect 58 (v0=114799), euler #=-29 (142387,426223,283807) : difference with theory (-27) = 2 CORRECTING DEFECT 59 (vertices=80, convex hull=119, v0=114936) After retessellation of defect 59 (v0=114936), euler #=-28 (142403,426330,283899) : difference with theory (-26) = 2 CORRECTING DEFECT 60 (vertices=79, convex hull=94, v0=115839) After retessellation of defect 60 (v0=115839), euler #=-27 (142445,426494,284022) : difference with theory (-25) = 2 CORRECTING DEFECT 61 (vertices=20, convex hull=32, v0=116240) After retessellation of defect 61 (v0=116240), euler #=-26 (142450,426519,284043) : difference with theory (-24) = 2 CORRECTING DEFECT 62 (vertices=132, convex hull=46, v0=118208) After retessellation of defect 62 (v0=118208), euler #=-25 (142463,426577,284089) : difference with theory (-23) = 2 CORRECTING DEFECT 63 (vertices=7, convex hull=16, v0=118247) After retessellation of defect 63 (v0=118247), euler #=-24 (142463,426582,284095) : difference with theory (-22) = 2 CORRECTING DEFECT 64 (vertices=27, convex hull=58, v0=118935) After retessellation of defect 64 (v0=118935), euler #=-23 (142475,426641,284143) : difference with theory (-21) = 2 CORRECTING DEFECT 65 (vertices=12, convex hull=27, v0=119736) After retessellation of defect 65 (v0=119736), euler #=-22 (142478,426657,284157) : difference with theory (-20) = 2 CORRECTING DEFECT 66 (vertices=18, convex hull=17, v0=119890) After retessellation of defect 66 (v0=119890), euler #=-21 (142481,426669,284167) : difference with theory (-19) = 2 CORRECTING DEFECT 67 (vertices=25, convex hull=62, v0=120312) After retessellation of defect 67 (v0=120312), euler #=-20 (142489,426715,284206) : difference with theory (-18) = 2 CORRECTING DEFECT 68 (vertices=63, convex hull=48, v0=120780) After retessellation of defect 68 (v0=120780), euler #=-19 (142499,426767,284249) : difference with theory (-17) = 2 CORRECTING DEFECT 69 (vertices=428, convex hull=166, v0=121501) After retessellation of defect 69 (v0=121501), euler #=-18 (142607,427185,284560) : difference with theory (-16) = 2 CORRECTING DEFECT 70 (vertices=48, convex hull=77, v0=122014) After retessellation of defect 70 (v0=122014), euler #=-17 (142630,427292,284645) : difference with theory (-15) = 2 CORRECTING DEFECT 71 (vertices=43, convex hull=86, v0=123135) After retessellation of defect 71 (v0=123135), euler #=-16 (142645,427374,284713) : difference with theory (-14) = 2 CORRECTING DEFECT 72 (vertices=83, convex hull=129, v0=123368) After retessellation of defect 72 (v0=123368), euler #=-14 (142683,427544,284847) : difference with theory (-13) = 1 CORRECTING DEFECT 73 (vertices=30, convex hull=76, v0=126173) After retessellation of defect 73 (v0=126173), euler #=-13 (142698,427622,284911) : difference with theory (-12) = 1 CORRECTING DEFECT 74 (vertices=21, convex hull=44, v0=126703) After retessellation of defect 74 (v0=126703), euler #=-12 (142701,427647,284934) : difference with theory (-11) = 1 CORRECTING DEFECT 75 (vertices=15, convex hull=56, v0=126737) After retessellation of defect 75 (v0=126737), euler #=-11 (142710,427698,284977) : difference with theory (-10) = 1 CORRECTING DEFECT 76 (vertices=28, convex hull=25, v0=127604) After retessellation of defect 76 (v0=127604), euler #=-10 (142712,427712,284990) : difference with theory (-9) = 1 CORRECTING DEFECT 77 (vertices=113, convex hull=72, v0=128238) After retessellation of defect 77 (v0=128238), euler #=-9 (142734,427809,285066) : difference with theory (-8) = 1 CORRECTING DEFECT 78 (vertices=24, convex hull=59, v0=131664) After retessellation of defect 78 (v0=131664), euler #=-8 (142745,427867,285114) : difference with theory (-7) = 1 CORRECTING DEFECT 79 (vertices=129, convex hull=159, v0=133466) After retessellation of defect 79 (v0=133466), euler #=-7 (142777,428033,285249) : difference with theory (-6) = 1 CORRECTING DEFECT 80 (vertices=23, convex hull=51, v0=137233) After retessellation of defect 80 (v0=137233), euler #=-6 (142787,428081,285288) : difference with theory (-5) = 1 CORRECTING DEFECT 81 (vertices=32, convex hull=64, v0=137784) After retessellation of defect 81 (v0=137784), euler #=-5 (142796,428134,285333) : difference with theory (-4) = 1 CORRECTING DEFECT 82 (vertices=139, convex hull=105, v0=138044) After retessellation of defect 82 (v0=138044), euler #=-4 (142845,428330,285481) : difference with theory (-3) = 1 CORRECTING DEFECT 83 (vertices=102, convex hull=136, v0=138750) After retessellation of defect 83 (v0=138750), euler #=-2 (142865,428461,285594) : difference with theory (-2) = 0 CORRECTING DEFECT 84 (vertices=50, convex hull=94, v0=142269) After retessellation of defect 84 (v0=142269), euler #=-1 (142892,428584,285691) : difference with theory (-1) = 0 CORRECTING DEFECT 85 (vertices=33, convex hull=73, v0=145238) After retessellation of defect 85 (v0=145238), euler #=0 (142910,428666,285756) : difference with theory (0) = 0 CORRECTING DEFECT 86 (vertices=30, convex hull=91, v0=145290) After retessellation of defect 86 (v0=145290), euler #=1 (142925,428751,285827) : difference with theory (1) = 0 CORRECTING DEFECT 87 (vertices=22, convex hull=48, v0=145393) After retessellation of defect 87 (v0=145393), euler #=2 (142936,428802,285868) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.25 (0.05-->8.44) (max @ vno 133060 --> 136991) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.25 (0.05-->8.44) (max @ vno 133060 --> 136991) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 286 mutations (33.4%), 570 crossovers (66.6%), 256 vertices were eliminated building final representation... 3730 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=142936, nf=285868, ne=428802, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 55.0 minutes 0 defective edges removing intersecting faces 000: 602 intersecting 001: 10 intersecting mris_fix_topology utimesec 3302.841891 mris_fix_topology stimesec 0.292955 mris_fix_topology ru_maxrss 458016 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 58086 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 30984 mris_fix_topology ru_oublock 13976 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 565 mris_fix_topology ru_nivcsw 8875 FSRUNTIME@ mris_fix_topology lh 0.9172 hours 1 threads mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050660 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=-186 (nv=152648, nf=305668, ne=458502, g=94) 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 13 iterations marking ambiguous vertices... 11866 ambiguous faces found in tessellation segmenting defects... 112 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 4 into 3 -merging segment 9 into 7 -merging segment 23 into 22 -merging segment 73 into 65 -merging segment 82 into 69 -merging segment 88 into 69 -merging segment 81 into 76 -merging segment 92 into 89 -merging segment 95 into 89 -merging segment 102 into 99 -merging segment 101 into 99 -merging segment 103 into 99 100 defects to be corrected 0 vertices coincident reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2148 (-4.6074) -vertex loglikelihood: -5.9062 (-2.9531) -normal dot loglikelihood: -3.5490 (-3.5490) -quad curv loglikelihood: -6.5135 (-3.2568) Total Loglikelihood : -25.1836 CORRECTING DEFECT 0 (vertices=60, convex hull=70, v0=159) After retessellation of defect 0 (v0=159), euler #=-104 (145361,433107,287642) : difference with theory (-97) = 7 CORRECTING DEFECT 1 (vertices=27, convex hull=25, v0=1319) After retessellation of defect 1 (v0=1319), euler #=-103 (145367,433135,287665) : difference with theory (-96) = 7 CORRECTING DEFECT 2 (vertices=32, convex hull=70, v0=1549) After retessellation of defect 2 (v0=1549), euler #=-102 (145381,433203,287720) : difference with theory (-95) = 7 CORRECTING DEFECT 3 (vertices=85, convex hull=137, v0=5450) After retessellation of defect 3 (v0=5450), euler #=-100 (145411,433353,287842) : difference with theory (-94) = 6 CORRECTING DEFECT 4 (vertices=34, convex hull=36, v0=7920) After retessellation of defect 4 (v0=7920), euler #=-99 (145412,433372,287861) : difference with theory (-93) = 6 CORRECTING DEFECT 5 (vertices=297, convex hull=185, v0=10734) After retessellation of defect 5 (v0=10734), euler #=-98 (145488,433695,288109) : difference with theory (-92) = 6 CORRECTING DEFECT 6 (vertices=80, convex hull=88, v0=11151) After retessellation of defect 6 (v0=11151), euler #=-96 (145508,433795,288191) : difference with theory (-91) = 5 CORRECTING DEFECT 7 (vertices=68, convex hull=38, v0=11271) After retessellation of defect 7 (v0=11271), euler #=-95 (145511,433819,288213) : difference with theory (-90) = 5 CORRECTING DEFECT 8 (vertices=7, convex hull=17, v0=19741) After retessellation of defect 8 (v0=19741), euler #=-94 (145511,433821,288216) : difference with theory (-89) = 5 CORRECTING DEFECT 9 (vertices=26, convex hull=20, v0=20437) After retessellation of defect 9 (v0=20437), euler #=-93 (145513,433835,288229) : difference with theory (-88) = 5 CORRECTING DEFECT 10 (vertices=25, convex hull=55, v0=20820) After retessellation of defect 10 (v0=20820), euler #=-92 (145522,433882,288268) : difference with theory (-87) = 5 CORRECTING DEFECT 11 (vertices=28, convex hull=59, v0=21012) After retessellation of defect 11 (v0=21012), euler #=-91 (145530,433929,288308) : difference with theory (-86) = 5 CORRECTING DEFECT 12 (vertices=50, convex hull=95, v0=21166) After retessellation of defect 12 (v0=21166), euler #=-90 (145547,434017,288380) : difference with theory (-85) = 5 CORRECTING DEFECT 13 (vertices=74, convex hull=87, v0=21556) After retessellation of defect 13 (v0=21556), euler #=-89 (145582,434159,288488) : difference with theory (-84) = 5 CORRECTING DEFECT 14 (vertices=92, convex hull=133, v0=22318) After retessellation of defect 14 (v0=22318), euler #=-88 (145625,434341,288628) : difference with theory (-83) = 5 CORRECTING DEFECT 15 (vertices=28, convex hull=59, v0=24583) After retessellation of defect 15 (v0=24583), euler #=-87 (145635,434390,288668) : difference with theory (-82) = 5 CORRECTING DEFECT 16 (vertices=25, convex hull=59, v0=24624) After retessellation of defect 16 (v0=24624), euler #=-86 (145644,434441,288711) : difference with theory (-81) = 5 CORRECTING DEFECT 17 (vertices=5, convex hull=19, v0=24941) After retessellation of defect 17 (v0=24941), euler #=-85 (145644,434445,288716) : difference with theory (-80) = 5 CORRECTING DEFECT 18 (vertices=50, convex hull=65, v0=25277) After retessellation of defect 18 (v0=25277), euler #=-84 (145674,434559,288801) : difference with theory (-79) = 5 CORRECTING DEFECT 19 (vertices=34, convex hull=56, v0=28661) After retessellation of defect 19 (v0=28661), euler #=-83 (145683,434607,288841) : difference with theory (-78) = 5 CORRECTING DEFECT 20 (vertices=15, convex hull=45, v0=28924) After retessellation of defect 20 (v0=28924), euler #=-81 (145687,434638,288870) : difference with theory (-77) = 4 CORRECTING DEFECT 21 (vertices=43, convex hull=65, v0=41923) After retessellation of defect 21 (v0=41923), euler #=-80 (145712,434741,288949) : difference with theory (-76) = 4 CORRECTING DEFECT 22 (vertices=14, convex hull=26, v0=42321) After retessellation of defect 22 (v0=42321), euler #=-79 (145714,434754,288961) : difference with theory (-75) = 4 CORRECTING DEFECT 23 (vertices=58, convex hull=100, v0=50977) After retessellation of defect 23 (v0=50977), euler #=-78 (145742,434884,289064) : difference with theory (-74) = 4 CORRECTING DEFECT 24 (vertices=17, convex hull=54, v0=55856) After retessellation of defect 24 (v0=55856), euler #=-77 (145751,434932,289104) : difference with theory (-73) = 4 CORRECTING DEFECT 25 (vertices=24, convex hull=59, v0=62724) After retessellation of defect 25 (v0=62724), euler #=-76 (145762,434989,289151) : difference with theory (-72) = 4 CORRECTING DEFECT 26 (vertices=20, convex hull=23, v0=62791) After retessellation of defect 26 (v0=62791), euler #=-75 (145768,435014,289171) : difference with theory (-71) = 4 CORRECTING DEFECT 27 (vertices=47, convex hull=34, v0=63173) After retessellation of defect 27 (v0=63173), euler #=-74 (145772,435036,289190) : difference with theory (-70) = 4 CORRECTING DEFECT 28 (vertices=18, convex hull=18, v0=63194) After retessellation of defect 28 (v0=63194), euler #=-73 (145775,435051,289203) : difference with theory (-69) = 4 CORRECTING DEFECT 29 (vertices=133, convex hull=164, v0=63942) After retessellation of defect 29 (v0=63942), euler #=-72 (145789,435170,289309) : difference with theory (-68) = 4 CORRECTING DEFECT 30 (vertices=5, convex hull=18, v0=65085) After retessellation of defect 30 (v0=65085), euler #=-71 (145790,435177,289316) : difference with theory (-67) = 4 CORRECTING DEFECT 31 (vertices=1268, convex hull=445, v0=66465) L defect detected... After retessellation of defect 31 (v0=66465), euler #=-70 (146007,436039,289962) : difference with theory (-66) = 4 CORRECTING DEFECT 32 (vertices=23, convex hull=53, v0=66607) After retessellation of defect 32 (v0=66607), euler #=-69 (146019,436092,290004) : difference with theory (-65) = 4 CORRECTING DEFECT 33 (vertices=56, convex hull=67, v0=66918) After retessellation of defect 33 (v0=66918), euler #=-68 (146029,436153,290056) : difference with theory (-64) = 4 CORRECTING DEFECT 34 (vertices=19, convex hull=44, v0=68053) After retessellation of defect 34 (v0=68053), euler #=-67 (146038,436195,290090) : difference with theory (-63) = 4 CORRECTING DEFECT 35 (vertices=50, convex hull=86, v0=69210) After retessellation of defect 35 (v0=69210), euler #=-66 (146055,436279,290158) : difference with theory (-62) = 4 CORRECTING DEFECT 36 (vertices=32, convex hull=60, v0=71482) After retessellation of defect 36 (v0=71482), euler #=-65 (146069,436346,290212) : difference with theory (-61) = 4 CORRECTING DEFECT 37 (vertices=15, convex hull=32, v0=71689) After retessellation of defect 37 (v0=71689), euler #=-64 (146070,436360,290226) : difference with theory (-60) = 4 CORRECTING DEFECT 38 (vertices=19, convex hull=34, v0=74222) After retessellation of defect 38 (v0=74222), euler #=-63 (146070,436375,290242) : difference with theory (-59) = 4 CORRECTING DEFECT 39 (vertices=91, convex hull=95, v0=74550) After retessellation of defect 39 (v0=74550), euler #=-63 (146109,436539,290367) : difference with theory (-58) = 5 CORRECTING DEFECT 40 (vertices=17, convex hull=17, v0=75738) After retessellation of defect 40 (v0=75738), euler #=-62 (146111,436550,290377) : difference with theory (-57) = 5 CORRECTING DEFECT 41 (vertices=36, convex hull=68, v0=78220) After retessellation of defect 41 (v0=78220), euler #=-61 (146135,436646,290450) : difference with theory (-56) = 5 CORRECTING DEFECT 42 (vertices=7, convex hull=18, v0=81281) After retessellation of defect 42 (v0=81281), euler #=-60 (146136,436654,290458) : difference with theory (-55) = 5 CORRECTING DEFECT 43 (vertices=10, convex hull=32, v0=81981) After retessellation of defect 43 (v0=81981), euler #=-59 (146140,436673,290474) : difference with theory (-54) = 5 CORRECTING DEFECT 44 (vertices=18, convex hull=46, v0=82612) After retessellation of defect 44 (v0=82612), euler #=-58 (146148,436714,290508) : difference with theory (-53) = 5 CORRECTING DEFECT 45 (vertices=5, convex hull=18, v0=83734) After retessellation of defect 45 (v0=83734), euler #=-57 (146149,436721,290515) : difference with theory (-52) = 5 CORRECTING DEFECT 46 (vertices=81, convex hull=46, v0=83746) After retessellation of defect 46 (v0=83746), euler #=-56 (146158,436761,290547) : difference with theory (-51) = 5 CORRECTING DEFECT 47 (vertices=66, convex hull=38, v0=84607) After retessellation of defect 47 (v0=84607), euler #=-55 (146170,436810,290585) : difference with theory (-50) = 5 CORRECTING DEFECT 48 (vertices=16, convex hull=50, v0=84860) After retessellation of defect 48 (v0=84860), euler #=-54 (146178,436851,290619) : difference with theory (-49) = 5 CORRECTING DEFECT 49 (vertices=46, convex hull=90, v0=85165) After retessellation of defect 49 (v0=85165), euler #=-53 (146211,436991,290727) : difference with theory (-48) = 5 CORRECTING DEFECT 50 (vertices=65, convex hull=26, v0=87077) After retessellation of defect 50 (v0=87077), euler #=-52 (146214,437005,290739) : difference with theory (-47) = 5 CORRECTING DEFECT 51 (vertices=12, convex hull=22, v0=87487) After retessellation of defect 51 (v0=87487), euler #=-51 (146216,437017,290750) : difference with theory (-46) = 5 CORRECTING DEFECT 52 (vertices=20, convex hull=45, v0=87501) After retessellation of defect 52 (v0=87501), euler #=-50 (146225,437061,290786) : difference with theory (-45) = 5 CORRECTING DEFECT 53 (vertices=29, convex hull=51, v0=89393) After retessellation of defect 53 (v0=89393), euler #=-49 (146244,437138,290845) : difference with theory (-44) = 5 CORRECTING DEFECT 54 (vertices=25, convex hull=29, v0=93891) After retessellation of defect 54 (v0=93891), euler #=-48 (146248,437159,290863) : difference with theory (-43) = 5 CORRECTING DEFECT 55 (vertices=17, convex hull=22, v0=94477) After retessellation of defect 55 (v0=94477), euler #=-47 (146251,437175,290877) : difference with theory (-42) = 5 CORRECTING DEFECT 56 (vertices=65, convex hull=89, v0=96058) After retessellation of defect 56 (v0=96058), euler #=-46 (146279,437295,290970) : difference with theory (-41) = 5 CORRECTING DEFECT 57 (vertices=12, convex hull=22, v0=98488) After retessellation of defect 57 (v0=98488), euler #=-45 (146281,437309,290983) : difference with theory (-40) = 5 CORRECTING DEFECT 58 (vertices=68, convex hull=49, v0=101623) After retessellation of defect 58 (v0=101623), euler #=-44 (146290,437355,291021) : difference with theory (-39) = 5 CORRECTING DEFECT 59 (vertices=19, convex hull=52, v0=103510) After retessellation of defect 59 (v0=103510), euler #=-43 (146302,437413,291068) : difference with theory (-38) = 5 CORRECTING DEFECT 60 (vertices=10, convex hull=34, v0=103829) After retessellation of defect 60 (v0=103829), euler #=-42 (146305,437432,291085) : difference with theory (-37) = 5 CORRECTING DEFECT 61 (vertices=55, convex hull=103, v0=105005) After retessellation of defect 61 (v0=105005), euler #=-41 (146343,437590,291206) : difference with theory (-36) = 5 CORRECTING DEFECT 62 (vertices=110, convex hull=73, v0=105585) After retessellation of defect 62 (v0=105585), euler #=-39 (146366,437689,291284) : difference with theory (-35) = 4 CORRECTING DEFECT 63 (vertices=27, convex hull=62, v0=105723) After retessellation of defect 63 (v0=105723), euler #=-38 (146377,437746,291331) : difference with theory (-34) = 4 CORRECTING DEFECT 64 (vertices=60, convex hull=69, v0=105784) After retessellation of defect 64 (v0=105784), euler #=-37 (146408,437872,291427) : difference with theory (-33) = 4 CORRECTING DEFECT 65 (vertices=9, convex hull=14, v0=106251) After retessellation of defect 65 (v0=106251), euler #=-36 (146409,437879,291434) : difference with theory (-32) = 4 CORRECTING DEFECT 66 (vertices=795, convex hull=417, v0=108005) L defect detected... After retessellation of defect 66 (v0=108005), euler #=-35 (146546,438528,291947) : difference with theory (-31) = 4 CORRECTING DEFECT 67 (vertices=28, convex hull=57, v0=108320) After retessellation of defect 67 (v0=108320), euler #=-34 (146556,438580,291990) : difference with theory (-30) = 4 CORRECTING DEFECT 68 (vertices=7, convex hull=15, v0=109352) After retessellation of defect 68 (v0=109352), euler #=-33 (146557,438586,291996) : difference with theory (-29) = 4 CORRECTING DEFECT 69 (vertices=46, convex hull=64, v0=110189) After retessellation of defect 69 (v0=110189), euler #=-32 (146581,438684,292071) : difference with theory (-28) = 4 CORRECTING DEFECT 70 (vertices=131, convex hull=61, v0=111617) After retessellation of defect 70 (v0=111617), euler #=-32 (146605,438787,292150) : difference with theory (-27) = 5 CORRECTING DEFECT 71 (vertices=32, convex hull=36, v0=111797) After retessellation of defect 71 (v0=111797), euler #=-31 (146608,438808,292169) : difference with theory (-26) = 5 CORRECTING DEFECT 72 (vertices=82, convex hull=139, v0=112405) After retessellation of defect 72 (v0=112405), euler #=-29 (146656,439014,292329) : difference with theory (-25) = 4 CORRECTING DEFECT 73 (vertices=49, convex hull=87, v0=117091) After retessellation of defect 73 (v0=117091), euler #=-29 (146685,439143,292429) : difference with theory (-24) = 5 CORRECTING DEFECT 74 (vertices=110, convex hull=34, v0=117789) After retessellation of defect 74 (v0=117789), euler #=-28 (146695,439182,292459) : difference with theory (-23) = 5 CORRECTING DEFECT 75 (vertices=22, convex hull=45, v0=117844) After retessellation of defect 75 (v0=117844), euler #=-27 (146698,439208,292483) : difference with theory (-22) = 5 CORRECTING DEFECT 76 (vertices=24, convex hull=15, v0=118215) After retessellation of defect 76 (v0=118215), euler #=-26 (146699,439216,292491) : difference with theory (-21) = 5 CORRECTING DEFECT 77 (vertices=112, convex hull=80, v0=122118) After retessellation of defect 77 (v0=122118), euler #=-25 (146738,439372,292609) : difference with theory (-20) = 5 CORRECTING DEFECT 78 (vertices=56, convex hull=39, v0=123226) After retessellation of defect 78 (v0=123226), euler #=-24 (146739,439390,292627) : difference with theory (-19) = 5 CORRECTING DEFECT 79 (vertices=32, convex hull=65, v0=123827) After retessellation of defect 79 (v0=123827), euler #=-23 (146759,439479,292697) : difference with theory (-18) = 5 CORRECTING DEFECT 80 (vertices=36, convex hull=21, v0=124386) After retessellation of defect 80 (v0=124386), euler #=-22 (146766,439507,292719) : difference with theory (-17) = 5 CORRECTING DEFECT 81 (vertices=99, convex hull=123, v0=125172) After retessellation of defect 81 (v0=125172), euler #=-21 (146807,439690,292862) : difference with theory (-16) = 5 CORRECTING DEFECT 82 (vertices=249, convex hull=299, v0=125497) After retessellation of defect 82 (v0=125497), euler #=-18 (146926,440201,293257) : difference with theory (-15) = 3 CORRECTING DEFECT 83 (vertices=59, convex hull=67, v0=126186) After retessellation of defect 83 (v0=126186), euler #=-17 (146950,440306,293339) : difference with theory (-14) = 3 CORRECTING DEFECT 84 (vertices=27, convex hull=20, v0=126211) After retessellation of defect 84 (v0=126211), euler #=-16 (146956,440331,293359) : difference with theory (-13) = 3 CORRECTING DEFECT 85 (vertices=66, convex hull=78, v0=126587) After retessellation of defect 85 (v0=126587), euler #=-15 (146984,440448,293449) : difference with theory (-12) = 3 CORRECTING DEFECT 86 (vertices=33, convex hull=68, v0=127831) After retessellation of defect 86 (v0=127831), euler #=-14 (146993,440504,293497) : difference with theory (-11) = 3 CORRECTING DEFECT 87 (vertices=14, convex hull=19, v0=129329) After retessellation of defect 87 (v0=129329), euler #=-13 (146994,440513,293506) : difference with theory (-10) = 3 CORRECTING DEFECT 88 (vertices=59, convex hull=85, v0=129869) After retessellation of defect 88 (v0=129869), euler #=-12 (147021,440634,293601) : difference with theory (-9) = 3 CORRECTING DEFECT 89 (vertices=58, convex hull=60, v0=131755) After retessellation of defect 89 (v0=131755), euler #=-11 (147037,440709,293661) : difference with theory (-8) = 3 CORRECTING DEFECT 90 (vertices=187, convex hull=201, v0=132609) After retessellation of defect 90 (v0=132609), euler #=-7 (147105,441016,293904) : difference with theory (-7) = 0 CORRECTING DEFECT 91 (vertices=46, convex hull=39, v0=133514) After retessellation of defect 91 (v0=133514), euler #=-6 (147114,441056,293936) : difference with theory (-6) = 0 CORRECTING DEFECT 92 (vertices=62, convex hull=68, v0=136970) After retessellation of defect 92 (v0=136970), euler #=-5 (147124,441113,293984) : difference with theory (-5) = 0 CORRECTING DEFECT 93 (vertices=496, convex hull=246, v0=138592) After retessellation of defect 93 (v0=138592), euler #=-4 (147169,441372,294199) : difference with theory (-4) = 0 CORRECTING DEFECT 94 (vertices=49, convex hull=54, v0=140593) After retessellation of defect 94 (v0=140593), euler #=-3 (147180,441428,294245) : difference with theory (-3) = 0 CORRECTING DEFECT 95 (vertices=20, convex hull=60, v0=142137) After retessellation of defect 95 (v0=142137), euler #=-2 (147192,441485,294291) : difference with theory (-2) = 0 CORRECTING DEFECT 96 (vertices=96, convex hull=91, v0=145260) After retessellation of defect 96 (v0=145260), euler #=-1 (147217,441599,294381) : difference with theory (-1) = 0 CORRECTING DEFECT 97 (vertices=59, convex hull=31, v0=149665) After retessellation of defect 97 (v0=149665), euler #=0 (147222,441628,294406) : difference with theory (0) = 0 CORRECTING DEFECT 98 (vertices=30, convex hull=24, v0=150810) After retessellation of defect 98 (v0=150810), euler #=1 (147228,441654,294427) : difference with theory (1) = 0 CORRECTING DEFECT 99 (vertices=24, convex hull=56, v0=152366) After retessellation of defect 99 (v0=152366), euler #=2 (147238,441708,294472) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.25 (0.07-->8.74) (max @ vno 135352 --> 140393) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.25 (0.07-->8.74) (max @ vno 135352 --> 140393) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 349 mutations (36.5%), 608 crossovers (63.5%), 613 vertices were eliminated building final representation... 5410 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=147238, nf=294472, ne=441708, g=0) writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 66.2 minutes 0 defective edges removing intersecting faces 000: 682 intersecting 001: 5 intersecting 002: 2 intersecting expanding nbhd size to 2 003: 5 intersecting mris_fix_topology utimesec 3974.638763 mris_fix_topology stimesec 0.307953 mris_fix_topology ru_maxrss 493396 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 57039 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 21504 mris_fix_topology ru_oublock 14424 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 720 mris_fix_topology ru_nivcsw 5407 FSRUNTIME@ mris_fix_topology rh 1.1034 hours 1 threads PIDs (16152 16155) completed and logs appended. mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 142936 - 428802 + 285868 = 2 --> 0 holes F =2V-4: 285868 = 285872-4 (0) 2E=3F: 857604 = 857604 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 147238 - 441708 + 294472 = 2 --> 0 holes F =2V-4: 294472 = 294476-4 (0) 2E=3F: 883416 = 883416 (0) total defect index = 0 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 90 intersecting 001: 2 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 71 intersecting 001: 4 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Sat Oct 7 21:02:57 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050660 lh #-------------------------------------------- #@# Make White Surf rh Sat Oct 7 21:02:57 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050660 rh Waiting for PID 18583 of (18583 18586) to complete... Waiting for PID 18586 of (18583 18586) to complete... mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz... 43243 bright wm thresholded. 11304 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.orig... computing class statistics... border white: 307857 voxels (1.83%) border gray 349309 voxels (2.08%) WM (102.0): 101.7 +- 6.8 [70.0 --> 110.0] GM (82.0) : 80.2 +- 11.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 68.3 (was 70) setting MAX_BORDER_WHITE to 110.8 (was 105) setting MIN_BORDER_WHITE to 80.0 (was 85) setting MAX_CSF to 56.6 (was 40) setting MAX_GRAY to 97.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 44.9 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.23 (0.02-->4.53) (max @ vno 105751 --> 142272) face area 0.27 +- 0.13 (0.00-->5.32) mean absolute distance = 0.76 +- 0.95 3717 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+-5.2, GM=80+-5.2 mean inside = 97.9, mean outside = 84.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=87.4, 116 (116) missing vertices, mean dist 0.3 [0.7 (%32.4)->0.8 (%67.6))] %68 local maxima, %27 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, 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-->4.43) (max @ vno 142271 --> 142272) face area 0.27 +- 0.13 (0.00-->4.49) mean absolute distance = 0.38 +- 0.58 4173 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2237115.2, rms=7.734 001: dt: 0.5000, sse=1384283.2, rms=5.491 (29.004%) 002: dt: 0.5000, sse=1024193.1, rms=4.124 (24.890%) 003: dt: 0.5000, sse=859031.9, rms=3.343 (18.949%) 004: dt: 0.5000, sse=784022.9, rms=2.908 (13.009%) 005: dt: 0.5000, sse=754972.8, rms=2.710 (6.800%) 006: dt: 0.5000, sse=742163.1, rms=2.607 (3.818%) rms = 2.57, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=735211.8, rms=2.572 (1.331%) 008: dt: 0.2500, sse=663791.3, rms=1.880 (26.896%) 009: dt: 0.2500, sse=653436.4, rms=1.754 (6.722%) rms = 1.73, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=650629.2, rms=1.727 (1.546%) rms = 1.70, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=647457.9, rms=1.703 (1.391%) positioning took 1.2 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=89.7, 121 (30) missing vertices, mean dist -0.2 [0.4 (%70.9)->0.3 (%29.1))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, 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 +- 0.26 (0.08-->4.37) (max @ vno 105751 --> 142272) face area 0.34 +- 0.17 (0.00-->5.70) mean absolute distance = 0.28 +- 0.40 4179 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1049101.5, rms=3.569 012: dt: 0.5000, sse=843576.1, rms=2.264 (36.574%) 013: dt: 0.5000, sse=824512.9, rms=2.091 (7.621%) rms = 2.11, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=782066.2, rms=1.731 (17.233%) 015: dt: 0.2500, sse=769284.2, rms=1.530 (11.626%) rms = 1.49, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=763040.8, rms=1.490 (2.620%) rms = 1.46, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=761428.7, rms=1.464 (1.711%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=91.4, 143 (19) missing vertices, mean dist -0.1 [0.3 (%68.6)->0.2 (%31.4))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.26 (0.08-->4.36) (max @ vno 142271 --> 142272) face area 0.33 +- 0.16 (0.00-->5.79) mean absolute distance = 0.24 +- 0.33 4006 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=866523.1, rms=2.561 018: dt: 0.5000, sse=793712.9, rms=1.894 (26.064%) rms = 1.92, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=757049.6, rms=1.545 (18.424%) 020: dt: 0.2500, sse=745023.6, rms=1.368 (11.476%) rms = 1.33, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=736452.4, rms=1.332 (2.608%) rms = 1.31, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=733422.7, rms=1.309 (1.747%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=91.9, 171 (15) missing vertices, mean dist -0.0 [0.3 (%55.6)->0.2 (%44.4))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=743371.6, rms=1.516 023: dt: 0.5000, sse=730006.0, rms=1.186 (21.771%) rms = 1.64, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=707105.6, rms=1.025 (13.569%) rms = 1.05, time step reduction 2 of 3 to 0.125... rms = 1.01, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=704690.9, rms=1.013 (1.199%) positioning took 0.5 minutes generating cortex label... 17 non-cortical segments detected only using segment with 7817 vertices erasing segment 0 (vno[0] = 56287) erasing segment 2 (vno[0] = 65714) erasing segment 3 (vno[0] = 80862) erasing segment 4 (vno[0] = 84792) erasing segment 5 (vno[0] = 86834) erasing segment 6 (vno[0] = 104720) erasing segment 7 (vno[0] = 104826) erasing segment 8 (vno[0] = 108390) erasing segment 9 (vno[0] = 110202) erasing segment 10 (vno[0] = 111163) erasing segment 11 (vno[0] = 111246) erasing segment 12 (vno[0] = 112149) erasing segment 13 (vno[0] = 112970) erasing segment 14 (vno[0] = 127928) erasing segment 15 (vno[0] = 129027) erasing segment 16 (vno[0] = 129041) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.area vertex spacing 0.89 +- 0.26 (0.03-->4.43) (max @ vno 64534 --> 65725) face area 0.33 +- 0.16 (0.00-->5.57) refinement took 4.8 minutes mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz... 43243 bright wm thresholded. 11304 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.orig... computing class statistics... border white: 307857 voxels (1.83%) border gray 349309 voxels (2.08%) WM (102.0): 101.7 +- 6.8 [70.0 --> 110.0] GM (82.0) : 80.2 +- 11.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 69.3 (was 70) setting MAX_BORDER_WHITE to 111.8 (was 105) setting MIN_BORDER_WHITE to 81.0 (was 85) setting MAX_CSF to 57.6 (was 40) setting MAX_GRAY to 98.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 45.9 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.23 (0.01-->4.73) (max @ vno 88443 --> 145903) face area 0.27 +- 0.13 (0.00-->4.33) mean absolute distance = 0.77 +- 0.97 4600 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-5.2, GM=81+-5.2 mean inside = 98.4, mean outside = 84.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=88.4, 224 (224) missing vertices, mean dist 0.3 [0.7 (%34.1)->0.8 (%65.9))] %69 local maxima, %27 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, 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 0.90 +- 0.26 (0.07-->4.85) (max @ vno 88443 --> 145903) face area 0.27 +- 0.13 (0.00-->3.71) mean absolute distance = 0.40 +- 0.60 4885 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2264461.0, rms=7.591 001: dt: 0.5000, sse=1399175.1, rms=5.396 (28.918%) 002: dt: 0.5000, sse=1042671.7, rms=4.075 (24.478%) 003: dt: 0.5000, sse=876481.7, rms=3.290 (19.268%) 004: dt: 0.5000, sse=798692.9, rms=2.828 (14.044%) 005: dt: 0.5000, sse=766698.9, rms=2.626 (7.127%) 006: dt: 0.5000, sse=779717.2, rms=2.527 (3.798%) 007: dt: 0.5000, sse=747066.6, rms=2.468 (2.328%) rms = 2.43, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=746688.8, rms=2.426 (1.672%) 009: dt: 0.2500, sse=680093.6, rms=1.791 (26.195%) 010: dt: 0.2500, sse=664924.8, rms=1.667 (6.932%) rms = 1.66, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=670105.4, rms=1.657 (0.582%) rms = 1.62, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=661498.6, rms=1.622 (2.097%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=90.7, 134 (42) missing vertices, mean dist -0.2 [0.4 (%71.4)->0.3 (%28.6))] %84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, 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 +- 0.26 (0.06-->4.66) (max @ vno 88443 --> 145903) face area 0.34 +- 0.17 (0.00-->4.85) mean absolute distance = 0.29 +- 0.40 4860 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1068600.1, rms=3.488 013: dt: 0.5000, sse=873401.1, rms=2.219 (36.372%) 014: dt: 0.5000, sse=849802.9, rms=2.038 (8.166%) rms = 2.04, time step reduction 1 of 3 to 0.250... 015: dt: 0.2500, sse=810634.9, rms=1.723 (15.451%) 016: dt: 0.2500, sse=792845.6, rms=1.542 (10.532%) rms = 1.50, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=813124.5, rms=1.497 (2.929%) rms = 1.47, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=786193.6, rms=1.467 (1.989%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 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 removing 2 vertex label from ripped group mean border=92.3, 151 (21) missing vertices, mean dist -0.1 [0.3 (%69.1)->0.2 (%30.9))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, 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 +- 0.26 (0.05-->4.73) (max @ vno 145887 --> 84131) face area 0.33 +- 0.16 (0.00-->4.87) mean absolute distance = 0.24 +- 0.33 4186 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=889796.4, rms=2.541 019: dt: 0.5000, sse=838684.1, rms=1.874 (26.246%) rms = 1.86, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=808869.9, rms=1.856 (1.005%) 021: dt: 0.2500, sse=773662.1, rms=1.400 (24.542%) 022: dt: 0.2500, sse=763412.7, rms=1.325 (5.362%) rms = 1.32, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=762087.8, rms=1.323 (0.149%) rms = 1.30, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=774165.2, rms=1.296 (2.050%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 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 removing 2 vertex label from ripped group mean border=92.8, 165 (17) missing vertices, mean dist -0.0 [0.3 (%55.5)->0.2 (%44.5))] %92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=782316.1, rms=1.499 025: dt: 0.5000, sse=759666.2, rms=1.188 (20.752%) rms = 1.60, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=729637.8, rms=1.041 (12.384%) rms = 1.08, time step reduction 2 of 3 to 0.125... rms = 1.03, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=724795.3, rms=1.025 (1.505%) positioning took 0.5 minutes generating cortex label... 20 non-cortical segments detected only using segment with 7437 vertices erasing segment 1 (vno[0] = 66975) erasing segment 2 (vno[0] = 67408) erasing segment 3 (vno[0] = 80271) erasing segment 4 (vno[0] = 94783) erasing segment 5 (vno[0] = 98848) erasing segment 6 (vno[0] = 102197) erasing segment 7 (vno[0] = 103062) erasing segment 8 (vno[0] = 107515) erasing segment 9 (vno[0] = 110160) erasing segment 10 (vno[0] = 110247) erasing segment 11 (vno[0] = 110306) erasing segment 12 (vno[0] = 111222) erasing segment 13 (vno[0] = 112098) erasing segment 14 (vno[0] = 112118) erasing segment 15 (vno[0] = 114058) erasing segment 16 (vno[0] = 115085) erasing segment 17 (vno[0] = 115985) erasing segment 18 (vno[0] = 116938) erasing segment 19 (vno[0] = 117897) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.area vertex spacing 0.88 +- 0.26 (0.04-->4.84) (max @ vno 84131 --> 145887) face area 0.33 +- 0.16 (0.00-->4.88) refinement took 5.1 minutes PIDs (18583 18586) completed and logs appended. #-------------------------------------------- #@# Smooth2 lh Sat Oct 7 21:08:01 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Sat Oct 7 21:08:01 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 18845 of (18845 18848) to complete... Waiting for PID 18848 of (18845 18848) to complete... 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... 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... PIDs (18845 18848) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Sat Oct 7 21:08:07 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Sat Oct 7 21:08:07 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 18894 of (18894 18897) to complete... Waiting for PID 18897 of (18894 18897) to complete... mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 49.3 mm, total surface area = 85080 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.184 (target=0.015) step 005: RMS=0.129 (target=0.015) step 010: RMS=0.096 (target=0.015) step 015: RMS=0.081 (target=0.015) step 020: RMS=0.067 (target=0.015) step 025: RMS=0.057 (target=0.015) step 030: RMS=0.047 (target=0.015) step 035: RMS=0.040 (target=0.015) step 040: RMS=0.034 (target=0.015) step 045: RMS=0.031 (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 0.7 minutes mris_inflate utimesec 42.765498 mris_inflate stimesec 0.115982 mris_inflate ru_maxrss 209464 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 30458 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11192 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2333 mris_inflate ru_nivcsw 3306 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 48.3 mm, total surface area = 86882 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.184 (target=0.015) step 005: RMS=0.129 (target=0.015) step 010: RMS=0.098 (target=0.015) step 015: RMS=0.082 (target=0.015) step 020: RMS=0.068 (target=0.015) step 025: RMS=0.058 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.041 (target=0.015) step 040: RMS=0.037 (target=0.015) step 045: RMS=0.033 (target=0.015) step 050: RMS=0.030 (target=0.015) step 055: RMS=0.027 (target=0.015) step 060: RMS=0.026 (target=0.015) inflation complete. inflation took 0.7 minutes mris_inflate utimesec 44.374254 mris_inflate stimesec 0.118981 mris_inflate ru_maxrss 216116 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 31609 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 10360 mris_inflate ru_oublock 11528 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 2321 mris_inflate ru_nivcsw 3340 PIDs (18894 18897) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Sat Oct 7 21:08:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf mris_curvature -w lh.white.preaparc 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 #-------------------------------------------- #@# Curv .H and .K rh Sat Oct 7 21:08:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf mris_curvature -w rh.white.preaparc 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 cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts/recon-all.log mris_curvature_white_lh.cmd rm_curvature_white_lh.H.cmd ln_curvature_white_lh.H.cmd rm_curvature_white_lh.K.cmd ln_curvature_white_lh.K.cmd mris_curvature_inflated_lh.cmd mris_curvature_white_rh.cmd rm_curvature_white_rh.H.cmd ln_curvature_white_rh.H.cmd rm_curvature_white_rh.K.cmd ln_curvature_white_rh.K.cmd mris_curvature_inflated_rh.cmd Waiting for PID 18994 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete... Waiting for PID 18997 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete... Waiting for PID 19000 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete... Waiting for PID 19003 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete... Waiting for PID 19006 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete... Waiting for PID 19009 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete... Waiting for PID 19012 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete... Waiting for PID 19015 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete... Waiting for PID 19018 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete... Waiting for PID 19022 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete... Waiting for PID 19025 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete... Waiting for PID 19028 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete... mris_curvature -w lh.white.preaparc total integrated curvature = 17.590*4pi (221.042) --> -17 handles ICI = 211.1, FI = 2154.7, variation=33892.318 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 172 vertices thresholded to be in k1 ~ [-0.29 0.46], k2 ~ [-0.09 0.06] total integrated curvature = 0.540*4pi (6.790) --> 0 handles ICI = 1.5, FI = 10.1, variation=168.251 123 vertices thresholded to be in [-0.02 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 134 vertices thresholded to be in [-0.13 0.20] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.022 done. mris_curvature -w rh.white.preaparc total integrated curvature = 19.193*4pi (241.185) --> -18 handles ICI = 222.7, FI = 2146.1, variation=34182.067 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 234 vertices thresholded to be in k1 ~ [-0.26 1.05], k2 ~ [-0.15 0.30] total integrated curvature = 0.473*4pi (5.938) --> 1 handles ICI = 1.4, FI = 9.8, variation=163.019 170 vertices thresholded to be in [-0.07 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 128 vertices thresholded to be in [-0.13 0.35] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.022 done. PIDs (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) completed and logs appended. #----------------------------------------- #@# Curvature Stats lh Sat Oct 7 21:10:22 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050660 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 [ 0050660/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 [ 264 ] Gb_filter = 0 WARN: S lookup min: -0.618221 WARN: S explicit min: 0.000000 vertex = 317 #----------------------------------------- #@# Curvature Stats rh Sat Oct 7 21:10:26 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050660 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 [ 0050660/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 [ 279 ] Gb_filter = 0 WARN: S lookup min: -0.928958 WARN: S explicit min: 0.000000 vertex = 4 #-------------------------------------------- #@# Sphere lh Sat Oct 7 21:10:31 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Sat Oct 7 21:10:31 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 19187 of (19187 19191) to complete... Waiting for PID 19191 of (19187 19191) to complete... mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 = 2 == scaling brain by 0.298... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.11 pass 1: epoch 2 of 3 starting distance error %20.10 unfolding complete - removing small folds... starting distance error %20.05 removing remaining folds... final distance error %20.07 MRISunfold() return, current seed 1234 -01: dt=0.0000, 343 negative triangles 193: dt=0.9900, 343 negative triangles 194: dt=0.9900, 176 negative triangles 195: dt=0.9900, 138 negative triangles 196: dt=0.9900, 136 negative triangles 197: dt=0.9900, 124 negative triangles 198: dt=0.9900, 117 negative triangles 199: dt=0.9900, 120 negative triangles 200: dt=0.9900, 109 negative triangles 201: dt=0.9900, 117 negative triangles 202: dt=0.9900, 117 negative triangles 203: dt=0.9900, 113 negative triangles 204: dt=0.9900, 100 negative triangles 205: dt=0.9900, 99 negative triangles 206: dt=0.9900, 100 negative triangles 207: dt=0.9900, 102 negative triangles 208: dt=0.9900, 96 negative triangles 209: dt=0.9900, 88 negative triangles 210: dt=0.9900, 91 negative triangles 211: dt=0.9900, 98 negative triangles 212: dt=0.9900, 95 negative triangles 213: dt=0.9900, 93 negative triangles 214: dt=0.9900, 91 negative triangles 215: dt=0.9900, 89 negative triangles 216: dt=0.9900, 92 negative triangles 217: dt=0.9900, 88 negative triangles 218: dt=0.9900, 76 negative triangles 219: dt=0.9900, 90 negative triangles 220: dt=0.9900, 79 negative triangles 221: dt=0.9900, 83 negative triangles 222: dt=0.9900, 78 negative triangles 223: dt=0.9900, 83 negative triangles 224: dt=0.9900, 75 negative triangles 225: dt=0.9900, 82 negative triangles 226: dt=0.9900, 78 negative triangles 227: dt=0.9900, 79 negative triangles 228: dt=0.9900, 68 negative triangles 229: dt=0.9900, 73 negative triangles 230: dt=0.9900, 60 negative triangles 231: dt=0.9900, 72 negative triangles 232: dt=0.9900, 62 negative triangles 233: dt=0.9900, 66 negative triangles 234: dt=0.9900, 60 negative triangles 235: dt=0.9900, 68 negative triangles 236: dt=0.9900, 58 negative triangles 237: dt=0.9900, 64 negative triangles 238: dt=0.9900, 60 negative triangles 239: dt=0.9900, 55 negative triangles 240: dt=0.9900, 60 negative triangles 241: dt=0.9900, 58 negative triangles 242: dt=0.9900, 61 negative triangles 243: dt=0.9900, 57 negative triangles 244: dt=0.9900, 52 negative triangles 245: dt=0.9900, 52 negative triangles 246: dt=0.9900, 48 negative triangles 247: dt=0.9900, 46 negative triangles 248: dt=0.9900, 49 negative triangles 249: dt=0.9900, 44 negative triangles 250: dt=0.9900, 47 negative triangles 251: dt=0.9900, 49 negative triangles 252: dt=0.9900, 48 negative triangles 253: dt=0.9900, 44 negative triangles 254: dt=0.9900, 49 negative triangles 255: dt=0.9900, 43 negative triangles 256: dt=0.9900, 43 negative triangles 257: dt=0.9900, 46 negative triangles 258: dt=0.9900, 49 negative triangles 259: dt=0.9900, 45 negative triangles 260: dt=0.9900, 39 negative triangles 261: dt=0.9900, 38 negative triangles 262: dt=0.9900, 29 negative triangles 263: dt=0.9900, 28 negative triangles 264: dt=0.9900, 25 negative triangles 265: dt=0.9900, 28 negative triangles 266: dt=0.9900, 31 negative triangles 267: dt=0.9900, 30 negative triangles 268: dt=0.9900, 30 negative triangles 269: dt=0.9900, 26 negative triangles 270: dt=0.9900, 26 negative triangles 271: dt=0.9900, 20 negative triangles 272: dt=0.9900, 22 negative triangles 273: dt=0.9900, 18 negative triangles 274: dt=0.9900, 24 negative triangles 275: dt=0.9900, 17 negative triangles 276: dt=0.9900, 17 negative triangles 277: dt=0.9900, 17 negative triangles 278: dt=0.9900, 16 negative triangles 279: dt=0.9900, 13 negative triangles 280: dt=0.9900, 14 negative triangles 281: dt=0.9900, 15 negative triangles 282: dt=0.9900, 11 negative triangles 283: dt=0.9900, 11 negative triangles 284: dt=0.9900, 10 negative triangles 285: dt=0.9900, 10 negative triangles 286: dt=0.9900, 9 negative triangles 287: dt=0.9900, 14 negative triangles 288: dt=0.9900, 8 negative triangles 289: dt=0.9900, 6 negative triangles 290: dt=0.9900, 8 negative triangles 291: dt=0.9900, 6 negative triangles 292: dt=0.9900, 3 negative triangles 293: dt=0.9900, 7 negative triangles 294: dt=0.9900, 3 negative triangles 295: dt=0.9900, 5 negative triangles 296: dt=0.9900, 4 negative triangles 297: dt=0.9900, 3 negative triangles 298: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 1.03 hours mris_sphere utimesec 3829.167878 mris_sphere stimesec 1.925707 mris_sphere ru_maxrss 290884 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 50943 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10120 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 157319 mris_sphere ru_nivcsw 301698 FSRUNTIME@ mris_sphere 1.0291 hours 1 threads mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 = 2 == scaling brain by 0.296... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.37 pass 1: epoch 2 of 3 starting distance error %19.31 unfolding complete - removing small folds... starting distance error %19.23 removing remaining folds... final distance error %19.25 MRISunfold() return, current seed 1234 -01: dt=0.0000, 280 negative triangles 215: dt=0.9900, 280 negative triangles 216: dt=0.9900, 118 negative triangles 217: dt=0.9900, 105 negative triangles 218: dt=0.9900, 90 negative triangles 219: dt=0.9900, 94 negative triangles 220: dt=0.9900, 83 negative triangles 221: dt=0.9900, 72 negative triangles 222: dt=0.9900, 65 negative triangles 223: dt=0.9900, 52 negative triangles 224: dt=0.9900, 61 negative triangles 225: dt=0.9900, 52 negative triangles 226: dt=0.9900, 40 negative triangles 227: dt=0.9900, 46 negative triangles 228: dt=0.9900, 46 negative triangles 229: dt=0.9900, 43 negative triangles 230: dt=0.9900, 37 negative triangles 231: dt=0.9900, 37 negative triangles 232: dt=0.9900, 43 negative triangles 233: dt=0.9900, 39 negative triangles 234: dt=0.9900, 38 negative triangles 235: dt=0.9900, 37 negative triangles 236: dt=0.9900, 41 negative triangles 237: dt=0.9900, 37 negative triangles 238: dt=0.9900, 39 negative triangles 239: dt=0.9900, 40 negative triangles 240: dt=0.9405, 38 negative triangles 241: dt=0.9405, 39 negative triangles 242: dt=0.9405, 34 negative triangles 243: dt=0.9405, 31 negative triangles 244: dt=0.9405, 29 negative triangles 245: dt=0.9405, 35 negative triangles 246: dt=0.9405, 35 negative triangles 247: dt=0.9405, 31 negative triangles 248: dt=0.9405, 33 negative triangles 249: dt=0.9405, 32 negative triangles 250: dt=0.9405, 33 negative triangles 251: dt=0.9405, 31 negative triangles 252: dt=0.9405, 31 negative triangles 253: dt=0.9405, 33 negative triangles 254: dt=0.8935, 34 negative triangles 255: dt=0.8935, 33 negative triangles 256: dt=0.8935, 30 negative triangles 257: dt=0.8935, 25 negative triangles 258: dt=0.8935, 24 negative triangles 259: dt=0.8935, 27 negative triangles 260: dt=0.8935, 27 negative triangles 261: dt=0.8935, 25 negative triangles 262: dt=0.8935, 26 negative triangles 263: dt=0.8935, 26 negative triangles 264: dt=0.8935, 27 negative triangles 265: dt=0.8935, 28 negative triangles 266: dt=0.8935, 26 negative triangles 267: dt=0.8935, 26 negative triangles 268: dt=0.8935, 23 negative triangles 269: dt=0.8935, 24 negative triangles 270: dt=0.8935, 25 negative triangles 271: dt=0.8935, 26 negative triangles 272: dt=0.8935, 26 negative triangles 273: dt=0.8935, 24 negative triangles 274: dt=0.8935, 27 negative triangles 275: dt=0.8935, 26 negative triangles 276: dt=0.8935, 24 negative triangles 277: dt=0.8935, 23 negative triangles 278: dt=0.8488, 26 negative triangles 279: dt=0.8488, 23 negative triangles 280: dt=0.8488, 23 negative triangles 281: dt=0.8488, 24 negative triangles 282: dt=0.8488, 24 negative triangles 283: dt=0.8488, 26 negative triangles 284: dt=0.8488, 24 negative triangles 285: dt=0.8488, 25 negative triangles 286: dt=0.8488, 24 negative triangles 287: dt=0.8488, 20 negative triangles 288: dt=0.8488, 20 negative triangles 289: dt=0.8488, 20 negative triangles 290: dt=0.8488, 21 negative triangles 291: dt=0.8488, 19 negative triangles 292: dt=0.8488, 21 negative triangles 293: dt=0.8488, 21 negative triangles 294: dt=0.8488, 19 negative triangles 295: dt=0.8488, 19 negative triangles 296: dt=0.8488, 17 negative triangles 297: dt=0.8488, 16 negative triangles 298: dt=0.8488, 16 negative triangles 299: dt=0.8488, 17 negative triangles 300: dt=0.8488, 13 negative triangles 301: dt=0.8488, 12 negative triangles 302: dt=0.8488, 9 negative triangles 303: dt=0.8488, 12 negative triangles 304: dt=0.8488, 10 negative triangles 305: dt=0.8488, 9 negative triangles 306: dt=0.8488, 9 negative triangles 307: dt=0.8488, 8 negative triangles 308: dt=0.8488, 3 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.99 hours mris_sphere utimesec 3572.316925 mris_sphere stimesec 1.672745 mris_sphere ru_maxrss 299800 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 52162 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 10456 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 139107 mris_sphere ru_nivcsw 301499 FSRUNTIME@ mris_sphere 0.9914 hours 1 threads PIDs (19187 19191) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Sat Oct 7 22:12:16 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Surf Reg rh Sat Oct 7 22:12:16 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg Waiting for PID 21737 of (21737 21740) to complete... Waiting for PID 21740 of (21737 21740) to complete... mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/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 /pasteur/homes/ntraut/bin/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=tars-, 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=tars-, 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 = 5.334 curvature mean = 0.040, std = 0.818 curvature mean = 0.019, std = 0.857 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, -16.00) sse = 365414.2, tmin=1.0521 d=32.00 min @ (8.00, 8.00, -8.00) sse = 304869.6, tmin=2.1364 d=16.00 min @ (-4.00, 0.00, 4.00) sse = 299375.3, tmin=3.2420 d=8.00 min @ (2.00, -2.00, -2.00) sse = 292485.5, tmin=4.3544 d=4.00 min @ (0.00, 0.00, -1.00) sse = 291669.4, tmin=5.4752 d=1.00 min @ (-0.25, 0.25, 0.25) sse = 291621.5, tmin=7.7291 d=0.50 min @ (0.12, 0.00, -0.12) sse = 291602.3, tmin=8.8535 tol=1.0e+00, sigma=0.5, host=tars-, 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 8.85 min curvature mean = -0.004, std = 0.821 curvature mean = 0.007, std = 0.944 curvature mean = -0.011, std = 0.829 curvature mean = 0.003, std = 0.977 curvature mean = -0.016, std = 0.828 curvature mean = 0.001, std = 0.991 2 Reading smoothwm curvature mean = -0.025, std = 0.335 curvature mean = 0.038, std = 0.247 curvature mean = 0.054, std = 0.295 curvature mean = 0.032, std = 0.307 curvature mean = 0.031, std = 0.457 curvature mean = 0.031, std = 0.333 curvature mean = 0.017, std = 0.588 curvature mean = 0.031, std = 0.344 curvature mean = 0.006, std = 0.716 MRISregister() return, current seed 0 -01: dt=0.0000, 138 negative triangles 115: dt=0.9900, 138 negative triangles expanding nbhd size to 1 116: dt=0.9900, 166 negative triangles 117: dt=0.9900, 124 negative triangles 118: dt=0.9900, 119 negative triangles 119: dt=0.9900, 113 negative triangles 120: dt=0.9900, 105 negative triangles 121: dt=0.9900, 100 negative triangles 122: dt=0.9900, 94 negative triangles 123: dt=0.9900, 90 negative triangles 124: dt=0.9900, 89 negative triangles 125: dt=0.9900, 80 negative triangles 126: dt=0.9900, 72 negative triangles 127: dt=0.9900, 67 negative triangles 128: dt=0.9900, 64 negative triangles 129: dt=0.9900, 67 negative triangles 130: dt=0.9900, 60 negative triangles 131: dt=0.9900, 58 negative triangles 132: dt=0.9900, 58 negative triangles 133: dt=0.9900, 55 negative triangles 134: dt=0.9900, 49 negative triangles 135: dt=0.9900, 51 negative triangles 136: dt=0.9900, 50 negative triangles 137: dt=0.9900, 48 negative triangles 138: dt=0.9900, 50 negative triangles 139: dt=0.9900, 55 negative triangles 140: dt=0.9900, 47 negative triangles 141: dt=0.9900, 45 negative triangles 142: dt=0.9900, 40 negative triangles 143: dt=0.9900, 36 negative triangles 144: dt=0.9900, 35 negative triangles 145: dt=0.9900, 35 negative triangles 146: dt=0.9900, 31 negative triangles 147: dt=0.9900, 30 negative triangles 148: dt=0.9900, 32 negative triangles 149: dt=0.9900, 31 negative triangles 150: dt=0.9900, 28 negative triangles 151: dt=0.9900, 29 negative triangles 152: dt=0.9900, 30 negative triangles 153: dt=0.9900, 27 negative triangles 154: dt=0.9900, 23 negative triangles 155: dt=0.9900, 22 negative triangles 156: dt=0.9900, 22 negative triangles 157: dt=0.9900, 21 negative triangles 158: dt=0.9900, 19 negative triangles 159: dt=0.9900, 18 negative triangles 160: dt=0.9900, 20 negative triangles 161: dt=0.9900, 22 negative triangles 162: dt=0.9900, 17 negative triangles 163: dt=0.9900, 14 negative triangles 164: dt=0.9900, 10 negative triangles 165: dt=0.9900, 10 negative triangles 166: dt=0.9900, 9 negative triangles 167: dt=0.9900, 10 negative triangles 168: dt=0.9900, 9 negative triangles 169: dt=0.9900, 8 negative triangles 170: dt=0.9900, 7 negative triangles 171: dt=0.9900, 8 negative triangles 172: dt=0.9900, 7 negative triangles 173: dt=0.9900, 8 negative triangles 174: dt=0.9900, 5 negative triangles 175: dt=0.9900, 3 negative triangles 176: dt=0.9900, 4 negative triangles 177: dt=0.9900, 3 negative triangles 178: dt=0.9900, 2 negative triangles 179: dt=0.9900, 4 negative triangles 180: dt=0.9900, 3 negative triangles 181: dt=0.9900, 1 negative triangles 182: dt=0.9900, 3 negative triangles 183: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.53 hours mris_register utimesec 5508.926515 mris_register stimesec 3.820419 mris_register ru_maxrss 262736 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 38036 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 10160 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 415602 mris_register ru_nivcsw 271577 FSRUNTIME@ mris_register 1.5305 hours 1 threads mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /pasteur/homes/ntraut/bin/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /pasteur/homes/ntraut/bin/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 /pasteur/homes/ntraut/bin/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=tars-, 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=tars-, 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 = 5.400 curvature mean = 0.034, std = 0.811 curvature mean = 0.021, std = 0.856 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, -16.00) sse = 376287.2, tmin=1.0833 d=32.00 min @ (8.00, 8.00, 0.00) sse = 304890.1, tmin=2.2099 d=8.00 min @ (0.00, -2.00, 0.00) sse = 297809.7, tmin=4.4810 d=2.00 min @ (0.50, 0.00, -0.50) sse = 297233.3, tmin=6.7609 d=1.00 min @ (0.00, 0.25, 0.25) sse = 297124.0, tmin=7.9158 d=0.50 min @ (0.00, -0.12, 0.00) sse = 297095.5, tmin=9.1034 tol=1.0e+00, sigma=0.5, host=tars-, 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 9.10 min curvature mean = 0.008, std = 0.822 curvature mean = 0.009, std = 0.945 curvature mean = 0.004, std = 0.831 curvature mean = 0.004, std = 0.977 curvature mean = 0.002, std = 0.833 curvature mean = 0.001, std = 0.990 2 Reading smoothwm curvature mean = -0.029, std = 0.339 curvature mean = 0.034, std = 0.243 curvature mean = 0.065, std = 0.289 curvature mean = 0.029, std = 0.299 curvature mean = 0.040, std = 0.447 curvature mean = 0.028, std = 0.325 curvature mean = 0.023, std = 0.576 curvature mean = 0.028, std = 0.335 curvature mean = 0.008, std = 0.684 MRISregister() return, current seed 0 -01: dt=0.0000, 212 negative triangles 119: dt=0.9900, 212 negative triangles 120: dt=0.9405, 249 negative triangles expanding nbhd size to 1 121: dt=0.9900, 243 negative triangles 122: dt=0.9900, 202 negative triangles 123: dt=0.9900, 190 negative triangles 124: dt=0.9900, 186 negative triangles 125: dt=0.9900, 165 negative triangles 126: dt=0.9900, 162 negative triangles 127: dt=0.9900, 150 negative triangles 128: dt=0.9900, 140 negative triangles 129: dt=0.9900, 138 negative triangles 130: dt=0.9900, 126 negative triangles 131: dt=0.9900, 119 negative triangles 132: dt=0.9900, 117 negative triangles 133: dt=0.9900, 108 negative triangles 134: dt=0.9900, 104 negative triangles 135: dt=0.9900, 99 negative triangles 136: dt=0.9900, 92 negative triangles 137: dt=0.9900, 91 negative triangles 138: dt=0.9900, 82 negative triangles 139: dt=0.9900, 87 negative triangles 140: dt=0.9900, 78 negative triangles 141: dt=0.9900, 80 negative triangles 142: dt=0.9900, 70 negative triangles 143: dt=0.9900, 65 negative triangles 144: dt=0.9900, 66 negative triangles 145: dt=0.9900, 57 negative triangles 146: dt=0.9900, 57 negative triangles 147: dt=0.9900, 51 negative triangles 148: dt=0.9900, 49 negative triangles 149: dt=0.9900, 46 negative triangles 150: dt=0.9900, 45 negative triangles 151: dt=0.9900, 42 negative triangles 152: dt=0.9900, 42 negative triangles 153: dt=0.9900, 44 negative triangles 154: dt=0.9900, 39 negative triangles 155: dt=0.9900, 41 negative triangles 156: dt=0.9900, 41 negative triangles 157: dt=0.9900, 39 negative triangles 158: dt=0.9900, 37 negative triangles 159: dt=0.9900, 37 negative triangles 160: dt=0.9900, 36 negative triangles 161: dt=0.9900, 42 negative triangles 162: dt=0.9900, 42 negative triangles 163: dt=0.9900, 35 negative triangles 164: dt=0.9900, 32 negative triangles 165: dt=0.9900, 34 negative triangles 166: dt=0.9900, 31 negative triangles 167: dt=0.9900, 33 negative triangles 168: dt=0.9900, 28 negative triangles 169: dt=0.9900, 28 negative triangles 170: dt=0.9900, 34 negative triangles 171: dt=0.9900, 32 negative triangles 172: dt=0.9900, 28 negative triangles 173: dt=0.9900, 24 negative triangles 174: dt=0.9900, 22 negative triangles 175: dt=0.9900, 24 negative triangles 176: dt=0.9900, 28 negative triangles 177: dt=0.9900, 26 negative triangles 178: dt=0.9900, 26 negative triangles 179: dt=0.9900, 25 negative triangles 180: dt=0.9900, 19 negative triangles 181: dt=0.9900, 18 negative triangles 182: dt=0.9900, 18 negative triangles 183: dt=0.9900, 16 negative triangles 184: dt=0.9900, 13 negative triangles 185: dt=0.9900, 12 negative triangles 186: dt=0.9900, 11 negative triangles 187: dt=0.9900, 10 negative triangles 188: dt=0.9900, 8 negative triangles 189: dt=0.9900, 6 negative triangles 190: dt=0.9900, 8 negative triangles 191: dt=0.9900, 7 negative triangles 192: dt=0.9900, 6 negative triangles 193: dt=0.9900, 7 negative triangles 194: dt=0.9900, 4 negative triangles 195: dt=0.9900, 2 negative triangles 196: dt=0.9900, 2 negative triangles 197: dt=0.9900, 1 negative triangles 198: dt=0.9900, 1 negative triangles 199: dt=0.9900, 2 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.55 hours mris_register utimesec 5610.953005 mris_register stimesec 3.844415 mris_register ru_maxrss 270668 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 38678 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 10448 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 408241 mris_register ru_nivcsw 271538 FSRUNTIME@ mris_register 1.5481 hours 1 threads PIDs (21737 21740) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Sat Oct 7 23:45:09 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Sat Oct 7 23:45:09 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 25704 of (25704 25707) to complete... Waiting for PID 25707 of (25704 25707) to complete... 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 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 PIDs (25704 25707) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Sat Oct 7 23:45:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mrisp_paint -a 5 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv #-------------------------------------------- #@# AvgCurv rh Sat Oct 7 23:45:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mrisp_paint -a 5 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv Waiting for PID 25750 of (25750 25753) to complete... Waiting for PID 25753 of (25750 25753) to complete... mrisp_paint -a 5 /pasteur/homes/ntraut/bin/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 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... mrisp_paint -a 5 /pasteur/homes/ntraut/bin/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 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... PIDs (25750 25753) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Sat Oct 7 23:45:13 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot #----------------------------------------- #@# Cortical Parc rh Sat Oct 7 23:45:13 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot Waiting for PID 25796 of (25796 25799) to complete... Waiting for PID 25799 of (25796 25799) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/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 /pasteur/homes/ntraut/bin/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... 1290 labels changed using aseg relabeling using gibbs priors... 000: 3121 changed, 142936 examined... 001: 697 changed, 13222 examined... 002: 175 changed, 3811 examined... 003: 49 changed, 1089 examined... 004: 28 changed, 276 examined... 005: 20 changed, 177 examined... 006: 7 changed, 112 examined... 007: 4 changed, 44 examined... 008: 5 changed, 24 examined... 009: 2 changed, 18 examined... 010: 1 changed, 12 examined... 011: 3 changed, 9 examined... 012: 2 changed, 15 examined... 013: 1 changed, 14 examined... 014: 0 changed, 6 examined... 293 labels changed using aseg 000: 125 total segments, 83 labels (344 vertices) changed 001: 42 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2037 vertices marked for relabeling... 2037 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 14 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/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 /pasteur/homes/ntraut/bin/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... 1029 labels changed using aseg relabeling using gibbs priors... 000: 3169 changed, 147238 examined... 001: 739 changed, 13552 examined... 002: 157 changed, 4080 examined... 003: 58 changed, 965 examined... 004: 15 changed, 365 examined... 005: 4 changed, 95 examined... 006: 1 changed, 26 examined... 007: 1 changed, 7 examined... 008: 2 changed, 7 examined... 009: 0 changed, 11 examined... 158 labels changed using aseg 000: 107 total segments, 64 labels (257 vertices) changed 001: 44 total segments, 1 labels (1 vertices) changed 002: 43 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... 2036 vertices marked for relabeling... 2036 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 15 seconds. PIDs (25796 25799) completed and logs appended. #-------------------------------------------- #@# Make Pial Surf lh Sat Oct 7 23:45:28 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050660 lh #-------------------------------------------- #@# Make Pial Surf rh Sat Oct 7 23:45:28 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050660 rh Waiting for PID 25844 of (25844 25847) to complete... Waiting for PID 25847 of (25844 25847) to complete... mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz... 43243 bright wm thresholded. 11304 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.orig... computing class statistics... border white: 307857 voxels (1.83%) border gray 349309 voxels (2.08%) WM (102.0): 101.7 +- 6.8 [70.0 --> 110.0] GM (82.0) : 80.2 +- 11.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 68.3 (was 70) setting MAX_BORDER_WHITE to 110.8 (was 105) setting MIN_BORDER_WHITE to 80.0 (was 85) setting MAX_CSF to 56.6 (was 40) setting MAX_GRAY to 97.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 44.9 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104+-5.2, GM=80+-5.2 mean inside = 97.9, mean outside = 84.1 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 0.89 +- 0.26 (0.03-->4.43) (max @ vno 64534 --> 65725) face area 0.33 +- 0.16 (0.00-->5.58) mean absolute distance = 0.67 +- 0.91 2971 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 44 points - only 0.00% unknown deleting segment 1 with 17 points - only 0.00% unknown deleting segment 2 with 104 points - only 0.00% unknown deleting segment 3 with 16 points - only 0.00% unknown deleting segment 5 with 6 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 284 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 7 points - only 0.00% unknown deleting segment 10 with 6 points - only 0.00% unknown deleting segment 11 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown deleting segment 13 with 22 points - only 0.00% unknown deleting segment 14 with 28 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 15 with 2 points - only 0.00% unknown mean border=87.2, 152 (152) missing vertices, mean dist 0.4 [1.2 (%12.9)->0.6 (%87.1))] %65 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.27 (0.08-->4.85) (max @ vno 65725 --> 64534) face area 0.33 +- 0.17 (0.00-->5.26) mean absolute distance = 0.37 +- 0.57 3541 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1662144.4, rms=5.995 001: dt: 0.5000, sse=1031686.4, rms=3.527 (41.164%) 002: dt: 0.5000, sse=867986.4, rms=2.567 (27.226%) 003: dt: 0.5000, sse=830388.2, rms=2.384 (7.122%) 004: dt: 0.5000, sse=818819.5, rms=2.292 (3.864%) rms = 2.35, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=781209.2, rms=1.912 (16.569%) 006: dt: 0.2500, sse=769272.8, rms=1.735 (9.282%) rms = 1.70, time step reduction 2 of 3 to 0.125... 007: dt: 0.2500, sse=764582.8, rms=1.695 (2.273%) rms = 1.67, time step reduction 3 of 3 to 0.062... 008: dt: 0.1250, sse=763054.5, rms=1.673 (1.337%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 37 points - only 0.00% unknown deleting segment 1 with 13 points - only 0.00% unknown deleting segment 2 with 98 points - only 0.00% unknown deleting segment 3 with 13 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 183 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown deleting segment 8 with 15 points - only 0.00% unknown deleting segment 9 with 33 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown mean border=89.6, 124 (32) missing vertices, mean dist -0.2 [0.4 (%70.6)->0.3 (%29.4))] %83 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, 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 +- 0.26 (0.07-->5.04) (max @ vno 65725 --> 64534) face area 0.34 +- 0.17 (0.00-->5.78) mean absolute distance = 0.28 +- 0.39 3940 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1040528.5, rms=3.448 009: dt: 0.5000, sse=844449.6, rms=2.155 (37.498%) 010: dt: 0.5000, sse=819941.4, rms=1.976 (8.318%) rms = 2.03, time step reduction 1 of 3 to 0.250... 011: dt: 0.2500, sse=784533.1, rms=1.620 (18.035%) 012: dt: 0.2500, sse=769961.3, rms=1.436 (11.316%) rms = 1.41, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=782523.9, rms=1.407 (2.057%) rms = 1.39, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=766032.9, rms=1.389 (1.271%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 44 points - only 0.00% unknown deleting segment 1 with 16 points - only 0.00% unknown deleting segment 2 with 99 points - only 0.00% unknown deleting segment 3 with 13 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 6 points - only 0.00% unknown deleting segment 6 with 229 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown deleting segment 8 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown deleting segment 10 with 20 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown deleting segment 13 with 5 points - only 0.00% unknown deleting segment 14 with 29 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown mean border=91.3, 157 (19) missing vertices, mean dist -0.1 [0.3 (%68.6)->0.2 (%31.4))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.26 (0.06-->5.15) (max @ vno 65725 --> 64534) face area 0.34 +- 0.17 (0.00-->5.40) mean absolute distance = 0.24 +- 0.33 3911 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=870098.4, rms=2.531 015: dt: 0.5000, sse=794961.1, rms=1.855 (26.707%) rms = 1.88, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=758971.2, rms=1.501 (19.113%) 017: dt: 0.2500, sse=745184.7, rms=1.321 (11.983%) rms = 1.29, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=751846.6, rms=1.289 (2.382%) rms = 1.27, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=740236.4, rms=1.270 (1.540%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 41 points - only 0.00% unknown deleting segment 1 with 16 points - only 0.00% unknown deleting segment 2 with 100 points - only 0.00% unknown deleting segment 3 with 13 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown deleting segment 5 with 227 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown deleting segment 13 with 5 points - only 0.00% unknown deleting segment 14 with 29 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 16 with 3 points - only 0.00% unknown mean border=91.9, 197 (16) missing vertices, mean dist -0.0 [0.3 (%55.6)->0.2 (%44.4))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=749861.8, rms=1.489 020: dt: 0.5000, sse=740426.2, rms=1.168 (21.548%) rms = 1.61, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=714586.5, rms=1.001 (14.337%) rms = 1.03, time step reduction 2 of 3 to 0.125... rms = 0.99, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=712339.4, rms=0.987 (1.398%) positioning took 0.5 minutes generating cortex label... 19 non-cortical segments detected only using segment with 7837 vertices erasing segment 0 (vno[0] = 56287) erasing segment 2 (vno[0] = 65714) erasing segment 3 (vno[0] = 66933) erasing segment 4 (vno[0] = 79786) erasing segment 5 (vno[0] = 85795) erasing segment 6 (vno[0] = 88746) erasing segment 7 (vno[0] = 89202) erasing segment 8 (vno[0] = 96108) erasing segment 9 (vno[0] = 104720) erasing segment 10 (vno[0] = 104826) erasing segment 11 (vno[0] = 108390) erasing segment 12 (vno[0] = 110202) erasing segment 13 (vno[0] = 111163) erasing segment 14 (vno[0] = 111246) erasing segment 15 (vno[0] = 112149) erasing segment 16 (vno[0] = 112970) erasing segment 17 (vno[0] = 127928) erasing segment 18 (vno[0] = 129027) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/lh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.curv writing smoothed area to lh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.area vertex spacing 0.89 +- 0.27 (0.05-->5.19) (max @ vno 64534 --> 65725) face area 0.33 +- 0.17 (0.00-->5.40) 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 57 points - only 0.00% unknown deleting segment 1 with 264 points - only 0.00% unknown deleting segment 2 with 21 points - only 0.00% unknown deleting segment 3 with 34 points - only 0.00% unknown deleting segment 5 with 17 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 9 with 16 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 14 with 31 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 15 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 16 with 3 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=66.8, 166 (166) missing vertices, mean dist 1.5 [0.3 (%0.0)->3.3 (%100.0))] %12 local maxima, %32 large gradients and %51 min vals, 267 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=tars-, 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=19130522.0, rms=26.012 001: dt: 0.0500, sse=17186392.0, rms=24.603 (5.417%) 002: dt: 0.0500, sse=15780930.0, rms=23.532 (4.355%) 003: dt: 0.0500, sse=14705449.0, rms=22.678 (3.630%) 004: dt: 0.0500, sse=13841601.0, rms=21.968 (3.132%) 005: dt: 0.0500, sse=13121071.0, rms=21.357 (2.780%) 006: dt: 0.0500, sse=12502312.0, rms=20.818 (2.522%) 007: dt: 0.0500, sse=11959097.0, rms=20.333 (2.329%) 008: dt: 0.0500, sse=11475302.0, rms=19.892 (2.173%) 009: dt: 0.0500, sse=11039302.0, rms=19.485 (2.045%) 010: dt: 0.0500, sse=10642330.0, rms=19.107 (1.940%) positioning took 1.0 minutes mean border=66.5, 146 (90) missing vertices, mean dist 1.3 [0.1 (%0.0)->2.8 (%100.0))] %14 local maxima, %33 large gradients and %49 min vals, 239 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, 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=11592862.0, rms=20.003 011: dt: 0.0500, sse=11224382.0, rms=19.662 (1.706%) 012: dt: 0.0500, sse=10884491.0, rms=19.342 (1.628%) 013: dt: 0.0500, sse=10569034.0, rms=19.040 (1.561%) 014: dt: 0.0500, sse=10275266.0, rms=18.754 (1.500%) 015: dt: 0.0500, sse=10001329.0, rms=18.484 (1.442%) 016: dt: 0.0500, sse=9744793.0, rms=18.227 (1.390%) 017: dt: 0.0500, sse=9504022.0, rms=17.982 (1.342%) 018: dt: 0.0500, sse=9277411.0, rms=17.749 (1.298%) 019: dt: 0.0500, sse=9063554.0, rms=17.526 (1.257%) 020: dt: 0.0500, sse=8861249.0, rms=17.312 (1.220%) positioning took 1.0 minutes mean border=66.4, 168 (57) missing vertices, mean dist 1.2 [0.1 (%0.3)->2.5 (%99.7))] %14 local maxima, %33 large gradients and %49 min vals, 232 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, 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=8980241.0, rms=17.443 021: dt: 0.0500, sse=8785763.0, rms=17.236 (1.184%) 022: dt: 0.0500, sse=8601212.0, rms=17.038 (1.151%) 023: dt: 0.0500, sse=8424750.0, rms=16.846 (1.126%) 024: dt: 0.0500, sse=8255496.5, rms=16.660 (1.106%) 025: dt: 0.0500, sse=8092972.5, rms=16.479 (1.086%) 026: dt: 0.0500, sse=7936089.5, rms=16.302 (1.072%) 027: dt: 0.0500, sse=7783654.0, rms=16.129 (1.064%) 028: dt: 0.0500, sse=7635242.0, rms=15.958 (1.059%) 029: dt: 0.0500, sse=7489611.0, rms=15.789 (1.062%) 030: dt: 0.0500, sse=7346553.5, rms=15.620 (1.066%) positioning took 1.0 minutes mean border=66.3, 230 (48) missing vertices, mean dist 1.1 [0.1 (%1.8)->2.2 (%98.2))] %14 local maxima, %33 large gradients and %48 min vals, 206 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, 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=7444955.0, rms=15.738 031: dt: 0.5000, sse=6344280.0, rms=14.388 (8.579%) 032: dt: 0.5000, sse=5419289.0, rms=13.142 (8.659%) 033: dt: 0.5000, sse=4655352.5, rms=12.016 (8.565%) 034: dt: 0.5000, sse=4001545.0, rms=10.959 (8.795%) 035: dt: 0.5000, sse=3468365.5, rms=10.015 (8.616%) 036: dt: 0.5000, sse=3008430.5, rms=9.121 (8.927%) 037: dt: 0.5000, sse=2632061.8, rms=8.321 (8.767%) 038: dt: 0.5000, sse=2323722.5, rms=7.601 (8.662%) 039: dt: 0.5000, sse=2099456.5, rms=7.034 (7.462%) 040: dt: 0.5000, sse=1922194.1, rms=6.550 (6.879%) 041: dt: 0.5000, sse=1806286.1, rms=6.213 (5.144%) 042: dt: 0.5000, sse=1712135.0, rms=5.925 (4.624%) 043: dt: 0.5000, sse=1663987.9, rms=5.772 (2.592%) 044: dt: 0.5000, sse=1617624.4, rms=5.620 (2.635%) 045: dt: 0.5000, sse=1597751.2, rms=5.553 (1.189%) 046: dt: 0.5000, sse=1570023.6, rms=5.458 (1.711%) rms = 5.44, time step reduction 1 of 3 to 0.250... 047: dt: 0.5000, sse=1564549.2, rms=5.440 (0.337%) 048: dt: 0.2500, sse=1438051.2, rms=4.945 (9.092%) 049: dt: 0.2500, sse=1399661.2, rms=4.800 (2.930%) rms = 4.82, time step reduction 2 of 3 to 0.125... 050: dt: 0.1250, sse=1383011.0, rms=4.732 (1.411%) 051: dt: 0.1250, sse=1361759.9, rms=4.643 (1.883%) rms = 4.63, time step reduction 3 of 3 to 0.062... 052: dt: 0.1250, sse=1357812.2, rms=4.626 (0.367%) positioning took 3.2 minutes mean border=65.4, 3968 (18) missing vertices, mean dist 0.1 [0.2 (%44.2)->0.6 (%55.8))] %25 local maxima, %23 large gradients and %44 min vals, 150 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, 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=1606659.8, rms=4.764 rms = 4.78, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1490080.9, rms=4.269 (10.377%) 054: dt: 0.2500, sse=1430163.4, rms=3.988 (6.583%) rms = 3.95, time step reduction 2 of 3 to 0.125... 055: dt: 0.2500, sse=1419752.1, rms=3.946 (1.068%) 056: dt: 0.1250, sse=1363760.8, rms=3.662 (7.191%) 057: dt: 0.1250, sse=1348435.1, rms=3.587 (2.039%) rms = 3.56, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1343571.1, rms=3.564 (0.645%) positioning took 1.1 minutes mean border=64.9, 4474 (16) missing vertices, mean dist 0.1 [0.2 (%43.7)->0.4 (%56.3))] %35 local maxima, %13 large gradients and %44 min vals, 186 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, 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=1365464.1, rms=3.699 rms = 4.31, time step reduction 1 of 3 to 0.250... 059: dt: 0.2500, sse=1335099.1, rms=3.541 (4.273%) rms = 3.56, time step reduction 2 of 3 to 0.125... rms = 3.52, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1330460.6, rms=3.516 (0.709%) positioning took 0.6 minutes mean border=64.4, 7914 (15) missing vertices, mean dist 0.1 [0.2 (%43.4)->0.3 (%56.6))] %36 local maxima, %12 large gradients and %42 min vals, 212 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1350630.4, rms=3.617 rms = 4.01, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1322391.5, rms=3.471 (4.029%) 062: dt: 0.2500, sse=1305931.2, rms=3.408 (1.824%) rms = 3.46, time step reduction 2 of 3 to 0.125... 063: dt: 0.1250, sse=1296637.8, rms=3.354 (1.584%) 064: dt: 0.1250, sse=1282163.0, rms=3.274 (2.384%) rms = 3.24, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=1274684.4, rms=3.237 (1.129%) positioning took 1.1 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.area.pial vertex spacing 1.02 +- 0.47 (0.09-->6.59) (max @ vno 64503 --> 64502) face area 0.41 +- 0.35 (0.00-->7.83) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 142936 vertices processed 25000 of 142936 vertices processed 50000 of 142936 vertices processed 75000 of 142936 vertices processed 100000 of 142936 vertices processed 125000 of 142936 vertices processed 0 of 142936 vertices processed 25000 of 142936 vertices processed 50000 of 142936 vertices processed 75000 of 142936 vertices processed 100000 of 142936 vertices processed 125000 of 142936 vertices processed thickness calculation complete, 558:1518 truncations. 25824 vertices at 0 distance 87942 vertices at 1 distance 90229 vertices at 2 distance 44182 vertices at 3 distance 16096 vertices at 4 distance 5455 vertices at 5 distance 1868 vertices at 6 distance 657 vertices at 7 distance 244 vertices at 8 distance 138 vertices at 9 distance 71 vertices at 10 distance 60 vertices at 11 distance 56 vertices at 12 distance 40 vertices at 13 distance 19 vertices at 14 distance 19 vertices at 15 distance 25 vertices at 16 distance 23 vertices at 17 distance 13 vertices at 18 distance 15 vertices at 19 distance 26 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.thickness positioning took 15.8 minutes mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/filled.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/brain.finalsurfs.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/../mri/aseg.presurf.mgz... reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz... 43243 bright wm thresholded. 11304 bright non-wm voxels segmented. reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.orig... computing class statistics... border white: 307857 voxels (1.83%) border gray 349309 voxels (2.08%) WM (102.0): 101.7 +- 6.8 [70.0 --> 110.0] GM (82.0) : 80.2 +- 11.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 69.3 (was 70) setting MAX_BORDER_WHITE to 111.8 (was 105) setting MIN_BORDER_WHITE to 81.0 (was 85) setting MAX_CSF to 57.6 (was 40) setting MAX_GRAY to 98.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 45.9 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-5.2, GM=81+-5.2 mean inside = 98.4, mean outside = 84.9 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.88 +- 0.26 (0.04-->4.84) (max @ vno 84131 --> 145887) face area 0.33 +- 0.16 (0.00-->4.88) mean absolute distance = 0.69 +- 0.92 3487 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 19 points - only 0.00% unknown deleting segment 7 with 130 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 37 points - only 0.00% unknown deleting segment 11 with 17 points - only 0.00% unknown deleting segment 12 with 19 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown mean border=88.3, 352 (351) missing vertices, mean dist 0.4 [1.2 (%12.9)->0.6 (%87.1))] %67 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, 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 0.90 +- 0.27 (0.04-->4.88) (max @ vno 145887 --> 84131) face area 0.33 +- 0.17 (0.00-->4.70) mean absolute distance = 0.38 +- 0.57 4118 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1644972.1, rms=5.797 001: dt: 0.5000, sse=1037951.8, rms=3.438 (40.691%) 002: dt: 0.5000, sse=887113.8, rms=2.504 (27.182%) 003: dt: 0.5000, sse=846604.8, rms=2.292 (8.456%) 004: dt: 0.5000, sse=833308.2, rms=2.177 (4.994%) rms = 2.23, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=794641.2, rms=1.835 (15.707%) 006: dt: 0.2500, sse=785070.5, rms=1.676 (8.682%) rms = 1.64, time step reduction 2 of 3 to 0.125... 007: dt: 0.2500, sse=777242.2, rms=1.640 (2.173%) rms = 1.61, time step reduction 3 of 3 to 0.062... 008: dt: 0.1250, sse=775650.2, rms=1.614 (1.535%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 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 78 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 6 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown mean border=90.6, 137 (44) missing vertices, mean dist -0.2 [0.4 (%71.8)->0.3 (%28.2))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, 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 +- 0.26 (0.06-->5.00) (max @ vno 145887 --> 84131) face area 0.34 +- 0.17 (0.00-->5.22) mean absolute distance = 0.29 +- 0.40 4390 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1047880.8, rms=3.343 009: dt: 0.5000, sse=858062.8, rms=2.081 (37.738%) 010: dt: 0.5000, sse=840345.6, rms=1.878 (9.775%) rms = 1.93, time step reduction 1 of 3 to 0.250... 011: dt: 0.2500, sse=798712.4, rms=1.561 (16.867%) 012: dt: 0.2500, sse=790508.3, rms=1.402 (10.219%) rms = 1.37, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=791362.4, rms=1.370 (2.221%) rms = 1.35, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=787017.2, rms=1.349 (1.580%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 12 points - only 0.00% unknown deleting segment 1 with 8 points - only 0.00% unknown deleting segment 2 with 102 points - only 0.00% unknown deleting segment 3 with 5 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 11 points - only 0.00% unknown deleting segment 6 with 13 points - only 0.00% unknown deleting segment 7 with 13 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown deleting segment 10 with 14 points - only 0.00% unknown mean border=92.2, 136 (22) missing vertices, mean dist -0.1 [0.3 (%69.1)->0.2 (%30.9))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, 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 +- 0.26 (0.06-->5.08) (max @ vno 145887 --> 84131) face area 0.33 +- 0.17 (0.00-->5.27) mean absolute distance = 0.24 +- 0.33 3954 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=887643.7, rms=2.474 015: dt: 0.5000, sse=820915.0, rms=1.802 (27.164%) rms = 1.80, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=805268.6, rms=1.795 (0.364%) 017: dt: 0.2500, sse=781915.5, rms=1.343 (25.204%) 018: dt: 0.2500, sse=760360.9, rms=1.276 (4.994%) rms = 1.28, time step reduction 2 of 3 to 0.125... rms = 1.26, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=756671.7, rms=1.264 (0.958%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 9 points - only 0.00% unknown deleting segment 1 with 8 points - only 0.00% unknown deleting segment 2 with 102 points - only 0.00% unknown deleting segment 3 with 5 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 15 points - only 0.00% unknown deleting segment 6 with 14 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown deleting segment 10 with 14 points - only 0.00% unknown mean border=92.8, 188 (14) missing vertices, mean dist -0.0 [0.3 (%55.6)->0.2 (%44.4))] %92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=766493.4, rms=1.482 020: dt: 0.5000, sse=752034.1, rms=1.238 (16.463%) rms = 1.67, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=732014.0, rms=1.034 (16.450%) rms = 1.06, time step reduction 2 of 3 to 0.125... rms = 1.01, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=730716.1, rms=1.015 (1.895%) positioning took 0.5 minutes generating cortex label... 25 non-cortical segments detected only using segment with 7412 vertices erasing segment 1 (vno[0] = 54235) erasing segment 2 (vno[0] = 66276) erasing segment 3 (vno[0] = 68539) erasing segment 4 (vno[0] = 80271) erasing segment 5 (vno[0] = 85273) erasing segment 6 (vno[0] = 94783) erasing segment 7 (vno[0] = 97800) erasing segment 8 (vno[0] = 102197) erasing segment 9 (vno[0] = 103062) erasing segment 10 (vno[0] = 103304) erasing segment 11 (vno[0] = 106192) erasing segment 12 (vno[0] = 107515) erasing segment 13 (vno[0] = 110160) erasing segment 14 (vno[0] = 110247) erasing segment 15 (vno[0] = 110306) erasing segment 16 (vno[0] = 111222) erasing segment 17 (vno[0] = 112098) erasing segment 18 (vno[0] = 112118) erasing segment 19 (vno[0] = 114058) erasing segment 20 (vno[0] = 115085) erasing segment 21 (vno[0] = 115985) erasing segment 22 (vno[0] = 116938) erasing segment 23 (vno[0] = 117897) erasing segment 24 (vno[0] = 127144) writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/rh.cortex.label... writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.curv writing smoothed area to rh.area writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.area vertex spacing 0.89 +- 0.27 (0.04-->5.05) (max @ vno 84131 --> 145887) face area 0.33 +- 0.17 (0.00-->5.20) 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 14 points - only 0.00% unknown deleting segment 1 with 28 points - only 0.00% unknown deleting segment 2 with 48 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown deleting segment 8 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 10 points - only 0.00% unknown deleting segment 13 with 9 points - only 0.00% unknown deleting segment 16 with 41 points - only 0.00% unknown deleting segment 17 with 6 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=67.9, 355 (355) missing vertices, mean dist 1.5 [1.3 (%0.0)->3.4 (%100.0))] %12 local maxima, %30 large gradients and %54 min vals, 234 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=tars-, 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=19541948.0, rms=25.857 001: dt: 0.0500, sse=17601898.0, rms=24.489 (5.288%) 002: dt: 0.0500, sse=16205534.0, rms=23.455 (4.221%) 003: dt: 0.0500, sse=15143400.0, rms=22.637 (3.488%) 004: dt: 0.0500, sse=14290057.0, rms=21.958 (3.002%) 005: dt: 0.0500, sse=13579627.0, rms=21.376 (2.652%) 006: dt: 0.0500, sse=12968860.0, rms=20.862 (2.403%) 007: dt: 0.0500, sse=12433268.0, rms=20.401 (2.211%) 008: dt: 0.0500, sse=11956473.0, rms=19.981 (2.056%) 009: dt: 0.0500, sse=11525825.0, rms=19.594 (1.935%) 010: dt: 0.0500, sse=11133810.0, rms=19.236 (1.831%) positioning took 1.0 minutes mean border=67.6, 241 (151) missing vertices, mean dist 1.3 [0.1 (%0.1)->2.9 (%99.9))] %13 local maxima, %31 large gradients and %52 min vals, 218 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, 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=12310116.0, rms=20.286 011: dt: 0.0500, sse=11943799.0, rms=19.963 (1.593%) 012: dt: 0.0500, sse=11605339.0, rms=19.660 (1.519%) 013: dt: 0.0500, sse=11291073.0, rms=19.374 (1.454%) 014: dt: 0.0500, sse=10998360.0, rms=19.104 (1.395%) 015: dt: 0.0500, sse=10724568.0, rms=18.848 (1.342%) 016: dt: 0.0500, sse=10468399.0, rms=18.605 (1.290%) 017: dt: 0.0500, sse=10226968.0, rms=18.372 (1.248%) 018: dt: 0.0500, sse=9999295.0, rms=18.151 (1.207%) 019: dt: 0.0500, sse=9783662.0, rms=17.938 (1.171%) 020: dt: 0.0500, sse=9579177.0, rms=17.734 (1.137%) positioning took 1.0 minutes mean border=67.4, 219 (86) missing vertices, mean dist 1.2 [0.1 (%0.5)->2.6 (%99.5))] %14 local maxima, %30 large gradients and %52 min vals, 228 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, 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=9715544.0, rms=17.873 021: dt: 0.0500, sse=9515791.0, rms=17.673 (1.119%) 022: dt: 0.0500, sse=9325783.0, rms=17.481 (1.089%) 023: dt: 0.0500, sse=9143169.0, rms=17.294 (1.070%) 024: dt: 0.0500, sse=8967546.0, rms=17.112 (1.051%) 025: dt: 0.0500, sse=8797847.0, rms=16.935 (1.038%) 026: dt: 0.0500, sse=8633783.0, rms=16.761 (1.025%) 027: dt: 0.0500, sse=8473965.0, rms=16.590 (1.020%) 028: dt: 0.0500, sse=8317540.0, rms=16.421 (1.019%) 029: dt: 0.0500, sse=8164277.0, rms=16.254 (1.019%) 030: dt: 0.0500, sse=8013510.0, rms=16.087 (1.024%) positioning took 1.0 minutes mean border=67.3, 298 (68) missing vertices, mean dist 1.0 [0.1 (%1.9)->2.3 (%98.1))] %14 local maxima, %31 large gradients and %51 min vals, 208 gradients ignored tol=1.0e-04, sigma=2.0, host=tars-, 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=8117616.0, rms=16.204 031: dt: 0.5000, sse=6980306.0, rms=14.898 (8.057%) 032: dt: 0.5000, sse=6046142.5, rms=13.729 (7.849%) 033: dt: 0.5000, sse=5251323.0, rms=12.649 (7.863%) 034: dt: 0.5000, sse=4559655.5, rms=11.627 (8.084%) 035: dt: 0.5000, sse=3965775.0, rms=10.671 (8.216%) 036: dt: 0.5000, sse=3434142.5, rms=9.736 (8.763%) 037: dt: 0.5000, sse=2983715.5, rms=8.870 (8.896%) 038: dt: 0.5000, sse=2595282.8, rms=8.047 (9.276%) 039: dt: 0.5000, sse=2305278.0, rms=7.376 (8.346%) 040: dt: 0.5000, sse=2081590.6, rms=6.811 (7.652%) 041: dt: 0.5000, sse=1942855.8, rms=6.437 (5.502%) 042: dt: 0.5000, sse=1833828.0, rms=6.125 (4.839%) 043: dt: 0.5000, sse=1775930.5, rms=5.953 (2.802%) 044: dt: 0.5000, sse=1725695.4, rms=5.798 (2.611%) 045: dt: 0.5000, sse=1698680.5, rms=5.715 (1.438%) 046: dt: 0.5000, sse=1676140.8, rms=5.641 (1.292%) rms = 5.61, time step reduction 1 of 3 to 0.250... 047: dt: 0.5000, sse=1666048.8, rms=5.609 (0.566%) 048: dt: 0.2500, sse=1531690.1, rms=5.118 (8.752%) 049: dt: 0.2500, sse=1490096.1, rms=4.971 (2.863%) rms = 4.99, time step reduction 2 of 3 to 0.125... 050: dt: 0.1250, sse=1467199.8, rms=4.885 (1.736%) 051: dt: 0.1250, sse=1436874.1, rms=4.767 (2.409%) rms = 4.75, time step reduction 3 of 3 to 0.062... 052: dt: 0.1250, sse=1431533.2, rms=4.746 (0.455%) positioning took 3.4 minutes mean border=66.6, 4994 (22) missing vertices, mean dist 0.1 [0.2 (%44.5)->0.6 (%55.5))] %23 local maxima, %22 large gradients and %47 min vals, 153 gradients ignored tol=1.0e-04, sigma=1.0, host=tars-, 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=1691833.1, rms=4.920 rms = 5.05, time step reduction 1 of 3 to 0.250... 053: dt: 0.2500, sse=1561506.1, rms=4.405 (10.471%) 054: dt: 0.2500, sse=1507521.2, rms=4.170 (5.331%) rms = 4.17, time step reduction 2 of 3 to 0.125... 055: dt: 0.1250, sse=1479779.5, rms=4.044 (3.015%) 056: dt: 0.1250, sse=1439883.9, rms=3.860 (4.570%) 057: dt: 0.1250, sse=1421692.8, rms=3.776 (2.159%) rms = 3.73, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1412254.1, rms=3.734 (1.109%) positioning took 1.3 minutes mean border=66.2, 5375 (16) missing vertices, mean dist 0.1 [0.2 (%44.6)->0.4 (%55.4))] %32 local maxima, %13 large gradients and %47 min vals, 163 gradients ignored tol=1.0e-04, sigma=0.5, host=tars-, 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=1434863.2, rms=3.870 rms = 4.58, time step reduction 1 of 3 to 0.250... 059: dt: 0.2500, sse=1398821.8, rms=3.700 (4.403%) rms = 3.78, time step reduction 2 of 3 to 0.125... rms = 3.67, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1393268.2, rms=3.673 (0.741%) positioning took 0.6 minutes mean border=65.8, 8839 (15) missing vertices, mean dist 0.1 [0.2 (%44.1)->0.3 (%55.9))] %33 local maxima, %12 large gradients and %45 min vals, 172 gradients ignored tol=1.0e-04, sigma=0.2, host=tars-, 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1408043.6, rms=3.739 rms = 4.24, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1376834.0, rms=3.590 (3.967%) rms = 3.57, time step reduction 2 of 3 to 0.125... 062: dt: 0.2500, sse=1367459.0, rms=3.571 (0.550%) 063: dt: 0.1250, sse=1339061.9, rms=3.421 (4.183%) 064: dt: 0.1250, sse=1326661.8, rms=3.363 (1.704%) rms = 3.34, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=1321399.4, rms=3.341 (0.665%) positioning took 1.1 minutes writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.area.pial vertex spacing 1.01 +- 0.47 (0.05-->6.52) (max @ vno 66223 --> 63851) face area 0.40 +- 0.34 (0.00-->10.40) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 147238 vertices processed 25000 of 147238 vertices processed 50000 of 147238 vertices processed 75000 of 147238 vertices processed 100000 of 147238 vertices processed 125000 of 147238 vertices processed 0 of 147238 vertices processed 25000 of 147238 vertices processed 50000 of 147238 vertices processed 75000 of 147238 vertices processed 100000 of 147238 vertices processed 125000 of 147238 vertices processed thickness calculation complete, 537:1299 truncations. 27997 vertices at 0 distance 89294 vertices at 1 distance 92530 vertices at 2 distance 46325 vertices at 3 distance 17051 vertices at 4 distance 5803 vertices at 5 distance 1991 vertices at 6 distance 757 vertices at 7 distance 240 vertices at 8 distance 145 vertices at 9 distance 85 vertices at 10 distance 72 vertices at 11 distance 77 vertices at 12 distance 46 vertices at 13 distance 32 vertices at 14 distance 26 vertices at 15 distance 23 vertices at 16 distance 18 vertices at 17 distance 24 vertices at 18 distance 20 vertices at 19 distance 26 vertices at 20 distance writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.thickness positioning took 16.6 minutes PIDs (25844 25847) completed and logs appended. #-------------------------------------------- #@# Surf Volume lh Sun Oct 8 00:02:04 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/lh.cortex.label Total face volume 285015 Total vertex volume 282017 (mask=0) #@# 0050660 lh 282017 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Sun Oct 8 00:02:07 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.volume masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/rh.cortex.label Total face volume 291096 Total vertex volume 287734 (mask=0) #@# 0050660 rh 287734 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Sun Oct 8 00:02:11 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 SUBJECTS_DIR is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 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 = 95 writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/ribbon.mgz mris_volmask took 15.01 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Sun Oct 8 00:17:12 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 lh white 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 0050660 lh pial #----------------------------------------- #@# Parcellation Stats rh Sun Oct 8 00:17:12 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 rh white 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 0050660 rh pial Waiting for PID 27287 of (27287 27290 27293 27296) to complete... Waiting for PID 27290 of (27287 27290 27293 27296) to complete... Waiting for PID 27293 of (27287 27290 27293 27296) to complete... Waiting for PID 27296 of (27287 27290 27293 27296) to complete... 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 0050660 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 285015 Total vertex volume 282017 (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) = 1471526 mm^3 (det: 1.323867 ) lhCtxGM: 279280.808 278491.000 diff= 789.8 pctdiff= 0.283 rhCtxGM: 284870.137 284689.000 diff= 181.1 pctdiff= 0.064 lhCtxWM: 233480.686 233866.500 diff= -385.8 pctdiff=-0.165 rhCtxWM: 237715.068 238592.500 diff= -877.4 pctdiff=-0.369 SubCortGMVol 68130.000 SupraTentVol 1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365 SupraTentVolNotVent 1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371 BrainSegVol 1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208 BrainSegVolNotVent 1261243.000 (1260795.700) diff=447.300 pctdiff=0.035 BrainSegVolNotVent 1261243.000 CerebellumVol 157288.000 VentChorVol 16563.000 3rd4th5thCSF 3560.000 CSFVol 898.000, OptChiasmVol 155.000 MaskVol 1664570.000 1210 911 2327 2.539 0.421 0.109 0.022 12 1.0 bankssts 875 596 1806 2.841 0.529 0.135 0.020 13 0.7 caudalanteriorcingulate 3461 2286 7426 2.843 0.460 0.125 0.032 41 4.6 caudalmiddlefrontal 2530 1623 3919 2.120 0.577 0.154 0.049 41 5.2 cuneus 785 565 2501 3.225 0.757 0.153 0.056 14 2.0 entorhinal 5543 3801 13707 3.038 0.623 0.139 0.041 104 9.5 fusiform 7263 4845 14559 2.739 0.464 0.119 0.026 97 7.4 inferiorparietal 6378 4395 16690 2.977 0.858 0.134 0.037 111 10.9 inferiortemporal 1998 1331 3872 2.367 1.081 0.125 0.034 30 2.6 isthmuscingulate 8727 5684 16613 2.559 0.615 0.140 0.035 127 12.3 lateraloccipital 4006 2712 8602 2.921 0.810 0.140 0.049 66 9.6 lateralorbitofrontal 4772 3139 7277 2.143 0.639 0.143 0.042 67 8.0 lingual 3183 2136 7191 2.815 0.899 0.142 0.049 78 6.6 medialorbitofrontal 5569 3923 15107 2.990 0.715 0.128 0.031 86 7.7 middletemporal 1318 903 3290 3.023 0.651 0.101 0.031 13 1.5 parahippocampal 2097 1212 3521 2.640 0.508 0.101 0.029 19 2.7 paracentral 2220 1460 5186 2.952 0.479 0.112 0.029 27 2.3 parsopercularis 1062 756 3256 3.121 0.585 0.160 0.054 27 2.4 parsorbitalis 1898 1313 4198 2.746 0.485 0.123 0.029 27 2.2 parstriangularis 1992 1347 1796 1.567 0.387 0.158 0.044 27 3.8 pericalcarine 6846 4383 11441 2.343 0.688 0.121 0.030 83 8.2 postcentral 1804 1183 3399 2.638 0.641 0.137 0.033 31 2.4 posteriorcingulate 8716 5111 15207 2.738 0.560 0.111 0.034 107 12.2 precentral 5563 3765 11280 2.755 0.504 0.123 0.027 73 6.2 precuneus 1221 796 3007 3.222 0.718 0.131 0.044 27 1.6 rostralanteriorcingulate 8730 5929 18701 2.698 0.511 0.141 0.037 171 14.0 rostralmiddlefrontal 9670 6575 21551 2.892 0.605 0.132 0.034 137 13.6 superiorfrontal 8262 5447 15922 2.560 0.541 0.125 0.028 103 9.1 superiorparietal 5327 3724 12749 2.937 0.600 0.124 0.027 61 6.1 superiortemporal 5996 4006 12686 2.851 0.477 0.131 0.034 94 7.9 supramarginal 412 285 1287 3.100 0.544 0.160 0.052 11 0.9 frontalpole 747 520 2425 3.116 0.896 0.147 0.053 15 1.7 temporalpole 774 501 1331 2.381 0.628 0.150 0.057 12 1.8 transversetemporal 3695 2431 8148 3.352 0.756 0.123 0.038 39 5.6 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 0050660 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 285015 Total vertex volume 282017 (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) = 1471526 mm^3 (det: 1.323867 ) lhCtxGM: 279280.808 278491.000 diff= 789.8 pctdiff= 0.283 rhCtxGM: 284870.137 284689.000 diff= 181.1 pctdiff= 0.064 lhCtxWM: 233480.686 233866.500 diff= -385.8 pctdiff=-0.165 rhCtxWM: 237715.068 238592.500 diff= -877.4 pctdiff=-0.369 SubCortGMVol 68130.000 SupraTentVol 1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365 SupraTentVolNotVent 1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371 BrainSegVol 1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208 BrainSegVolNotVent 1261243.000 (1260795.700) diff=447.300 pctdiff=0.035 BrainSegVolNotVent 1261243.000 CerebellumVol 157288.000 VentChorVol 16563.000 3rd4th5thCSF 3560.000 CSFVol 898.000, OptChiasmVol 155.000 MaskVol 1664570.000 1210 979 2327 2.539 0.421 0.132 0.028 22 1.5 bankssts 875 714 1806 2.841 0.529 0.149 0.029 34 0.8 caudalanteriorcingulate 3461 2833 7426 2.843 0.460 0.141 0.037 71 5.1 caudalmiddlefrontal 2530 1998 3919 2.120 0.577 0.149 0.041 40 4.6 cuneus 785 997 2501 3.225 0.757 0.209 0.065 20 2.8 entorhinal 5543 4930 13707 3.038 0.623 0.158 0.040 109 9.7 fusiform 7263 5816 14559 2.739 0.464 0.139 0.054 159 22.2 inferiorparietal 6378 6175 16690 2.977 0.858 0.161 0.038 119 12.1 inferiortemporal 1998 1744 3872 2.367 1.081 0.160 0.041 43 3.5 isthmuscingulate 8727 7023 16613 2.559 0.615 0.135 0.033 139 12.3 lateraloccipital 4006 3061 8602 2.921 0.810 0.139 0.036 67 6.1 lateralorbitofrontal 4772 3681 7277 2.143 0.639 0.140 0.040 75 8.1 lingual 3183 2816 7191 2.815 0.899 0.165 0.050 80 7.1 medialorbitofrontal 5569 5875 15107 2.990 0.715 0.157 0.031 70 8.4 middletemporal 1318 1283 3290 3.023 0.651 0.141 0.029 10 2.0 parahippocampal 2097 1437 3521 2.640 0.508 0.106 0.022 22 1.9 paracentral 2220 2012 5186 2.952 0.479 0.145 0.033 29 3.2 parsopercularis 1062 1257 3256 3.121 0.585 0.188 0.040 15 2.1 parsorbitalis 1898 1697 4198 2.746 0.485 0.149 0.030 22 2.6 parstriangularis 1992 1089 1796 1.567 0.387 0.110 0.032 35 2.6 pericalcarine 6846 5283 11441 2.343 0.688 0.125 0.026 68 8.4 postcentral 1804 1344 3399 2.638 0.641 0.150 0.044 79 3.2 posteriorcingulate 8716 5788 15207 2.738 0.560 0.107 0.027 121 10.3 precentral 5563 4212 11280 2.755 0.504 0.135 0.032 127 7.4 precuneus 1221 1105 3007 3.222 0.718 0.175 0.046 45 2.5 rostralanteriorcingulate 8730 7677 18701 2.698 0.511 0.160 0.038 135 14.8 rostralmiddlefrontal 9670 7940 21551 2.892 0.605 0.142 0.035 167 14.7 superiorfrontal 8262 6684 15922 2.560 0.541 0.137 0.036 127 10.8 superiorparietal 5327 4775 12749 2.937 0.600 0.146 0.033 86 7.9 superiortemporal 5996 4788 12686 2.851 0.477 0.143 0.052 275 17.0 supramarginal 412 536 1287 3.100 0.544 0.205 0.041 6 0.7 frontalpole 747 1025 2425 3.116 0.896 0.232 0.057 14 2.2 temporalpole 774 577 1331 2.381 0.628 0.127 0.032 8 1.0 transversetemporal 3695 2271 8148 3.352 0.756 0.134 0.040 71 6.6 insula 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 0050660 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 291096 Total vertex volume 287734 (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) = 1471526 mm^3 (det: 1.323867 ) lhCtxGM: 279280.808 278491.000 diff= 789.8 pctdiff= 0.283 rhCtxGM: 284870.137 284689.000 diff= 181.1 pctdiff= 0.064 lhCtxWM: 233480.686 233866.500 diff= -385.8 pctdiff=-0.165 rhCtxWM: 237715.068 238592.500 diff= -877.4 pctdiff=-0.369 SubCortGMVol 68130.000 SupraTentVol 1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365 SupraTentVolNotVent 1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371 BrainSegVol 1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208 BrainSegVolNotVent 1261243.000 (1260795.700) diff=447.300 pctdiff=0.035 BrainSegVolNotVent 1261243.000 CerebellumVol 157288.000 VentChorVol 16563.000 3rd4th5thCSF 3560.000 CSFVol 898.000, OptChiasmVol 155.000 MaskVol 1664570.000 1615 1129 3224 3.033 0.468 0.113 0.023 14 1.6 bankssts 891 611 1511 2.434 0.543 0.159 0.022 23 0.7 caudalanteriorcingulate 3234 2173 6458 2.718 0.427 0.125 0.031 41 3.8 caudalmiddlefrontal 2299 1465 3207 2.001 0.479 0.145 0.043 34 4.2 cuneus 720 496 2302 3.282 0.780 0.129 0.046 10 1.5 entorhinal 6132 3962 12865 2.823 0.729 0.134 0.049 119 11.9 fusiform 9099 5996 18795 2.850 0.482 0.126 0.032 122 11.3 inferiorparietal 5879 3837 14228 2.963 0.849 0.118 0.036 90 9.0 inferiortemporal 1430 912 2682 2.430 0.972 0.129 0.029 24 1.7 isthmuscingulate 7591 5004 14817 2.565 0.603 0.139 0.039 102 11.9 lateraloccipital 3707 2524 8776 3.135 0.779 0.148 0.045 68 7.3 lateralorbitofrontal 3887 2536 5494 2.031 0.609 0.146 0.051 64 7.7 lingual 3410 2290 7595 2.767 0.680 0.127 0.038 63 5.2 medialorbitofrontal 5957 4130 16241 3.170 0.737 0.127 0.033 92 8.0 middletemporal 1336 855 2967 2.818 0.686 0.098 0.028 12 1.7 parahippocampal 3150 1936 5371 2.591 0.502 0.126 0.036 42 4.8 paracentral 2159 1429 5084 2.955 0.420 0.122 0.035 30 2.7 parsopercularis 1310 872 3213 2.944 0.629 0.142 0.047 31 2.3 parsorbitalis 2275 1542 5043 2.801 0.538 0.130 0.031 34 2.7 parstriangularis 2164 1429 2149 1.693 0.443 0.144 0.044 27 3.9 pericalcarine 7925 4792 12615 2.330 0.675 0.116 0.034 98 12.4 postcentral 2126 1399 4219 2.579 0.721 0.132 0.030 33 2.7 posteriorcingulate 9763 5839 16276 2.578 0.632 0.119 0.037 140 14.9 precentral 5171 3418 10299 2.764 0.532 0.118 0.029 58 6.4 precuneus 810 505 1853 2.997 0.783 0.129 0.031 14 1.1 rostralanteriorcingulate 8124 5583 17973 2.765 0.576 0.143 0.037 149 13.1 rostralmiddlefrontal 10094 6789 22498 2.853 0.586 0.132 0.039 389 18.0 superiorfrontal 8089 5237 14806 2.514 0.480 0.124 0.032 108 10.3 superiorparietal 5989 4083 15625 3.194 0.660 0.119 0.027 71 6.5 superiortemporal 7085 4749 15400 2.855 0.525 0.131 0.035 101 10.0 supramarginal 500 334 1519 3.302 0.539 0.168 0.043 13 0.8 frontalpole 674 448 2730 3.742 0.690 0.141 0.049 10 1.4 temporalpole 590 360 1051 2.790 0.465 0.140 0.036 8 0.8 transversetemporal 4321 2834 8780 3.038 0.970 0.127 0.040 58 6.2 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 0050660 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 291096 Total vertex volume 287734 (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) = 1471526 mm^3 (det: 1.323867 ) lhCtxGM: 279280.808 278491.000 diff= 789.8 pctdiff= 0.283 rhCtxGM: 284870.137 284689.000 diff= 181.1 pctdiff= 0.064 lhCtxWM: 233480.686 233866.500 diff= -385.8 pctdiff=-0.165 rhCtxWM: 237715.068 238592.500 diff= -877.4 pctdiff=-0.369 SubCortGMVol 68130.000 SupraTentVol 1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365 SupraTentVolNotVent 1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371 BrainSegVol 1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208 BrainSegVolNotVent 1261243.000 (1260795.700) diff=447.300 pctdiff=0.035 BrainSegVolNotVent 1261243.000 CerebellumVol 157288.000 VentChorVol 16563.000 3rd4th5thCSF 3560.000 CSFVol 898.000, OptChiasmVol 155.000 MaskVol 1664570.000 1615 980 3224 3.033 0.468 0.119 0.031 25 2.1 bankssts 891 657 1511 2.434 0.543 0.177 0.044 66 1.4 caudalanteriorcingulate 3234 2538 6458 2.718 0.427 0.132 0.030 62 4.2 caudalmiddlefrontal 2299 1773 3207 2.001 0.479 0.136 0.035 29 3.6 cuneus 720 827 2302 3.282 0.780 0.183 0.073 60 1.3 entorhinal 6132 4852 12865 2.823 0.729 0.145 0.040 129 10.6 fusiform 9099 7042 18795 2.850 0.482 0.137 0.033 139 13.3 inferiorparietal 5879 5391 14228 2.963 0.849 0.147 0.034 116 9.3 inferiortemporal 1430 1143 2682 2.430 0.972 0.149 0.040 26 2.2 isthmuscingulate 7591 6331 14817 2.565 0.603 0.135 0.033 128 10.5 lateraloccipital 3707 2969 8776 3.135 0.779 0.153 0.038 111 6.4 lateralorbitofrontal 3887 2945 5494 2.031 0.609 0.139 0.038 60 6.6 lingual 3410 3071 7595 2.767 0.680 0.158 0.038 50 5.6 medialorbitofrontal 5957 5908 16241 3.170 0.737 0.155 0.035 91 9.0 middletemporal 1336 1218 2967 2.818 0.686 0.136 0.037 17 2.5 parahippocampal 3150 2128 5371 2.591 0.502 0.117 0.032 47 4.2 paracentral 2159 1974 5084 2.955 0.420 0.156 0.034 28 3.5 parsopercularis 1310 1279 3213 2.944 0.629 0.154 0.029 15 1.7 parsorbitalis 2275 1984 5043 2.801 0.538 0.155 0.035 31 3.6 parstriangularis 2164 1243 2149 1.693 0.443 0.107 0.030 47 2.6 pericalcarine 7925 5939 12615 2.330 0.675 0.116 0.027 73 9.9 postcentral 2126 1737 4219 2.579 0.721 0.154 0.034 58 3.2 posteriorcingulate 9763 6461 16276 2.578 0.632 0.108 0.029 124 11.3 precentral 5171 3848 10299 2.764 0.532 0.131 0.033 82 6.7 precuneus 810 730 1853 2.997 0.783 0.199 0.076 26 3.3 rostralanteriorcingulate 8124 7223 17973 2.765 0.576 0.161 0.038 144 14.4 rostralmiddlefrontal 10094 8510 22498 2.853 0.586 0.145 0.041 176 17.0 superiorfrontal 8089 6390 14806 2.514 0.480 0.131 0.028 100 9.5 superiorparietal 5989 5440 15625 3.194 0.660 0.137 0.029 62 7.8 superiortemporal 7085 5767 15400 2.855 0.525 0.144 0.036 110 11.0 supramarginal 500 587 1519 3.302 0.539 0.198 0.038 7 0.9 frontalpole 674 970 2730 3.742 0.690 0.235 0.048 7 1.6 temporalpole 590 395 1051 2.790 0.465 0.112 0.034 5 0.8 transversetemporal 4321 2730 8780 3.038 0.970 0.135 0.043 99 8.0 insula PIDs (27287 27290 27293 27296) completed and logs appended. #----------------------------------------- #@# Cortical Parc 2 lh Sun Oct 8 00:18:32 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot #----------------------------------------- #@# Cortical Parc 2 rh Sun Oct 8 00:18:32 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot Waiting for PID 27374 of (27374 27377) to complete... Waiting for PID 27377 of (27374 27377) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/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 /pasteur/homes/ntraut/bin/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... 40 labels changed using aseg relabeling using gibbs priors... 000: 9013 changed, 142936 examined... 001: 2095 changed, 35640 examined... 002: 664 changed, 10990 examined... 003: 283 changed, 3670 examined... 004: 130 changed, 1631 examined... 005: 65 changed, 734 examined... 006: 36 changed, 377 examined... 007: 25 changed, 197 examined... 008: 7 changed, 126 examined... 009: 2 changed, 38 examined... 010: 2 changed, 11 examined... 011: 1 changed, 8 examined... 012: 2 changed, 8 examined... 013: 0 changed, 12 examined... 10 labels changed using aseg 000: 254 total segments, 170 labels (1460 vertices) changed 001: 88 total segments, 4 labels (9 vertices) changed 002: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 42 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1224 vertices marked for relabeling... 1224 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 19 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/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 /pasteur/homes/ntraut/bin/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... 7 labels changed using aseg relabeling using gibbs priors... 000: 9597 changed, 147238 examined... 001: 2179 changed, 37405 examined... 002: 651 changed, 11445 examined... 003: 277 changed, 3670 examined... 004: 140 changed, 1578 examined... 005: 66 changed, 785 examined... 006: 30 changed, 373 examined... 007: 15 changed, 167 examined... 008: 8 changed, 97 examined... 009: 4 changed, 35 examined... 010: 2 changed, 24 examined... 011: 0 changed, 9 examined... 14 labels changed using aseg 000: 288 total segments, 202 labels (2388 vertices) changed 001: 104 total segments, 18 labels (128 vertices) changed 002: 87 total segments, 1 labels (1 vertices) changed 003: 86 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 52 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1553 vertices marked for relabeling... 1553 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 20 seconds. PIDs (27374 27377) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Sun Oct 8 00:18:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 lh white #----------------------------------------- #@# Parcellation Stats 2 rh Sun Oct 8 00:18:52 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 rh white Waiting for PID 27443 of (27443 27446) to complete... Waiting for PID 27446 of (27443 27446) to complete... 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 0050660 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 285015 Total vertex volume 282017 (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) = 1471526 mm^3 (det: 1.323867 ) lhCtxGM: 279280.808 278491.000 diff= 789.8 pctdiff= 0.283 rhCtxGM: 284870.137 284689.000 diff= 181.1 pctdiff= 0.064 lhCtxWM: 233480.686 233866.500 diff= -385.8 pctdiff=-0.165 rhCtxWM: 237715.068 238592.500 diff= -877.4 pctdiff=-0.369 SubCortGMVol 68130.000 SupraTentVol 1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365 SupraTentVolNotVent 1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371 BrainSegVol 1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208 BrainSegVolNotVent 1261243.000 (1260795.700) diff=447.300 pctdiff=0.035 BrainSegVolNotVent 1261243.000 CerebellumVol 157288.000 VentChorVol 16563.000 3rd4th5thCSF 3560.000 CSFVol 898.000, OptChiasmVol 155.000 MaskVol 1664570.000 1546 1078 3738 2.833 0.735 0.144 0.036 29 2.3 G&S_frontomargin 1653 1140 4008 2.944 0.568 0.149 0.035 28 2.2 G&S_occipital_inf 1579 824 2538 2.506 0.490 0.106 0.034 19 1.9 G&S_paracentral 1631 1096 4159 3.126 0.621 0.134 0.033 23 2.1 G&S_subcentral 746 520 2009 2.922 0.423 0.159 0.048 20 1.5 G&S_transv_frontopol 2379 1609 5606 3.170 0.587 0.136 0.044 43 3.6 G&S_cingul-Ant 1025 736 2187 2.815 0.421 0.111 0.019 10 0.7 G&S_cingul-Mid-Ant 1199 842 2352 2.751 0.393 0.126 0.034 15 1.8 G&S_cingul-Mid-Post 861 580 2420 3.134 0.733 0.148 0.039 14 1.3 G_cingul-Post-dorsal 323 214 911 2.910 1.185 0.144 0.044 6 0.4 G_cingul-Post-ventral 2272 1443 3759 2.079 0.717 0.150 0.050 38 4.7 G_cuneus 1514 978 4086 3.056 0.491 0.128 0.037 26 2.0 G_front_inf-Opercular 407 267 1321 3.246 0.367 0.130 0.032 6 0.6 G_front_inf-Orbital 1162 766 3099 2.881 0.508 0.144 0.040 24 2.0 G_front_inf-Triangul 4955 3259 12653 2.876 0.480 0.150 0.045 118 9.4 G_front_middle 7088 4654 17296 2.978 0.622 0.139 0.040 131 12.1 G_front_sup 716 494 1830 3.533 0.775 0.164 0.059 14 1.8 G_Ins_lg&S_cent_ins 845 524 2803 3.876 0.716 0.122 0.042 12 1.4 G_insular_short 3106 1950 7710 2.923 0.511 0.134 0.032 59 3.7 G_occipital_middle 1604 975 2942 2.399 0.656 0.136 0.037 25 2.4 G_occipital_sup 2193 1444 6102 3.093 0.553 0.151 0.050 49 4.4 G_oc-temp_lat-fusifor 3322 2138 5232 2.053 0.643 0.159 0.053 59 7.0 G_oc-temp_med-Lingual 1728 1210 5165 3.149 0.745 0.130 0.047 27 3.2 G_oc-temp_med-Parahip 2689 1764 7230 2.972 0.859 0.162 0.069 75 9.1 G_orbital 2648 1721 6680 2.932 0.565 0.137 0.038 54 4.0 G_pariet_inf-Angular 2959 1935 7246 2.996 0.477 0.142 0.040 58 4.6 G_pariet_inf-Supramar 3031 1994 7296 2.773 0.519 0.137 0.035 52 3.7 G_parietal_sup 2554 1549 4523 2.294 0.581 0.131 0.037 40 4.0 G_postcentral 3396 1698 6653 2.917 0.570 0.107 0.042 63 6.0 G_precentral 2651 1760 7026 2.979 0.519 0.144 0.036 58 3.9 G_precuneus 938 606 2795 2.957 0.899 0.160 0.055 35 2.4 G_rectus 738 478 1425 2.473 1.270 0.122 0.066 15 1.7 G_subcallosal 698 435 1352 2.404 0.651 0.160 0.065 14 1.7 G_temp_sup-G_T_transv 1762 1253 6112 3.162 0.613 0.143 0.038 32 2.7 G_temp_sup-Lateral 601 475 2097 3.532 0.726 0.105 0.021 4 0.5 G_temp_sup-Plan_polar 824 580 1913 2.808 0.356 0.093 0.019 6 0.5 G_temp_sup-Plan_tempo 3421 2346 10882 3.035 0.964 0.150 0.048 85 7.8 G_temporal_inf 3170 2261 10499 3.182 0.774 0.139 0.035 63 5.0 G_temporal_middle 380 265 677 2.851 0.583 0.097 0.017 2 0.2 Lat_Fis-ant-Horizont 330 231 610 2.620 0.438 0.085 0.014 1 0.2 Lat_Fis-ant-Vertical 1165 775 1654 2.672 0.455 0.111 0.025 8 1.1 Lat_Fis-post 2061 1317 3857 2.380 0.694 0.145 0.046 32 3.6 Pole_occipital 2092 1433 6901 3.198 0.830 0.154 0.054 45 5.0 Pole_temporal 2509 1733 2617 1.815 0.601 0.142 0.034 28 3.6 S_calcarine 3563 2313 4024 2.063 0.518 0.114 0.028 27 4.3 S_central 884 633 1405 2.519 0.350 0.093 0.015 4 0.6 S_cingul-Marginalis 540 361 1062 3.304 0.530 0.099 0.020 2 0.5 S_circular_insula_ant 1410 972 2249 3.007 0.604 0.101 0.022 7 1.3 S_circular_insula_inf 1712 1168 2564 2.765 0.425 0.103 0.021 8 1.6 S_circular_insula_sup 1232 835 2504 3.049 0.830 0.113 0.029 23 1.7 S_collat_transv_ant 635 445 839 2.356 0.344 0.135 0.028 5 0.8 S_collat_transv_post 1843 1271 2832 2.617 0.387 0.111 0.025 16 1.9 S_front_inf 1558 1068 2382 2.471 0.331 0.117 0.024 14 1.5 S_front_middle 2532 1781 4355 2.556 0.410 0.114 0.024 19 2.8 S_front_sup 265 180 385 2.493 0.249 0.114 0.020 2 0.3 S_interm_prim-Jensen 3162 2120 4705 2.520 0.378 0.108 0.019 25 2.5 S_intrapariet&P_trans 1515 1033 2090 2.335 0.456 0.128 0.025 13 1.6 S_oc_middle&Lunatus 1519 1024 2028 2.215 0.386 0.121 0.025 14 1.5 S_oc_sup&transversal 775 538 1243 2.676 0.379 0.127 0.024 11 0.8 S_occipital_ant 1017 718 1785 2.869 0.508 0.119 0.027 7 1.2 S_oc-temp_lat 2438 1716 4184 2.757 0.482 0.112 0.024 17 2.3 S_oc-temp_med&Lingual 391 263 659 2.757 0.444 0.098 0.017 2 0.3 S_orbital_lateral 687 500 1182 2.778 0.715 0.126 0.024 5 0.8 S_orbital_med-olfact 1422 1007 2872 2.877 0.744 0.134 0.036 18 2.2 S_orbital-H_Shaped 2274 1529 3396 2.373 0.397 0.125 0.029 22 2.7 S_parieto_occipital 1627 951 1435 1.998 1.006 0.122 0.025 29 1.5 S_pericallosal 3476 2328 5354 2.498 0.375 0.113 0.023 28 3.3 S_postcentral 1648 1110 3043 2.825 0.373 0.103 0.019 12 1.2 S_precentral-inf-part 1680 1135 2567 2.615 0.397 0.121 0.025 13 1.8 S_precentral-sup-part 785 539 1296 2.671 0.573 0.129 0.026 8 0.9 S_suborbital 1459 1000 2314 2.641 0.345 0.108 0.021 11 1.2 S_subparietal 2337 1623 3588 2.640 0.460 0.109 0.021 16 2.0 S_temporal_inf 5423 3803 9120 2.657 0.462 0.113 0.022 46 5.0 S_temporal_sup 419 303 581 2.332 0.472 0.137 0.023 4 0.5 S_temporal_transverse 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 0050660 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 291096 Total vertex volume 287734 (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) = 1471526 mm^3 (det: 1.323867 ) lhCtxGM: 279280.808 278491.000 diff= 789.8 pctdiff= 0.283 rhCtxGM: 284870.137 284689.000 diff= 181.1 pctdiff= 0.064 lhCtxWM: 233480.686 233866.500 diff= -385.8 pctdiff=-0.165 rhCtxWM: 237715.068 238592.500 diff= -877.4 pctdiff=-0.369 SubCortGMVol 68130.000 SupraTentVol 1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365 SupraTentVolNotVent 1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371 BrainSegVol 1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208 BrainSegVolNotVent 1261243.000 (1260795.700) diff=447.300 pctdiff=0.035 BrainSegVolNotVent 1261243.000 CerebellumVol 157288.000 VentChorVol 16563.000 3rd4th5thCSF 3560.000 CSFVol 898.000, OptChiasmVol 155.000 MaskVol 1664570.000 1009 680 2366 2.981 0.598 0.152 0.039 22 1.6 G&S_frontomargin 1548 1043 3846 2.901 0.561 0.137 0.038 24 2.3 G&S_occipital_inf 1774 1053 2886 2.353 0.545 0.129 0.042 28 3.2 G&S_paracentral 1767 1206 4665 3.215 0.447 0.142 0.039 25 2.8 G&S_subcentral 984 711 3087 3.310 0.596 0.175 0.050 26 1.9 G&S_transv_frontopol 3395 2287 7183 2.897 0.525 0.130 0.032 50 4.5 G&S_cingul-Ant 1307 916 2646 2.823 0.423 0.127 0.026 18 1.3 G&S_cingul-Mid-Ant 1773 1187 3446 2.730 0.424 0.121 0.028 21 2.1 G&S_cingul-Mid-Post 522 364 1703 3.054 0.783 0.152 0.035 9 0.8 G_cingul-Post-dorsal 343 219 1005 3.182 0.881 0.152 0.044 9 0.6 G_cingul-Post-ventral 2135 1339 3016 1.949 0.525 0.146 0.046 34 4.1 G_cuneus 1665 1077 4511 3.102 0.406 0.134 0.041 30 2.5 G_front_inf-Opercular 429 287 1177 2.968 0.608 0.145 0.037 10 0.6 G_front_inf-Orbital 757 513 2084 2.983 0.433 0.143 0.037 16 1.0 G_front_inf-Triangul 4088 2766 10604 2.794 0.569 0.157 0.048 103 8.5 G_front_middle 6641 4254 15793 2.877 0.616 0.140 0.047 365 14.9 G_front_sup 850 570 2131 3.608 0.659 0.140 0.041 14 1.2 G_Ins_lg&S_cent_ins 1064 695 2923 3.282 0.905 0.153 0.053 23 2.1 G_insular_short 2136 1343 5409 3.003 0.472 0.143 0.043 38 3.4 G_occipital_middle 1536 880 2733 2.417 0.623 0.134 0.042 25 2.9 G_occipital_sup 2597 1642 6229 2.944 0.735 0.144 0.048 52 5.0 G_oc-temp_lat-fusifor 2139 1371 3373 2.051 0.632 0.156 0.057 40 4.5 G_oc-temp_med-Lingual 1830 1206 4969 2.981 0.808 0.125 0.047 28 4.0 G_oc-temp_med-Parahip 2699 1811 8158 3.284 0.777 0.154 0.053 69 6.0 G_orbital 4004 2563 10618 3.036 0.522 0.145 0.046 86 7.2 G_pariet_inf-Angular 3596 2412 8867 2.956 0.569 0.140 0.035 59 5.2 G_pariet_inf-Supramar 2682 1773 6030 2.669 0.464 0.139 0.036 49 4.0 G_parietal_sup 3079 1579 4625 2.211 0.573 0.123 0.049 53 7.1 G_postcentral 3894 2100 7223 2.673 0.627 0.121 0.047 58 8.0 G_precentral 2294 1503 5837 2.911 0.571 0.135 0.036 39 3.7 G_precuneus 946 648 2929 2.973 0.817 0.166 0.060 30 2.0 G_rectus 746 423 896 1.872 1.325 0.100 0.049 10 1.2 G_subcallosal 444 264 948 2.842 0.484 0.141 0.035 7 0.6 G_temp_sup-G_T_transv 2087 1407 7303 3.603 0.640 0.148 0.041 42 3.3 G_temp_sup-Lateral 740 516 2136 3.480 0.567 0.094 0.019 4 0.6 G_temp_sup-Plan_polar 1184 805 2639 2.936 0.582 0.114 0.028 11 1.3 G_temp_sup-Plan_tempo 3086 1959 8882 3.154 0.876 0.128 0.044 64 5.9 G_temporal_inf 3617 2459 12155 3.445 0.724 0.140 0.042 74 5.9 G_temporal_middle 542 357 1049 2.712 0.560 0.109 0.024 6 0.5 Lat_Fis-ant-Horizont 204 148 312 2.409 0.512 0.118 0.019 1 0.2 Lat_Fis-ant-Vertical 1591 1077 2465 2.710 0.416 0.118 0.027 14 1.8 Lat_Fis-post 3391 2200 5374 2.112 0.662 0.154 0.055 57 7.3 Pole_occipital 2040 1408 7374 3.391 0.842 0.157 0.060 43 5.1 Pole_temporal 2011 1382 2348 1.987 0.663 0.133 0.036 20 3.0 S_calcarine 3622 2316 3794 1.940 0.609 0.112 0.031 52 4.4 S_central 1626 1116 2788 2.652 0.323 0.118 0.027 14 1.7 S_cingul-Marginalis 628 420 1058 3.129 0.459 0.101 0.021 3 0.5 S_circular_insula_ant 1036 717 1605 2.829 0.526 0.088 0.018 4 0.8 S_circular_insula_inf 1379 928 2280 2.939 0.505 0.103 0.020 6 1.2 S_circular_insula_sup 1353 873 2321 2.777 0.715 0.106 0.038 13 1.9 S_collat_transv_ant 532 367 755 2.279 0.391 0.133 0.041 6 0.9 S_collat_transv_post 1866 1265 3145 2.569 0.356 0.115 0.024 18 1.8 S_front_inf 1878 1304 3016 2.553 0.458 0.126 0.027 14 2.2 S_front_middle 2856 1947 5239 2.622 0.451 0.117 0.025 30 2.8 S_front_sup 263 177 435 2.890 0.345 0.116 0.025 2 0.3 S_interm_prim-Jensen 3702 2476 6157 2.533 0.360 0.106 0.021 32 3.0 S_intrapariet&P_trans 776 520 990 2.321 0.318 0.120 0.030 5 1.0 S_oc_middle&Lunatus 1071 739 1415 2.220 0.481 0.123 0.027 9 1.1 S_oc_sup&transversal 1139 743 1676 2.556 0.410 0.116 0.023 10 1.2 S_occipital_ant 1488 1010 2423 2.650 0.663 0.102 0.023 12 1.6 S_oc-temp_lat 2618 1709 3867 2.476 0.579 0.115 0.037 41 3.6 S_oc-temp_med&Lingual 595 394 1017 2.850 0.644 0.123 0.025 6 0.6 S_orbital_lateral 747 526 1263 2.606 0.593 0.099 0.019 5 0.4 S_orbital_med-olfact 1542 1046 3150 3.014 0.716 0.144 0.044 22 2.9 S_orbital-H_Shaped 2149 1416 3113 2.407 0.478 0.114 0.027 20 2.4 S_parieto_occipital 1493 874 1179 1.808 0.680 0.135 0.025 29 1.4 S_pericallosal 3278 2184 4618 2.461 0.410 0.110 0.021 26 2.8 S_postcentral 1699 1148 2806 2.794 0.354 0.109 0.021 12 1.5 S_precentral-inf-part 2245 1479 3529 2.601 0.384 0.107 0.020 19 1.7 S_precentral-sup-part 417 294 650 2.551 0.478 0.133 0.028 4 0.6 S_suborbital 1043 701 1821 2.822 0.463 0.104 0.019 6 0.8 S_subparietal 1758 1198 2513 2.595 0.471 0.100 0.016 11 1.1 S_temporal_inf 7266 5018 12669 2.821 0.439 0.106 0.019 52 6.2 S_temporal_sup 297 201 488 2.970 0.409 0.111 0.022 2 0.3 S_temporal_transverse PIDs (27443 27446) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Sun Oct 8 00:19:33 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot #----------------------------------------- #@# Cortical Parc 3 rh Sun Oct 8 00:19:34 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot Waiting for PID 27498 of (27498 27501) to complete... Waiting for PID 27501 of (27498 27501) to complete... mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/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 /pasteur/homes/ntraut/bin/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... 1376 labels changed using aseg relabeling using gibbs priors... 000: 2077 changed, 142936 examined... 001: 484 changed, 9606 examined... 002: 118 changed, 2767 examined... 003: 46 changed, 738 examined... 004: 20 changed, 297 examined... 005: 11 changed, 109 examined... 006: 14 changed, 73 examined... 007: 7 changed, 78 examined... 008: 7 changed, 47 examined... 009: 1 changed, 41 examined... 010: 1 changed, 6 examined... 011: 1 changed, 7 examined... 012: 1 changed, 7 examined... 013: 2 changed, 7 examined... 014: 0 changed, 8 examined... 202 labels changed using aseg 000: 55 total segments, 22 labels (183 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... 1020 vertices marked for relabeling... 1020 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 15 seconds. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/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 /pasteur/homes/ntraut/bin/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... 1393 labels changed using aseg relabeling using gibbs priors... 000: 2253 changed, 147238 examined... 001: 564 changed, 10452 examined... 002: 160 changed, 3153 examined... 003: 64 changed, 906 examined... 004: 48 changed, 392 examined... 005: 25 changed, 246 examined... 006: 19 changed, 162 examined... 007: 6 changed, 105 examined... 008: 2 changed, 39 examined... 009: 1 changed, 14 examined... 010: 0 changed, 7 examined... 299 labels changed using aseg 000: 69 total segments, 36 labels (499 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 15 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1127 vertices marked for relabeling... 1127 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 16 seconds. PIDs (27498 27501) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Sun Oct 8 00:19:50 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 lh white #----------------------------------------- #@# Parcellation Stats 3 rh Sun Oct 8 00:19:50 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 rh white Waiting for PID 27552 of (27552 27555) to complete... Waiting for PID 27555 of (27552 27555) to complete... 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 0050660 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 285015 Total vertex volume 282017 (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) = 1471526 mm^3 (det: 1.323867 ) lhCtxGM: 279280.808 278491.000 diff= 789.8 pctdiff= 0.283 rhCtxGM: 284870.137 284689.000 diff= 181.1 pctdiff= 0.064 lhCtxWM: 233480.686 233866.500 diff= -385.8 pctdiff=-0.165 rhCtxWM: 237715.068 238592.500 diff= -877.4 pctdiff=-0.369 SubCortGMVol 68130.000 SupraTentVol 1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365 SupraTentVolNotVent 1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371 BrainSegVol 1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208 BrainSegVolNotVent 1261243.000 (1260795.700) diff=447.300 pctdiff=0.035 BrainSegVolNotVent 1261243.000 CerebellumVol 157288.000 VentChorVol 16563.000 3rd4th5thCSF 3560.000 CSFVol 898.000, OptChiasmVol 155.000 MaskVol 1664570.000 1502 1030 2954 2.818 0.473 0.133 0.022 20 1.3 caudalanteriorcingulate 3711 2455 7864 2.856 0.455 0.126 0.032 43 4.9 caudalmiddlefrontal 3365 2178 5557 2.239 0.631 0.143 0.042 49 5.8 cuneus 677 493 2096 3.180 0.792 0.149 0.051 12 1.5 entorhinal 5013 3430 11805 2.993 0.573 0.138 0.040 92 8.3 fusiform 7377 4908 14956 2.748 0.475 0.122 0.027 107 7.9 inferiorparietal 6382 4378 17671 3.057 0.888 0.139 0.041 119 12.0 inferiortemporal 1998 1318 3805 2.365 1.075 0.124 0.034 31 2.5 isthmuscingulate 8742 5685 16844 2.563 0.625 0.138 0.035 126 12.0 lateraloccipital 4396 2989 10024 2.919 0.832 0.146 0.051 82 10.8 lateralorbitofrontal 4939 3256 7485 2.134 0.636 0.144 0.042 69 8.2 lingual 2472 1655 5887 2.833 0.814 0.142 0.048 60 4.9 medialorbitofrontal 7088 5058 18143 2.909 0.692 0.125 0.029 102 9.1 middletemporal 1371 939 3438 3.039 0.643 0.102 0.033 14 1.6 parahippocampal 2477 1466 4248 2.666 0.513 0.102 0.028 21 3.1 paracentral 2058 1352 4672 2.932 0.463 0.112 0.029 26 2.0 parsopercularis 1095 720 2798 3.059 0.543 0.127 0.043 18 2.1 parsorbitalis 2342 1603 4905 2.715 0.489 0.123 0.029 30 2.8 parstriangularis 1998 1348 1822 1.575 0.394 0.158 0.044 27 3.9 pericalcarine 7724 4978 12879 2.366 0.672 0.122 0.030 92 9.5 postcentral 1929 1259 3543 2.633 0.651 0.134 0.033 31 2.5 posteriorcingulate 8533 4994 14932 2.733 0.560 0.110 0.034 105 12.1 precentral 5403 3679 11369 2.774 0.506 0.124 0.028 74 6.2 precuneus 1771 1144 3808 3.037 0.929 0.131 0.048 36 3.0 rostralanteriorcingulate 6221 4235 13891 2.755 0.528 0.143 0.039 122 10.6 rostralmiddlefrontal 11086 7594 25238 2.853 0.610 0.137 0.036 191 16.6 superiorfrontal 6625 4351 12620 2.562 0.508 0.125 0.028 82 7.2 superiorparietal 7096 4954 16990 2.928 0.630 0.127 0.031 87 9.4 superiortemporal 5478 3641 11311 2.834 0.462 0.129 0.034 79 7.1 supramarginal 752 485 1288 2.375 0.625 0.149 0.058 12 1.7 transversetemporal 3078 2039 7175 3.458 0.724 0.118 0.033 31 4.0 insula 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 0050660 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 291096 Total vertex volume 287734 (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) = 1471526 mm^3 (det: 1.323867 ) lhCtxGM: 279280.808 278491.000 diff= 789.8 pctdiff= 0.283 rhCtxGM: 284870.137 284689.000 diff= 181.1 pctdiff= 0.064 lhCtxWM: 233480.686 233866.500 diff= -385.8 pctdiff=-0.165 rhCtxWM: 237715.068 238592.500 diff= -877.4 pctdiff=-0.369 SubCortGMVol 68130.000 SupraTentVol 1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365 SupraTentVolNotVent 1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371 BrainSegVol 1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208 BrainSegVolNotVent 1261243.000 (1260795.700) diff=447.300 pctdiff=0.035 BrainSegVolNotVent 1261243.000 CerebellumVol 157288.000 VentChorVol 16563.000 3rd4th5thCSF 3560.000 CSFVol 898.000, OptChiasmVol 155.000 MaskVol 1664570.000 1106 752 2110 2.544 0.615 0.157 0.024 27 1.0 caudalanteriorcingulate 3376 2267 6720 2.713 0.425 0.125 0.030 44 3.8 caudalmiddlefrontal 2682 1715 3785 2.061 0.494 0.140 0.041 36 4.6 cuneus 642 449 2074 3.374 0.615 0.125 0.039 6 1.0 entorhinal 5568 3594 11284 2.803 0.699 0.132 0.048 104 10.3 fusiform 8900 5875 18548 2.854 0.484 0.129 0.033 124 11.4 inferiorparietal 6356 4175 15920 2.982 0.867 0.120 0.038 101 10.1 inferiortemporal 1451 925 2709 2.443 0.963 0.128 0.029 24 1.7 isthmuscingulate 7773 5095 14952 2.535 0.611 0.138 0.039 104 12.2 lateraloccipital 4513 3043 11117 3.154 0.787 0.150 0.048 94 8.8 lateralorbitofrontal 3789 2483 5399 2.045 0.601 0.150 0.051 64 7.7 lingual 2647 1720 5882 2.599 1.011 0.134 0.046 52 4.4 medialorbitofrontal 7309 5053 18954 3.137 0.705 0.123 0.031 101 9.2 middletemporal 1446 915 3096 2.776 0.713 0.101 0.033 17 2.3 parahippocampal 3294 2025 5752 2.608 0.522 0.126 0.037 43 5.0 paracentral 2459 1649 5617 2.912 0.424 0.124 0.034 33 3.1 parsopercularis 1130 738 2123 2.619 0.510 0.113 0.027 15 1.2 parsorbitalis 2270 1533 5158 2.832 0.537 0.128 0.031 36 2.6 parstriangularis 2180 1405 2140 1.693 0.445 0.144 0.048 29 4.3 pericalcarine 8673 5287 13646 2.335 0.659 0.119 0.034 107 13.3 postcentral 2169 1418 4251 2.599 0.719 0.131 0.031 32 2.8 posteriorcingulate 9258 5535 15696 2.594 0.638 0.119 0.038 133 14.5 precentral 5324 3523 10782 2.751 0.537 0.118 0.029 61 6.5 precuneus 1115 710 2235 2.865 0.786 0.117 0.027 16 1.3 rostralanteriorcingulate 5793 3927 12192 2.713 0.567 0.143 0.039 103 9.8 rostralmiddlefrontal 13261 8971 29507 2.840 0.580 0.136 0.040 459 23.8 superiorfrontal 6769 4393 12614 2.547 0.476 0.122 0.031 90 8.6 superiorparietal 7702 5260 20233 3.200 0.662 0.121 0.029 94 8.9 superiortemporal 6692 4483 14644 2.856 0.534 0.130 0.034 94 9.4 supramarginal 585 358 1029 2.772 0.459 0.141 0.036 8 0.8 transversetemporal 3296 2234 7567 3.337 0.670 0.125 0.032 39 4.2 insula PIDs (27552 27555) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Sun Oct 8 00:20:30 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts pctsurfcon --s 0050660 --lh-only #----------------------------------------- #@# WM/GM Contrast rh Sun Oct 8 00:20:30 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts pctsurfcon --s 0050660 --rh-only Waiting for PID 27636 of (27636 27648) to complete... Waiting for PID 27648 of (27636 27648) to complete... pctsurfcon --s 0050660 --lh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts/pctsurfcon.log Sun Oct 8 00:20:30 CEST 2017 setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux tars-542 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27636/lh.wm.mgh --regheader 0050660 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 INFO: changing type to float Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 = 77480 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27636/lh.wm.mgh Dim: 142936 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27636/lh.gm.mgh --projfrac 0.3 --regheader 0050660 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 INFO: changing type to float Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/lh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 = 93123 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/lh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27636/lh.gm.mgh Dim: 142936 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27636/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27636/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.w-g.pct.mgh --annot 0050660 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.w-g.pct.mgh --annot 0050660 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/stats/lh.w-g.pct.stats --snr sysname Linux hostname tars-542 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.w-g.pct.mgh Vertex Area is 0.664865 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 pctsurfcon --s 0050660 --rh-only Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts/pctsurfcon.log Sun Oct 8 00:20:30 CEST 2017 setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux tars-542 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27648/rh.wm.mgh --regheader 0050660 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 INFO: changing type to float Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 = 78821 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27648/rh.wm.mgh Dim: 147238 1 1 mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27648/rh.gm.mgh --projfrac 0.3 --regheader 0050660 --cortex srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 INFO: changing type to float Done loading volume Computing registration from header. Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/rh.cortex.label Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Done reading source surface Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 = 95188 Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/rh.cortex.label Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27648/rh.gm.mgh Dim: 147238 1 1 mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27648/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27648/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.w-g.pct.mgh mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.w-g.pct.mgh --annot 0050660 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.w-g.pct.mgh --annot 0050660 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/stats/rh.w-g.pct.stats --snr sysname Linux hostname tars-542 machine x86_64 user ntraut UseRobust 0 Constructing seg from annotation Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.w-g.pct.mgh Vertex Area is 0.657735 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 PIDs (27636 27648) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Sun Oct 8 00:20:36 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 2795 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 3281 voxels changed to hypointensity... 5979 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Sun Oct 8 00:21:00 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660 mri_aparc2aseg --s 0050660 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt #----------------------------------------- #@# AParc-to-ASeg a2009s Sun Oct 8 00:21:00 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660 mri_aparc2aseg --s 0050660 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s #----------------------------------------- #@# AParc-to-ASeg DKTatlas Sun Oct 8 00:21:00 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660 mri_aparc2aseg --s 0050660 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/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 Waiting for PID 27815 of (27815 27818 27821) to complete... Waiting for PID 27818 of (27815 27818 27821) to complete... Waiting for PID 27821 of (27815 27818 27821) to complete... mri_aparc2aseg --s 0050660 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/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: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 subject 0050660 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 7.19 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 107 rescaling Left_Cerebral_Cortex from 61 --> 73 rescaling Left_Lateral_Ventricle from 13 --> 32 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 88 rescaling Left_Cerebellum_Cortex from 60 --> 70 rescaling Left_Thalamus from 94 --> 105 rescaling Left_Thalamus_Proper from 84 --> 93 rescaling Left_Caudate from 75 --> 88 rescaling Left_Putamen from 80 --> 92 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 48 rescaling Fourth_Ventricle from 22 --> 32 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 70 rescaling Left_Amygdala from 56 --> 69 rescaling CSF from 32 --> 70 rescaling Left_Accumbens_area from 62 --> 71 rescaling Left_VentralDC from 87 --> 90 rescaling Right_Cerebral_White_Matter from 105 --> 105 rescaling Right_Cerebral_Cortex from 58 --> 75 rescaling Right_Lateral_Ventricle from 13 --> 28 rescaling Right_Inf_Lat_Vent from 25 --> 29 rescaling Right_Cerebellum_White_Matter from 87 --> 89 rescaling Right_Cerebellum_Cortex from 59 --> 71 rescaling Right_Thalamus_Proper from 85 --> 88 rescaling Right_Caudate from 62 --> 83 rescaling Right_Putamen from 80 --> 86 rescaling Right_Pallidum from 97 --> 103 rescaling Right_Hippocampus from 53 --> 71 rescaling Right_Amygdala from 55 --> 73 rescaling Right_Accumbens_area from 65 --> 82 rescaling Right_VentralDC from 86 --> 95 rescaling Fifth_Ventricle from 40 --> 58 rescaling WM_hypointensities from 78 --> 80 rescaling non_WM_hypointensities from 40 --> 56 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 564001 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 184 changed. pass 2: 15 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/aparc+aseg.mgz mri_aparc2aseg --s 0050660 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/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: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 subject 0050660 outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 7.19 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 107 rescaling Left_Cerebral_Cortex from 61 --> 73 rescaling Left_Lateral_Ventricle from 13 --> 32 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 88 rescaling Left_Cerebellum_Cortex from 60 --> 70 rescaling Left_Thalamus from 94 --> 105 rescaling Left_Thalamus_Proper from 84 --> 93 rescaling Left_Caudate from 75 --> 88 rescaling Left_Putamen from 80 --> 92 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 48 rescaling Fourth_Ventricle from 22 --> 32 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 70 rescaling Left_Amygdala from 56 --> 69 rescaling CSF from 32 --> 70 rescaling Left_Accumbens_area from 62 --> 71 rescaling Left_VentralDC from 87 --> 90 rescaling Right_Cerebral_White_Matter from 105 --> 105 rescaling Right_Cerebral_Cortex from 58 --> 75 rescaling Right_Lateral_Ventricle from 13 --> 28 rescaling Right_Inf_Lat_Vent from 25 --> 29 rescaling Right_Cerebellum_White_Matter from 87 --> 89 rescaling Right_Cerebellum_Cortex from 59 --> 71 rescaling Right_Thalamus_Proper from 85 --> 88 rescaling Right_Caudate from 62 --> 83 rescaling Right_Putamen from 80 --> 86 rescaling Right_Pallidum from 97 --> 103 rescaling Right_Hippocampus from 53 --> 71 rescaling Right_Amygdala from 55 --> 73 rescaling Right_Accumbens_area from 65 --> 82 rescaling Right_VentralDC from 86 --> 95 rescaling Fifth_Ventricle from 40 --> 58 rescaling WM_hypointensities from 78 --> 80 rescaling non_WM_hypointensities from 40 --> 56 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 564054 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 184 changed. pass 2: 15 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/aparc.a2009s+aseg.mgz mri_aparc2aseg --s 0050660 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/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: /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 subject 0050660 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 7.19 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 107 rescaling Left_Cerebral_Cortex from 61 --> 73 rescaling Left_Lateral_Ventricle from 13 --> 32 rescaling Left_Inf_Lat_Vent from 34 --> 33 rescaling Left_Cerebellum_White_Matter from 86 --> 88 rescaling Left_Cerebellum_Cortex from 60 --> 70 rescaling Left_Thalamus from 94 --> 105 rescaling Left_Thalamus_Proper from 84 --> 93 rescaling Left_Caudate from 75 --> 88 rescaling Left_Putamen from 80 --> 92 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 48 rescaling Fourth_Ventricle from 22 --> 32 rescaling Brain_Stem from 81 --> 82 rescaling Left_Hippocampus from 57 --> 70 rescaling Left_Amygdala from 56 --> 69 rescaling CSF from 32 --> 70 rescaling Left_Accumbens_area from 62 --> 71 rescaling Left_VentralDC from 87 --> 90 rescaling Right_Cerebral_White_Matter from 105 --> 105 rescaling Right_Cerebral_Cortex from 58 --> 75 rescaling Right_Lateral_Ventricle from 13 --> 28 rescaling Right_Inf_Lat_Vent from 25 --> 29 rescaling Right_Cerebellum_White_Matter from 87 --> 89 rescaling Right_Cerebellum_Cortex from 59 --> 71 rescaling Right_Thalamus_Proper from 85 --> 88 rescaling Right_Caudate from 62 --> 83 rescaling Right_Putamen from 80 --> 86 rescaling Right_Pallidum from 97 --> 103 rescaling Right_Hippocampus from 53 --> 71 rescaling Right_Amygdala from 55 --> 73 rescaling Right_Accumbens_area from 65 --> 82 rescaling Right_VentralDC from 86 --> 95 rescaling Fifth_Ventricle from 40 --> 58 rescaling WM_hypointensities from 78 --> 80 rescaling non_WM_hypointensities from 40 --> 56 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 564054 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 184 changed. pass 2: 15 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz PIDs (27815 27818 27821) completed and logs appended. #----------------------------------------- #@# APas-to-ASeg Sun Oct 8 00:28:44 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Sun Oct 8 00:28:44 CEST 2017 setenv SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 cd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri /pasteur/homes/ntraut/bin/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 tars-542 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 tars-542 machine x86_64 user ntraut 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 Sun Oct 8 00:28:44 CEST 2017 Ended at Sun Oct 8 00:28:50 CEST 2017 Apas2aseg-Run-Time-Sec 6 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Sun Oct 8 00:28:50 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660 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 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/ASegStatsLUT.txt --subject 0050660 $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 /pasteur/homes/ntraut/bin/freesurfer-6.0.0/ASegStatsLUT.txt --subject 0050660 sysname Linux hostname tars-542 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1471526 mm^3 (det: 1.323867 ) Computing euler number orig.nofix lheno = -164, rheno = -186 orig.nofix lhholes = 83, rhholes = 94 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 279280.808 278491.000 diff= 789.8 pctdiff= 0.283 rhCtxGM: 284870.137 284689.000 diff= 181.1 pctdiff= 0.064 lhCtxWM: 233480.686 233866.500 diff= -385.8 pctdiff=-0.165 rhCtxWM: 237715.068 238592.500 diff= -877.4 pctdiff=-0.369 SubCortGMVol 68130.000 SupraTentVol 1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365 SupraTentVolNotVent 1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371 BrainSegVol 1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208 BrainSegVolNotVent 1261243.000 (1260795.700) diff=447.300 pctdiff=0.035 BrainSegVolNotVent 1261243.000 CerebellumVol 157288.000 VentChorVol 16563.000 3rd4th5thCSF 3560.000 CSFVol 898.000, OptChiasmVol 155.000 MaskVol 1664570.000 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 Sun Oct 8 00:30:34 CEST 2017 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660 mri_aparc2aseg --s 0050660 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 subject 0050660 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/aparc+aseg.mgz Reading lh white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading lh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading rh pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/ribbon.mgz Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 8286 vertices from left hemi Ripped 7732 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/aseg.mgz Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 = 1033055 Used brute-force search on 169 voxels Fixing Parahip LH WM Found 17 clusters 0 k 1.000000 1 k 1.000000 2 k 2.000000 3 k 9.000000 4 k 101.000000 5 k 2.000000 6 k 1.000000 7 k 1.000000 8 k 6.000000 9 k 1.000000 10 k 1.000000 11 k 1.000000 12 k 1.000000 13 k 1720.000000 14 k 42.000000 15 k 2.000000 16 k 10.000000 Fixing Parahip RH WM Found 20 clusters 0 k 1.000000 1 k 1.000000 2 k 4.000000 3 k 5.000000 4 k 1.000000 5 k 7.000000 6 k 1.000000 7 k 122.000000 8 k 4.000000 9 k 4.000000 10 k 44.000000 11 k 1627.000000 12 k 3.000000 13 k 1.000000 14 k 1.000000 15 k 1.000000 16 k 1.000000 17 k 1.000000 18 k 1.000000 19 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 0050660 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/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 0050660 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv sysname Linux hostname tars-542 machine x86_64 user ntraut UseRobust 0 atlas_icv (eTIV) = 1471526 mm^3 (det: 1.323867 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 279280.808 278491.000 diff= 789.8 pctdiff= 0.283 rhCtxGM: 284870.137 284689.000 diff= 181.1 pctdiff= 0.064 lhCtxWM: 233480.686 233866.500 diff= -385.8 pctdiff=-0.165 rhCtxWM: 237715.068 238592.500 diff= -877.4 pctdiff=-0.369 SubCortGMVol 68130.000 SupraTentVol 1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365 SupraTentVolNotVent 1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371 BrainSegVol 1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208 BrainSegVolNotVent 1261243.000 (1260795.700) diff=447.300 pctdiff=0.035 BrainSegVolNotVent 1261243.000 CerebellumVol 157288.000 VentChorVol 16563.000 3rd4th5thCSF 3560.000 CSFVol 898.000, OptChiasmVol 155.000 MaskVol 1664570.000 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label #-------------------------------------------- #@# BA_exvivo Labels lh Sun Oct 8 00:39:15 CEST 2017 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.label --trgsubject 0050660 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.label --trgsubject 0050660 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.label --trgsubject 0050660 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.label --trgsubject 0050660 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.label --trgsubject 0050660 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 28514 of (28514 28520 28526 28531 28537) to complete... Waiting for PID 28520 of (28514 28520 28526 28531 28537) to complete... Waiting for PID 28526 of (28514 28520 28526 28531 28537) to complete... Waiting for PID 28531 of (28514 28520 28526 28531 28537) to complete... Waiting for PID 28537 of (28514 28520 28526 28531 28537) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.label --trgsubject 0050660 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 423 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4552 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.label --trgsubject 0050660 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 797 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8706 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.label --trgsubject 0050660 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 274 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4351 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.label --trgsubject 0050660 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 517 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6500 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.label --trgsubject 0050660 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 947 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6731 mri_label2label: Done PIDs (28514 28520 28526 28531 28537) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.label --trgsubject 0050660 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.label --trgsubject 0050660 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.label --trgsubject 0050660 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.label --trgsubject 0050660 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 28579 of (28579 28585 28591 28596) to complete... Waiting for PID 28585 of (28579 28585 28591 28596) to complete... Waiting for PID 28591 of (28579 28585 28591 28596) to complete... Waiting for PID 28596 of (28579 28585 28591 28596) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.label --trgsubject 0050660 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 514 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4584 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.label --trgsubject 0050660 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 1730 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 15319 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.label --trgsubject 0050660 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 269 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4450 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.label --trgsubject 0050660 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 633 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4055 mri_label2label: Done PIDs (28579 28585 28591 28596) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.label --trgsubject 0050660 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.label --trgsubject 0050660 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.label --trgsubject 0050660 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject 0050660 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject 0050660 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 28671 of (28671 28677 28683 28688 28693) to complete... Waiting for PID 28677 of (28671 28677 28683 28688 28693) to complete... Waiting for PID 28683 of (28671 28677 28683 28688 28693) to complete... Waiting for PID 28688 of (28671 28677 28683 28688 28693) to complete... Waiting for PID 28693 of (28671 28677 28683 28688 28693) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.label --trgsubject 0050660 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 1382 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 6023 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.label --trgsubject 0050660 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 3232 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 11346 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.label --trgsubject 0050660 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 585 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2603 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject 0050660 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 272 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1562 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject 0050660 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 284 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1483 mri_label2label: Done PIDs (28671 28677 28683 28688 28693) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 28738 of (28738 28744 28750 28756 28761) to complete... Waiting for PID 28744 of (28738 28744 28750 28756 28761) to complete... Waiting for PID 28750 of (28738 28744 28750 28756 28761) to complete... Waiting for PID 28756 of (28738 28744 28750 28756 28761) to complete... Waiting for PID 28761 of (28738 28744 28750 28756 28761) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 162 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1176 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 186 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2278 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 72 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1576 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 182 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2178 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 501 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2820 mri_label2label: Done PIDs (28738 28744 28750 28756 28761) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 28808 of (28808 28814 28820 28825) to complete... Waiting for PID 28814 of (28808 28814 28820 28825) to complete... Waiting for PID 28820 of (28808 28814 28820 28825) to complete... Waiting for PID 28825 of (28808 28814 28820 28825) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 148 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1697 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 813 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7848 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 156 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2068 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 256 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1407 mri_label2label: Done PIDs (28808 28814 28820 28825) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 28892 of (28892 28898 28904 28910 28916) to complete... Waiting for PID 28898 of (28892 28898 28904 28910 28916) to complete... Waiting for PID 28904 of (28892 28898 28904 28910 28916) to complete... Waiting for PID 28910 of (28892 28898 28904 28910 28916) to complete... Waiting for PID 28916 of (28892 28898 28904 28910 28916) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 912 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4317 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 1426 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4760 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 143 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 656 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 109 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 579 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject 0050660 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936 Number of reverse mapping hits = 94 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 544 mri_label2label: Done PIDs (28892 28898 28904 28910 28916) completed and logs appended. mris_label2annot --s 0050660 --hemi lh --ctab /pasteur/homes/ntraut/bin/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 /pasteur/homes/ntraut/bin/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label cmdline mris_label2annot --s 0050660 --hemi lh --ctab /pasteur/homes/ntraut/bin/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 tars-542 machine x86_64 user ntraut subject 0050660 hemi lh SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 ColorTable /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 98817 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/lh.BA_exvivo.annot mris_label2annot --s 0050660 --hemi lh --ctab /pasteur/homes/ntraut/bin/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 /pasteur/homes/ntraut/bin/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label cmdline mris_label2annot --s 0050660 --hemi lh --ctab /pasteur/homes/ntraut/bin/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 tars-542 machine x86_64 user ntraut subject 0050660 hemi lh SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 ColorTable /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 116936 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 285015 Total vertex volume 282017 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /pasteur/homes/ntraut/bin/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) = 1471526 mm^3 (det: 1.323867 ) lhCtxGM: 279280.808 278491.000 diff= 789.8 pctdiff= 0.283 rhCtxGM: 284870.137 284689.000 diff= 181.1 pctdiff= 0.064 lhCtxWM: 233480.686 233866.500 diff= -385.8 pctdiff=-0.165 rhCtxWM: 237715.068 238592.500 diff= -877.4 pctdiff=-0.369 SubCortGMVol 68130.000 SupraTentVol 1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365 SupraTentVolNotVent 1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371 BrainSegVol 1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208 BrainSegVolNotVent 1261243.000 (1260795.700) diff=447.300 pctdiff=0.035 BrainSegVolNotVent 1261243.000 CerebellumVol 157288.000 VentChorVol 16563.000 3rd4th5thCSF 3560.000 CSFVol 898.000, OptChiasmVol 155.000 MaskVol 1664570.000 1265 750 2282 2.301 0.560 0.142 0.043 25 2.3 BA1_exvivo 4513 2964 7790 2.543 0.456 0.117 0.025 43 4.6 BA2_exvivo 1093 744 1074 1.896 0.376 0.142 0.036 11 1.6 BA3a_exvivo 2566 1640 4280 2.161 0.740 0.118 0.029 34 2.9 BA3b_exvivo 2072 985 3221 2.761 0.516 0.098 0.040 23 4.0 BA4a_exvivo 1542 897 2096 2.529 0.454 0.103 0.031 10 1.9 BA4p_exvivo 9735 6167 20973 2.892 0.577 0.124 0.034 143 13.5 BA6_exvivo 2129 1394 4685 2.936 0.470 0.114 0.029 27 2.3 BA44_exvivo 2918 1995 6550 2.750 0.505 0.126 0.034 47 4.0 BA45_exvivo 3475 2324 4440 1.781 0.656 0.152 0.045 50 6.5 V1_exvivo 8870 5660 14235 2.235 0.638 0.147 0.044 139 15.7 V2_exvivo 2333 1568 4797 2.788 0.509 0.129 0.025 26 2.7 MT_exvivo 747 506 2146 3.085 0.745 0.115 0.040 10 1.2 perirhinal_exvivo 861 656 3062 3.333 0.719 0.146 0.051 16 1.7 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 0050660 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 285015 Total vertex volume 282017 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /pasteur/homes/ntraut/bin/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) = 1471526 mm^3 (det: 1.323867 ) lhCtxGM: 279280.808 278491.000 diff= 789.8 pctdiff= 0.283 rhCtxGM: 284870.137 284689.000 diff= 181.1 pctdiff= 0.064 lhCtxWM: 233480.686 233866.500 diff= -385.8 pctdiff=-0.165 rhCtxWM: 237715.068 238592.500 diff= -877.4 pctdiff=-0.369 SubCortGMVol 68130.000 SupraTentVol 1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365 SupraTentVolNotVent 1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371 BrainSegVol 1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208 BrainSegVolNotVent 1261243.000 (1260795.700) diff=447.300 pctdiff=0.035 BrainSegVolNotVent 1261243.000 CerebellumVol 157288.000 VentChorVol 16563.000 3rd4th5thCSF 3560.000 CSFVol 898.000, OptChiasmVol 155.000 MaskVol 1664570.000 895 504 1474 2.153 0.545 0.147 0.047 19 1.7 BA1_exvivo 1699 1100 2903 2.461 0.396 0.110 0.025 15 1.5 BA2_exvivo 880 594 819 1.886 0.355 0.143 0.037 9 1.4 BA3a_exvivo 1568 1015 1833 1.742 0.382 0.103 0.021 13 1.4 BA3b_exvivo 2166 1022 3248 2.770 0.503 0.093 0.036 21 3.5 BA4a_exvivo 1213 730 1648 2.484 0.451 0.108 0.034 9 1.6 BA4p_exvivo 5514 3363 11416 2.864 0.581 0.123 0.036 92 8.1 BA6_exvivo 1419 920 3230 2.948 0.430 0.115 0.028 20 1.6 BA44_exvivo 1227 832 3417 2.921 0.530 0.141 0.041 23 1.9 BA45_exvivo 3670 2451 4851 1.817 0.674 0.149 0.044 53 6.6 V1_exvivo 4362 2766 6737 2.166 0.631 0.152 0.048 72 8.5 V2_exvivo 594 388 1355 2.849 0.480 0.132 0.029 8 0.7 MT_exvivo 356 253 1056 3.091 0.721 0.083 0.019 1 0.3 perirhinal_exvivo 437 348 1447 3.415 0.749 0.150 0.050 8 0.8 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Sun Oct 8 00:42:17 CEST 2017 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.label --trgsubject 0050660 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.label --trgsubject 0050660 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.label --trgsubject 0050660 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.label --trgsubject 0050660 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.label --trgsubject 0050660 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 29032 of (29032 29038 29044 29050 29056) to complete... Waiting for PID 29038 of (29032 29038 29044 29050 29056) to complete... Waiting for PID 29044 of (29032 29038 29044 29050 29056) to complete... Waiting for PID 29050 of (29032 29038 29044 29050 29056) to complete... Waiting for PID 29056 of (29032 29038 29044 29050 29056) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.label --trgsubject 0050660 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 826 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4788 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.label --trgsubject 0050660 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 1070 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7757 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.label --trgsubject 0050660 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 317 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4297 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.label --trgsubject 0050660 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 540 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 5062 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.label --trgsubject 0050660 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 1150 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6897 mri_label2label: Done PIDs (29032 29038 29044 29050 29056) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.label --trgsubject 0050660 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.label --trgsubject 0050660 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.label --trgsubject 0050660 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.label --trgsubject 0050660 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 29099 of (29099 29105 29111 29116) to complete... Waiting for PID 29105 of (29099 29105 29111 29116) to complete... Waiting for PID 29111 of (29099 29105 29111 29116) to complete... Waiting for PID 29116 of (29099 29105 29111 29116) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.label --trgsubject 0050660 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 514 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4987 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.label --trgsubject 0050660 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 2175 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 14431 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.label --trgsubject 0050660 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 789 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7701 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.label --trgsubject 0050660 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 1013 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6368 mri_label2label: Done PIDs (29099 29105 29111 29116) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.label --trgsubject 0050660 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.label --trgsubject 0050660 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.label --trgsubject 0050660 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject 0050660 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject 0050660 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 29177 of (29177 29183 29189 29194 29199) to complete... Waiting for PID 29183 of (29177 29183 29189 29194 29199) to complete... Waiting for PID 29189 of (29177 29183 29189 29194 29199) to complete... Waiting for PID 29194 of (29177 29183 29189 29194 29199) to complete... Waiting for PID 29199 of (29177 29183 29189 29194 29199) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.label --trgsubject 0050660 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 1468 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6195 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.label --trgsubject 0050660 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 2056 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10072 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.label --trgsubject 0050660 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 867 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2799 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject 0050660 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 346 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1384 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject 0050660 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 275 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 1027 mri_label2label: Done PIDs (29177 29183 29189 29194 29199) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 29245 of (29245 29251 29257 29263 29269) to complete... Waiting for PID 29251 of (29245 29251 29257 29263 29269) to complete... Waiting for PID 29257 of (29245 29251 29257 29263 29269) to complete... Waiting for PID 29263 of (29245 29251 29257 29263 29269) to complete... Waiting for PID 29269 of (29245 29251 29257 29263 29269) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 353 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 1229 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 358 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 3046 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 104 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1802 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 284 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2467 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 185 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1573 mri_label2label: Done PIDs (29245 29251 29257 29263 29269) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 29315 of (29315 29321 29327 29333) to complete... Waiting for PID 29321 of (29315 29321 29327 29333) to complete... Waiting for PID 29327 of (29315 29321 29327 29333) to complete... Waiting for PID 29333 of (29315 29321 29327 29333) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 210 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1699 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 1543 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 8502 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 196 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1208 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 162 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1340 mri_label2label: Done PIDs (29315 29321 29327 29333) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 29386 of (29386 29392 29398 29404 29410) to complete... Waiting for PID 29392 of (29386 29392 29398 29404 29410) to complete... Waiting for PID 29398 of (29386 29392 29398 29404 29410) to complete... Waiting for PID 29404 of (29386 29392 29398 29404 29410) to complete... Waiting for PID 29410 of (29386 29392 29398 29404 29410) to complete... mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 1052 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4284 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 911 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4348 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 155 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 423 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 234 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 928 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject 0050660 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = 0050660 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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 FREESURFER_HOME /pasteur/homes/ntraut/bin/freesurfer-6.0.0 Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white Reading target registration /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238 Number of reverse mapping hits = 157 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 448 mri_label2label: Done PIDs (29386 29392 29398 29404 29410) completed and logs appended. mris_label2annot --s 0050660 --hemi rh --ctab /pasteur/homes/ntraut/bin/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 /pasteur/homes/ntraut/bin/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label cmdline mris_label2annot --s 0050660 --hemi rh --ctab /pasteur/homes/ntraut/bin/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 tars-542 machine x86_64 user ntraut subject 0050660 hemi rh SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 ColorTable /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 102130 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/rh.BA_exvivo.annot mris_label2annot --s 0050660 --hemi rh --ctab /pasteur/homes/ntraut/bin/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 /pasteur/homes/ntraut/bin/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 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label cmdline mris_label2annot --s 0050660 --hemi rh --ctab /pasteur/homes/ntraut/bin/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 tars-542 machine x86_64 user ntraut subject 0050660 hemi rh SUBJECTS_DIR /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0 ColorTable /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 120851 unhit vertices Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 291096 Total vertex volume 287734 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /pasteur/homes/ntraut/bin/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) = 1471526 mm^3 (det: 1.323867 ) lhCtxGM: 279280.808 278491.000 diff= 789.8 pctdiff= 0.283 rhCtxGM: 284870.137 284689.000 diff= 181.1 pctdiff= 0.064 lhCtxWM: 233480.686 233866.500 diff= -385.8 pctdiff=-0.165 rhCtxWM: 237715.068 238592.500 diff= -877.4 pctdiff=-0.369 SubCortGMVol 68130.000 SupraTentVol 1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365 SupraTentVolNotVent 1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371 BrainSegVol 1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208 BrainSegVolNotVent 1261243.000 (1260795.700) diff=447.300 pctdiff=0.035 BrainSegVolNotVent 1261243.000 CerebellumVol 157288.000 VentChorVol 16563.000 3rd4th5thCSF 3560.000 CSFVol 898.000, OptChiasmVol 155.000 MaskVol 1664570.000 1295 656 1851 2.140 0.662 0.131 0.056 24 3.5 BA1_exvivo 4236 2674 6511 2.440 0.445 0.111 0.028 44 5.4 BA2_exvivo 1257 833 1143 1.827 0.535 0.133 0.033 12 1.6 BA3a_exvivo 2389 1463 3412 2.067 0.647 0.106 0.027 23 2.5 BA3b_exvivo 2039 1065 3079 2.549 0.605 0.107 0.039 22 3.5 BA4a_exvivo 1599 949 1976 2.257 0.667 0.123 0.048 43 3.1 BA4p_exvivo 9632 5999 18875 2.726 0.575 0.125 0.039 377 16.6 BA6_exvivo 3760 2481 8067 2.922 0.468 0.120 0.031 46 4.2 BA44_exvivo 4232 2842 9580 2.810 0.532 0.130 0.034 70 5.5 BA45_exvivo 3796 2441 4857 1.843 0.595 0.147 0.053 59 8.1 V1_exvivo 6973 4552 10646 2.147 0.598 0.146 0.044 102 12.4 V2_exvivo 2577 1654 4990 2.687 0.449 0.127 0.034 33 3.3 MT_exvivo 736 529 2234 3.189 0.669 0.112 0.040 9 1.2 perirhinal_exvivo 587 378 1758 3.004 1.057 0.172 0.085 18 2.3 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 0050660 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz... reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white... reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial... reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 291096 Total vertex volume 287734 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /pasteur/homes/ntraut/bin/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) = 1471526 mm^3 (det: 1.323867 ) lhCtxGM: 279280.808 278491.000 diff= 789.8 pctdiff= 0.283 rhCtxGM: 284870.137 284689.000 diff= 181.1 pctdiff= 0.064 lhCtxWM: 233480.686 233866.500 diff= -385.8 pctdiff=-0.165 rhCtxWM: 237715.068 238592.500 diff= -877.4 pctdiff=-0.369 SubCortGMVol 68130.000 SupraTentVol 1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365 SupraTentVolNotVent 1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371 BrainSegVol 1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208 BrainSegVolNotVent 1261243.000 (1260795.700) diff=447.300 pctdiff=0.035 BrainSegVolNotVent 1261243.000 CerebellumVol 157288.000 VentChorVol 16563.000 3rd4th5thCSF 3560.000 CSFVol 898.000, OptChiasmVol 155.000 MaskVol 1664570.000 1097 483 1181 1.878 0.474 0.122 0.058 21 3.0 BA1_exvivo 2422 1490 3891 2.383 0.398 0.112 0.027 29 3.1 BA2_exvivo 1108 735 941 1.757 0.474 0.136 0.034 11 1.4 BA3a_exvivo 1903 1167 2373 1.917 0.586 0.102 0.025 16 1.9 BA3b_exvivo 1179 620 1675 2.359 0.582 0.120 0.045 16 2.4 BA4a_exvivo 1317 797 1645 2.298 0.711 0.123 0.043 38 2.2 BA4p_exvivo 6771 4097 12802 2.701 0.594 0.124 0.042 342 12.8 BA6_exvivo 982 661 2195 2.849 0.405 0.127 0.040 18 1.3 BA44_exvivo 1032 705 2688 2.927 0.496 0.141 0.040 19 1.6 BA45_exvivo 3614 2325 4451 1.820 0.580 0.147 0.054 56 7.8 V1_exvivo 3678 2457 5500 1.983 0.547 0.154 0.046 59 6.7 V2_exvivo 413 248 812 2.595 0.380 0.123 0.032 5 0.5 MT_exvivo 468 325 1196 3.104 0.647 0.118 0.046 7 1.0 perirhinal_exvivo 403 270 959 2.560 1.001 0.191 0.092 13 1.9 entorhinal_exvivo Started at Sat Oct 7 16:10:09 CEST 2017 Ended at Sun Oct 8 00:45:20 CEST 2017 #@#%# recon-all-run-time-hours 8.586 recon-all -s 0050660 finished without error at Sun Oct 8 00:45:20 CEST 2017