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- Sat Oct 7 16:15:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669
- /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
- -subjid 0050669 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/CMU_b/0050669/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
- subjid 0050669
- 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-385 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: 264648740 256040768 8607972 1734888 0 251338120
- -/+ buffers/cache: 4702648 259946092
- 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: ntraut Machine: tars-385 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: 2017/10/07-14:15:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: ntraut Machine: tars-385 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: 2017/10/07-14:15:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: ntraut Machine: tars-385 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: 2017/10/07-14:15:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: ntraut Machine: tars-385 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: 2017/10/07-14:15:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: ntraut Machine: tars-385 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: 2017/10/07-14:15:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: ntraut Machine: tars-385 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: 2017/10/07-14:15:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: ntraut Machine: tars-385 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: 2017/10/07-14:15:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: ntraut Machine: tars-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:11-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-385 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: 2017/10/07-14:15:12-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-385 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: 2017/10/07-14:15:12-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-385 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: 2017/10/07-14:15:12-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-385 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: 2017/10/07-14:15:12-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-385 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: 2017/10/07-14:15:12-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-385 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-6.0.0/0050669
- mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/CMU_b/0050669/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/orig/001.mgz
- mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/CMU_b/0050669/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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_b/0050669/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-6.0.0/0050669/mri/orig/001.mgz...
- #--------------------------------------------
- #@# MotionCor Sat Oct 7 16:15:14 CEST 2017
- Found 1 runs
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/rawavg.mgz
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669
- mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/orig.mgz --conform
- mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/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-6.0.0/0050669/mri/orig.mgz...
- mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Sat Oct 7 16:15:26 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/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-385 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 16:15:26 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.30635
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30635/nu0.mnc -odt float
- mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.30635/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.30635/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Sat Oct 7 16:15:29 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.30635/nu0.mnc ./tmp.mri_nu_correct.mni.30635/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.30635/0/ -iterations 1000 -distance 50
- [ntraut@tars-385:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/] [2017-10-07 16:15:29] 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.30635/0/ ./tmp.mri_nu_correct.mni.30635/nu0.mnc ./tmp.mri_nu_correct.mni.30635/nu1.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
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- Processing:.................................................................Done
- Processing:.................................................................Done
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- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
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- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
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- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 42
- CV of field change: 0.000979467
-
-
-
- mri_convert ./tmp.mri_nu_correct.mni.30635/nu1.mnc orig_nu.mgz --like orig.mgz --conform
- mri_convert.bin ./tmp.mri_nu_correct.mni.30635/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.30635/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 16:16:38 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 16:16:38 CEST 2017
- Ended at Sat Oct 7 16:17:22 CEST 2017
- talairach_avi done
- cp transforms/talairach.auto.xfm transforms/talairach.xfm
- #--------------------------------------------
- #@# Talairach Failure Detection Sat Oct 7 16:17:24 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7496, pval=0.6675 >= 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-6.0.0/0050669/mri/transforms/talairach_avi.log
- tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/transforms/talairach_avi.log
- TalAviQA: 0.97746
- z-score: 0
- #--------------------------------------------
- #@# Nu Intensity Correction Sat Oct 7 16:17:24 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-6.0.0/0050669/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-385 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 16:17:25 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.31440
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.31440/nu0.mnc -odt float
- mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.31440/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.31440/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Sat Oct 7 16:17:27 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.31440/nu0.mnc ./tmp.mri_nu_correct.mni.31440/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.31440/0/
- [ntraut@tars-385:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/] [2017-10-07 16:17:27] 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.31440/0/ ./tmp.mri_nu_correct.mni.31440/nu0.mnc ./tmp.mri_nu_correct.mni.31440/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
- Number of iterations: 35
- CV of field change: 0.000962069
-
-
- --------------------------------------------------------
- Iteration 2 Sat Oct 7 16:18:13 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.31440/nu1.mnc ./tmp.mri_nu_correct.mni.31440/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.31440/1/
- [ntraut@tars-385:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/] [2017-10-07 16:18:13] 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.31440/1/ ./tmp.mri_nu_correct.mni.31440/nu1.mnc ./tmp.mri_nu_correct.mni.31440/nu2.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 11
- CV of field change: 0.000969084
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.31440/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.31440/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-6.0.0/0050669/mri
- cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.31440/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.31440/ones.mgz
- sysname Linux
- hostname tars-385
- machine x86_64
- user ntraut
- input ./tmp.mri_nu_correct.mni.31440/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.31440/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.31440/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.31440/sum.junk --avgwf ./tmp.mri_nu_correct.mni.31440/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.31440/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.31440/sum.junk --avgwf ./tmp.mri_nu_correct.mni.31440/input.mean.dat
- sysname Linux
- hostname tars-385
- machine x86_64
- user ntraut
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.31440/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.31440/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.31440/ones.mgz --i ./tmp.mri_nu_correct.mni.31440/nu2.mnc --sum ./tmp.mri_nu_correct.mni.31440/sum.junk --avgwf ./tmp.mri_nu_correct.mni.31440/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.31440/ones.mgz --i ./tmp.mri_nu_correct.mni.31440/nu2.mnc --sum ./tmp.mri_nu_correct.mni.31440/sum.junk --avgwf ./tmp.mri_nu_correct.mni.31440/output.mean.dat
- sysname Linux
- hostname tars-385
- machine x86_64
- user ntraut
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.31440/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.31440/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.31440/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.31440/nu2.mnc ./tmp.mri_nu_correct.mni.31440/nu2.mnc mul .88675258821043735474
- Saving result to './tmp.mri_nu_correct.mni.31440/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.31440/nu2.mnc nu.mgz --like orig.mgz
- mri_convert.bin ./tmp.mri_nu_correct.mni.31440/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.31440/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 11 seconds.
- mapping ( 5, 142) to ( 3, 110)
-
-
- Sat Oct 7 16:19:28 CEST 2017
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Sat Oct 7 16:19:29 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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
- 1.06200 -0.00084 0.04552 -3.61380;
- 0.00860 0.97481 0.21911 4.12947;
- -0.07634 -0.20614 1.11086 -27.96796;
- 0.00000 0.00000 0.00000 1.00000;
- processing without aseg, no1d=0
- MRInormInit():
- INFO: Modifying talairach volume c_(r,a,s) based on average_305
- MRInormalize():
- MRIsplineNormalize(): npeaks = 19
- Starting OpenSpline(): npoints = 19
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 110
- white matter peak found at 110
- gm peak at 85 (85), valley at 39 (39)
- csf peak at 43, setting threshold to 71
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 110
- white matter peak found at 110
- gm peak at 83 (83), valley at 40 (40)
- csf peak at 42, setting threshold to 69
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to T1.mgz
- 3D bias adjustment took 2 minutes and 16 seconds.
- #--------------------------------------------
- #@# Skull Stripping Sat Oct 7 16:21:45 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri
- mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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=5.0
- skull bounding box = (46, 29, 0) --> (204, 172, 204)
- using (99, 77, 102) as brain centroid...
- mean wm in atlas = 108, using box (80,59,77) --> (118, 94,127) to find MRI wm
- before smoothing, mri peak at 107
- robust fit to distribution - 106 +- 4.7
- after smoothing, mri peak at 107, scaling input intensities by 1.009
- scaling channel 0 by 1.00935
- initial log_p = -4.621
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.492417 @ (9.091, 27.273, 9.091)
- max log p = -4.407197 @ (-4.545, -4.545, -4.545)
- max log p = -4.334916 @ (-6.818, -2.273, 2.273)
- max log p = -4.334916 @ (0.000, 0.000, 0.000)
- max log p = -4.323277 @ (3.977, -0.568, 2.841)
- max log p = -4.318295 @ (-1.989, 1.989, -3.125)
- Found translation: (-0.3, 21.9, 6.5): log p = -4.318
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.167, old_max_log_p =-4.318 (thresh=-4.3)
- 1.07500 0.00000 0.00000 -9.67105;
- 0.00000 1.11081 0.29764 -22.52648;
- 0.00000 -0.25882 0.96593 41.22679;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.167, old_max_log_p =-4.167 (thresh=-4.2)
- 1.07500 0.00000 0.00000 -9.67105;
- 0.00000 1.11081 0.29764 -22.52648;
- 0.00000 -0.25882 0.96593 41.22679;
- 0.00000 0.00000 0.00000 1.00000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 2 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.105, old_max_log_p =-4.167 (thresh=-4.2)
- 1.03413 0.03798 0.00903 -8.18774;
- -0.03449 1.18177 0.28087 -22.99484;
- 0.00000 -0.23067 1.01172 36.80895;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.088, old_max_log_p =-4.105 (thresh=-4.1)
- 1.03358 0.04550 -0.02408 -5.69154;
- -0.03578 1.22608 0.29140 -29.18869;
- 0.03320 -0.22501 0.99250 32.09047;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.088, old_max_log_p =-4.088 (thresh=-4.1)
- 1.03358 0.04550 -0.02408 -5.69154;
- -0.03578 1.22608 0.29140 -29.18869;
- 0.03320 -0.22501 0.99250 32.09047;
- 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=-4.070, old_max_log_p =-4.088 (thresh=-4.1)
- 1.02973 0.05981 0.00503 -9.42254;
- -0.05288 1.22955 0.29252 -26.66528;
- 0.00780 -0.22543 0.98927 37.00425;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.070, old_max_log_p =-4.070 (thresh=-4.1)
- 1.02973 0.05981 0.00503 -9.42254;
- -0.05294 1.23099 0.29286 -26.86314;
- 0.00781 -0.22569 0.99043 36.91763;
- 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
- 1.02973 0.05981 0.00503 -9.42254;
- -0.05294 1.23099 0.29286 -26.86314;
- 0.00781 -0.22569 0.99043 36.91763;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3243
- Quasinewton: input matrix
- 1.02973 0.05981 0.00503 -9.42254;
- -0.05294 1.23099 0.29286 -26.86314;
- 0.00781 -0.22569 0.99043 36.91763;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.02973 0.05981 0.00503 -9.42254;
- -0.05294 1.23099 0.29286 -26.86314;
- 0.00781 -0.22569 0.99043 36.91763;
- 0.00000 0.00000 0.00000 1.00000;
- pass 1, spacing 8: log(p) = -4.070 (old=-4.621)
- transform before final EM align:
- 1.02973 0.05981 0.00503 -9.42254;
- -0.05294 1.23099 0.29286 -26.86314;
- 0.00781 -0.22569 0.99043 36.91763;
- 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
- 1.02973 0.05981 0.00503 -9.42254;
- -0.05294 1.23099 0.29286 -26.86314;
- 0.00781 -0.22569 0.99043 36.91763;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 364799
- Quasinewton: input matrix
- 1.02973 0.05981 0.00503 -9.42254;
- -0.05294 1.23099 0.29286 -26.86314;
- 0.00781 -0.22569 0.99043 36.91763;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 011: -log(p) = 4.5 tol 0.000000
- final transform:
- 1.02973 0.05981 0.00503 -9.42254;
- -0.05294 1.23099 0.29286 -26.86314;
- 0.00781 -0.22569 0.99043 36.91763;
- 0.00000 0.00000 0.00000 1.00000;
- writing output transformation to transforms/talairach_with_skull.lta...
- mri_em_register utimesec 1328.743000
- mri_em_register stimesec 1.769730
- 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 157569
- mri_em_register ru_majflt 0
- mri_em_register ru_nswap 0
- mri_em_register ru_inblock 148912
- 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 4409
- mri_em_register ru_nivcsw 3775
- registration took 11 minutes and 40 seconds.
- mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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=125 y=99 z=97 r=66
- first estimation of the main basin volume: 1218802 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 16 found in the rest of the brain
- global maximum in x=106, y=80, z=65, Imax=255
- CSF=17, 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=8473992071 voxels, voxel volume =1.000
- = 8473992071 mmm3 = 8473992.192 cm3
- done.
- PostAnalyze...Basin Prior
- 11 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=124,y=103, z=93, r=10154 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=41 , nb = 43965
- RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=13 , nb = -1038412316
- LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=12 , nb = -1039800221
- RIGHT_BRAIN CSF_MIN=0, CSF_intensity=4, CSF_MAX=54 , nb = 1068584228
- LEFT_BRAIN CSF_MIN=0, CSF_intensity=4, CSF_MAX=45 , nb = 1079880414
- OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=10 , nb = 1067203420
- Problem with the least square interpolation in GM_MIN calculation.
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 41, 52, 59, 79
- after analyzing : 41, 56, 59, 61
- RIGHT_CER
- before analyzing : 13, 24, 54, 84
- after analyzing : 13, 44, 54, 54
- LEFT_CER
- before analyzing : 12, 24, 55, 80
- after analyzing : 12, 44, 55, 53
- RIGHT_BRAIN
- before analyzing : 54, 56, 58, 79
- after analyzing : 54, 57, 58, 62
- LEFT_BRAIN
- before analyzing : 45, 54, 59, 79
- after analyzing : 45, 57, 59, 62
- OTHER
- before analyzing : 10, 19, 59, 92
- after analyzing : 10, 45, 59, 56
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...67 iterations
- *********************VALIDATION*********************
- curvature mean = -0.013, std = 0.011
- curvature mean = 69.612, std = 7.533
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 1.74, sigma = 2.93
- after rotation: sse = 1.74, sigma = 2.93
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 1.78, its var is 2.46
- before Erosion-Dilatation 0.11% of inacurate vertices
- after Erosion-Dilatation 0.00% of inacurate vertices
- Validation of the shape of the surface done.
- Scaling of atlas fields onto current surface fields
- ********FINAL ITERATIVE TEMPLATE DEFORMATION********
- Compute Local values csf/gray
- Fine Segmentation...44 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1697615 voxels, voxel volume = 1.000 mm3
- = 1697615 mmm3 = 1697.615 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- mri_watershed utimesec 28.013741
- mri_watershed stimesec 0.416936
- mri_watershed ru_maxrss 822640
- mri_watershed ru_ixrss 0
- mri_watershed ru_idrss 0
- mri_watershed ru_isrss 0
- mri_watershed ru_minflt 212986
- mri_watershed ru_majflt 0
- mri_watershed ru_nswap 0
- mri_watershed ru_inblock 7552
- mri_watershed ru_oublock 2624
- mri_watershed ru_msgsnd 0
- mri_watershed ru_msgrcv 0
- mri_watershed ru_nsignals 0
- mri_watershed ru_nvcsw 2134
- mri_watershed ru_nivcsw 1214
- mri_watershed done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Sat Oct 7 16:33:54 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri
- mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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=22.9
- skull bounding box = (56, 40, 15) --> (191, 170, 184)
- using (101, 83, 100) as brain centroid...
- mean wm in atlas = 107, using box (84,67,79) --> (117, 98,120) to find MRI wm
- before smoothing, mri peak at 106
- robust fit to distribution - 106 +- 4.3
- after smoothing, mri peak at 106, scaling input intensities by 1.009
- scaling channel 0 by 1.00943
- initial log_p = -4.382
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.150100 @ (-9.091, 9.091, 9.091)
- max log p = -3.848802 @ (13.636, 4.545, -4.545)
- max log p = -3.782086 @ (-2.273, 2.273, 2.273)
- max log p = -3.745925 @ (1.136, 1.136, 1.136)
- max log p = -3.745925 @ (0.000, 0.000, 0.000)
- max log p = -3.737440 @ (-1.420, -0.284, 0.852)
- Found translation: (2.0, 16.8, 8.8): log p = -3.737
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.636, old_max_log_p =-3.737 (thresh=-3.7)
- 0.99144 0.14816 0.02206 -14.26666;
- -0.12074 1.04098 0.15500 12.64237;
- 0.00000 -0.11161 0.99651 20.58754;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.636, old_max_log_p =-3.636 (thresh=-3.6)
- 0.99144 0.14816 0.02206 -14.26666;
- -0.12074 1.04098 0.15500 12.64237;
- 0.00000 -0.11161 0.99651 20.58754;
- 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=-3.499, old_max_log_p =-3.636 (thresh=-3.6)
- 1.03451 0.07629 0.03519 -15.29060;
- -0.05559 1.04403 0.28769 -6.75315;
- -0.01781 -0.24225 0.94961 44.41359;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.496, old_max_log_p =-3.499 (thresh=-3.5)
- 1.03215 0.11065 0.04356 -19.27103;
- -0.08879 1.04834 0.25517 0.02460;
- -0.01998 -0.21186 0.97648 39.10121;
- 0.00000 0.00000 0.00000 1.00000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 4 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.462, old_max_log_p =-3.496 (thresh=-3.5)
- 1.03100 0.07790 0.02687 -13.75638;
- -0.05526 1.04660 0.27192 -6.06200;
- -0.01032 -0.22775 0.97017 40.56639;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.459, old_max_log_p =-3.462 (thresh=-3.5)
- 1.02984 0.07967 0.01891 -13.05690;
- -0.05520 1.04537 0.27160 -5.91510;
- -0.00189 -0.22737 0.97149 38.87303;
- 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
- 1.02984 0.07967 0.01891 -13.05690;
- -0.05520 1.04537 0.27160 -5.91510;
- -0.00189 -0.22737 0.97149 38.87303;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2830
- Quasinewton: input matrix
- 1.02984 0.07967 0.01891 -13.05690;
- -0.05520 1.04537 0.27160 -5.91510;
- -0.00189 -0.22737 0.97149 38.87303;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.02984 0.07967 0.01891 -13.05690;
- -0.05520 1.04537 0.27160 -5.91510;
- -0.00189 -0.22737 0.97149 38.87303;
- 0.00000 0.00000 0.00000 1.00000;
- pass 1, spacing 8: log(p) = -3.459 (old=-4.382)
- transform before final EM align:
- 1.02984 0.07967 0.01891 -13.05690;
- -0.05520 1.04537 0.27160 -5.91510;
- -0.00189 -0.22737 0.97149 38.87303;
- 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
- 1.02984 0.07967 0.01891 -13.05690;
- -0.05520 1.04537 0.27160 -5.91510;
- -0.00189 -0.22737 0.97149 38.87303;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 315557
- Quasinewton: input matrix
- 1.02984 0.07967 0.01891 -13.05690;
- -0.05520 1.04537 0.27160 -5.91510;
- -0.00189 -0.22737 0.97149 38.87303;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 010: -log(p) = 4.0 tol 0.000000
- final transform:
- 1.02984 0.07967 0.01891 -13.05690;
- -0.05520 1.04537 0.27160 -5.91510;
- -0.00189 -0.22737 0.97149 38.87303;
- 0.00000 0.00000 0.00000 1.00000;
- writing output transformation to transforms/talairach.lta...
- mri_em_register utimesec 925.958232
- mri_em_register stimesec 1.481774
- 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 158988
- 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 141
- mri_em_register ru_nivcsw 3053
- registration took 8 minutes and 1 seconds.
- #--------------------------------------
- #@# CA Normalize Sat Oct 7 16:41:55 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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=21.9
- skull bounding box = (56, 40, 14) --> (191, 170, 184)
- using (101, 83, 99) as brain centroid...
- mean wm in atlas = 107, using box (84,67,78) --> (117, 98,119) to find MRI wm
- before smoothing, mri peak at 106
- robust fit to distribution - 106 +- 4.3
- 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
- 1.02984 0.07967 0.01891 -13.05690;
- -0.05520 1.04537 0.27160 -5.91510;
- -0.00189 -0.22737 0.97149 38.87303;
- 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 (123, 41, 17) --> (191, 151, 181)
- Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
- 0 of 680 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (62, 40, 16) --> (129, 144, 181)
- Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
- 0 of 610 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (124, 127, 46) --> (170, 169, 99)
- Left_Cerebellum_White_Matter: limiting intensities to 101.0 --> 132.0
- 0 of 10 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (79, 127, 43) --> (124, 164, 100)
- Right_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0
- 0 of 19 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (107, 113, 81) --> (141, 179, 111)
- Brain_Stem: limiting intensities to 106.0 --> 132.0
- 7 of 9 (77.8%) samples deleted
- using 1328 total control points for intensity normalization...
- bias field = 0.970 +- 0.048
- 16 of 1321 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 39915 control points for structure...
- bounding box (123, 41, 17) --> (191, 151, 181)
- Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0
- 0 of 828 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (62, 40, 16) --> (129, 144, 181)
- Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0
- 1 of 1017 (0.1%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (124, 127, 46) --> (170, 169, 99)
- Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 4 of 104 (3.8%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (79, 127, 43) --> (124, 164, 100)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 3 of 78 (3.8%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (107, 113, 81) --> (141, 179, 111)
- Brain_Stem: limiting intensities to 88.0 --> 132.0
- 1 of 85 (1.2%) samples deleted
- using 2112 total control points for intensity normalization...
- bias field = 1.013 +- 0.066
- 6 of 2062 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 39915 control points for structure...
- bounding box (123, 41, 17) --> (191, 151, 181)
- Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0
- 0 of 840 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (62, 40, 16) --> (129, 144, 181)
- Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
- 2 of 1038 (0.2%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (124, 127, 46) --> (170, 169, 99)
- Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 35 of 86 (40.7%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (79, 127, 43) --> (124, 164, 100)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 37 of 71 (52.1%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (107, 113, 81) --> (141, 179, 111)
- Brain_Stem: limiting intensities to 88.0 --> 132.0
- 83 of 195 (42.6%) samples deleted
- using 2230 total control points for intensity normalization...
- bias field = 1.023 +- 0.053
- 10 of 2049 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 1 minutes and 53 seconds.
- #--------------------------------------
- #@# CA Reg Sat Oct 7 16:43:49 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri
- mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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=0.824, neg=0, invalid=762
- 0001: dt=204.530880, rms=0.767 (6.880%), neg=0, invalid=762
- 0002: dt=176.519856, rms=0.751 (2.152%), neg=0, invalid=762
- 0003: dt=221.952000, rms=0.742 (1.123%), neg=0, invalid=762
- 0004: dt=148.173913, rms=0.738 (0.550%), neg=0, invalid=762
- 0005: dt=443.904000, rms=0.733 (0.709%), neg=0, invalid=762
- 0006: dt=110.976000, rms=0.730 (0.388%), neg=0, invalid=762
- 0007: dt=1775.616000, rms=0.721 (1.257%), neg=0, invalid=762
- 0008: dt=110.976000, rms=0.718 (0.379%), neg=0, invalid=762
- 0009: dt=517.888000, rms=0.716 (0.322%), neg=0, invalid=762
- 0010: dt=92.480000, rms=0.715 (0.077%), neg=0, invalid=762
- 0011: dt=92.480000, rms=0.715 (0.017%), neg=0, invalid=762
- 0012: dt=92.480000, rms=0.715 (0.062%), neg=0, invalid=762
- 0013: dt=92.480000, rms=0.714 (0.057%), neg=0, invalid=762
- 0014: dt=92.480000, rms=0.714 (0.088%), neg=0, invalid=762
- 0015: dt=92.480000, rms=0.713 (0.154%), neg=0, invalid=762
- 0016: dt=92.480000, rms=0.712 (0.158%), neg=0, invalid=762
- 0017: dt=92.480000, rms=0.711 (0.102%), neg=0, invalid=762
- 0018: dt=92.480000, rms=0.710 (0.095%), neg=0, invalid=762
- 0019: dt=1183.744000, rms=0.709 (0.105%), neg=0, invalid=762
- 0020: dt=129.472000, rms=0.709 (0.085%), neg=0, invalid=762
- 0021: dt=129.472000, rms=0.709 (0.024%), neg=0, invalid=762
- 0022: dt=129.472000, rms=0.708 (0.043%), neg=0, invalid=762
- 0023: dt=129.472000, rms=0.708 (0.068%), neg=0, invalid=762
- 0024: dt=129.472000, rms=0.708 (0.045%), neg=0, invalid=762
- 0025: dt=129.472000, rms=0.707 (0.084%), neg=0, invalid=762
- 0026: dt=129.472000, rms=0.706 (0.070%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.707, neg=0, invalid=762
- 0027: dt=221.952000, rms=0.702 (0.784%), neg=0, invalid=762
- 0028: dt=129.472000, rms=0.701 (0.060%), neg=0, invalid=762
- 0029: dt=129.472000, rms=0.701 (0.042%), neg=0, invalid=762
- 0030: dt=129.472000, rms=0.700 (0.090%), neg=0, invalid=762
- 0031: dt=129.472000, rms=0.699 (0.113%), neg=0, invalid=762
- 0032: dt=129.472000, rms=0.699 (0.099%), neg=0, invalid=762
- 0033: dt=129.472000, rms=0.698 (0.112%), neg=0, invalid=762
- 0034: dt=129.472000, rms=0.697 (0.091%), neg=0, invalid=762
- 0035: dt=517.888000, rms=0.697 (0.032%), neg=0, invalid=762
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.704, neg=0, invalid=762
- 0036: dt=36.288000, rms=0.703 (0.268%), neg=0, invalid=762
- 0037: dt=145.152000, rms=0.698 (0.657%), neg=0, invalid=762
- 0038: dt=250.200647, rms=0.681 (2.429%), neg=0, invalid=762
- 0039: dt=25.386018, rms=0.678 (0.462%), neg=0, invalid=762
- 0040: dt=9.072000, rms=0.678 (0.015%), neg=0, invalid=762
- 0041: dt=9.072000, rms=0.678 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.678, neg=0, invalid=762
- 0042: dt=155.773585, rms=0.673 (0.818%), neg=0, invalid=762
- 0043: dt=36.288000, rms=0.671 (0.270%), neg=0, invalid=762
- 0044: dt=331.776000, rms=0.666 (0.683%), neg=0, invalid=762
- 0045: dt=36.288000, rms=0.665 (0.291%), neg=0, invalid=762
- 0046: dt=82.944000, rms=0.664 (0.140%), neg=0, invalid=762
- 0047: dt=82.944000, rms=0.662 (0.179%), neg=0, invalid=762
- 0048: dt=82.944000, rms=0.661 (0.257%), neg=0, invalid=762
- 0049: dt=82.944000, rms=0.659 (0.311%), neg=0, invalid=762
- 0050: dt=82.944000, rms=0.656 (0.361%), neg=0, invalid=762
- 0051: dt=82.944000, rms=0.654 (0.418%), neg=0, invalid=762
- 0052: dt=82.944000, rms=0.651 (0.419%), neg=0, invalid=762
- 0053: dt=82.944000, rms=0.648 (0.381%), neg=0, invalid=762
- 0054: dt=82.944000, rms=0.646 (0.321%), neg=0, invalid=762
- 0055: dt=82.944000, rms=0.644 (0.314%), neg=0, invalid=762
- 0056: dt=82.944000, rms=0.642 (0.289%), neg=0, invalid=762
- 0057: dt=82.944000, rms=0.641 (0.281%), neg=0, invalid=762
- 0058: dt=82.944000, rms=0.639 (0.247%), neg=0, invalid=762
- 0059: dt=82.944000, rms=0.638 (0.193%), neg=0, invalid=762
- 0060: dt=82.944000, rms=0.636 (0.200%), neg=0, invalid=762
- 0061: dt=82.944000, rms=0.635 (0.172%), neg=0, invalid=762
- 0062: dt=82.944000, rms=0.634 (0.187%), neg=0, invalid=762
- 0063: dt=82.944000, rms=0.633 (0.162%), neg=0, invalid=762
- 0064: dt=82.944000, rms=0.632 (0.133%), neg=0, invalid=762
- 0065: dt=82.944000, rms=0.632 (0.083%), neg=0, invalid=762
- 0066: dt=82.944000, rms=0.631 (0.124%), neg=0, invalid=762
- 0067: dt=82.944000, rms=0.631 (0.053%), neg=0, invalid=762
- 0068: dt=36.288000, rms=0.630 (0.040%), neg=0, invalid=762
- 0069: dt=36.288000, rms=0.630 (0.008%), neg=0, invalid=762
- 0070: dt=36.288000, rms=0.630 (0.006%), neg=0, invalid=762
- 0071: dt=36.288000, rms=0.630 (0.008%), neg=0, invalid=762
- 0072: dt=36.288000, rms=0.630 (0.021%), neg=0, invalid=762
- 0073: dt=36.288000, rms=0.630 (0.019%), neg=0, invalid=762
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.658, neg=0, invalid=762
- 0074: dt=2.800000, rms=0.657 (0.133%), neg=0, invalid=762
- 0075: dt=2.800000, rms=0.657 (0.013%), neg=0, invalid=762
- 0076: dt=2.800000, rms=0.657 (-0.004%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.658, neg=0, invalid=762
- 0077: dt=2.800000, rms=0.657 (0.117%), neg=0, invalid=762
- 0078: dt=0.700000, rms=0.657 (-0.002%), neg=0, invalid=762
- setting smoothness coefficient to 2.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.733, neg=0, invalid=762
- 0079: dt=6.429967, rms=0.707 (3.429%), neg=0, invalid=762
- 0080: dt=7.987539, rms=0.703 (0.689%), neg=0, invalid=762
- 0081: dt=5.636364, rms=0.702 (0.091%), neg=0, invalid=762
- 0082: dt=5.636364, rms=0.701 (0.095%), neg=0, invalid=762
- 0083: dt=5.636364, rms=0.701 (0.021%), neg=0, invalid=762
- 0084: dt=5.636364, rms=0.701 (-0.173%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.702, neg=0, invalid=762
- 0085: dt=0.000000, rms=0.701 (0.087%), neg=0, invalid=762
- 0086: dt=0.000000, rms=0.701 (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=0.737, neg=0, invalid=762
- 0087: dt=0.000000, rms=0.736 (0.079%), neg=0, invalid=762
- 0088: dt=0.000000, rms=0.736 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.737, neg=0, invalid=762
- 0089: dt=0.000000, rms=0.736 (0.079%), neg=0, invalid=762
- 0090: dt=0.000000, rms=0.736 (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=0.677, neg=0, invalid=762
- 0091: dt=0.714474, rms=0.663 (2.032%), neg=0, invalid=762
- 0092: dt=0.064000, rms=0.663 (0.077%), neg=0, invalid=762
- 0093: dt=0.064000, rms=0.663 (-0.054%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.663, neg=0, invalid=762
- 0094: dt=0.028000, rms=0.663 (0.113%), neg=0, invalid=762
- 0095: dt=0.007000, rms=0.663 (0.001%), neg=0, invalid=762
- 0096: dt=0.007000, rms=0.663 (-0.001%), neg=0, invalid=762
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.10027 (20)
- mri peak = 0.11149 (30)
- Left_Lateral_Ventricle (4): linear fit = 1.78 x + 0.0 (979 voxels, overlap=0.218)
- Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (979 voxels, peak = 36), gca=30.0
- gca peak = 0.15565 (16)
- mri peak = 0.10922 (34)
- Right_Lateral_Ventricle (43): linear fit = 2.07 x + 0.0 (710 voxels, overlap=0.075)
- Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (710 voxels, peak = 33), gca=24.0
- gca peak = 0.26829 (96)
- mri peak = 0.11759 (97)
- Right_Pallidum (52): linear fit = 1.05 x + 0.0 (992 voxels, overlap=0.986)
- Right_Pallidum (52): linear fit = 1.05 x + 0.0 (992 voxels, peak = 101), gca=101.3
- gca peak = 0.20183 (93)
- mri peak = 0.08305 (98)
- Left_Pallidum (13): linear fit = 1.04 x + 0.0 (860 voxels, overlap=1.006)
- Left_Pallidum (13): linear fit = 1.04 x + 0.0 (860 voxels, peak = 97), gca=97.2
- gca peak = 0.21683 (55)
- mri peak = 0.07860 (74)
- Right_Hippocampus (53): linear fit = 1.29 x + 0.0 (1086 voxels, overlap=0.014)
- Right_Hippocampus (53): linear fit = 1.29 x + 0.0 (1086 voxels, peak = 71), gca=71.2
- gca peak = 0.30730 (58)
- mri peak = 0.09186 (75)
- Left_Hippocampus (17): linear fit = 1.28 x + 0.0 (952 voxels, overlap=0.015)
- Left_Hippocampus (17): linear fit = 1.28 x + 0.0 (952 voxels, peak = 75), gca=74.5
- gca peak = 0.11430 (101)
- mri peak = 0.10645 (104)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (74703 voxels, overlap=0.687)
- Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (74703 voxels, peak = 105), gca=104.5
- gca peak = 0.12076 (102)
- mri peak = 0.09844 (106)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (75845 voxels, overlap=0.656)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (75845 voxels, peak = 107), gca=106.6
- gca peak = 0.14995 (59)
- mri peak = 0.04216 (78)
- Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (30225 voxels, overlap=0.000)
- Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (30225 voxels, peak = 79), gca=79.4
- gca peak = 0.15082 (58)
- mri peak = 0.04902 (78)
- Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (35001 voxels, overlap=0.000)
- Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (35001 voxels, peak = 77), gca=76.9
- gca peak = 0.14161 (67)
- mri peak = 0.11747 (84)
- Right_Caudate (50): linear fit = 1.25 x + 0.0 (682 voxels, overlap=0.012)
- Right_Caudate (50): linear fit = 1.25 x + 0.0 (682 voxels, peak = 83), gca=83.4
- gca peak = 0.15243 (71)
- mri peak = 0.10752 (88)
- Left_Caudate (11): linear fit = 1.21 x + 0.0 (1186 voxels, overlap=0.010)
- Left_Caudate (11): linear fit = 1.21 x + 0.0 (1186 voxels, peak = 86), gca=85.6
- gca peak = 0.13336 (57)
- mri peak = 0.04397 (74)
- Left_Cerebellum_Cortex (8): linear fit = 1.35 x + 0.0 (20811 voxels, overlap=0.001)
- Left_Cerebellum_Cortex (8): linear fit = 1.35 x + 0.0 (20811 voxels, peak = 77), gca=76.7
- gca peak = 0.13252 (56)
- mri peak = 0.04593 (74)
- Right_Cerebellum_Cortex (47): linear fit = 1.35 x + 0.0 (25125 voxels, overlap=0.001)
- Right_Cerebellum_Cortex (47): linear fit = 1.35 x + 0.0 (25125 voxels, peak = 75), gca=75.3
- gca peak = 0.18181 (84)
- mri peak = 0.07578 (89)
- Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (9271 voxels, overlap=0.826)
- Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (9271 voxels, peak = 89), gca=89.5
- gca peak = 0.20573 (83)
- mri peak = 0.06191 (88)
- Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (7362 voxels, overlap=0.990)
- Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (7362 voxels, peak = 88), gca=87.6
- gca peak = 0.21969 (57)
- mri peak = 0.08602 (74)
- Left_Amygdala (18): linear fit = 1.27 x + 0.0 (462 voxels, overlap=0.049)
- Left_Amygdala (18): linear fit = 1.27 x + 0.0 (462 voxels, peak = 73), gca=72.7
- gca peak = 0.39313 (56)
- mri peak = 0.10811 (72)
- Right_Amygdala (54): linear fit = 1.27 x + 0.0 (524 voxels, overlap=0.032)
- Right_Amygdala (54): linear fit = 1.27 x + 0.0 (524 voxels, peak = 71), gca=71.4
- gca peak = 0.14181 (85)
- mri peak = 0.08629 (97)
- Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (6003 voxels, overlap=0.339)
- Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (6003 voxels, peak = 96), gca=96.5
- gca peak = 0.11978 (83)
- mri peak = 0.09187 (93)
- Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4945 voxels, overlap=0.247)
- Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4945 voxels, peak = 93), gca=92.5
- gca peak = 0.13399 (79)
- mri peak = 0.06469 (94)
- Left_Putamen (12): linear fit = 1.17 x + 0.0 (2749 voxels, overlap=0.068)
- Left_Putamen (12): linear fit = 1.17 x + 0.0 (2749 voxels, peak = 93), gca=92.8
- gca peak = 0.14159 (79)
- mri peak = 0.08126 (93)
- Right_Putamen (51): linear fit = 1.18 x + 0.0 (2731 voxels, overlap=0.048)
- Right_Putamen (51): linear fit = 1.18 x + 0.0 (2731 voxels, peak = 94), gca=93.6
- gca peak = 0.10025 (80)
- mri peak = 0.09365 (86)
- Brain_Stem (16): linear fit = 1.11 x + 0.0 (12312 voxels, overlap=0.402)
- Brain_Stem (16): linear fit = 1.11 x + 0.0 (12312 voxels, peak = 88), gca=88.4
- gca peak = 0.13281 (86)
- mri peak = 0.07563 (94)
- Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1311 voxels, overlap=0.462)
- Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1311 voxels, peak = 93), gca=93.3
- gca peak = 0.12801 (89)
- mri peak = 0.08498 (98)
- Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1600 voxels, overlap=0.621)
- Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1600 voxels, peak = 97), gca=96.6
- gca peak = 0.20494 (23)
- uniform distribution in MR - rejecting arbitrary fit
- gca peak = 0.15061 (21)
- mri peak = 0.10112 (33)
- Fourth_Ventricle (15): linear fit = 1.86 x + 0.0 (517 voxels, overlap=0.217)
- Fourth_Ventricle (15): linear fit = 1.86 x + 0.0 (517 voxels, peak = 39), gca=39.0
- gca peak Unknown = 0.94835 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.18056 (32)
- gca peak Left_Thalamus = 0.64095 (94)
- gca peak Third_Ventricle = 0.20494 (23)
- gca peak Fourth_Ventricle = 0.15061 (21)
- gca peak CSF = 0.20999 (34)
- gca peak Left_Accumbens_area = 0.39030 (62)
- gca peak Left_undetermined = 0.95280 (25)
- gca peak Left_vessel = 0.67734 (53)
- gca peak Left_choroid_plexus = 0.09433 (44)
- gca peak Right_Inf_Lat_Vent = 0.23544 (26)
- gca peak Right_Accumbens_area = 0.30312 (64)
- gca peak Right_vessel = 0.46315 (51)
- gca peak Right_choroid_plexus = 0.14086 (44)
- gca peak Fifth_Ventricle = 0.51669 (36)
- gca peak WM_hypointensities = 0.09722 (76)
- gca peak non_WM_hypointensities = 0.11899 (47)
- gca peak Optic_Chiasm = 0.39033 (72)
- label assignment complete, 0 changed (0.00%)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.30 x + 0.0
- estimating mean wm scale to be 1.04 x + 0.0
- estimating mean csf scale to be 1.50 x + 0.0
- saving intensity scales to talairach.label_intensities.txt
- **************** pass 1 of 1 ************************
- enabling zero nodes
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.652, neg=0, invalid=762
- 0097: dt=86.370173, rms=0.625 (4.183%), neg=0, invalid=762
- 0098: dt=110.976000, rms=0.623 (0.310%), neg=0, invalid=762
- 0099: dt=221.952000, rms=0.621 (0.353%), neg=0, invalid=762
- 0100: dt=517.888000, rms=0.617 (0.611%), neg=0, invalid=762
- 0101: dt=369.920000, rms=0.615 (0.273%), neg=0, invalid=762
- 0102: dt=110.976000, rms=0.614 (0.101%), neg=0, invalid=762
- 0103: dt=1183.744000, rms=0.610 (0.660%), neg=0, invalid=762
- 0104: dt=32.368000, rms=0.610 (0.066%), neg=0, invalid=762
- 0105: dt=32.368000, rms=0.610 (0.015%), neg=0, invalid=762
- 0106: dt=32.368000, rms=0.610 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.610, neg=0, invalid=762
- 0107: dt=295.936000, rms=0.608 (0.385%), neg=0, invalid=762
- 0108: dt=110.976000, rms=0.607 (0.120%), neg=0, invalid=762
- 0109: dt=1183.744000, rms=0.606 (0.244%), neg=0, invalid=762
- 0110: dt=129.472000, rms=0.604 (0.209%), neg=0, invalid=762
- 0111: dt=129.472000, rms=0.604 (0.021%), neg=0, invalid=762
- 0112: dt=129.472000, rms=0.604 (0.018%), neg=0, invalid=762
- 0113: dt=129.472000, rms=0.604 (0.036%), neg=0, invalid=762
- 0114: dt=129.472000, rms=0.604 (0.054%), neg=0, invalid=762
- 0115: dt=129.472000, rms=0.603 (0.069%), neg=0, invalid=762
- 0116: dt=129.472000, rms=0.603 (0.086%), neg=0, invalid=762
- 0117: dt=129.472000, rms=0.602 (0.093%), neg=0, invalid=762
- 0118: dt=129.472000, rms=0.601 (0.097%), neg=0, invalid=762
- 0119: dt=129.472000, rms=0.601 (0.089%), neg=0, invalid=762
- 0120: dt=129.472000, rms=0.600 (0.086%), neg=0, invalid=762
- 0121: dt=129.472000, rms=0.600 (0.085%), neg=0, invalid=762
- 0122: dt=129.472000, rms=0.599 (0.080%), neg=0, invalid=762
- 0123: dt=129.472000, rms=0.599 (0.074%), neg=0, invalid=762
- 0124: dt=129.472000, rms=0.599 (0.069%), neg=0, invalid=762
- 0125: dt=129.472000, rms=0.598 (0.066%), neg=0, invalid=762
- 0126: dt=129.472000, rms=0.598 (0.067%), neg=0, invalid=762
- 0127: dt=129.472000, rms=0.597 (0.067%), neg=0, invalid=762
- 0128: dt=129.472000, rms=0.597 (0.060%), neg=0, invalid=762
- 0129: dt=129.472000, rms=0.597 (0.057%), neg=0, invalid=762
- 0130: dt=129.472000, rms=0.596 (0.056%), neg=0, invalid=762
- 0131: dt=129.472000, rms=0.596 (0.057%), neg=0, invalid=762
- 0132: dt=129.472000, rms=0.596 (0.052%), neg=0, invalid=762
- 0133: dt=129.472000, rms=0.595 (0.049%), neg=0, invalid=762
- 0134: dt=129.472000, rms=0.595 (0.039%), neg=0, invalid=762
- 0135: dt=129.472000, rms=0.595 (0.039%), neg=0, invalid=762
- 0136: dt=129.472000, rms=0.595 (0.051%), neg=0, invalid=762
- 0137: dt=129.472000, rms=0.594 (0.047%), neg=0, invalid=762
- 0138: dt=129.472000, rms=0.594 (0.044%), neg=0, invalid=762
- 0139: dt=129.472000, rms=0.594 (0.042%), neg=0, invalid=762
- 0140: dt=129.472000, rms=0.594 (0.037%), neg=0, invalid=762
- 0141: dt=129.472000, rms=0.593 (0.033%), neg=0, invalid=762
- 0142: dt=129.472000, rms=0.593 (0.034%), neg=0, invalid=762
- 0143: dt=129.472000, rms=0.593 (0.034%), neg=0, invalid=762
- 0144: dt=129.472000, rms=0.593 (0.034%), neg=0, invalid=762
- 0145: dt=129.472000, rms=0.593 (0.033%), neg=0, invalid=762
- 0146: dt=129.472000, rms=0.592 (0.034%), neg=0, invalid=762
- 0147: dt=129.472000, rms=0.592 (0.032%), neg=0, invalid=762
- 0148: dt=129.472000, rms=0.592 (0.028%), neg=0, invalid=762
- 0149: dt=129.472000, rms=0.592 (0.026%), neg=0, invalid=762
- 0150: dt=129.472000, rms=0.592 (0.028%), neg=0, invalid=762
- 0151: dt=129.472000, rms=0.592 (0.028%), neg=0, invalid=762
- 0152: dt=129.472000, rms=0.591 (0.028%), neg=0, invalid=762
- 0153: dt=129.472000, rms=0.591 (0.023%), neg=0, invalid=762
- 0154: dt=129.472000, rms=0.591 (0.021%), neg=0, invalid=762
- 0155: dt=517.888000, rms=0.591 (0.010%), neg=0, invalid=762
- 0156: dt=517.888000, rms=0.591 (-0.059%), neg=0, invalid=762
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.592, neg=0, invalid=762
- 0157: dt=25.920000, rms=0.592 (0.063%), neg=0, invalid=762
- 0158: dt=36.288000, rms=0.591 (0.037%), neg=0, invalid=762
- 0159: dt=36.288000, rms=0.591 (0.061%), neg=0, invalid=762
- 0160: dt=36.288000, rms=0.590 (0.102%), neg=0, invalid=762
- 0161: dt=36.288000, rms=0.590 (0.152%), neg=0, invalid=762
- 0162: dt=36.288000, rms=0.588 (0.224%), neg=0, invalid=762
- 0163: dt=36.288000, rms=0.586 (0.303%), neg=0, invalid=762
- 0164: dt=36.288000, rms=0.584 (0.387%), neg=0, invalid=762
- 0165: dt=36.288000, rms=0.582 (0.404%), neg=0, invalid=762
- 0166: dt=36.288000, rms=0.580 (0.365%), neg=0, invalid=762
- 0167: dt=36.288000, rms=0.578 (0.337%), neg=0, invalid=762
- 0168: dt=36.288000, rms=0.576 (0.290%), neg=0, invalid=762
- 0169: dt=36.288000, rms=0.576 (0.078%), neg=0, invalid=762
- 0170: dt=36.288000, rms=0.575 (0.127%), neg=0, invalid=762
- 0171: dt=36.288000, rms=0.574 (0.163%), neg=0, invalid=762
- 0172: dt=36.288000, rms=0.573 (0.194%), neg=0, invalid=762
- 0173: dt=36.288000, rms=0.572 (0.224%), neg=0, invalid=762
- 0174: dt=9.072000, rms=0.571 (0.012%), neg=0, invalid=762
- 0175: dt=2.268000, rms=0.571 (0.002%), neg=0, invalid=762
- 0176: dt=0.405000, rms=0.571 (0.000%), neg=0, invalid=762
- 0177: dt=0.050625, rms=0.571 (0.000%), neg=0, invalid=762
- 0178: dt=0.012656, rms=0.571 (0.000%), neg=0, invalid=762
- 0179: dt=0.003164, rms=0.571 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.572, neg=0, invalid=762
- 0180: dt=145.152000, rms=0.566 (0.930%), neg=0, invalid=762
- 0181: dt=62.208000, rms=0.566 (0.077%), neg=0, invalid=762
- 0182: dt=580.608000, rms=0.562 (0.696%), neg=0, invalid=762
- 0183: dt=36.288000, rms=0.561 (0.171%), neg=0, invalid=762
- 0184: dt=82.944000, rms=0.561 (0.053%), neg=0, invalid=762
- 0185: dt=145.152000, rms=0.560 (0.180%), neg=0, invalid=762
- 0186: dt=25.920000, rms=0.560 (0.021%), neg=0, invalid=762
- 0187: dt=25.920000, rms=0.560 (0.008%), neg=0, invalid=762
- 0188: dt=25.920000, rms=0.560 (0.011%), neg=0, invalid=762
- 0189: dt=25.920000, rms=0.559 (0.027%), neg=0, invalid=762
- 0190: dt=25.920000, rms=0.559 (0.061%), neg=0, invalid=762
- 0191: dt=25.920000, rms=0.559 (0.088%), neg=0, invalid=762
- 0192: dt=25.920000, rms=0.558 (0.103%), neg=0, invalid=762
- 0193: dt=25.920000, rms=0.558 (0.099%), neg=0, invalid=762
- 0194: dt=25.920000, rms=0.557 (0.098%), neg=0, invalid=762
- 0195: dt=25.920000, rms=0.556 (0.089%), neg=0, invalid=762
- 0196: dt=25.920000, rms=0.556 (0.085%), neg=0, invalid=762
- 0197: dt=25.920000, rms=0.555 (0.089%), neg=0, invalid=762
- 0198: dt=25.920000, rms=0.555 (0.099%), neg=0, invalid=762
- 0199: dt=25.920000, rms=0.554 (0.110%), neg=0, invalid=762
- 0200: dt=25.920000, rms=0.554 (0.111%), neg=0, invalid=762
- 0201: dt=25.920000, rms=0.553 (0.101%), neg=0, invalid=762
- 0202: dt=25.920000, rms=0.553 (0.095%), neg=0, invalid=762
- 0203: dt=25.920000, rms=0.552 (0.081%), neg=0, invalid=762
- 0204: dt=25.920000, rms=0.552 (0.077%), neg=0, invalid=762
- 0205: dt=25.920000, rms=0.551 (0.080%), neg=0, invalid=762
- 0206: dt=25.920000, rms=0.551 (0.087%), neg=0, invalid=762
- 0207: dt=25.920000, rms=0.550 (0.083%), neg=0, invalid=762
- 0208: dt=25.920000, rms=0.550 (0.085%), neg=0, invalid=762
- 0209: dt=25.920000, rms=0.549 (0.079%), neg=0, invalid=762
- 0210: dt=25.920000, rms=0.549 (0.068%), neg=0, invalid=762
- 0211: dt=25.920000, rms=0.549 (0.063%), neg=0, invalid=762
- 0212: dt=25.920000, rms=0.548 (0.059%), neg=0, invalid=762
- 0213: dt=25.920000, rms=0.548 (0.065%), neg=0, invalid=762
- 0214: dt=25.920000, rms=0.548 (0.070%), neg=0, invalid=762
- 0215: dt=25.920000, rms=0.547 (0.071%), neg=0, invalid=762
- 0216: dt=25.920000, rms=0.547 (0.068%), neg=0, invalid=762
- 0217: dt=25.920000, rms=0.547 (0.064%), neg=0, invalid=762
- 0218: dt=25.920000, rms=0.546 (0.053%), neg=0, invalid=762
- 0219: dt=25.920000, rms=0.546 (0.051%), neg=0, invalid=762
- 0220: dt=25.920000, rms=0.546 (0.046%), neg=0, invalid=762
- 0221: dt=25.920000, rms=0.546 (0.048%), neg=0, invalid=762
- 0222: dt=25.920000, rms=0.545 (0.046%), neg=0, invalid=762
- 0223: dt=25.920000, rms=0.545 (0.048%), neg=0, invalid=762
- 0224: dt=25.920000, rms=0.545 (0.047%), neg=0, invalid=762
- 0225: dt=25.920000, rms=0.545 (0.043%), neg=0, invalid=762
- 0226: dt=25.920000, rms=0.544 (0.044%), neg=0, invalid=762
- 0227: dt=25.920000, rms=0.544 (0.041%), neg=0, invalid=762
- 0228: dt=25.920000, rms=0.544 (0.043%), neg=0, invalid=762
- 0229: dt=25.920000, rms=0.544 (0.043%), neg=0, invalid=762
- 0230: dt=25.920000, rms=0.543 (0.038%), neg=0, invalid=762
- 0231: dt=25.920000, rms=0.543 (0.041%), neg=0, invalid=762
- 0232: dt=25.920000, rms=0.543 (0.036%), neg=0, invalid=762
- 0233: dt=25.920000, rms=0.543 (0.033%), neg=0, invalid=762
- 0234: dt=25.920000, rms=0.543 (0.034%), neg=0, invalid=762
- 0235: dt=25.920000, rms=0.542 (0.039%), neg=0, invalid=762
- 0236: dt=25.920000, rms=0.542 (0.038%), neg=0, invalid=762
- 0237: dt=25.920000, rms=0.542 (0.034%), neg=0, invalid=762
- 0238: dt=25.920000, rms=0.542 (0.031%), neg=0, invalid=762
- 0239: dt=25.920000, rms=0.542 (0.034%), neg=0, invalid=762
- 0240: dt=25.920000, rms=0.541 (0.030%), neg=0, invalid=762
- 0241: dt=25.920000, rms=0.541 (0.029%), neg=0, invalid=762
- 0242: dt=25.920000, rms=0.541 (0.031%), neg=0, invalid=762
- 0243: dt=25.920000, rms=0.541 (0.030%), neg=0, invalid=762
- 0244: dt=25.920000, rms=0.541 (0.029%), neg=0, invalid=762
- 0245: dt=25.920000, rms=0.541 (0.029%), neg=0, invalid=762
- 0246: dt=25.920000, rms=0.541 (0.024%), neg=0, invalid=762
- 0247: dt=25.920000, rms=0.540 (0.027%), neg=0, invalid=762
- 0248: dt=25.920000, rms=0.540 (0.028%), neg=0, invalid=762
- 0249: dt=25.920000, rms=0.540 (0.027%), neg=0, invalid=762
- 0250: dt=25.920000, rms=0.540 (0.028%), neg=0, invalid=762
- 0251: dt=25.920000, rms=0.540 (0.025%), neg=0, invalid=762
- 0252: dt=25.920000, rms=0.540 (0.027%), neg=0, invalid=762
- 0253: dt=25.920000, rms=0.540 (0.025%), neg=0, invalid=762
- 0254: dt=25.920000, rms=0.539 (0.023%), neg=0, invalid=762
- 0255: dt=25.920000, rms=0.539 (0.025%), neg=0, invalid=762
- 0256: dt=25.920000, rms=0.539 (0.021%), neg=0, invalid=762
- 0257: dt=25.920000, rms=0.539 (0.020%), neg=0, invalid=762
- 0258: dt=124.416000, rms=0.539 (0.005%), neg=0, invalid=762
- 0259: dt=124.416000, rms=0.539 (0.011%), neg=0, invalid=762
- 0260: dt=124.416000, rms=0.539 (0.015%), neg=0, invalid=762
- 0261: dt=124.416000, rms=0.539 (0.022%), neg=0, invalid=762
- 0262: dt=124.416000, rms=0.539 (0.021%), neg=0, invalid=762
- 0263: dt=124.416000, rms=0.538 (0.036%), neg=0, invalid=762
- 0264: dt=124.416000, rms=0.538 (0.047%), neg=0, invalid=762
- 0265: dt=124.416000, rms=0.538 (0.046%), neg=0, invalid=762
- 0266: dt=124.416000, rms=0.538 (0.035%), neg=0, invalid=762
- 0267: dt=124.416000, rms=0.537 (0.059%), neg=0, invalid=762
- 0268: dt=124.416000, rms=0.537 (0.040%), neg=0, invalid=762
- 0269: dt=124.416000, rms=0.537 (0.046%), neg=0, invalid=762
- 0270: dt=124.416000, rms=0.537 (0.063%), neg=0, invalid=762
- 0271: dt=124.416000, rms=0.536 (0.055%), neg=0, invalid=762
- 0272: dt=124.416000, rms=0.536 (0.076%), neg=0, invalid=762
- 0273: dt=124.416000, rms=0.536 (0.046%), neg=0, invalid=762
- 0274: dt=124.416000, rms=0.536 (0.028%), neg=0, invalid=762
- 0275: dt=124.416000, rms=0.535 (0.093%), neg=0, invalid=762
- 0276: dt=124.416000, rms=0.535 (0.028%), neg=0, invalid=762
- 0277: dt=124.416000, rms=0.535 (0.059%), neg=0, invalid=762
- 0278: dt=124.416000, rms=0.534 (0.100%), neg=0, invalid=762
- 0279: dt=124.416000, rms=0.534 (0.018%), neg=0, invalid=762
- 0280: dt=124.416000, rms=0.534 (0.064%), neg=0, invalid=762
- 0281: dt=124.416000, rms=0.533 (0.043%), neg=0, invalid=762
- 0282: dt=124.416000, rms=0.533 (0.061%), neg=0, invalid=762
- 0283: dt=124.416000, rms=0.533 (0.071%), neg=0, invalid=762
- 0284: dt=124.416000, rms=0.533 (-0.019%), neg=0, invalid=762
- 0285: dt=20.736000, rms=0.533 (0.002%), neg=0, invalid=762
- 0286: dt=9.072000, rms=0.533 (0.002%), neg=0, invalid=762
- 0287: dt=36.288000, rms=0.533 (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=0.541, neg=0, invalid=762
- 0288: dt=8.000000, rms=0.540 (0.094%), neg=0, invalid=762
- 0289: dt=6.400000, rms=0.540 (0.011%), neg=0, invalid=762
- 0290: dt=6.400000, rms=0.540 (0.005%), neg=0, invalid=762
- 0291: dt=6.400000, rms=0.540 (-0.019%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.540, neg=0, invalid=762
- 0292: dt=85.968727, rms=0.536 (0.878%), neg=0, invalid=762
- 0293: dt=25.600000, rms=0.534 (0.218%), neg=0, invalid=762
- 0294: dt=102.400000, rms=0.532 (0.441%), neg=0, invalid=762
- 0295: dt=23.627907, rms=0.531 (0.271%), neg=0, invalid=762
- 0296: dt=87.561358, rms=0.528 (0.407%), neg=0, invalid=762
- 0297: dt=11.200000, rms=0.528 (0.167%), neg=0, invalid=762
- 0298: dt=32.000000, rms=0.527 (0.096%), neg=0, invalid=762
- 0299: dt=44.800000, rms=0.526 (0.216%), neg=0, invalid=762
- 0300: dt=25.600000, rms=0.525 (0.082%), neg=0, invalid=762
- 0301: dt=44.800000, rms=0.525 (0.183%), neg=0, invalid=762
- 0302: dt=32.000000, rms=0.524 (0.081%), neg=0, invalid=762
- 0303: dt=44.800000, rms=0.523 (0.146%), neg=0, invalid=762
- 0304: dt=25.600000, rms=0.523 (0.094%), neg=0, invalid=762
- 0305: dt=44.800000, rms=0.522 (0.132%), neg=0, invalid=762
- 0306: dt=25.600000, rms=0.522 (0.075%), neg=0, invalid=762
- 0307: dt=44.800000, rms=0.521 (0.115%), neg=0, invalid=762
- 0308: dt=25.600000, rms=0.521 (0.069%), neg=0, invalid=762
- 0309: dt=44.800000, rms=0.520 (0.102%), neg=0, invalid=762
- 0310: dt=25.600000, rms=0.520 (0.062%), neg=0, invalid=762
- 0311: dt=44.800000, rms=0.519 (0.086%), neg=0, invalid=762
- 0312: dt=19.200000, rms=0.519 (0.055%), neg=0, invalid=762
- 0313: dt=128.000000, rms=0.518 (0.160%), neg=0, invalid=762
- 0314: dt=25.600000, rms=0.518 (0.128%), neg=0, invalid=762
- 0315: dt=44.800000, rms=0.517 (0.089%), neg=0, invalid=762
- 0316: dt=25.600000, rms=0.517 (0.047%), neg=0, invalid=762
- 0317: dt=25.600000, rms=0.517 (0.054%), neg=0, invalid=762
- 0318: dt=25.600000, rms=0.516 (0.072%), neg=0, invalid=762
- 0319: dt=25.600000, rms=0.516 (0.110%), neg=0, invalid=762
- 0320: dt=25.600000, rms=0.515 (0.127%), neg=0, invalid=762
- 0321: dt=25.600000, rms=0.514 (0.149%), neg=0, invalid=762
- 0322: dt=25.600000, rms=0.514 (0.162%), neg=0, invalid=762
- 0323: dt=25.600000, rms=0.513 (0.024%), neg=0, invalid=762
- 0324: dt=12.800000, rms=0.513 (0.014%), neg=0, invalid=762
- 0325: dt=2.800000, rms=0.513 (0.006%), neg=0, invalid=762
- 0326: dt=1.400000, rms=0.513 (0.001%), neg=0, invalid=762
- 0327: dt=0.350000, rms=0.513 (0.001%), neg=0, invalid=762
- 0328: dt=0.175000, rms=0.513 (0.001%), neg=0, invalid=762
- 0329: dt=0.087500, rms=0.513 (-0.001%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.528, neg=0, invalid=762
- 0330: dt=0.000000, rms=0.528 (0.059%), neg=0, invalid=762
- 0331: dt=0.000000, rms=0.528 (0.000%), neg=0, invalid=762
- 0332: dt=0.150000, rms=0.528 (-0.007%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.528, neg=0, invalid=762
- 0333: dt=0.000000, rms=0.528 (0.059%), neg=0, invalid=762
- 0334: dt=0.000000, rms=0.528 (0.000%), neg=0, invalid=762
- 0335: dt=0.150000, rms=0.528 (-0.004%), neg=0, invalid=762
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.558, neg=0, invalid=762
- 0336: dt=1.792000, rms=0.555 (0.698%), neg=0, invalid=762
- 0337: dt=0.448000, rms=0.554 (0.018%), neg=0, invalid=762
- 0338: dt=0.448000, rms=0.554 (-0.005%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.555, neg=0, invalid=762
- 0339: dt=1.836364, rms=0.552 (0.427%), neg=0, invalid=762
- 0340: dt=1.536000, rms=0.552 (0.072%), neg=0, invalid=762
- 0341: dt=0.448000, rms=0.552 (0.005%), neg=0, invalid=762
- 0342: dt=0.448000, rms=0.552 (0.002%), neg=0, invalid=762
- 0343: dt=0.448000, rms=0.552 (-0.011%), 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=0.527, neg=0, invalid=762
- 0344: dt=1.280000, rms=0.496 (5.780%), neg=0, invalid=762
- 0345: dt=0.000000, rms=0.496 (0.013%), neg=0, invalid=762
- 0346: dt=0.050000, rms=0.496 (-0.162%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.496, neg=0, invalid=762
- 0347: dt=0.000000, rms=0.496 (0.076%), neg=0, invalid=762
- 0348: dt=0.000000, rms=0.496 (0.000%), neg=0, invalid=762
- 0349: dt=0.050000, rms=0.496 (-0.061%), 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=0.489, neg=0, invalid=762
- 0350: dt=0.000000, rms=0.488 (0.078%), neg=0, invalid=762
- 0351: dt=0.000000, rms=0.488 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.489, neg=0, invalid=762
- 0352: dt=92.480000, rms=0.488 (0.090%), neg=0, invalid=762
- 0353: dt=369.920000, rms=0.488 (0.047%), neg=0, invalid=762
- 0354: dt=369.920000, rms=0.488 (-0.041%), neg=0, invalid=762
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.489, neg=0, invalid=762
- 0355: dt=6.480000, rms=0.488 (0.085%), neg=0, invalid=762
- 0356: dt=2.268000, rms=0.488 (0.001%), neg=0, invalid=762
- 0357: dt=2.268000, rms=0.488 (0.001%), neg=0, invalid=762
- 0358: dt=2.268000, rms=0.488 (-0.002%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.489, neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0359: dt=145.152000, rms=0.485 (0.746%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0360: dt=36.288000, rms=0.485 (0.054%), neg=0, invalid=762
- 0361: dt=36.288000, rms=0.484 (0.073%), neg=0, invalid=762
- 0362: dt=36.288000, rms=0.484 (0.112%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0363: dt=36.288000, rms=0.483 (0.144%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0364: dt=36.288000, rms=0.482 (0.147%), neg=0, invalid=762
- 0365: dt=36.288000, rms=0.482 (0.147%), neg=0, invalid=762
- 0366: dt=36.288000, rms=0.481 (0.126%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0367: dt=36.288000, rms=0.481 (0.108%), neg=0, invalid=762
- 0368: dt=36.288000, rms=0.480 (0.097%), neg=0, invalid=762
- 0369: dt=145.152000, rms=0.480 (0.075%), neg=0, invalid=762
- 0370: dt=145.152000, rms=0.480 (-0.068%), neg=0, invalid=762
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.481, neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0371: dt=11.200000, rms=0.480 (0.242%), neg=0, invalid=762
- 0372: dt=11.200000, rms=0.479 (0.086%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0373: dt=11.200000, rms=0.479 (0.069%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 1 iterations, nbhd size=0, neg = 0
- 0374: dt=11.200000, rms=0.479 (0.039%), neg=0, invalid=762
- iter 0, gcam->neg = 7
- after 7 iterations, nbhd size=1, neg = 0
- 0375: dt=11.200000, rms=0.479 (-0.063%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.479, neg=0, invalid=762
- iter 0, gcam->neg = 7
- after 9 iterations, nbhd size=1, neg = 0
- 0376: dt=56.433048, rms=0.471 (1.700%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0377: dt=23.612903, rms=0.469 (0.447%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0378: dt=44.800000, rms=0.467 (0.316%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0379: dt=25.600000, rms=0.466 (0.198%), neg=0, invalid=762
- 0380: dt=25.600000, rms=0.466 (0.184%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 1 iterations, nbhd size=0, neg = 0
- 0381: dt=25.600000, rms=0.464 (0.267%), neg=0, invalid=762
- 0382: dt=25.600000, rms=0.463 (0.332%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 2 iterations, nbhd size=0, neg = 0
- 0383: dt=25.600000, rms=0.461 (0.328%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 10 iterations, nbhd size=1, neg = 0
- 0384: dt=25.600000, rms=0.460 (0.319%), neg=0, invalid=762
- iter 0, gcam->neg = 5
- after 8 iterations, nbhd size=1, neg = 0
- 0385: dt=25.600000, rms=0.458 (0.320%), neg=0, invalid=762
- iter 0, gcam->neg = 5
- after 9 iterations, nbhd size=1, neg = 0
- 0386: dt=25.600000, rms=0.457 (0.270%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0387: dt=25.600000, rms=0.456 (0.237%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 6 iterations, nbhd size=1, neg = 0
- 0388: dt=25.600000, rms=0.455 (0.186%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0389: dt=25.600000, rms=0.454 (0.187%), neg=0, invalid=762
- 0390: dt=25.600000, rms=0.454 (0.152%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 6 iterations, nbhd size=1, neg = 0
- 0391: dt=25.600000, rms=0.453 (0.105%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 7 iterations, nbhd size=1, neg = 0
- 0392: dt=25.600000, rms=0.453 (0.082%), neg=0, invalid=762
- 0393: dt=11.200000, rms=0.453 (0.020%), neg=0, invalid=762
- 0394: dt=11.200000, rms=0.453 (0.013%), neg=0, invalid=762
- 0395: dt=11.200000, rms=0.453 (0.009%), neg=0, invalid=762
- 0396: dt=11.200000, rms=0.453 (0.010%), neg=0, invalid=762
- 0397: dt=11.200000, rms=0.453 (0.001%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.460, neg=0, invalid=762
- 0398: dt=0.000000, rms=0.459 (0.081%), neg=0, invalid=762
- 0399: dt=0.000000, rms=0.459 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.460, neg=0, invalid=762
- 0400: dt=1.728000, rms=0.459 (0.095%), neg=0, invalid=762
- 0401: dt=0.864000, rms=0.459 (0.003%), neg=0, invalid=762
- 0402: dt=0.864000, rms=0.459 (0.001%), neg=0, invalid=762
- 0403: dt=0.864000, rms=0.459 (-0.011%), neg=0, invalid=762
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.473, neg=0, invalid=762
- 0404: dt=0.000000, rms=0.472 (0.078%), neg=0, invalid=762
- 0405: dt=0.000000, rms=0.472 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.473, neg=0, invalid=762
- 0406: dt=1.024000, rms=0.472 (0.206%), neg=0, invalid=762
- 0407: dt=0.256000, rms=0.472 (0.005%), neg=0, invalid=762
- 0408: dt=0.256000, rms=0.472 (-0.004%), 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=0.455, neg=0, invalid=762
- iter 0, gcam->neg = 405
- after 15 iterations, nbhd size=1, neg = 0
- 0409: dt=1.792000, rms=0.437 (3.992%), neg=0, invalid=762
- 0410: dt=0.016000, rms=0.437 (0.008%), neg=0, invalid=762
- 0411: dt=0.016000, rms=0.437 (-0.002%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.438, neg=0, invalid=762
- 0412: dt=0.112000, rms=0.437 (0.176%), neg=0, invalid=762
- 0413: dt=0.007000, rms=0.437 (0.005%), neg=0, invalid=762
- 0414: dt=0.007000, rms=0.437 (-0.001%), 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=0.428, neg=0, invalid=762
- 0415: dt=0.000000, rms=0.428 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.428, neg=0, invalid=762
- 0416: dt=3.468000, rms=0.428 (0.000%), neg=0, invalid=762
- 0417: dt=0.433500, rms=0.428 (0.000%), neg=0, invalid=762
- 0418: dt=0.433500, rms=0.428 (-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=0.428, neg=0, invalid=762
- 0419: dt=0.000000, rms=0.428 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.428, neg=0, invalid=762
- 0420: dt=36.288000, rms=0.428 (0.015%), neg=0, invalid=762
- 0421: dt=82.944000, rms=0.428 (0.012%), neg=0, invalid=762
- 0422: dt=82.944000, rms=0.428 (0.025%), neg=0, invalid=762
- 0423: dt=82.944000, rms=0.428 (0.019%), neg=0, invalid=762
- 0424: dt=82.944000, rms=0.428 (0.004%), neg=0, invalid=762
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.428, neg=0, invalid=762
- 0425: dt=0.700000, rms=0.428 (0.001%), neg=0, invalid=762
- 0426: dt=0.600000, rms=0.428 (0.000%), neg=0, invalid=762
- 0427: dt=0.600000, rms=0.428 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.428, neg=0, invalid=762
- iter 0, gcam->neg = 5
- after 8 iterations, nbhd size=1, neg = 0
- 0428: dt=121.435897, rms=0.425 (0.676%), neg=0, invalid=762
- 0429: dt=25.600000, rms=0.425 (0.133%), neg=0, invalid=762
- 0430: dt=25.600000, rms=0.424 (0.087%), neg=0, invalid=762
- 0431: dt=25.600000, rms=0.424 (0.103%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0432: dt=25.600000, rms=0.423 (0.111%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0433: dt=25.600000, rms=0.423 (0.120%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0434: dt=25.600000, rms=0.422 (0.147%), neg=0, invalid=762
- iter 0, gcam->neg = 5
- after 10 iterations, nbhd size=1, neg = 0
- 0435: dt=25.600000, rms=0.422 (0.112%), neg=0, invalid=762
- iter 0, gcam->neg = 10
- after 4 iterations, nbhd size=0, neg = 0
- 0436: dt=25.600000, rms=0.421 (0.107%), neg=0, invalid=762
- 0437: dt=25.600000, rms=0.421 (0.006%), neg=0, invalid=762
- 0438: dt=25.600000, rms=0.421 (0.019%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 7 iterations, nbhd size=1, neg = 0
- 0439: dt=25.600000, rms=0.421 (0.009%), neg=0, invalid=762
- 0440: dt=25.600000, rms=0.421 (0.028%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 2 iterations, nbhd size=0, neg = 0
- 0441: dt=25.600000, rms=0.421 (0.032%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0442: dt=25.600000, rms=0.421 (0.044%), neg=0, invalid=762
- 0443: dt=25.600000, rms=0.420 (0.049%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 8 iterations, nbhd size=1, neg = 0
- 0444: dt=25.600000, rms=0.420 (0.042%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.423, neg=0, invalid=762
- 0445: dt=0.000113, rms=0.423 (0.000%), neg=0, invalid=762
- 0446: dt=0.000000, rms=0.423 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.423, neg=0, invalid=762
- 0447: dt=11.844156, rms=0.423 (0.146%), neg=0, invalid=762
- iter 0, gcam->neg = 12
- after 10 iterations, nbhd size=1, neg = 0
- 0448: dt=37.174917, rms=0.421 (0.332%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0449: dt=11.462687, rms=0.421 (0.119%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0450: dt=11.462687, rms=0.420 (0.130%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 6 iterations, nbhd size=1, neg = 0
- 0451: dt=11.462687, rms=0.420 (0.150%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 1 iterations, nbhd size=0, neg = 0
- 0452: dt=11.462687, rms=0.419 (0.131%), neg=0, invalid=762
- 0453: dt=11.462687, rms=0.418 (0.113%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 1 iterations, nbhd size=0, neg = 0
- 0454: dt=11.462687, rms=0.418 (0.113%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 9 iterations, nbhd size=1, neg = 0
- 0455: dt=11.462687, rms=0.418 (0.085%), neg=0, invalid=762
- 0456: dt=4.032000, rms=0.418 (0.005%), neg=0, invalid=762
- 0457: dt=4.032000, rms=0.418 (0.003%), neg=0, invalid=762
- 0458: dt=4.032000, rms=0.418 (0.004%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0459: dt=4.032000, rms=0.418 (0.005%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0460: dt=4.032000, rms=0.418 (0.008%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0461: dt=4.032000, rms=0.418 (0.012%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 1 iterations, nbhd size=0, neg = 0
- 0462: dt=4.032000, rms=0.417 (0.009%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0463: dt=4.032000, rms=0.417 (0.009%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0464: dt=4.032000, rms=0.417 (0.006%), neg=0, invalid=762
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.422, neg=0, invalid=762
- 0465: dt=0.000000, rms=0.422 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.422, neg=0, invalid=762
- 0466: dt=0.000050, rms=0.422 (0.000%), neg=0, invalid=762
- 0467: dt=0.000000, rms=0.422 (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=0.414, neg=0, invalid=762
- iter 0, gcam->neg = 302
- after 14 iterations, nbhd size=1, neg = 0
- 0468: dt=1.280000, rms=0.408 (1.557%), neg=0, invalid=762
- 0469: dt=0.000023, rms=0.408 (0.000%), neg=0, invalid=762
- 0470: dt=0.000023, rms=0.408 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.408, neg=0, invalid=762
- 0471: dt=0.192000, rms=0.407 (0.167%), neg=0, invalid=762
- 0472: dt=0.256000, rms=0.407 (0.089%), neg=0, invalid=762
- 0473: dt=0.256000, rms=0.406 (0.126%), neg=0, invalid=762
- 0474: dt=0.256000, rms=0.406 (0.117%), neg=0, invalid=762
- iter 0, gcam->neg = 22
- after 11 iterations, nbhd size=1, neg = 0
- 0475: dt=0.256000, rms=0.406 (-0.005%), neg=0, invalid=762
- 0476: dt=0.448000, rms=0.405 (0.158%), neg=0, invalid=762
- 0477: dt=0.448000, rms=0.405 (0.107%), neg=0, invalid=762
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- mri_ca_register took 2 hours, 29 minutes and 12 seconds.
- mri_ca_register utimesec 9904.731251
- mri_ca_register stimesec 10.264439
- mri_ca_register ru_maxrss 1335624
- mri_ca_register ru_ixrss 0
- mri_ca_register ru_idrss 0
- mri_ca_register ru_isrss 0
- mri_ca_register ru_minflt 5549070
- mri_ca_register ru_majflt 0
- mri_ca_register ru_nswap 0
- mri_ca_register ru_inblock 0
- mri_ca_register ru_oublock 64448
- mri_ca_register ru_msgsnd 0
- mri_ca_register ru_msgrcv 0
- mri_ca_register ru_nsignals 0
- mri_ca_register ru_nvcsw 6781
- mri_ca_register ru_nivcsw 28397
- FSRUNTIME@ mri_ca_register 2.4867 hours 2 threads
- #--------------------------------------
- #@# SubCort Seg Sat Oct 7 19:13:01 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-385
- 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-6.0.0/0050669/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 7.18
- 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 = 0.10764 (32)
- Left_Lateral_Ventricle (4): linear fit = 1.68 x + 0.0 (865 voxels, overlap=0.084)
- Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (865 voxels, peak = 34), gca=30.0
- gca peak = 0.17677 (13)
- mri peak = 0.11317 (31)
- Right_Lateral_Ventricle (43): linear fit = 2.31 x + 0.0 (965 voxels, overlap=0.084)
- Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (965 voxels, peak = 30), gca=19.5
- gca peak = 0.28129 (95)
- mri peak = 0.12078 (97)
- Right_Pallidum (52): linear fit = 1.03 x + 0.0 (693 voxels, overlap=0.957)
- Right_Pallidum (52): linear fit = 1.03 x + 0.0 (693 voxels, peak = 98), gca=98.3
- gca peak = 0.16930 (96)
- mri peak = 0.11072 (101)
- Left_Pallidum (13): linear fit = 1.04 x + 0.0 (711 voxels, overlap=0.747)
- Left_Pallidum (13): linear fit = 1.04 x + 0.0 (711 voxels, peak = 100), gca=100.3
- gca peak = 0.24553 (55)
- mri peak = 0.08889 (73)
- Right_Hippocampus (53): linear fit = 1.32 x + 0.0 (1170 voxels, overlap=0.022)
- Right_Hippocampus (53): linear fit = 1.32 x + 0.0 (1170 voxels, peak = 72), gca=72.3
- gca peak = 0.30264 (59)
- mri peak = 0.09519 (76)
- Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (920 voxels, overlap=0.021)
- Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (920 voxels, peak = 76), gca=76.4
- gca peak = 0.07580 (103)
- mri peak = 0.11662 (104)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (55217 voxels, overlap=0.691)
- Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (55217 voxels, peak = 105), gca=104.5
- gca peak = 0.07714 (104)
- mri peak = 0.10845 (106)
- Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (56805 voxels, overlap=0.612)
- Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (56805 voxels, peak = 106), gca=105.6
- gca peak = 0.09712 (58)
- mri peak = 0.04710 (78)
- Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (34102 voxels, overlap=0.001)
- Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (34102 voxels, peak = 78), gca=78.0
- gca peak = 0.11620 (58)
- mri peak = 0.05098 (76)
- Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (34913 voxels, overlap=0.001)
- Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (34913 voxels, peak = 75), gca=75.1
- gca peak = 0.30970 (66)
- mri peak = 0.11091 (88)
- Right_Caudate (50): linear fit = 1.29 x + 0.0 (1118 voxels, overlap=0.021)
- Right_Caudate (50): linear fit = 1.29 x + 0.0 (1118 voxels, peak = 85), gca=85.5
- gca peak = 0.15280 (69)
- mri peak = 0.11347 (88)
- Left_Caudate (11): linear fit = 1.16 x + 0.0 (1151 voxels, overlap=0.021)
- Left_Caudate (11): linear fit = 1.16 x + 0.0 (1151 voxels, peak = 80), gca=80.4
- gca peak = 0.13902 (56)
- mri peak = 0.06130 (74)
- Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (26150 voxels, overlap=0.001)
- Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (26150 voxels, peak = 74), gca=74.2
- gca peak = 0.14777 (55)
- mri peak = 0.06638 (74)
- Right_Cerebellum_Cortex (47): linear fit = 1.34 x + 0.0 (29827 voxels, overlap=0.001)
- Right_Cerebellum_Cortex (47): linear fit = 1.34 x + 0.0 (29827 voxels, peak = 73), gca=73.4
- gca peak = 0.16765 (84)
- mri peak = 0.11117 (90)
- Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (7995 voxels, overlap=0.530)
- Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (7995 voxels, peak = 89), gca=89.5
- gca peak = 0.18739 (84)
- mri peak = 0.12852 (88)
- Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (7532 voxels, overlap=0.556)
- Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (7532 voxels, peak = 89), gca=89.5
- gca peak = 0.29869 (57)
- mri peak = 0.10055 (76)
- Left_Amygdala (18): linear fit = 1.28 x + 0.0 (545 voxels, overlap=0.065)
- Left_Amygdala (18): linear fit = 1.28 x + 0.0 (545 voxels, peak = 73), gca=73.2
- gca peak = 0.33601 (57)
- mri peak = 0.09214 (75)
- Right_Amygdala (54): linear fit = 1.30 x + 0.0 (625 voxels, overlap=0.049)
- Right_Amygdala (54): linear fit = 1.30 x + 0.0 (625 voxels, peak = 74), gca=74.4
- gca peak = 0.11131 (90)
- mri peak = 0.08748 (97)
- Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (5647 voxels, overlap=0.477)
- Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (5647 voxels, peak = 99), gca=98.6
- gca peak = 0.11793 (83)
- mri peak = 0.09023 (93)
- Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5271 voxels, overlap=0.259)
- Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5271 voxels, peak = 93), gca=92.5
- gca peak = 0.08324 (81)
- mri peak = 0.08807 (91)
- Left_Putamen (12): linear fit = 1.17 x + 0.0 (1869 voxels, overlap=0.078)
- Left_Putamen (12): linear fit = 1.17 x + 0.0 (1869 voxels, peak = 95), gca=95.2
- gca peak = 0.10360 (77)
- mri peak = 0.08788 (91)
- Right_Putamen (51): linear fit = 1.17 x + 0.0 (1980 voxels, overlap=0.098)
- Right_Putamen (51): linear fit = 1.17 x + 0.0 (1980 voxels, peak = 90), gca=90.5
- gca peak = 0.08424 (78)
- mri peak = 0.09275 (86)
- Brain_Stem (16): linear fit = 1.08 x + 0.0 (15547 voxels, overlap=0.476)
- Brain_Stem (16): linear fit = 1.08 x + 0.0 (15547 voxels, peak = 84), gca=83.9
- gca peak = 0.12631 (89)
- mri peak = 0.08875 (94)
- Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1735 voxels, overlap=0.491)
- Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1735 voxels, peak = 97), gca=97.5
- gca peak = 0.14500 (87)
- mri peak = 0.08324 (98)
- Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1889 voxels, overlap=0.726)
- Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1889 voxels, peak = 94), gca=93.5
- gca peak = 0.14975 (24)
- mri peak = 0.09880 (33)
- gca peak = 0.19357 (14)
- mri peak = 0.14047 (31)
- Fourth_Ventricle (15): linear fit = 2.01 x + 0.0 (296 voxels, overlap=0.123)
- Fourth_Ventricle (15): linear fit = 2.01 x + 0.0 (296 voxels, peak = 28), gca=28.1
- 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 1.31 x + 0.0
- estimating mean wm scale to be 1.01 x + 0.0
- estimating mean csf scale to be 1.50 x + 0.0
- Left_Putamen too bright - rescaling by 0.993 (from 1.175) to 94.5 (was 95.2)
- saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.12544 (31)
- mri peak = 0.10764 (32)
- Left_Lateral_Ventricle (4): linear fit = 1.11 x + 0.0 (865 voxels, overlap=0.717)
- Left_Lateral_Ventricle (4): linear fit = 1.11 x + 0.0 (865 voxels, peak = 34), gca=34.3
- gca peak = 0.13981 (19)
- mri peak = 0.11317 (31)
- Right_Lateral_Ventricle (43): linear fit = 1.57 x + 0.0 (965 voxels, overlap=0.321)
- Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (965 voxels, peak = 30), gca=28.5
- gca peak = 0.28323 (99)
- mri peak = 0.12078 (97)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (693 voxels, overlap=1.006)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (693 voxels, peak = 99), gca=99.5
- gca peak = 0.16204 (100)
- mri peak = 0.11072 (101)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (711 voxels, overlap=1.000)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (711 voxels, peak = 100), gca=100.5
- gca peak = 0.23800 (73)
- mri peak = 0.08889 (73)
- Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (1170 voxels, overlap=1.000)
- Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (1170 voxels, peak = 71), gca=71.2
- gca peak = 0.27094 (73)
- mri peak = 0.09519 (76)
- Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (920 voxels, overlap=1.004)
- Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (920 voxels, peak = 72), gca=71.9
- gca peak = 0.07771 (104)
- mri peak = 0.11662 (104)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (55217 voxels, overlap=0.737)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (55217 voxels, peak = 103), gca=103.5
- gca peak = 0.07820 (106)
- mri peak = 0.10845 (106)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (56805 voxels, overlap=0.680)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (56805 voxels, peak = 107), gca=106.5
- gca peak = 0.07302 (78)
- mri peak = 0.04710 (78)
- Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (34102 voxels, overlap=0.923)
- Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (34102 voxels, peak = 77), gca=76.8
- gca peak = 0.09082 (75)
- mri peak = 0.05098 (76)
- Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (34913 voxels, overlap=0.939)
- Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (34913 voxels, peak = 75), gca=75.0
- gca peak = 0.21576 (85)
- mri peak = 0.11091 (88)
- Right_Caudate (50): linear fit = 0.99 x + 0.0 (1118 voxels, overlap=0.999)
- Right_Caudate (50): linear fit = 0.99 x + 0.0 (1118 voxels, peak = 84), gca=83.7
- gca peak = 0.14945 (90)
- mri peak = 0.11347 (88)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (1151 voxels, overlap=0.952)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (1151 voxels, peak = 90), gca=90.0
- gca peak = 0.10891 (73)
- mri peak = 0.06130 (74)
- Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (26150 voxels, overlap=0.963)
- Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (26150 voxels, peak = 73), gca=73.0
- gca peak = 0.11369 (73)
- mri peak = 0.06638 (74)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (29827 voxels, overlap=0.966)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (29827 voxels, peak = 72), gca=71.9
- gca peak = 0.15873 (90)
- mri peak = 0.11117 (90)
- Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (7995 voxels, overlap=0.904)
- Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (7995 voxels, peak = 91), gca=91.3
- gca peak = 0.15163 (90)
- mri peak = 0.12852 (88)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7532 voxels, overlap=0.909)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7532 voxels, peak = 90), gca=89.6
- gca peak = 0.27864 (73)
- mri peak = 0.10055 (76)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (545 voxels, overlap=1.012)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (545 voxels, peak = 73), gca=73.0
- gca peak = 0.33228 (74)
- mri peak = 0.09214 (75)
- Right_Amygdala (54): linear fit = 0.98 x + 0.0 (625 voxels, overlap=1.004)
- Right_Amygdala (54): linear fit = 0.98 x + 0.0 (625 voxels, peak = 72), gca=72.2
- gca peak = 0.10984 (97)
- mri peak = 0.08748 (97)
- Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (5647 voxels, overlap=0.878)
- Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (5647 voxels, peak = 96), gca=95.5
- gca peak = 0.10417 (90)
- mri peak = 0.09023 (93)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5271 voxels, overlap=0.883)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5271 voxels, peak = 90), gca=90.4
- gca peak = 0.07568 (88)
- mri peak = 0.08807 (91)
- Left_Putamen (12): linear fit = 1.01 x + 0.0 (1869 voxels, overlap=0.810)
- Left_Putamen (12): linear fit = 1.01 x + 0.0 (1869 voxels, peak = 89), gca=89.3
- gca peak = 0.08774 (92)
- mri peak = 0.08788 (91)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1980 voxels, overlap=0.842)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1980 voxels, peak = 92), gca=91.5
- gca peak = 0.08828 (84)
- mri peak = 0.09275 (86)
- Brain_Stem (16): linear fit = 1.01 x + 0.0 (15547 voxels, overlap=0.758)
- Brain_Stem (16): linear fit = 1.01 x + 0.0 (15547 voxels, peak = 85), gca=85.3
- gca peak = 0.12704 (92)
- mri peak = 0.08875 (94)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1735 voxels, overlap=0.827)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1735 voxels, peak = 92), gca=91.5
- gca peak = 0.15761 (92)
- mri peak = 0.08324 (98)
- Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1889 voxels, overlap=0.916)
- Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1889 voxels, peak = 93), gca=93.4
- gca peak = 0.12656 (38)
- mri peak = 0.09880 (33)
- gca peak = 0.16542 (24)
- mri peak = 0.14047 (31)
- Fourth_Ventricle (15): linear fit = 1.32 x + 0.0 (296 voxels, overlap=0.325)
- Fourth_Ventricle (15): linear fit = 1.32 x + 0.0 (296 voxels, peak = 32), gca=31.6
- gca peak Unknown = 0.94835 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.17746 (35)
- gca peak Left_Thalamus = 0.36646 (104)
- gca peak Third_Ventricle = 0.12656 (38)
- gca peak CSF = 0.15446 (55)
- gca peak Left_Accumbens_area = 0.54589 (73)
- gca peak Left_undetermined = 0.95280 (34)
- gca peak Left_vessel = 0.75997 (52)
- gca peak Left_choroid_plexus = 0.12303 (35)
- gca peak Right_Inf_Lat_Vent = 0.19792 (30)
- gca peak Right_Accumbens_area = 0.29821 (84)
- gca peak Right_vessel = 0.82168 (52)
- gca peak Right_choroid_plexus = 0.14504 (37)
- gca peak Fifth_Ventricle = 0.51780 (46)
- gca peak WM_hypointensities = 0.07786 (78)
- gca peak non_WM_hypointensities = 0.09187 (44)
- gca peak Optic_Chiasm = 0.68724 (75)
- not using caudate to estimate GM means
- estimating mean gm scale to be 0.99 x + 0.0
- estimating mean wm scale to be 1.00 x + 0.0
- estimating mean csf scale to be 1.31 x + 0.0
- Left_Pallidum too bright - rescaling by 1.013 (from 1.005) to 101.9 (was 100.5)
- saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
- saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt
- 91012 voxels changed in iteration 0 of unlikely voxel relabeling
- 283 voxels changed in iteration 1 of unlikely voxel relabeling
- 29 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
- 81379 gm and wm labels changed (%36 to gray, %64 to white out of all changed labels)
- 403 hippocampal voxels changed.
- 1 amygdala voxels changed.
- pass 1: 90408 changed. image ll: -2.123, PF=0.500
- pass 2: 24675 changed. image ll: -2.121, PF=0.500
- pass 3: 7074 changed.
- pass 4: 2394 changed.
- 75905 voxels changed in iteration 0 of unlikely voxel relabeling
- 572 voxels changed in iteration 1 of unlikely voxel relabeling
- 24 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
- 7693 voxels changed in iteration 0 of unlikely voxel relabeling
- 108 voxels changed in iteration 1 of unlikely voxel relabeling
- 1 voxels changed in iteration 2 of unlikely voxel relabeling
- 0 voxels changed in iteration 3 of unlikely voxel relabeling
- 5248 voxels changed in iteration 0 of unlikely voxel relabeling
- 79 voxels changed in iteration 1 of unlikely voxel relabeling
- 21 voxels changed in iteration 2 of unlikely voxel relabeling
- 1 voxels changed in iteration 3 of unlikely voxel relabeling
- 0 voxels changed in iteration 4 of unlikely voxel relabeling
- 5197 voxels changed in iteration 0 of unlikely voxel relabeling
- 37 voxels changed in iteration 1 of unlikely voxel relabeling
- 2 voxels changed in iteration 2 of unlikely voxel relabeling
- 0 voxels changed in iteration 3 of unlikely voxel relabeling
- MRItoUCHAR: min=0, max=85
- MRItoUCHAR: converting to UCHAR
- writing labeled volume to aseg.auto_noCCseg.mgz
- mri_ca_label utimesec 4934.699811
- mri_ca_label stimesec 1.791727
- mri_ca_label ru_maxrss 2103956
- mri_ca_label ru_ixrss 0
- mri_ca_label ru_idrss 0
- mri_ca_label ru_isrss 0
- mri_ca_label ru_minflt 690728
- mri_ca_label ru_majflt 0
- mri_ca_label ru_nswap 0
- mri_ca_label ru_inblock 64440
- mri_ca_label ru_oublock 480
- mri_ca_label ru_msgsnd 0
- mri_ca_label ru_msgrcv 0
- mri_ca_label ru_nsignals 0
- mri_ca_label ru_nvcsw 272
- mri_ca_label ru_nivcsw 6196
- auto-labeling took 81 minutes and 26 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/transforms/cc_up.lta 0050669
- 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-6.0.0/0050669/mri/transforms/cc_up.lta
- reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/aseg.auto_noCCseg.mgz
- reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/norm.mgz
- 45017 voxels in left wm, 45687 in right wm, xrange [122, 131]
- searching rotation angles z=[-10 4], y=[-6 8]
-
searching scale 1 Z rot -10.0
searching scale 1 Z rot -9.7
searching scale 1 Z rot -9.5
searching scale 1 Z rot -9.2
searching scale 1 Z rot -9.0
searching scale 1 Z rot -8.7
searching scale 1 Z rot -8.5
searching scale 1 Z rot -8.2
searching scale 1 Z rot -8.0
searching scale 1 Z rot -7.7
searching scale 1 Z rot -7.5
searching scale 1 Z rot -7.2
searching scale 1 Z rot -7.0
searching scale 1 Z rot -6.7
searching scale 1 Z rot -6.5
searching scale 1 Z rot -6.2
searching scale 1 Z rot -6.0
searching scale 1 Z rot -5.7
searching scale 1 Z rot -5.5
searching scale 1 Z rot -5.2
searching scale 1 Z rot -5.0
searching scale 1 Z rot -4.7
searching scale 1 Z rot -4.5
searching scale 1 Z rot -4.2
searching scale 1 Z rot -4.0
searching scale 1 Z rot -3.7
searching scale 1 Z rot -3.5
searching scale 1 Z rot -3.2
searching scale 1 Z rot -3.0
searching scale 1 Z rot -2.7
searching scale 1 Z rot -2.5
searching scale 1 Z rot -2.2
searching scale 1 Z rot -2.0
searching scale 1 Z rot -1.7
searching scale 1 Z rot -1.5
searching scale 1 Z rot -1.2
searching scale 1 Z rot -1.0
searching scale 1 Z rot -0.7
searching scale 1 Z rot -0.5
searching scale 1 Z rot -0.2
searching scale 1 Z rot 0.0
searching scale 1 Z rot 0.3
searching scale 1 Z rot 0.5
searching scale 1 Z rot 0.8
searching scale 1 Z rot 1.0
searching scale 1 Z rot 1.3
searching scale 1 Z rot 1.5
searching scale 1 Z rot 1.8
searching scale 1 Z rot 2.0
searching scale 1 Z rot 2.3
searching scale 1 Z rot 2.5
searching scale 1 Z rot 2.8
searching scale 1 Z rot 3.0
searching scale 1 Z rot 3.3
searching scale 1 Z rot 3.5
searching scale 1 Z rot 3.8 global minimum found at slice 126.3, rotations (0.70, -2.99)
- final transformation (x=126.3, yr=0.698, zr=-2.986):
- 0.99857 0.05210 0.01216 -3.59922;
- -0.05209 0.99864 -0.00063 50.75103;
- -0.01218 0.00000 0.99993 40.54474;
- 0.00000 0.00000 0.00000 1.00000;
- updating x range to be [126, 130] in xformed coordinates
- best xformed slice 128
- cc center is found at 128 84 89
- eigenvectors:
- -0.00135 -0.00515 0.99999;
- -0.10339 -0.99463 -0.00526;
- 0.99464 -0.10339 0.00081;
- writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/aseg.auto.mgz...
- corpus callosum segmentation took 0.9 minutes
- #--------------------------------------
- #@# Merge ASeg Sat Oct 7 20:35:19 CEST 2017
- cp aseg.auto.mgz aseg.presurf.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Sat Oct 7 20:35:19 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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...
- 812 control points removed
- Building bias image
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 0...
- Smoothing with sigma 8
- Applying bias correction
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 110
- white matter peak found at 110
- gm peak at 84 (84), valley at 20 (20)
- csf peak at 43, setting threshold to 70
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 110
- white matter peak found at 110
- gm peak at 83 (83), valley at 20 (20)
- csf peak at 42, setting threshold to 69
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to brain.mgz
- 3D bias adjustment took 3 minutes and 19 seconds.
- #--------------------------------------------
- #@# Mask BFS Sat Oct 7 20:38:40 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1654456 voxels in mask (pct= 9.86)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Sat Oct 7 20:38:41 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): 104.1 +- 5.8 [79.0 --> 125.0]
- GM (78.0) : 75.7 +- 13.0 [30.0 --> 95.0]
- setting bottom of white matter range to 88.7
- setting top of gray matter range to 101.7
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- using local geometry to label remaining ambiguous voxels...
- reclassifying voxels using Gaussian border classifier...
- removing voxels with positive offset direction...
- smoothing T1 volume with sigma = 0.250
- removing 1-dimensional structures...
- 13506 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 4588 filled
- 2276 bright non-wm voxels segmented.
- 6591 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 0.51 minutes
- reading wm segmentation from wm.seg.mgz...
- 100 voxels added to wm to prevent paths from MTL structures to cortex
- 3711 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 39488 voxels turned on, 53195 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+): 18 found - 18 modified | TOTAL: 18
- pass 2 (xy+): 0 found - 18 modified | TOTAL: 18
- pass 1 (xy-): 29 found - 29 modified | TOTAL: 47
- pass 2 (xy-): 0 found - 29 modified | TOTAL: 47
- pass 1 (yz+): 28 found - 28 modified | TOTAL: 75
- pass 2 (yz+): 0 found - 28 modified | TOTAL: 75
- pass 1 (yz-): 38 found - 38 modified | TOTAL: 113
- pass 2 (yz-): 0 found - 38 modified | TOTAL: 113
- pass 1 (xz+): 30 found - 30 modified | TOTAL: 143
- pass 2 (xz+): 0 found - 30 modified | TOTAL: 143
- pass 1 (xz-): 18 found - 18 modified | TOTAL: 161
- pass 2 (xz-): 0 found - 18 modified | TOTAL: 161
- Iteration Number : 1
- pass 1 (+++): 23 found - 23 modified | TOTAL: 23
- pass 2 (+++): 0 found - 23 modified | TOTAL: 23
- pass 1 (+++): 36 found - 36 modified | TOTAL: 59
- pass 2 (+++): 0 found - 36 modified | TOTAL: 59
- pass 1 (+++): 18 found - 18 modified | TOTAL: 77
- pass 2 (+++): 0 found - 18 modified | TOTAL: 77
- pass 1 (+++): 16 found - 16 modified | TOTAL: 93
- pass 2 (+++): 0 found - 16 modified | TOTAL: 93
- Iteration Number : 1
- pass 1 (++): 204 found - 204 modified | TOTAL: 204
- pass 2 (++): 0 found - 204 modified | TOTAL: 204
- pass 1 (+-): 173 found - 173 modified | TOTAL: 377
- pass 2 (+-): 0 found - 173 modified | TOTAL: 377
- pass 1 (--): 164 found - 164 modified | TOTAL: 541
- pass 2 (--): 0 found - 164 modified | TOTAL: 541
- pass 1 (-+): 169 found - 169 modified | TOTAL: 710
- pass 2 (-+): 0 found - 169 modified | TOTAL: 710
- Iteration Number : 2
- pass 1 (xy+): 5 found - 5 modified | TOTAL: 5
- pass 2 (xy+): 0 found - 5 modified | TOTAL: 5
- pass 1 (xy-): 6 found - 6 modified | TOTAL: 11
- pass 2 (xy-): 0 found - 6 modified | TOTAL: 11
- pass 1 (yz+): 9 found - 9 modified | TOTAL: 20
- pass 2 (yz+): 0 found - 9 modified | TOTAL: 20
- pass 1 (yz-): 8 found - 8 modified | TOTAL: 28
- pass 2 (yz-): 0 found - 8 modified | TOTAL: 28
- pass 1 (xz+): 4 found - 4 modified | TOTAL: 32
- pass 2 (xz+): 0 found - 4 modified | TOTAL: 32
- pass 1 (xz-): 11 found - 11 modified | TOTAL: 43
- pass 2 (xz-): 0 found - 11 modified | TOTAL: 43
- 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 (++): 4 found - 4 modified | TOTAL: 4
- pass 2 (++): 0 found - 4 modified | TOTAL: 4
- pass 1 (+-): 2 found - 2 modified | TOTAL: 6
- pass 2 (+-): 0 found - 2 modified | TOTAL: 6
- pass 1 (--): 2 found - 2 modified | TOTAL: 8
- pass 2 (--): 0 found - 2 modified | TOTAL: 8
- pass 1 (-+): 3 found - 3 modified | TOTAL: 11
- pass 2 (-+): 0 found - 3 modified | TOTAL: 11
- Iteration Number : 3
- 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-): 0 found - 0 modified | TOTAL: 2
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 2
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 2
- Iteration Number : 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (++): 1 found - 1 modified | TOTAL: 1
- pass 2 (++): 0 found - 1 modified | TOTAL: 1
- pass 1 (+-): 0 found - 0 modified | TOTAL: 1
- pass 1 (--): 0 found - 0 modified | TOTAL: 1
- pass 1 (-+): 0 found - 0 modified | TOTAL: 1
- Iteration Number : 4
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 4
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 4
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 1021 (out of 582438: 0.175298)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Sat Oct 7 20:41:20 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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
- 1.02984 0.07967 0.01891 -13.05690;
- -0.05520 1.04537 0.27160 -5.91510;
- -0.00189 -0.22737 0.97149 38.87304;
- 0.00000 0.00000 0.00000 1.00000;
- voxel to talairach voxel transform
- 1.02984 0.07967 0.01891 -13.05690;
- -0.05520 1.04537 0.27160 -5.91510;
- -0.00189 -0.22737 0.97149 38.87304;
- 0.00000 0.00000 0.00000 1.00000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 1167 (min = 350, max = 1400), aspect = 0.47 (min = 0.10, max = 0.75)
- no need to search
- using seed (125, 122, 153), TAL = (3.0, 25.0, 6.0)
- talairach voxel to voxel transform
- 0.96710 -0.07334 0.00168 12.12828;
- 0.04768 0.89815 -0.25202 15.73193;
- 0.01304 0.21006 0.97037 -36.30833;
- 0.00000 0.00000 0.00000 1.00000;
- segmentation indicates cc at (125, 122, 153) --> (3.0, 25.0, 6.0)
- done.
- writing output to filled.mgz...
- filling took 0.7 minutes
- talairach cc position changed to (3.00, 25.00, 6.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(21.00, 25.00, 6.00) SRC: (106.92, 91.85, 139.18)
- search lh wm seed point around talairach space (-15.00, 25.00, 6.00), SRC: (141.73, 93.56, 139.65)
- 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 20:42:06 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- Iteration Number : 1
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 2 found - 2 modified | TOTAL: 2
- pass 2 (xy-): 0 found - 2 modified | TOTAL: 2
- pass 1 (yz+): 1 found - 1 modified | TOTAL: 3
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 3
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 4
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 4
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 5
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 5
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 5
- 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 (+-): 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 = 6 (out of 278867: 0.002152)
- 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 20: 1120 vertices, 1249 faces
- slice 30: 6874 vertices, 7123 faces
- slice 40: 15748 vertices, 16079 faces
- slice 50: 26436 vertices, 26817 faces
- slice 60: 37285 vertices, 37696 faces
- slice 70: 48592 vertices, 49004 faces
- slice 80: 59789 vertices, 60205 faces
- slice 90: 71331 vertices, 71756 faces
- slice 100: 82911 vertices, 83358 faces
- slice 110: 93841 vertices, 94276 faces
- slice 120: 104772 vertices, 105203 faces
- slice 130: 114831 vertices, 115265 faces
- slice 140: 123443 vertices, 123807 faces
- slice 150: 130638 vertices, 130988 faces
- slice 160: 137237 vertices, 137568 faces
- slice 170: 142538 vertices, 142816 faces
- slice 180: 145555 vertices, 145720 faces
- slice 190: 145808 vertices, 145918 faces
- slice 200: 145808 vertices, 145918 faces
- slice 210: 145808 vertices, 145918 faces
- slice 220: 145808 vertices, 145918 faces
- slice 230: 145808 vertices, 145918 faces
- slice 240: 145808 vertices, 145918 faces
- slice 250: 145808 vertices, 145918 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...
- 145808 voxel in cpt #1: X=-110 [v=145808,e=437754,f=291836] located at (-25.056505, -36.079391, 29.290560)
- For the whole surface: X=-110 [v=145808,e=437754,f=291836]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Tessellate rh Sat Oct 7 20:42:12 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
- Iteration Number : 1
- pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 1
- pass 1 (yz+): 1 found - 1 modified | TOTAL: 2
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 2
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 2
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 3
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 3
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 3
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 3 (out of 282079: 0.001064)
- 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 20: 836 vertices, 935 faces
- slice 30: 6082 vertices, 6327 faces
- slice 40: 14820 vertices, 15178 faces
- slice 50: 25967 vertices, 26357 faces
- slice 60: 38051 vertices, 38446 faces
- slice 70: 49592 vertices, 49993 faces
- slice 80: 61523 vertices, 61963 faces
- slice 90: 73503 vertices, 73950 faces
- slice 100: 84974 vertices, 85415 faces
- slice 110: 96025 vertices, 96450 faces
- slice 120: 107384 vertices, 107795 faces
- slice 130: 117378 vertices, 117786 faces
- slice 140: 125491 vertices, 125874 faces
- slice 150: 132772 vertices, 133099 faces
- slice 160: 139348 vertices, 139664 faces
- slice 170: 144550 vertices, 144822 faces
- slice 180: 147470 vertices, 147616 faces
- slice 190: 147584 vertices, 147698 faces
- slice 200: 147584 vertices, 147698 faces
- slice 210: 147584 vertices, 147698 faces
- slice 220: 147584 vertices, 147698 faces
- slice 230: 147584 vertices, 147698 faces
- slice 240: 147584 vertices, 147698 faces
- slice 250: 147584 vertices, 147698 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...
- 147584 voxel in cpt #1: X=-114 [v=147584,e=443094,f=295396] located at (30.062988, -36.532822, 33.160885)
- For the whole surface: X=-114 [v=147584,e=443094,f=295396]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Sat Oct 7 20:42:18 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- #--------------------------------------------
- #@# Smooth1 rh Sat Oct 7 20:42:18 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- Waiting for PID 14317 of (14317 14320) to complete...
- Waiting for PID 14320 of (14317 14320) 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 (14317 14320) completed and logs appended.
- #--------------------------------------------
- #@# Inflation1 lh Sat Oct 7 20:42:25 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- #--------------------------------------------
- #@# Inflation1 rh Sat Oct 7 20:42:25 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- Waiting for PID 14370 of (14370 14373) to complete...
- Waiting for PID 14373 of (14370 14373) 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 = 47.6 mm, total surface area = 75239 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 0.8 minutes
-
step 000: RMS=0.161 (target=0.015)
step 005: RMS=0.121 (target=0.015)
step 010: RMS=0.091 (target=0.015)
step 015: RMS=0.077 (target=0.015)
step 020: RMS=0.067 (target=0.015)
step 025: RMS=0.059 (target=0.015)
step 030: RMS=0.053 (target=0.015)
step 035: RMS=0.049 (target=0.015)
step 040: RMS=0.045 (target=0.015)
step 045: RMS=0.043 (target=0.015)
step 050: RMS=0.042 (target=0.015)
step 055: RMS=0.042 (target=0.015)
step 060: RMS=0.041 (target=0.015)
- inflation complete.
- Not saving sulc
- mris_inflate utimesec 46.639909
- mris_inflate stimesec 0.106983
- mris_inflate ru_maxrss 213320
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 30782
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 10264
- mris_inflate ru_oublock 10280
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2103
- mris_inflate ru_nivcsw 3423
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- Not saving sulc
- Reading ../surf/rh.smoothwm.nofix
- avg radius = 47.5 mm, total surface area = 75980 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 0.7 minutes
-
step 000: RMS=0.161 (target=0.015)
step 005: RMS=0.121 (target=0.015)
step 010: RMS=0.092 (target=0.015)
step 015: RMS=0.079 (target=0.015)
step 020: RMS=0.069 (target=0.015)
step 025: RMS=0.060 (target=0.015)
step 030: RMS=0.055 (target=0.015)
step 035: RMS=0.050 (target=0.015)
step 040: RMS=0.048 (target=0.015)
step 045: RMS=0.045 (target=0.015)
step 050: RMS=0.044 (target=0.015)
step 055: RMS=0.045 (target=0.015)
step 060: RMS=0.045 (target=0.015)
- inflation complete.
- Not saving sulc
- mris_inflate utimesec 44.388251
- mris_inflate stimesec 0.126980
- mris_inflate ru_maxrss 216284
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 31011
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 0
- mris_inflate ru_oublock 10408
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2342
- mris_inflate ru_nivcsw 3276
- PIDs (14370 14373) completed and logs appended.
- #--------------------------------------------
- #@# QSphere lh Sat Oct 7 20:43:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- #--------------------------------------------
- #@# QSphere rh Sat Oct 7 20:43:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- Waiting for PID 14438 of (14438 14442) to complete...
- Waiting for PID 14442 of (14438 14442) 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 0.96 +- 0.57 (0.00-->6.70) (max @ vno 59492 --> 60695)
- face area 0.02 +- 0.03 (-0.38-->0.45)
- == Number of threads available to mris_sphere for OpenMP = 2 ==
- scaling brain by 0.301...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.976, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.714, avgs=0
- 010/300: dt: 0.9000, rms radial error=176.154, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.420, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.587, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.695, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.769, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.828, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.880, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.931, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.982, avgs=0
- 055/300: dt: 0.9000, rms radial error=168.037, avgs=0
- 060/300: dt: 0.9000, rms radial error=167.095, avgs=0
- 065/300: dt: 0.9000, rms radial error=166.159, avgs=0
- 070/300: dt: 0.9000, rms radial error=165.228, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.301, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.379, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.462, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.551, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.644, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.742, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.845, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.953, avgs=0
- 115/300: dt: 0.9000, rms radial error=157.066, avgs=0
- 120/300: dt: 0.9000, rms radial error=156.184, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.307, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.434, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.567, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.704, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.845, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.992, avgs=0
- 155/300: dt: 0.9000, rms radial error=150.143, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.299, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.459, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.624, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.794, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.968, avgs=0
- 185/300: dt: 0.9000, rms radial error=145.147, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.330, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.518, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.710, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.907, avgs=0
- 210/300: dt: 0.9000, rms radial error=141.108, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.313, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.523, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.737, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.955, avgs=0
- 235/300: dt: 0.9000, rms radial error=137.178, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.405, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.636, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.872, avgs=0
- 255/300: dt: 0.9000, rms radial error=134.111, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.356, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.604, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.857, avgs=0
- 275/300: dt: 0.9000, rms radial error=131.113, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.374, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.640, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.909, avgs=0
- 295/300: dt: 0.9000, rms radial error=128.182, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.460, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 17303.03
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00010
- epoch 2 (K=40.0), pass 1, starting sse = 2987.75
- 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 = 327.70
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.04/10 = 0.00444
- epoch 4 (K=640.0), pass 1, starting sse = 24.24
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.08/13 = 0.00651
- final distance error %28.48
- writing spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.07 hours
- mris_sphere utimesec 262.494094
- mris_sphere stimesec 0.185971
- mris_sphere ru_maxrss 213520
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 30831
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 10304
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 8991
- mris_sphere ru_nivcsw 19617
- FSRUNTIME@ mris_sphere 0.0730 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 0.95 +- 0.57 (0.00-->6.95) (max @ vno 65176 --> 66321)
- face area 0.02 +- 0.03 (-0.16-->0.60)
- == Number of threads available to mris_sphere for OpenMP = 2 ==
- scaling brain by 0.301...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.869, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.609, avgs=0
- 010/300: dt: 0.9000, rms radial error=176.051, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.318, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.484, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.591, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.666, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.725, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.780, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.833, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.887, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.943, avgs=0
- 060/300: dt: 0.9000, rms radial error=167.002, avgs=0
- 065/300: dt: 0.9000, rms radial error=166.065, avgs=0
- 070/300: dt: 0.9000, rms radial error=165.133, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.205, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.283, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.365, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.452, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.545, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.642, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.743, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.850, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.961, avgs=0
- 120/300: dt: 0.9000, rms radial error=156.078, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.199, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.324, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.455, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.590, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.730, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.875, avgs=0
- 155/300: dt: 0.9000, rms radial error=150.025, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.179, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.338, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.501, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.670, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.843, avgs=0
- 185/300: dt: 0.9000, rms radial error=145.021, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.203, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.390, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.582, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.778, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.978, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.183, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.393, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.607, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.826, avgs=0
- 235/300: dt: 0.9000, rms radial error=137.049, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.276, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.508, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.745, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.985, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.230, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.479, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.733, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.990, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.252, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.518, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.788, avgs=0
- 295/300: dt: 0.9000, rms radial error=128.062, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.340, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 17509.67
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00016
- epoch 2 (K=40.0), pass 1, starting sse = 2998.97
- 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 = 332.22
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.07/11 = 0.00599
- epoch 4 (K=640.0), pass 1, starting sse = 26.59
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.15/15 = 0.00982
- final distance error %27.26
- writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.07 hours
- mris_sphere utimesec 272.907511
- mris_sphere stimesec 0.219966
- mris_sphere ru_maxrss 216488
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 31060
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 10392
- mris_sphere ru_oublock 10432
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 9441
- mris_sphere ru_nivcsw 19557
- FSRUNTIME@ mris_sphere 0.0748 hours 1 threads
- PIDs (14438 14442) completed and logs appended.
- #--------------------------------------------
- #@# Fix Topology Copy lh Sat Oct 7 20:47:41 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- cp ../surf/lh.orig.nofix ../surf/lh.orig
- cp ../surf/lh.inflated.nofix ../surf/lh.inflated
- #--------------------------------------------
- #@# Fix Topology Copy rh Sat Oct 7 20:47:41 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- cp ../surf/rh.orig.nofix ../surf/rh.orig
- cp ../surf/rh.inflated.nofix ../surf/rh.inflated
- #@# Fix Topology lh Sat Oct 7 20:47:41 CEST 2017
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050669 lh
- #@# Fix Topology rh Sat Oct 7 20:47:41 CEST 2017
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050669 rh
- Waiting for PID 14658 of (14658 14661) to complete...
- Waiting for PID 14661 of (14658 14661) to complete...
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050669 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=-110 (nv=145808, nf=291836, ne=437754, g=56)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 9 iterations
- marking ambiguous vertices...
- 5072 ambiguous faces found in tessellation
- segmenting defects...
- 61 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 36 into 33
- -merging segment 39 into 33
- -merging segment 42 into 33
- -merging segment 49 into 45
- 57 defects to be corrected
- 0 vertices coincident
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.0702 (-4.5351)
- -vertex loglikelihood: -5.7067 (-2.8534)
- -normal dot loglikelihood: -3.6121 (-3.6121)
- -quad curv loglikelihood: -6.6154 (-3.3077)
- Total Loglikelihood : -25.0045
- CORRECTING DEFECT 0 (vertices=24, convex hull=53, v0=381)
- After retessellation of defect 0 (v0=381), euler #=-58 (142618,426282,283606) : difference with theory (-54) = 4
- CORRECTING DEFECT 1 (vertices=36, convex hull=64, v0=700)
- After retessellation of defect 1 (v0=700), euler #=-57 (142627,426334,283650) : difference with theory (-53) = 4
- CORRECTING DEFECT 2 (vertices=43, convex hull=95, v0=1824)
- After retessellation of defect 2 (v0=1824), euler #=-56 (142651,426447,283740) : difference with theory (-52) = 4
- CORRECTING DEFECT 3 (vertices=24, convex hull=64, v0=3477)
- After retessellation of defect 3 (v0=3477), euler #=-55 (142661,426505,283789) : difference with theory (-51) = 4
- CORRECTING DEFECT 4 (vertices=18, convex hull=41, v0=8440)
- After retessellation of defect 4 (v0=8440), euler #=-54 (142668,426540,283818) : difference with theory (-50) = 4
- CORRECTING DEFECT 5 (vertices=18, convex hull=60, v0=10739)
- After retessellation of defect 5 (v0=10739), euler #=-53 (142676,426587,283858) : difference with theory (-49) = 4
- CORRECTING DEFECT 6 (vertices=22, convex hull=45, v0=13326)
- After retessellation of defect 6 (v0=13326), euler #=-52 (142687,426635,283896) : difference with theory (-48) = 4
- CORRECTING DEFECT 7 (vertices=25, convex hull=45, v0=15414)
- After retessellation of defect 7 (v0=15414), euler #=-51 (142696,426678,283931) : difference with theory (-47) = 4
- CORRECTING DEFECT 8 (vertices=28, convex hull=57, v0=23122)
- After retessellation of defect 8 (v0=23122), euler #=-50 (142711,426746,283985) : difference with theory (-46) = 4
- CORRECTING DEFECT 9 (vertices=27, convex hull=61, v0=24695)
- After retessellation of defect 9 (v0=24695), euler #=-49 (142726,426817,284042) : difference with theory (-45) = 4
- CORRECTING DEFECT 10 (vertices=27, convex hull=45, v0=28204)
- After retessellation of defect 10 (v0=28204), euler #=-48 (142733,426851,284070) : difference with theory (-44) = 4
- CORRECTING DEFECT 11 (vertices=26, convex hull=50, v0=46234)
- After retessellation of defect 11 (v0=46234), euler #=-47 (142749,426917,284121) : difference with theory (-43) = 4
- CORRECTING DEFECT 12 (vertices=25, convex hull=63, v0=46915)
- After retessellation of defect 12 (v0=46915), euler #=-46 (142758,426967,284163) : difference with theory (-42) = 4
- CORRECTING DEFECT 13 (vertices=41, convex hull=71, v0=52015)
- After retessellation of defect 13 (v0=52015), euler #=-45 (142767,427023,284211) : difference with theory (-41) = 4
- CORRECTING DEFECT 14 (vertices=374, convex hull=201, v0=54901)
- After retessellation of defect 14 (v0=54901), euler #=-44 (142809,427244,284391) : difference with theory (-40) = 4
- CORRECTING DEFECT 15 (vertices=61, convex hull=103, v0=54983)
- After retessellation of defect 15 (v0=54983), euler #=-43 (142839,427379,284497) : difference with theory (-39) = 4
- CORRECTING DEFECT 16 (vertices=36, convex hull=82, v0=59746)
- After retessellation of defect 16 (v0=59746), euler #=-42 (142863,427486,284581) : difference with theory (-38) = 4
- CORRECTING DEFECT 17 (vertices=8, convex hull=23, v0=61761)
- After retessellation of defect 17 (v0=61761), euler #=-41 (142864,427497,284592) : difference with theory (-37) = 4
- CORRECTING DEFECT 18 (vertices=6, convex hull=24, v0=63992)
- After retessellation of defect 18 (v0=63992), euler #=-40 (142865,427506,284601) : difference with theory (-36) = 4
- CORRECTING DEFECT 19 (vertices=88, convex hull=93, v0=64140)
- After retessellation of defect 19 (v0=64140), euler #=-39 (142905,427664,284720) : difference with theory (-35) = 4
- CORRECTING DEFECT 20 (vertices=42, convex hull=50, v0=64702)
- After retessellation of defect 20 (v0=64702), euler #=-38 (142914,427707,284755) : difference with theory (-34) = 4
- CORRECTING DEFECT 21 (vertices=58, convex hull=65, v0=65642)
- After retessellation of defect 21 (v0=65642), euler #=-37 (142929,427780,284814) : difference with theory (-33) = 4
- CORRECTING DEFECT 22 (vertices=34, convex hull=65, v0=75054)
- After retessellation of defect 22 (v0=75054), euler #=-36 (142941,427844,284867) : difference with theory (-32) = 4
- CORRECTING DEFECT 23 (vertices=33, convex hull=76, v0=86296)
- After retessellation of defect 23 (v0=86296), euler #=-35 (142961,427930,284934) : difference with theory (-31) = 4
- CORRECTING DEFECT 24 (vertices=6, convex hull=19, v0=86960)
- After retessellation of defect 24 (v0=86960), euler #=-34 (142963,427942,284945) : difference with theory (-30) = 4
- CORRECTING DEFECT 25 (vertices=12, convex hull=14, v0=88758)
- After retessellation of defect 25 (v0=88758), euler #=-33 (142966,427952,284953) : difference with theory (-29) = 4
- CORRECTING DEFECT 26 (vertices=12, convex hull=23, v0=89850)
- After retessellation of defect 26 (v0=89850), euler #=-32 (142967,427961,284962) : difference with theory (-28) = 4
- CORRECTING DEFECT 27 (vertices=13, convex hull=30, v0=90692)
- After retessellation of defect 27 (v0=90692), euler #=-31 (142968,427975,284976) : difference with theory (-27) = 4
- CORRECTING DEFECT 28 (vertices=16, convex hull=50, v0=94225)
- After retessellation of defect 28 (v0=94225), euler #=-30 (142978,428024,285016) : difference with theory (-26) = 4
- CORRECTING DEFECT 29 (vertices=26, convex hull=28, v0=95760)
- After retessellation of defect 29 (v0=95760), euler #=-29 (142981,428041,285031) : difference with theory (-25) = 4
- CORRECTING DEFECT 30 (vertices=34, convex hull=58, v0=97134)
- After retessellation of defect 30 (v0=97134), euler #=-28 (142998,428116,285090) : difference with theory (-24) = 4
- CORRECTING DEFECT 31 (vertices=19, convex hull=28, v0=97174)
- After retessellation of defect 31 (v0=97174), euler #=-27 (143000,428132,285105) : difference with theory (-23) = 4
- CORRECTING DEFECT 32 (vertices=29, convex hull=21, v0=99865)
- After retessellation of defect 32 (v0=99865), euler #=-26 (143003,428145,285116) : difference with theory (-22) = 4
- CORRECTING DEFECT 33 (vertices=221, convex hull=239, v0=99992)
- After retessellation of defect 33 (v0=99992), euler #=-22 (143095,428544,285427) : difference with theory (-21) = 1
- CORRECTING DEFECT 34 (vertices=70, convex hull=31, v0=100950)
- After retessellation of defect 34 (v0=100950), euler #=-21 (143112,428604,285471) : difference with theory (-20) = 1
- CORRECTING DEFECT 35 (vertices=19, convex hull=28, v0=100964)
- After retessellation of defect 35 (v0=100964), euler #=-20 (143116,428624,285488) : difference with theory (-19) = 1
- CORRECTING DEFECT 36 (vertices=158, convex hull=78, v0=103548)
- After retessellation of defect 36 (v0=103548), euler #=-19 (143151,428769,285599) : difference with theory (-18) = 1
- CORRECTING DEFECT 37 (vertices=27, convex hull=76, v0=103751)
- After retessellation of defect 37 (v0=103751), euler #=-18 (143165,428842,285659) : difference with theory (-17) = 1
- CORRECTING DEFECT 38 (vertices=506, convex hull=188, v0=105342)
- After retessellation of defect 38 (v0=105342), euler #=-17 (143289,429302,285996) : difference with theory (-16) = 1
- CORRECTING DEFECT 39 (vertices=11, convex hull=20, v0=106273)
- After retessellation of defect 39 (v0=106273), euler #=-16 (143293,429319,286010) : difference with theory (-15) = 1
- CORRECTING DEFECT 40 (vertices=23, convex hull=53, v0=110397)
- After retessellation of defect 40 (v0=110397), euler #=-15 (143308,429384,286061) : difference with theory (-14) = 1
- CORRECTING DEFECT 41 (vertices=65, convex hull=33, v0=110417)
- After retessellation of defect 41 (v0=110417), euler #=-14 (143319,429429,286096) : difference with theory (-13) = 1
- CORRECTING DEFECT 42 (vertices=209, convex hull=246, v0=110785)
- After retessellation of defect 42 (v0=110785), euler #=-12 (143393,429784,286379) : difference with theory (-12) = 0
- CORRECTING DEFECT 43 (vertices=40, convex hull=67, v0=112744)
- After retessellation of defect 43 (v0=112744), euler #=-11 (143411,429867,286445) : difference with theory (-11) = 0
- CORRECTING DEFECT 44 (vertices=36, convex hull=36, v0=115496)
- After retessellation of defect 44 (v0=115496), euler #=-10 (143415,429890,286465) : difference with theory (-10) = 0
- CORRECTING DEFECT 45 (vertices=34, convex hull=29, v0=116444)
- After retessellation of defect 45 (v0=116444), euler #=-9 (143419,429913,286485) : difference with theory (-9) = 0
- CORRECTING DEFECT 46 (vertices=91, convex hull=97, v0=120871)
- After retessellation of defect 46 (v0=120871), euler #=-8 (143451,430051,286592) : difference with theory (-8) = 0
- CORRECTING DEFECT 47 (vertices=48, convex hull=86, v0=121752)
- After retessellation of defect 47 (v0=121752), euler #=-7 (143479,430175,286689) : difference with theory (-7) = 0
- CORRECTING DEFECT 48 (vertices=62, convex hull=68, v0=122623)
- After retessellation of defect 48 (v0=122623), euler #=-6 (143502,430278,286770) : difference with theory (-6) = 0
- CORRECTING DEFECT 49 (vertices=33, convex hull=53, v0=128457)
- After retessellation of defect 49 (v0=128457), euler #=-5 (143514,430334,286815) : difference with theory (-5) = 0
- CORRECTING DEFECT 50 (vertices=34, convex hull=68, v0=129315)
- After retessellation of defect 50 (v0=129315), euler #=-4 (143526,430396,286866) : difference with theory (-4) = 0
- CORRECTING DEFECT 51 (vertices=32, convex hull=61, v0=133736)
- After retessellation of defect 51 (v0=133736), euler #=-3 (143541,430470,286926) : difference with theory (-3) = 0
- CORRECTING DEFECT 52 (vertices=32, convex hull=74, v0=136752)
- After retessellation of defect 52 (v0=136752), euler #=-2 (143557,430547,286988) : difference with theory (-2) = 0
- CORRECTING DEFECT 53 (vertices=30, convex hull=63, v0=137617)
- After retessellation of defect 53 (v0=137617), euler #=-1 (143571,430616,287044) : difference with theory (-1) = 0
- CORRECTING DEFECT 54 (vertices=42, convex hull=85, v0=141659)
- After retessellation of defect 54 (v0=141659), euler #=0 (143584,430689,287105) : difference with theory (0) = 0
- CORRECTING DEFECT 55 (vertices=17, convex hull=56, v0=142913)
- After retessellation of defect 55 (v0=142913), euler #=1 (143592,430735,287144) : difference with theory (1) = 0
- CORRECTING DEFECT 56 (vertices=64, convex hull=84, v0=145111)
- After retessellation of defect 56 (v0=145111), euler #=2 (143612,430830,287220) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.23 (0.09-->8.71) (max @ vno 61067 --> 62202)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.23 (0.09-->8.71) (max @ vno 61067 --> 62202)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 208 mutations (36.7%), 358 crossovers (63.3%), 197 vertices were eliminated
- building final representation...
- 2196 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=143612, nf=287220, ne=430830, g=0)
- writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 31.2 minutes
- 0 defective edges
- removing intersecting faces
- 000: 357 intersecting
- 001: 7 intersecting
- mris_fix_topology utimesec 1868.683916
- mris_fix_topology stimesec 0.276957
- mris_fix_topology ru_maxrss 454684
- mris_fix_topology ru_ixrss 0
- mris_fix_topology ru_idrss 0
- mris_fix_topology ru_isrss 0
- mris_fix_topology ru_minflt 56747
- mris_fix_topology ru_majflt 0
- mris_fix_topology ru_nswap 0
- mris_fix_topology ru_inblock 10264
- mris_fix_topology ru_oublock 13808
- mris_fix_topology ru_msgsnd 0
- mris_fix_topology ru_msgrcv 0
- mris_fix_topology ru_nsignals 0
- mris_fix_topology ru_nvcsw 428
- mris_fix_topology ru_nivcsw 4784
- FSRUNTIME@ mris_fix_topology lh 0.5192 hours 1 threads
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050669 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=-114 (nv=147584, nf=295396, ne=443094, g=58)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 9 iterations
- marking ambiguous vertices...
- 7429 ambiguous faces found in tessellation
- segmenting defects...
- 68 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 4 into 3
- -merging segment 19 into 16
- -merging segment 38 into 32
- -merging segment 37 into 35
- -merging segment 43 into 42
- -merging segment 63 into 60
- 62 defects to be corrected
- 0 vertices coincident
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -8.8917 (-4.4459)
- -vertex loglikelihood: -5.6909 (-2.8455)
- -normal dot loglikelihood: -3.5628 (-3.5628)
- -quad curv loglikelihood: -6.3005 (-3.1502)
- Total Loglikelihood : -24.4459
- CORRECTING DEFECT 0 (vertices=29, convex hull=50, v0=137)
- After retessellation of defect 0 (v0=137), euler #=-64 (142960,426807,283783) : difference with theory (-59) = 5
- CORRECTING DEFECT 1 (vertices=820, convex hull=418, v0=1630)
- After retessellation of defect 1 (v0=1630), euler #=-63 (143047,427262,284152) : difference with theory (-58) = 5
- CORRECTING DEFECT 2 (vertices=5, convex hull=16, v0=1703)
- After retessellation of defect 2 (v0=1703), euler #=-62 (143047,427267,284158) : difference with theory (-57) = 5
- CORRECTING DEFECT 3 (vertices=50, convex hull=107, v0=2940)
- After retessellation of defect 3 (v0=2940), euler #=-60 (143056,427347,284231) : difference with theory (-56) = 4
- CORRECTING DEFECT 4 (vertices=41, convex hull=73, v0=7696)
- After retessellation of defect 4 (v0=7696), euler #=-59 (143083,427460,284318) : difference with theory (-55) = 4
- CORRECTING DEFECT 5 (vertices=31, convex hull=61, v0=12272)
- After retessellation of defect 5 (v0=12272), euler #=-58 (143098,427531,284375) : difference with theory (-54) = 4
- CORRECTING DEFECT 6 (vertices=7, convex hull=19, v0=14465)
- After retessellation of defect 6 (v0=14465), euler #=-57 (143099,427538,284382) : difference with theory (-53) = 4
- CORRECTING DEFECT 7 (vertices=60, convex hull=79, v0=18218)
- After retessellation of defect 7 (v0=18218), euler #=-56 (143128,427658,284474) : difference with theory (-52) = 4
- CORRECTING DEFECT 8 (vertices=33, convex hull=54, v0=30411)
- After retessellation of defect 8 (v0=30411), euler #=-55 (143139,427708,284514) : difference with theory (-51) = 4
- CORRECTING DEFECT 9 (vertices=45, convex hull=84, v0=32796)
- After retessellation of defect 9 (v0=32796), euler #=-54 (143170,427835,284611) : difference with theory (-50) = 4
- CORRECTING DEFECT 10 (vertices=34, convex hull=62, v0=39101)
- After retessellation of defect 10 (v0=39101), euler #=-53 (143180,427889,284656) : difference with theory (-49) = 4
- CORRECTING DEFECT 11 (vertices=52, convex hull=68, v0=50339)
- After retessellation of defect 11 (v0=50339), euler #=-52 (143196,427967,284719) : difference with theory (-48) = 4
- CORRECTING DEFECT 12 (vertices=27, convex hull=50, v0=54669)
- After retessellation of defect 12 (v0=54669), euler #=-51 (143205,428010,284754) : difference with theory (-47) = 4
- CORRECTING DEFECT 13 (vertices=248, convex hull=191, v0=56318)
- After retessellation of defect 13 (v0=56318), euler #=-51 (143236,428201,284914) : difference with theory (-46) = 5
- CORRECTING DEFECT 14 (vertices=32, convex hull=84, v0=57596)
- After retessellation of defect 14 (v0=57596), euler #=-50 (143251,428277,284976) : difference with theory (-45) = 5
- CORRECTING DEFECT 15 (vertices=25, convex hull=46, v0=63695)
- After retessellation of defect 15 (v0=63695), euler #=-48 (143258,428313,285007) : difference with theory (-44) = 4
- CORRECTING DEFECT 16 (vertices=28, convex hull=62, v0=64055)
- After retessellation of defect 16 (v0=64055), euler #=-47 (143272,428379,285060) : difference with theory (-43) = 4
- CORRECTING DEFECT 17 (vertices=300, convex hull=240, v0=65140)
- After retessellation of defect 17 (v0=65140), euler #=-46 (143365,428773,285362) : difference with theory (-42) = 4
- CORRECTING DEFECT 18 (vertices=91, convex hull=100, v0=68724)
- After retessellation of defect 18 (v0=68724), euler #=-45 (143407,428954,285502) : difference with theory (-41) = 4
- CORRECTING DEFECT 19 (vertices=91, convex hull=140, v0=73815)
- After retessellation of defect 19 (v0=73815), euler #=-44 (143416,429047,285587) : difference with theory (-40) = 4
- CORRECTING DEFECT 20 (vertices=27, convex hull=59, v0=74129)
- After retessellation of defect 20 (v0=74129), euler #=-43 (143427,429103,285633) : difference with theory (-39) = 4
- CORRECTING DEFECT 21 (vertices=19, convex hull=27, v0=77032)
- After retessellation of defect 21 (v0=77032), euler #=-42 (143430,429121,285649) : difference with theory (-38) = 4
- CORRECTING DEFECT 22 (vertices=14, convex hull=21, v0=81072)
- After retessellation of defect 22 (v0=81072), euler #=-41 (143434,429139,285664) : difference with theory (-37) = 4
- CORRECTING DEFECT 23 (vertices=28, convex hull=44, v0=82761)
- After retessellation of defect 23 (v0=82761), euler #=-40 (143445,429187,285702) : difference with theory (-36) = 4
- CORRECTING DEFECT 24 (vertices=33, convex hull=24, v0=83109)
- After retessellation of defect 24 (v0=83109), euler #=-39 (143447,429199,285713) : difference with theory (-35) = 4
- CORRECTING DEFECT 25 (vertices=9, convex hull=22, v0=83405)
- After retessellation of defect 25 (v0=83405), euler #=-38 (143449,429210,285723) : difference with theory (-34) = 4
- CORRECTING DEFECT 26 (vertices=50, convex hull=63, v0=85667)
- After retessellation of defect 26 (v0=85667), euler #=-37 (143460,429264,285767) : difference with theory (-33) = 4
- CORRECTING DEFECT 27 (vertices=98, convex hull=35, v0=85842)
- After retessellation of defect 27 (v0=85842), euler #=-36 (143466,429293,285791) : difference with theory (-32) = 4
- CORRECTING DEFECT 28 (vertices=22, convex hull=35, v0=87916)
- After retessellation of defect 28 (v0=87916), euler #=-35 (143470,429317,285812) : difference with theory (-31) = 4
- CORRECTING DEFECT 29 (vertices=31, convex hull=62, v0=92857)
- After retessellation of defect 29 (v0=92857), euler #=-34 (143487,429393,285872) : difference with theory (-30) = 4
- CORRECTING DEFECT 30 (vertices=300, convex hull=261, v0=93912)
- After retessellation of defect 30 (v0=93912), euler #=-32 (143607,429875,286236) : difference with theory (-29) = 3
- CORRECTING DEFECT 31 (vertices=31, convex hull=74, v0=95722)
- After retessellation of defect 31 (v0=95722), euler #=-31 (143624,429951,286296) : difference with theory (-28) = 3
- CORRECTING DEFECT 32 (vertices=105, convex hull=40, v0=97984)
- After retessellation of defect 32 (v0=97984), euler #=-30 (143632,429992,286330) : difference with theory (-27) = 3
- CORRECTING DEFECT 33 (vertices=194, convex hull=149, v0=100043)
- After retessellation of defect 33 (v0=100043), euler #=-28 (143702,430276,286546) : difference with theory (-26) = 2
- CORRECTING DEFECT 34 (vertices=20, convex hull=24, v0=100508)
- After retessellation of defect 34 (v0=100508), euler #=-27 (143705,430292,286560) : difference with theory (-25) = 2
- CORRECTING DEFECT 35 (vertices=34, convex hull=31, v0=106322)
- After retessellation of defect 35 (v0=106322), euler #=-26 (143711,430321,286584) : difference with theory (-24) = 2
- CORRECTING DEFECT 36 (vertices=33, convex hull=27, v0=106576)
- After retessellation of defect 36 (v0=106576), euler #=-25 (143720,430355,286610) : difference with theory (-23) = 2
- CORRECTING DEFECT 37 (vertices=57, convex hull=73, v0=108039)
- After retessellation of defect 37 (v0=108039), euler #=-24 (143739,430445,286682) : difference with theory (-22) = 2
- CORRECTING DEFECT 38 (vertices=191, convex hull=126, v0=108067)
- After retessellation of defect 38 (v0=108067), euler #=-22 (143762,430571,286787) : difference with theory (-21) = 1
- CORRECTING DEFECT 39 (vertices=30, convex hull=65, v0=110719)
- After retessellation of defect 39 (v0=110719), euler #=-21 (143772,430625,286832) : difference with theory (-20) = 1
- CORRECTING DEFECT 40 (vertices=7, convex hull=13, v0=110748)
- After retessellation of defect 40 (v0=110748), euler #=-20 (143772,430627,286835) : difference with theory (-19) = 1
- CORRECTING DEFECT 41 (vertices=10, convex hull=26, v0=110983)
- After retessellation of defect 41 (v0=110983), euler #=-19 (143777,430652,286856) : difference with theory (-18) = 1
- CORRECTING DEFECT 42 (vertices=26, convex hull=56, v0=111022)
- After retessellation of defect 42 (v0=111022), euler #=-18 (143793,430721,286910) : difference with theory (-17) = 1
- CORRECTING DEFECT 43 (vertices=22, convex hull=68, v0=111723)
- After retessellation of defect 43 (v0=111723), euler #=-17 (143807,430790,286966) : difference with theory (-16) = 1
- CORRECTING DEFECT 44 (vertices=64, convex hull=104, v0=112341)
- After retessellation of defect 44 (v0=112341), euler #=-16 (143834,430913,287063) : difference with theory (-15) = 1
- CORRECTING DEFECT 45 (vertices=27, convex hull=37, v0=113148)
- After retessellation of defect 45 (v0=113148), euler #=-15 (143836,430932,287081) : difference with theory (-14) = 1
- CORRECTING DEFECT 46 (vertices=63, convex hull=94, v0=114420)
- After retessellation of defect 46 (v0=114420), euler #=-14 (143866,431063,287183) : difference with theory (-13) = 1
- CORRECTING DEFECT 47 (vertices=35, convex hull=81, v0=114522)
- After retessellation of defect 47 (v0=114522), euler #=-13 (143883,431147,287251) : difference with theory (-12) = 1
- CORRECTING DEFECT 48 (vertices=45, convex hull=71, v0=117323)
- After retessellation of defect 48 (v0=117323), euler #=-12 (143905,431240,287323) : difference with theory (-11) = 1
- CORRECTING DEFECT 49 (vertices=57, convex hull=92, v0=117965)
- After retessellation of defect 49 (v0=117965), euler #=-11 (143931,431360,287418) : difference with theory (-10) = 1
- CORRECTING DEFECT 50 (vertices=60, convex hull=53, v0=122942)
- After retessellation of defect 50 (v0=122942), euler #=-10 (143941,431404,287453) : difference with theory (-9) = 1
- CORRECTING DEFECT 51 (vertices=29, convex hull=78, v0=123811)
- After retessellation of defect 51 (v0=123811), euler #=-9 (143950,431459,287500) : difference with theory (-8) = 1
- CORRECTING DEFECT 52 (vertices=35, convex hull=67, v0=123813)
- After retessellation of defect 52 (v0=123813), euler #=-8 (143960,431517,287549) : difference with theory (-7) = 1
- CORRECTING DEFECT 53 (vertices=34, convex hull=53, v0=123914)
- After retessellation of defect 53 (v0=123914), euler #=-7 (143974,431578,287597) : difference with theory (-6) = 1
- CORRECTING DEFECT 54 (vertices=39, convex hull=26, v0=125241)
- After retessellation of defect 54 (v0=125241), euler #=-6 (143977,431595,287612) : difference with theory (-5) = 1
- CORRECTING DEFECT 55 (vertices=375, convex hull=322, v0=125331)
- After retessellation of defect 55 (v0=125331), euler #=-4 (144121,432200,288075) : difference with theory (-4) = 0
- CORRECTING DEFECT 56 (vertices=27, convex hull=61, v0=126240)
- After retessellation of defect 56 (v0=126240), euler #=-3 (144130,432251,288118) : difference with theory (-3) = 0
- CORRECTING DEFECT 57 (vertices=68, convex hull=29, v0=129351)
- After retessellation of defect 57 (v0=129351), euler #=-2 (144136,432281,288143) : difference with theory (-2) = 0
- CORRECTING DEFECT 58 (vertices=25, convex hull=53, v0=136823)
- After retessellation of defect 58 (v0=136823), euler #=-1 (144148,432340,288191) : difference with theory (-1) = 0
- CORRECTING DEFECT 59 (vertices=45, convex hull=81, v0=137489)
- After retessellation of defect 59 (v0=137489), euler #=0 (144172,432443,288271) : difference with theory (0) = 0
- CORRECTING DEFECT 60 (vertices=134, convex hull=89, v0=144524)
- After retessellation of defect 60 (v0=144524), euler #=1 (144190,432537,288348) : difference with theory (1) = 0
- CORRECTING DEFECT 61 (vertices=30, convex hull=70, v0=147322)
- After retessellation of defect 61 (v0=147322), euler #=2 (144204,432606,288404) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.88 +- 0.24 (0.06-->9.04) (max @ vno 57500 --> 58640)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.88 +- 0.24 (0.06-->9.04) (max @ vno 57500 --> 58640)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 231 mutations (35.3%), 423 crossovers (64.7%), 462 vertices were eliminated
- building final representation...
- 3380 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=144204, nf=288404, ne=432606, g=0)
- writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 54.0 minutes
- 0 defective edges
- removing intersecting faces
- 000: 506 intersecting
- 001: 16 intersecting
- mris_fix_topology utimesec 3241.246255
- mris_fix_topology stimesec 0.198969
- mris_fix_topology ru_maxrss 458944
- mris_fix_topology ru_ixrss 0
- mris_fix_topology ru_idrss 0
- mris_fix_topology ru_isrss 0
- mris_fix_topology ru_minflt 60015
- mris_fix_topology ru_majflt 0
- mris_fix_topology ru_nswap 0
- mris_fix_topology ru_inblock 0
- mris_fix_topology ru_oublock 14008
- mris_fix_topology ru_msgsnd 0
- mris_fix_topology ru_msgrcv 0
- mris_fix_topology ru_nsignals 0
- mris_fix_topology ru_nvcsw 588
- mris_fix_topology ru_nivcsw 4531
- FSRUNTIME@ mris_fix_topology rh 0.9004 hours 1 threads
- PIDs (14658 14661) completed and logs appended.
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 143612 - 430830 + 287220 = 2 --> 0 holes
- F =2V-4: 287220 = 287224-4 (0)
- 2E=3F: 861660 = 861660 (0)
- total defect index = 0
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 144204 - 432606 + 288404 = 2 --> 0 holes
- F =2V-4: 288404 = 288408-4 (0)
- 2E=3F: 865212 = 865212 (0)
- total defect index = 0
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 22 intersecting
- 001: 2 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 45 intersecting
- 001: 2 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Sat Oct 7 21:41:55 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050669 lh
- #--------------------------------------------
- #@# Make White Surf rh Sat Oct 7 21:41:55 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050669 rh
- Waiting for PID 19761 of (19761 19764) to complete...
- Waiting for PID 19764 of (19761 19764) to complete...
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050669 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-6.0.0/0050669/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/wm.mgz...
- 37330 bright wm thresholded.
- 2468 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.orig...
- computing class statistics...
- border white: 295606 voxels (1.76%)
- border gray 303578 voxels (1.81%)
- WM (103.0): 103.2 +- 5.8 [70.0 --> 110.0]
- GM (85.0) : 83.8 +- 10.2 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 71.8 (was 70)
- setting MAX_BORDER_WHITE to 111.8 (was 105)
- setting MIN_BORDER_WHITE to 82.0 (was 85)
- setting MAX_CSF to 61.6 (was 40)
- setting MAX_GRAY to 100.2 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 71.8 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 51.3 (was 40)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.22 (0.04-->4.84) (max @ vno 58849 --> 142782)
- face area 0.27 +- 0.13 (0.00-->2.70)
- mean absolute distance = 0.82 +- 0.99
- 4144 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=106+-5.2, GM=82+-6.1
- mean inside = 99.9, mean outside = 87.1
- 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=89.8, 94 (94) missing vertices, mean dist 0.3 [0.7 (%32.7)->0.9 (%67.3))]
- %67 local maxima, %28 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 +- 0.26 (0.07-->6.09) (max @ vno 142791 --> 59998)
- face area 0.27 +- 0.13 (0.00-->3.31)
- mean absolute distance = 0.42 +- 0.65
- 4539 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=2149391.2, rms=7.530
- 001: dt: 0.5000, sse=1372783.4, rms=5.454 (27.572%)
- 002: dt: 0.5000, sse=1013611.6, rms=4.100 (24.832%)
- 003: dt: 0.5000, sse=842715.4, rms=3.235 (21.084%)
- 004: dt: 0.5000, sse=756240.8, rms=2.711 (16.201%)
- 005: dt: 0.5000, sse=717017.5, rms=2.433 (10.264%)
- 006: dt: 0.5000, sse=697453.4, rms=2.289 (5.899%)
- 007: dt: 0.5000, sse=692912.2, rms=2.217 (3.152%)
- rms = 2.18, time step reduction 1 of 3 to 0.250...
- 008: dt: 0.5000, sse=685517.1, rms=2.177 (1.810%)
- 009: dt: 0.2500, sse=637262.7, rms=1.604 (26.308%)
- 010: dt: 0.2500, sse=630475.1, rms=1.516 (5.517%)
- rms = 1.50, time step reduction 2 of 3 to 0.125...
- 011: dt: 0.2500, sse=631081.2, rms=1.501 (0.976%)
- rms = 1.49, time step reduction 3 of 3 to 0.062...
- 012: dt: 0.1250, sse=628111.9, rms=1.487 (0.958%)
- positioning took 1.3 minutes
- inhibiting deformation at non-cortical midline structures...
- mean border=91.7, 82 (11) missing vertices, mean dist -0.2 [0.5 (%67.5)->0.3 (%32.5))]
- %79 local maxima, %16 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 +- 0.25 (0.07-->6.50) (max @ vno 142791 --> 59998)
- face area 0.35 +- 0.16 (0.00-->4.64)
- mean absolute distance = 0.32 +- 0.42
- 4231 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1010764.6, rms=3.283
- 013: dt: 0.5000, sse=831017.2, rms=2.086 (36.482%)
- 014: dt: 0.5000, sse=794266.3, rms=1.776 (14.856%)
- rms = 1.75, time step reduction 1 of 3 to 0.250...
- 015: dt: 0.5000, sse=790644.9, rms=1.747 (1.594%)
- 016: dt: 0.2500, sse=761540.9, rms=1.352 (22.627%)
- rms = 1.30, time step reduction 2 of 3 to 0.125...
- 017: dt: 0.2500, sse=760545.1, rms=1.304 (3.560%)
- rms = 1.29, time step reduction 3 of 3 to 0.062...
- 018: dt: 0.1250, sse=757710.5, rms=1.287 (1.267%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- mean border=93.5, 57 (5) missing vertices, mean dist -0.2 [0.3 (%70.6)->0.3 (%29.4))]
- %89 local maxima, % 6 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 +- 0.25 (0.04-->6.73) (max @ vno 142791 --> 59998)
- face area 0.34 +- 0.16 (0.00-->4.63)
- mean absolute distance = 0.26 +- 0.35
- 3704 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=884918.2, rms=2.670
- 019: dt: 0.5000, sse=770354.6, rms=1.668 (37.541%)
- 020: dt: 0.5000, sse=757770.6, rms=1.566 (6.066%)
- rms = 1.65, time step reduction 1 of 3 to 0.250...
- 021: dt: 0.2500, sse=735994.7, rms=1.299 (17.054%)
- 022: dt: 0.2500, sse=732303.9, rms=1.183 (8.927%)
- rms = 1.18, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=728356.8, rms=1.176 (0.647%)
- rms = 1.16, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=727468.4, rms=1.164 (1.021%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- mean border=94.1, 72 (5) missing vertices, mean dist -0.1 [0.3 (%57.2)->0.2 (%42.8))]
- %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-6.0.0/0050669/surf/lh.white.preaparc...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=733897.6, rms=1.430
- 025: dt: 0.5000, sse=709139.0, rms=1.011 (29.313%)
- rms = 1.38, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.2500, sse=697827.1, rms=0.902 (10.751%)
- rms = 0.94, time step reduction 2 of 3 to 0.125...
- rms = 0.89, time step reduction 3 of 3 to 0.062...
- 027: dt: 0.1250, sse=697505.2, rms=0.894 (0.895%)
- positioning took 0.5 minutes
- generating cortex label...
- 11 non-cortical segments detected
- only using segment with 7886 vertices
- erasing segment 1 (vno[0] = 54313)
- erasing segment 2 (vno[0] = 59678)
- erasing segment 3 (vno[0] = 81051)
- erasing segment 4 (vno[0] = 81062)
- erasing segment 5 (vno[0] = 83338)
- erasing segment 6 (vno[0] = 88718)
- erasing segment 7 (vno[0] = 94036)
- erasing segment 8 (vno[0] = 106633)
- erasing segment 9 (vno[0] = 106653)
- erasing segment 10 (vno[0] = 111197)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/label/lh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.area
- vertex spacing 0.89 +- 0.25 (0.04-->6.79) (max @ vno 59998 --> 142791)
- face area 0.33 +- 0.16 (0.00-->4.58)
- refinement took 5.0 minutes
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050669 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-6.0.0/0050669/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/wm.mgz...
- 37330 bright wm thresholded.
- 2468 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.orig...
- computing class statistics...
- border white: 295606 voxels (1.76%)
- border gray 303578 voxels (1.81%)
- WM (103.0): 103.2 +- 5.8 [70.0 --> 110.0]
- GM (85.0) : 83.8 +- 10.2 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 71.8 (was 70)
- setting MAX_BORDER_WHITE to 111.8 (was 105)
- setting MIN_BORDER_WHITE to 82.0 (was 85)
- setting MAX_CSF to 61.6 (was 40)
- setting MAX_GRAY to 100.2 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 71.8 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 51.3 (was 40)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.23 (0.03-->4.58) (max @ vno 5723 --> 143000)
- face area 0.27 +- 0.13 (0.00-->3.17)
- mean absolute distance = 0.82 +- 1.01
- 4448 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=106+-5.2, GM=82+-7.0
- mean inside = 99.9, mean outside = 87.3
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- mean border=90.1, 105 (105) missing vertices, mean dist 0.3 [0.7 (%33.4)->0.9 (%66.6))]
- %70 local maxima, %26 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 0.91 +- 0.26 (0.09-->5.38) (max @ vno 143323 --> 143361)
- face area 0.27 +- 0.13 (0.00-->3.89)
- mean absolute distance = 0.42 +- 0.66
- 4664 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=2108989.5, rms=7.388
- 001: dt: 0.5000, sse=1350863.2, rms=5.319 (28.002%)
- 002: dt: 0.5000, sse=1002058.1, rms=3.976 (25.247%)
- 003: dt: 0.5000, sse=831881.3, rms=3.134 (21.193%)
- 004: dt: 0.5000, sse=750796.4, rms=2.624 (16.260%)
- 005: dt: 0.5000, sse=717230.8, rms=2.367 (9.810%)
- 006: dt: 0.5000, sse=700340.6, rms=2.235 (5.577%)
- 007: dt: 0.5000, sse=693960.4, rms=2.179 (2.471%)
- rms = 2.14, time step reduction 1 of 3 to 0.250...
- 008: dt: 0.5000, sse=691184.3, rms=2.142 (1.698%)
- 009: dt: 0.2500, sse=644150.7, rms=1.572 (26.623%)
- 010: dt: 0.2500, sse=636670.8, rms=1.483 (5.666%)
- rms = 1.47, time step reduction 2 of 3 to 0.125...
- 011: dt: 0.2500, sse=634121.6, rms=1.473 (0.700%)
- rms = 1.46, time step reduction 3 of 3 to 0.062...
- 012: dt: 0.1250, sse=632779.8, rms=1.457 (1.062%)
- positioning took 1.3 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=92.0, 61 (16) missing vertices, mean dist -0.2 [0.5 (%67.5)->0.3 (%32.5))]
- %81 local maxima, %15 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 +- 0.25 (0.12-->5.22) (max @ vno 55122 --> 55103)
- face area 0.34 +- 0.17 (0.00-->5.07)
- mean absolute distance = 0.33 +- 0.43
- 5047 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1008639.8, rms=3.228
- 013: dt: 0.5000, sse=836143.4, rms=2.047 (36.582%)
- 014: dt: 0.5000, sse=799365.6, rms=1.745 (14.728%)
- rms = 1.71, time step reduction 1 of 3 to 0.250...
- 015: dt: 0.5000, sse=794354.2, rms=1.714 (1.823%)
- 016: dt: 0.2500, sse=766803.8, rms=1.339 (21.863%)
- rms = 1.29, time step reduction 2 of 3 to 0.125...
- 017: dt: 0.2500, sse=775600.3, rms=1.293 (3.397%)
- rms = 1.28, time step reduction 3 of 3 to 0.062...
- 018: dt: 0.1250, sse=763611.9, rms=1.279 (1.158%)
- positioning took 0.6 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=93.7, 84 (7) missing vertices, mean dist -0.2 [0.4 (%70.6)->0.3 (%29.4))]
- %90 local maxima, % 6 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 +- 0.25 (0.06-->5.49) (max @ vno 55122 --> 55103)
- face area 0.34 +- 0.16 (0.00-->5.02)
- mean absolute distance = 0.26 +- 0.36
- 4242 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=882521.2, rms=2.576
- 019: dt: 0.5000, sse=776687.1, rms=1.658 (35.632%)
- 020: dt: 0.5000, sse=764299.9, rms=1.562 (5.828%)
- rms = 1.63, time step reduction 1 of 3 to 0.250...
- 021: dt: 0.2500, sse=744905.9, rms=1.305 (16.433%)
- 022: dt: 0.2500, sse=738057.6, rms=1.187 (9.079%)
- rms = 1.18, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=739030.2, rms=1.176 (0.887%)
- rms = 1.16, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=736031.9, rms=1.165 (0.959%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=94.2, 89 (6) missing vertices, mean dist -0.1 [0.3 (%57.5)->0.2 (%42.5))]
- %92 local maxima, % 3 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-6.0.0/0050669/surf/rh.white.preaparc...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=743911.1, rms=1.437
- 025: dt: 0.5000, sse=714177.9, rms=1.016 (29.272%)
- rms = 1.36, time step reduction 1 of 3 to 0.250...
- 026: dt: 0.2500, sse=709525.9, rms=0.914 (10.083%)
- rms = 0.95, time step reduction 2 of 3 to 0.125...
- rms = 0.91, time step reduction 3 of 3 to 0.062...
- 027: dt: 0.1250, sse=706863.8, rms=0.906 (0.891%)
- positioning took 0.5 minutes
- generating cortex label...
- 10 non-cortical segments detected
- only using segment with 7439 vertices
- erasing segment 1 (vno[0] = 61109)
- erasing segment 2 (vno[0] = 91907)
- erasing segment 3 (vno[0] = 93970)
- erasing segment 4 (vno[0] = 95973)
- erasing segment 5 (vno[0] = 104049)
- erasing segment 6 (vno[0] = 105933)
- erasing segment 7 (vno[0] = 107714)
- erasing segment 8 (vno[0] = 108685)
- erasing segment 9 (vno[0] = 114324)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/label/rh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.area
- vertex spacing 0.89 +- 0.25 (0.05-->5.54) (max @ vno 55103 --> 55122)
- face area 0.33 +- 0.16 (0.00-->4.98)
- refinement took 5.1 minutes
- PIDs (19761 19764) completed and logs appended.
- #--------------------------------------------
- #@# Smooth2 lh Sat Oct 7 21:46:59 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm
- #--------------------------------------------
- #@# Smooth2 rh Sat Oct 7 21:46:59 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm
- Waiting for PID 19994 of (19994 19997) to complete...
- Waiting for PID 19997 of (19994 19997) 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 (19994 19997) completed and logs appended.
- #--------------------------------------------
- #@# Inflation2 lh Sat Oct 7 21:47:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated
- #--------------------------------------------
- #@# Inflation2 rh Sat Oct 7 21:47:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated
- Waiting for PID 20046 of (20046 20049) to complete...
- Waiting for PID 20049 of (20046 20049) to complete...
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated
- Reading ../surf/lh.smoothwm
- avg radius = 47.8 mm, total surface area = 85454 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.181 (target=0.015)
step 005: RMS=0.126 (target=0.015)
step 010: RMS=0.093 (target=0.015)
step 015: RMS=0.077 (target=0.015)
step 020: RMS=0.063 (target=0.015)
step 025: RMS=0.053 (target=0.015)
step 030: RMS=0.044 (target=0.015)
step 035: RMS=0.038 (target=0.015)
step 040: RMS=0.033 (target=0.015)
step 045: RMS=0.030 (target=0.015)
step 050: RMS=0.027 (target=0.015)
step 055: RMS=0.025 (target=0.015)
step 060: RMS=0.023 (target=0.015)
- inflation complete.
- inflation took 0.9 minutes
- mris_inflate utimesec 54.704683
- mris_inflate stimesec 0.139978
- mris_inflate ru_maxrss 210248
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 30653
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 10104
- mris_inflate ru_oublock 11248
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 1879
- mris_inflate ru_nivcsw 3321
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated
- Reading ../surf/rh.smoothwm
- avg radius = 47.7 mm, total surface area = 85920 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.181 (target=0.015)
step 005: RMS=0.126 (target=0.015)
step 010: RMS=0.095 (target=0.015)
step 015: RMS=0.077 (target=0.015)
step 020: RMS=0.064 (target=0.015)
step 025: RMS=0.053 (target=0.015)
step 030: RMS=0.044 (target=0.015)
step 035: RMS=0.037 (target=0.015)
step 040: RMS=0.032 (target=0.015)
step 045: RMS=0.028 (target=0.015)
step 050: RMS=0.026 (target=0.015)
step 055: RMS=0.024 (target=0.015)
step 060: RMS=0.022 (target=0.015)
- inflation complete.
- inflation took 0.7 minutes
- mris_inflate utimesec 44.345258
- mris_inflate stimesec 0.127980
- mris_inflate ru_maxrss 211516
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 30969
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 10144
- mris_inflate ru_oublock 11288
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2078
- mris_inflate ru_nivcsw 3408
- PIDs (20046 20049) completed and logs appended.
- #--------------------------------------------
- #@# Curv .H and .K lh Sat Oct 7 21:48:02 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 21:48:02 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/surf
- reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 20163 of (20163 20166 20169 20172 20175 20178 20181 20184 20187 20190 20193 20196) to complete...
- Waiting for PID 20166 of (20163 20166 20169 20172 20175 20178 20181 20184 20187 20190 20193 20196) to complete...
- Waiting for PID 20169 of (20163 20166 20169 20172 20175 20178 20181 20184 20187 20190 20193 20196) to complete...
- Waiting for PID 20172 of (20163 20166 20169 20172 20175 20178 20181 20184 20187 20190 20193 20196) to complete...
- Waiting for PID 20175 of (20163 20166 20169 20172 20175 20178 20181 20184 20187 20190 20193 20196) to complete...
- Waiting for PID 20178 of (20163 20166 20169 20172 20175 20178 20181 20184 20187 20190 20193 20196) to complete...
- Waiting for PID 20181 of (20163 20166 20169 20172 20175 20178 20181 20184 20187 20190 20193 20196) to complete...
- Waiting for PID 20184 of (20163 20166 20169 20172 20175 20178 20181 20184 20187 20190 20193 20196) to complete...
- Waiting for PID 20187 of (20163 20166 20169 20172 20175 20178 20181 20184 20187 20190 20193 20196) to complete...
- Waiting for PID 20190 of (20163 20166 20169 20172 20175 20178 20181 20184 20187 20190 20193 20196) to complete...
- Waiting for PID 20193 of (20163 20166 20169 20172 20175 20178 20181 20184 20187 20190 20193 20196) to complete...
- Waiting for PID 20196 of (20163 20166 20169 20172 20175 20178 20181 20184 20187 20190 20193 20196) to complete...
- mris_curvature -w lh.white.preaparc
- total integrated curvature = 8.684*4pi (109.122) --> -8 handles
- ICI = 191.9, FI = 1948.1, variation=30800.488
- 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
- 188 vertices thresholded to be in k1 ~ [-0.25 0.66], k2 ~ [-0.12 0.07]
- total integrated curvature = 0.555*4pi (6.970) --> 0 handles
- ICI = 1.5, FI = 9.7, variation=165.326
- 125 vertices thresholded to be in [-0.02 0.02]
- writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 157 vertices thresholded to be in [-0.15 0.28]
- done.
- writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.023
- done.
- mris_curvature -w rh.white.preaparc
- total integrated curvature = 8.742*4pi (109.853) --> -8 handles
- ICI = 196.6, FI = 1977.8, variation=31342.749
- 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
- 189 vertices thresholded to be in k1 ~ [-0.16 0.49], k2 ~ [-0.09 0.06]
- total integrated curvature = 0.595*4pi (7.476) --> 0 handles
- ICI = 1.5, FI = 9.2, variation=157.678
- 124 vertices thresholded to be in [-0.02 0.01]
- writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 153 vertices thresholded to be in [-0.10 0.22]
- done.
- writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.022
- done.
- PIDs (20163 20166 20169 20172 20175 20178 20181 20184 20187 20190 20193 20196) completed and logs appended.
- #-----------------------------------------
- #@# Curvature Stats lh Sat Oct 7 21:49:33 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050669 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 [ 0050669/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 [ 256 ]
- Gb_filter = 0
- WARN: S lookup min: -0.213844
- WARN: S explicit min: 0.000000 vertex = 387
- #-----------------------------------------
- #@# Curvature Stats rh Sat Oct 7 21:49:38 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050669 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 [ 0050669/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 [ 256 ]
- Gb_filter = 0
- WARN: S lookup min: -0.506026
- WARN: S explicit min: 0.000000 vertex = 28
- #--------------------------------------------
- #@# Sphere lh Sat Oct 7 21:49:43 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
- #--------------------------------------------
- #@# Sphere rh Sat Oct 7 21:49:43 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere
- Waiting for PID 20336 of (20336 20339) to complete...
- Waiting for PID 20339 of (20336 20339) to complete...
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 0.281...
- 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 %20.03
- pass 1: epoch 2 of 3 starting distance error %20.01
- unfolding complete - removing small folds...
- starting distance error %19.96
- removing remaining folds...
- final distance error %19.97
- MRISunfold() return, current seed 1234
- -01: dt=0.0000, 249 negative triangles
- 190: dt=0.9900, 249 negative triangles
- 191: dt=0.9900, 132 negative triangles
- 192: dt=0.9900, 107 negative triangles
- 193: dt=0.9900, 101 negative triangles
- 194: dt=0.9900, 72 negative triangles
- 195: dt=0.9900, 74 negative triangles
- 196: dt=0.9900, 60 negative triangles
- 197: dt=0.9900, 61 negative triangles
- 198: dt=0.9900, 53 negative triangles
- 199: dt=0.9900, 49 negative triangles
- 200: dt=0.9900, 51 negative triangles
- 201: dt=0.9900, 49 negative triangles
- 202: dt=0.9900, 45 negative triangles
- 203: dt=0.9900, 37 negative triangles
- 204: dt=0.9900, 41 negative triangles
- 205: dt=0.9900, 37 negative triangles
- 206: dt=0.9900, 38 negative triangles
- 207: dt=0.9900, 39 negative triangles
- 208: dt=0.9900, 42 negative triangles
- 209: dt=0.9900, 34 negative triangles
- 210: dt=0.9900, 36 negative triangles
- 211: dt=0.9900, 36 negative triangles
- 212: dt=0.9900, 32 negative triangles
- 213: dt=0.9900, 29 negative triangles
- 214: dt=0.9900, 30 negative triangles
- 215: dt=0.9900, 27 negative triangles
- 216: dt=0.9900, 28 negative triangles
- 217: dt=0.9900, 29 negative triangles
- 218: dt=0.9900, 26 negative triangles
- 219: dt=0.9900, 25 negative triangles
- 220: dt=0.9900, 25 negative triangles
- 221: dt=0.9900, 21 negative triangles
- 222: dt=0.9900, 24 negative triangles
- 223: dt=0.9900, 22 negative triangles
- 224: dt=0.9900, 23 negative triangles
- 225: dt=0.9900, 25 negative triangles
- 226: dt=0.9900, 22 negative triangles
- 227: dt=0.9900, 20 negative triangles
- 228: dt=0.9900, 19 negative triangles
- 229: dt=0.9900, 18 negative triangles
- 230: dt=0.9900, 18 negative triangles
- 231: dt=0.9900, 22 negative triangles
- 232: dt=0.9900, 21 negative triangles
- 233: dt=0.9900, 17 negative triangles
- 234: dt=0.9900, 17 negative triangles
- 235: dt=0.9900, 14 negative triangles
- 236: dt=0.9900, 18 negative triangles
- 237: dt=0.9900, 13 negative triangles
- 238: dt=0.9900, 12 negative triangles
- 239: dt=0.9900, 12 negative triangles
- 240: dt=0.9900, 12 negative triangles
- 241: dt=0.9900, 7 negative triangles
- 242: dt=0.9900, 8 negative triangles
- 243: dt=0.9900, 9 negative triangles
- 244: dt=0.9900, 3 negative triangles
- 245: dt=0.9900, 3 negative triangles
- 246: dt=0.9900, 6 negative triangles
- 247: dt=0.9900, 3 negative triangles
- 248: dt=0.9900, 2 negative triangles
- 249: dt=0.9900, 3 negative triangles
- 250: dt=0.9900, 3 negative triangles
- 251: dt=0.9900, 1 negative triangles
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 1.10 hours
- mris_sphere utimesec 4076.472282
- mris_sphere stimesec 1.750733
- mris_sphere ru_maxrss 294820
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 51946
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 10152
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 124247
- mris_sphere ru_nivcsw 308790
- FSRUNTIME@ mris_sphere 1.0956 hours 1 threads
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 0.283...
- 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
- singular matrix in quadratic form
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %19.34
- pass 1: epoch 2 of 3 starting distance error %19.31
- unfolding complete - removing small folds...
- starting distance error %19.26
- removing remaining folds...
- final distance error %19.27
- MRISunfold() return, current seed 1234
- -01: dt=0.0000, 182 negative triangles
- 174: dt=0.9900, 182 negative triangles
- 175: dt=0.9900, 59 negative triangles
- 176: dt=0.9900, 52 negative triangles
- 177: dt=0.9900, 34 negative triangles
- 178: dt=0.9900, 34 negative triangles
- 179: dt=0.9900, 32 negative triangles
- 180: dt=0.9900, 29 negative triangles
- 181: dt=0.9900, 32 negative triangles
- 182: dt=0.9900, 30 negative triangles
- 183: dt=0.9900, 25 negative triangles
- 184: dt=0.9900, 23 negative triangles
- 185: dt=0.9900, 18 negative triangles
- 186: dt=0.9900, 16 negative triangles
- 187: dt=0.9900, 20 negative triangles
- 188: dt=0.9900, 19 negative triangles
- 189: dt=0.9900, 15 negative triangles
- 190: dt=0.9900, 14 negative triangles
- 191: dt=0.9900, 13 negative triangles
- 192: dt=0.9900, 12 negative triangles
- 193: dt=0.9900, 9 negative triangles
- 194: dt=0.9900, 8 negative triangles
- 195: dt=0.9900, 6 negative triangles
- 196: dt=0.9900, 9 negative triangles
- 197: dt=0.9900, 4 negative triangles
- 198: dt=0.9900, 5 negative triangles
- 199: dt=0.9900, 4 negative triangles
- 200: dt=0.9900, 1 negative triangles
- 201: dt=0.9900, 1 negative triangles
- 202: dt=0.9900, 2 negative triangles
- 203: dt=0.9900, 1 negative triangles
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 1.03 hours
- mris_sphere utimesec 3670.001075
- mris_sphere stimesec 1.572760
- mris_sphere ru_maxrss 296716
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 52417
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 10200
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 114393
- mris_sphere ru_nivcsw 314432
- FSRUNTIME@ mris_sphere 1.0310 hours 1 threads
- PIDs (20336 20339) completed and logs appended.
- #--------------------------------------------
- #@# Surf Reg lh Sat Oct 7 22:55:27 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 22:55:27 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 22681 of (22681 22684) to complete...
- Waiting for PID 22684 of (22681 22684) to complete...
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/scripts
- cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 = 5.396
- curvature mean = 0.026, std = 0.822
- curvature mean = 0.017, std = 0.856
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, -16.00, 0.00) sse = 242504.0, tmin=1.1037
- d=16.00 min @ (0.00, 4.00, 0.00) sse = 224727.0, tmin=3.3439
- d=8.00 min @ (2.00, 0.00, 0.00) sse = 217047.1, tmin=4.4760
- d=4.00 min @ (-1.00, -1.00, 1.00) sse = 215354.8, tmin=5.6179
- d=2.00 min @ (0.50, 0.00, -0.50) sse = 214309.7, tmin=6.7675
- d=0.50 min @ (0.00, 0.00, 0.12) sse = 214296.5, tmin=9.0326
- 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 9.03 min
- curvature mean = -0.005, std = 0.838
- curvature mean = 0.007, std = 0.945
- curvature mean = -0.008, std = 0.848
- curvature mean = 0.003, std = 0.978
- curvature mean = -0.011, std = 0.850
- curvature mean = 0.000, std = 0.992
- 2 Reading smoothwm
- curvature mean = -0.024, std = 0.310
- curvature mean = 0.038, std = 0.246
- curvature mean = 0.056, std = 0.323
- curvature mean = 0.035, std = 0.303
- curvature mean = 0.030, std = 0.501
- curvature mean = 0.035, std = 0.329
- curvature mean = 0.017, std = 0.638
- curvature mean = 0.035, std = 0.340
- curvature mean = 0.005, std = 0.757
- MRISregister() return, current seed 0
- -01: dt=0.0000, 70 negative triangles
- 114: dt=0.9900, 70 negative triangles
- expanding nbhd size to 1
- 115: dt=0.9900, 98 negative triangles
- 116: dt=0.9900, 65 negative triangles
- 117: dt=0.9900, 71 negative triangles
- 118: dt=0.9900, 72 negative triangles
- 119: dt=0.9900, 69 negative triangles
- 120: dt=0.9900, 63 negative triangles
- 121: dt=0.9900, 62 negative triangles
- 122: dt=0.9900, 60 negative triangles
- 123: dt=0.9900, 56 negative triangles
- 124: dt=0.9900, 46 negative triangles
- 125: dt=0.9900, 40 negative triangles
- 126: dt=0.9900, 46 negative triangles
- 127: dt=0.9900, 38 negative triangles
- 128: dt=0.9900, 36 negative triangles
- 129: dt=0.9900, 32 negative triangles
- 130: dt=0.9900, 26 negative triangles
- 131: dt=0.9900, 20 negative triangles
- 132: dt=0.9900, 19 negative triangles
- 133: dt=0.9900, 19 negative triangles
- 134: dt=0.9900, 16 negative triangles
- 135: dt=0.9900, 20 negative triangles
- 136: dt=0.9900, 21 negative triangles
- 137: dt=0.9900, 13 negative triangles
- 138: dt=0.9900, 14 negative triangles
- 139: dt=0.9900, 12 negative triangles
- 140: dt=0.9900, 12 negative triangles
- 141: dt=0.9900, 10 negative triangles
- 142: dt=0.9900, 13 negative triangles
- 143: dt=0.9900, 13 negative triangles
- 144: dt=0.9900, 11 negative triangles
- 145: dt=0.9900, 8 negative triangles
- 146: dt=0.9900, 9 negative triangles
- 147: dt=0.9900, 7 negative triangles
- 148: dt=0.9900, 7 negative triangles
- 149: dt=0.9900, 6 negative triangles
- 150: dt=0.9900, 5 negative triangles
- 151: dt=0.9900, 7 negative triangles
- 152: dt=0.9900, 6 negative triangles
- 153: dt=0.9900, 3 negative triangles
- 154: dt=0.9900, 2 negative triangles
- 155: dt=0.9900, 1 negative triangles
- 156: dt=0.9900, 4 negative triangles
- 157: dt=0.9900, 4 negative triangles
- 158: dt=0.9900, 1 negative triangles
- 159: dt=0.9900, 4 negative triangles
- 160: dt=0.9900, 2 negative triangles
- 161: dt=0.9900, 2 negative triangles
- writing registered surface to ../surf/lh.sphere.reg...
- registration took 1.28 hours
- mris_register utimesec 4509.410465
- mris_register stimesec 4.083379
- mris_register ru_maxrss 262840
- mris_register ru_ixrss 0
- mris_register ru_idrss 0
- mris_register ru_isrss 0
- mris_register ru_minflt 38492
- mris_register ru_majflt 0
- mris_register ru_nswap 0
- mris_register ru_inblock 0
- mris_register ru_oublock 10200
- mris_register ru_msgsnd 0
- mris_register ru_msgrcv 0
- mris_register ru_nsignals 0
- mris_register ru_nvcsw 334078
- mris_register ru_nivcsw 228015
- FSRUNTIME@ mris_register 1.2751 hours 1 threads
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/scripts
- cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 = 5.480
- curvature mean = 0.029, std = 0.814
- curvature mean = 0.018, std = 0.860
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, -16.00, 0.00) sse = 372140.6, tmin=1.2812
- d=32.00 min @ (8.00, 8.00, 0.00) sse = 294640.7, tmin=2.5735
- d=16.00 min @ (0.00, -4.00, 0.00) sse = 278811.2, tmin=3.8719
- d=8.00 min @ (2.00, 2.00, 2.00) sse = 269107.2, tmin=5.1732
- d=4.00 min @ (0.00, 0.00, -1.00) sse = 267551.8, tmin=6.4829
- d=1.00 min @ (0.00, -0.25, 0.00) sse = 267420.8, tmin=9.0969
- d=0.50 min @ (0.00, 0.00, -0.12) sse = 267415.3, tmin=10.4198
- 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 10.42 min
- curvature mean = -0.008, std = 0.824
- curvature mean = 0.007, std = 0.947
- curvature mean = -0.015, std = 0.833
- curvature mean = 0.003, std = 0.978
- curvature mean = -0.018, std = 0.833
- curvature mean = 0.000, std = 0.991
- 2 Reading smoothwm
- curvature mean = -0.024, std = 0.310
- curvature mean = 0.032, std = 0.241
- curvature mean = 0.056, std = 0.319
- curvature mean = 0.028, std = 0.300
- curvature mean = 0.033, std = 0.494
- curvature mean = 0.027, std = 0.325
- curvature mean = 0.020, std = 0.629
- curvature mean = 0.027, std = 0.337
- curvature mean = 0.007, std = 0.737
- MRISregister() return, current seed 0
- -01: dt=0.0000, 35 negative triangles
- 113: dt=0.9900, 35 negative triangles
- expanding nbhd size to 1
- 114: dt=0.9900, 55 negative triangles
- 115: dt=0.9900, 32 negative triangles
- 116: dt=0.9900, 35 negative triangles
- 117: dt=0.9900, 34 negative triangles
- 118: dt=0.9900, 30 negative triangles
- 119: dt=0.9900, 37 negative triangles
- 120: dt=0.9900, 29 negative triangles
- 121: dt=0.9900, 22 negative triangles
- 122: dt=0.9900, 22 negative triangles
- 123: dt=0.9900, 24 negative triangles
- 124: dt=0.9900, 20 negative triangles
- 125: dt=0.9900, 17 negative triangles
- 126: dt=0.9900, 14 negative triangles
- 127: dt=0.9900, 19 negative triangles
- 128: dt=0.9900, 16 negative triangles
- 129: dt=0.9900, 14 negative triangles
- 130: dt=0.9900, 9 negative triangles
- 131: dt=0.9900, 6 negative triangles
- 132: dt=0.9900, 3 negative triangles
- 133: dt=0.9900, 6 negative triangles
- 134: dt=0.9900, 2 negative triangles
- 135: dt=0.9900, 2 negative triangles
- 136: dt=0.9900, 1 negative triangles
- writing registered surface to ../surf/rh.sphere.reg...
- registration took 1.60 hours
- mris_register utimesec 6491.621123
- mris_register stimesec 4.804269
- mris_register ru_maxrss 268300
- mris_register ru_ixrss 0
- mris_register ru_idrss 0
- mris_register ru_isrss 0
- mris_register ru_minflt 37521
- mris_register ru_majflt 0
- mris_register ru_nswap 0
- mris_register ru_inblock 0
- mris_register ru_oublock 10240
- mris_register ru_msgsnd 0
- mris_register ru_msgrcv 0
- mris_register ru_nsignals 0
- mris_register ru_nvcsw 348434
- mris_register ru_nivcsw 202889
- FSRUNTIME@ mris_register 1.5993 hours 1 threads
- PIDs (22681 22684) completed and logs appended.
- #--------------------------------------------
- #@# Jacobian white lh Sun Oct 8 00:31:24 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white
- #--------------------------------------------
- #@# Jacobian white rh Sun Oct 8 00:31:24 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white
- Waiting for PID 30575 of (30575 30578) to complete...
- Waiting for PID 30578 of (30575 30578) 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 (30575 30578) completed and logs appended.
- #--------------------------------------------
- #@# AvgCurv lh Sun Oct 8 00:31:27 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 Sun Oct 8 00:31:27 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 30621 of (30621 30624) to complete...
- Waiting for PID 30624 of (30621 30624) 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 (30621 30624) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc lh Sun Oct 8 00:31:29 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050669 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 Sun Oct 8 00:31:29 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050669 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 30665 of (30665 30668) to complete...
- Waiting for PID 30668 of (30665 30668) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050669 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...
- 1142 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3202 changed, 143612 examined...
- 001: 711 changed, 13606 examined...
- 002: 194 changed, 4028 examined...
- 003: 63 changed, 1196 examined...
- 004: 19 changed, 386 examined...
- 005: 4 changed, 107 examined...
- 006: 2 changed, 25 examined...
- 007: 1 changed, 8 examined...
- 008: 1 changed, 7 examined...
- 009: 0 changed, 7 examined...
- 189 labels changed using aseg
- 000: 115 total segments, 71 labels (374 vertices) changed
- 001: 45 total segments, 2 labels (5 vertices) changed
- 002: 43 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 2 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1836 vertices marked for relabeling...
- 1836 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 0 minutes and 15 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050669 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...
- 1248 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2777 changed, 144204 examined...
- 001: 649 changed, 12180 examined...
- 002: 141 changed, 3584 examined...
- 003: 41 changed, 881 examined...
- 004: 18 changed, 262 examined...
- 005: 5 changed, 99 examined...
- 006: 6 changed, 34 examined...
- 007: 1 changed, 29 examined...
- 008: 2 changed, 8 examined...
- 009: 2 changed, 10 examined...
- 010: 3 changed, 12 examined...
- 011: 2 changed, 17 examined...
- 012: 0 changed, 9 examined...
- 116 labels changed using aseg
- 000: 78 total segments, 39 labels (192 vertices) changed
- 001: 38 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 3 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1653 vertices marked for relabeling...
- 1653 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 0 minutes and 14 seconds.
- PIDs (30665 30668) completed and logs appended.
- #--------------------------------------------
- #@# Make Pial Surf lh Sun Oct 8 00:31:44 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050669 lh
- #--------------------------------------------
- #@# Make Pial Surf rh Sun Oct 8 00:31:44 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050669 rh
- Waiting for PID 30739 of (30739 30742) to complete...
- Waiting for PID 30742 of (30739 30742) to complete...
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050669 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-6.0.0/0050669/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/wm.mgz...
- 37330 bright wm thresholded.
- 2468 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.orig...
- computing class statistics...
- border white: 295606 voxels (1.76%)
- border gray 303578 voxels (1.81%)
- WM (103.0): 103.2 +- 5.8 [70.0 --> 110.0]
- GM (85.0) : 83.8 +- 10.2 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 71.8 (was 70)
- setting MAX_BORDER_WHITE to 111.8 (was 105)
- setting MIN_BORDER_WHITE to 82.0 (was 85)
- setting MAX_CSF to 61.6 (was 40)
- setting MAX_GRAY to 100.2 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 71.8 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 51.3 (was 40)
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106+-5.2, GM=82+-6.1
- mean inside = 99.9, mean outside = 87.1
- 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 +- 0.25 (0.04-->6.79) (max @ vno 59998 --> 142791)
- face area 0.33 +- 0.16 (0.00-->4.58)
- mean absolute distance = 0.72 +- 0.95
- 3116 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 1 with 18 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 3 with 14 points - only 0.00% unknown
- deleting segment 4 with 150 points - only 0.00% unknown
- deleting segment 5 with 24 points - only 0.00% unknown
- deleting segment 6 with 31 points - only 0.00% unknown
- deleting segment 7 with 163 points - only 0.00% unknown
- deleting segment 8 with 14 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 points - only 0.00% unknown
- deleting segment 11 with 7 points - only 0.00% unknown
- mean border=89.7, 157 (152) missing vertices, mean dist 0.4 [1.1 (%15.2)->0.6 (%84.8))]
- %66 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 +- 0.26 (0.07-->6.81) (max @ vno 142791 --> 59998)
- face area 0.33 +- 0.16 (0.00-->4.30)
- mean absolute distance = 0.40 +- 0.64
- 3471 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1586730.0, rms=5.751
- 001: dt: 0.5000, sse=1001555.1, rms=3.438 (40.222%)
- 002: dt: 0.5000, sse=832740.2, rms=2.397 (30.266%)
- 003: dt: 0.5000, sse=804771.6, rms=2.089 (12.861%)
- 004: dt: 0.5000, sse=778411.8, rms=1.958 (6.273%)
- rms = 1.96, time step reduction 1 of 3 to 0.250...
- 005: dt: 0.2500, sse=755939.4, rms=1.689 (13.757%)
- 006: dt: 0.2500, sse=747819.2, rms=1.550 (8.194%)
- rms = 1.51, time step reduction 2 of 3 to 0.125...
- 007: dt: 0.2500, sse=744136.8, rms=1.512 (2.461%)
- rms = 1.49, time step reduction 3 of 3 to 0.062...
- 008: dt: 0.1250, sse=743588.8, rms=1.491 (1.426%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 0 with 3 points - only 0.00% unknown
- deleting segment 1 with 12 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 2 with 1 points - only 0.00% unknown
- deleting segment 3 with 12 points - only 0.00% unknown
- deleting segment 4 with 20 points - only 0.00% unknown
- deleting segment 5 with 74 points - only 0.00% unknown
- deleting segment 6 with 27 points - only 0.00% unknown
- deleting segment 7 with 160 points - only 0.00% unknown
- deleting segment 8 with 14 points - only 0.00% unknown
- deleting segment 9 with 7 points - only 0.00% unknown
- mean border=91.7, 67 (21) missing vertices, mean dist -0.2 [0.5 (%66.7)->0.3 (%33.3))]
- %79 local maxima, %16 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 0.90 +- 0.26 (0.06-->6.95) (max @ vno 142791 --> 59998)
- face area 0.35 +- 0.17 (0.00-->4.75)
- mean absolute distance = 0.32 +- 0.42
- 4037 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=981040.8, rms=3.082
- 009: dt: 0.5000, sse=820917.2, rms=1.924 (37.568%)
- 010: dt: 0.5000, sse=788934.8, rms=1.646 (14.463%)
- rms = 1.67, time step reduction 1 of 3 to 0.250...
- 011: dt: 0.2500, sse=771954.0, rms=1.420 (13.707%)
- 012: dt: 0.2500, sse=767848.8, rms=1.297 (8.651%)
- rms = 1.27, time step reduction 2 of 3 to 0.125...
- 013: dt: 0.2500, sse=762480.1, rms=1.272 (1.919%)
- rms = 1.26, time step reduction 3 of 3 to 0.062...
- 014: dt: 0.1250, sse=761781.4, rms=1.256 (1.292%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- deleting segment 0 with 3 points - only 0.00% unknown
- deleting segment 1 with 12 points - only 0.00% unknown
- deleting segment 2 with 14 points - only 0.00% unknown
- deleting segment 3 with 118 points - only 0.00% unknown
- deleting segment 4 with 19 points - only 0.00% unknown
- deleting segment 5 with 166 points - only 0.00% unknown
- deleting segment 6 with 23 points - only 0.00% unknown
- deleting segment 7 with 14 points - only 0.00% unknown
- deleting segment 8 with 7 points - only 0.00% unknown
- mean border=93.5, 50 (12) missing vertices, mean dist -0.2 [0.3 (%70.6)->0.3 (%29.4))]
- %89 local maxima, % 6 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 +- 0.25 (0.06-->7.10) (max @ vno 142791 --> 59998)
- face area 0.34 +- 0.17 (0.00-->4.75)
- mean absolute distance = 0.26 +- 0.34
- 4574 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=891713.0, rms=2.667
- 015: dt: 0.5000, sse=776919.6, rms=1.653 (38.019%)
- 016: dt: 0.5000, sse=761592.8, rms=1.545 (6.562%)
- rms = 1.63, time step reduction 1 of 3 to 0.250...
- 017: dt: 0.2500, sse=741821.2, rms=1.282 (16.984%)
- 018: dt: 0.2500, sse=736788.6, rms=1.170 (8.726%)
- rms = 1.16, time step reduction 2 of 3 to 0.125...
- 019: dt: 0.2500, sse=735474.2, rms=1.165 (0.505%)
- rms = 1.15, time step reduction 3 of 3 to 0.062...
- 020: dt: 0.1250, sse=734087.9, rms=1.154 (0.929%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- deleting segment 0 with 4 points - only 0.00% unknown
- deleting segment 1 with 12 points - only 0.00% unknown
- deleting segment 2 with 12 points - only 0.00% unknown
- deleting segment 3 with 118 points - only 0.00% unknown
- deleting segment 4 with 18 points - only 0.00% unknown
- deleting segment 5 with 170 points - only 0.00% unknown
- deleting segment 6 with 23 points - only 0.00% unknown
- deleting segment 7 with 14 points - only 0.00% unknown
- deleting segment 8 with 8 points - only 0.00% unknown
- deleting segment 9 with 16 points - only 0.00% unknown
- mean border=94.1, 63 (10) missing vertices, mean dist -0.1 [0.3 (%57.2)->0.2 (%42.8))]
- %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-6.0.0/0050669/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=738815.1, rms=1.406
- 021: dt: 0.5000, sse=714488.1, rms=0.999 (28.923%)
- rms = 1.37, time step reduction 1 of 3 to 0.250...
- 022: dt: 0.2500, sse=705445.2, rms=0.898 (10.107%)
- rms = 0.93, time step reduction 2 of 3 to 0.125...
- rms = 0.89, time step reduction 3 of 3 to 0.062...
- 023: dt: 0.1250, sse=704108.4, rms=0.892 (0.693%)
- positioning took 0.5 minutes
- generating cortex label...
- 12 non-cortical segments detected
- only using segment with 7867 vertices
- erasing segment 0 (vno[0] = 38863)
- erasing segment 2 (vno[0] = 54313)
- erasing segment 3 (vno[0] = 59678)
- erasing segment 4 (vno[0] = 81051)
- erasing segment 5 (vno[0] = 81062)
- erasing segment 6 (vno[0] = 83338)
- erasing segment 7 (vno[0] = 88718)
- erasing segment 8 (vno[0] = 106633)
- erasing segment 9 (vno[0] = 106653)
- erasing segment 10 (vno[0] = 111197)
- erasing segment 11 (vno[0] = 118668)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/label/lh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.area
- vertex spacing 0.89 +- 0.26 (0.04-->7.14) (max @ vno 59998 --> 142791)
- face area 0.33 +- 0.16 (0.00-->4.66)
- 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 16 points - only 0.00% unknown
- deleting segment 1 with 54 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 2 with 2 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 4 with 4 points - only 0.00% unknown
- deleting segment 5 with 192 points - only 0.00% unknown
- deleting segment 7 with 21 points - only 0.00% unknown
- deleting segment 8 with 66 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
- deleting segment 11 with 30 points - only 0.00% unknown
- deleting segment 12 with 12 points - only 0.00% unknown
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from white.preaparc...
- mean border=70.2, 195 (195) missing vertices, mean dist 1.5 [0.7 (%0.0)->3.0 (%100.0))]
- %13 local maxima, %34 large gradients and %48 min vals, 189 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=17451786.0, rms=24.740
- 001: dt: 0.0500, sse=15790059.0, rms=23.483 (5.084%)
- 002: dt: 0.0500, sse=14586234.0, rms=22.527 (4.068%)
- 003: dt: 0.0500, sse=13663891.0, rms=21.767 (3.376%)
- 004: dt: 0.0500, sse=12918223.0, rms=21.132 (2.917%)
- 005: dt: 0.0500, sse=12293017.0, rms=20.584 (2.591%)
- 006: dt: 0.0500, sse=11753606.0, rms=20.100 (2.354%)
- 007: dt: 0.0500, sse=11277900.0, rms=19.663 (2.175%)
- 008: dt: 0.0500, sse=10851095.0, rms=19.262 (2.038%)
- 009: dt: 0.0500, sse=10463780.0, rms=18.891 (1.927%)
- 010: dt: 0.0500, sse=10108324.0, rms=18.544 (1.838%)
- positioning took 1.0 minutes
- mean border=70.0, 146 (103) missing vertices, mean dist 1.3 [0.3 (%0.1)->2.5 (%99.9))]
- %14 local maxima, %34 large gradients and %47 min vals, 179 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=10902006.0, rms=19.311
- 011: dt: 0.0500, sse=10571191.0, rms=18.996 (1.634%)
- 012: dt: 0.0500, sse=10263467.0, rms=18.697 (1.571%)
- 013: dt: 0.0500, sse=9975628.0, rms=18.414 (1.517%)
- 014: dt: 0.0500, sse=9705753.0, rms=18.144 (1.466%)
- 015: dt: 0.0500, sse=9451998.0, rms=17.886 (1.420%)
- 016: dt: 0.0500, sse=9212612.0, rms=17.639 (1.379%)
- 017: dt: 0.0500, sse=8986232.0, rms=17.403 (1.341%)
- 018: dt: 0.0500, sse=8771270.0, rms=17.175 (1.308%)
- 019: dt: 0.0500, sse=8566427.0, rms=16.955 (1.280%)
- 020: dt: 0.0500, sse=8370574.0, rms=16.742 (1.256%)
- positioning took 1.0 minutes
- mean border=69.9, 162 (79) missing vertices, mean dist 1.1 [0.1 (%0.4)->2.2 (%99.6))]
- %15 local maxima, %34 large gradients and %46 min vals, 181 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=8490202.0, rms=16.878
- 021: dt: 0.0500, sse=8299589.0, rms=16.670 (1.234%)
- 022: dt: 0.0500, sse=8116790.0, rms=16.467 (1.213%)
- 023: dt: 0.0500, sse=7940144.5, rms=16.269 (1.202%)
- 024: dt: 0.0500, sse=7769476.5, rms=16.076 (1.190%)
- 025: dt: 0.0500, sse=7603776.0, rms=15.885 (1.184%)
- 026: dt: 0.0500, sse=7442680.5, rms=15.698 (1.179%)
- 027: dt: 0.0500, sse=7285250.5, rms=15.513 (1.180%)
- 028: dt: 0.0500, sse=7130749.5, rms=15.329 (1.186%)
- 029: dt: 0.0500, sse=6979056.0, rms=15.146 (1.193%)
- 030: dt: 0.0500, sse=6830195.0, rms=14.964 (1.200%)
- positioning took 1.0 minutes
- mean border=69.8, 197 (67) missing vertices, mean dist 1.0 [0.1 (%2.3)->1.9 (%97.7))]
- %15 local maxima, %34 large gradients and %46 min vals, 167 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=6898373.0, rms=15.048
- 031: dt: 0.5000, sse=5770741.0, rms=13.601 (9.616%)
- 032: dt: 0.5000, sse=4854534.5, rms=12.296 (9.593%)
- 033: dt: 0.5000, sse=4095573.8, rms=11.102 (9.716%)
- 034: dt: 0.5000, sse=3432104.5, rms=9.937 (10.491%)
- 035: dt: 0.5000, sse=2897751.5, rms=8.890 (10.534%)
- 036: dt: 0.5000, sse=2440785.0, rms=7.884 (11.322%)
- 037: dt: 0.5000, sse=2087756.6, rms=7.010 (11.076%)
- 038: dt: 0.5000, sse=1815128.2, rms=6.251 (10.837%)
- 039: dt: 0.5000, sse=1650410.2, rms=5.745 (8.091%)
- 040: dt: 0.5000, sse=1525929.8, rms=5.328 (7.251%)
- 041: dt: 0.5000, sse=1460758.8, rms=5.098 (4.332%)
- 042: dt: 0.5000, sse=1407326.9, rms=4.898 (3.918%)
- 043: dt: 0.5000, sse=1389179.2, rms=4.828 (1.423%)
- 044: dt: 0.5000, sse=1363627.8, rms=4.728 (2.082%)
- rms = 4.71, time step reduction 1 of 3 to 0.250...
- 045: dt: 0.5000, sse=1360283.5, rms=4.715 (0.278%)
- 046: dt: 0.2500, sse=1228590.4, rms=4.113 (12.754%)
- 047: dt: 0.2500, sse=1191403.4, rms=3.943 (4.133%)
- rms = 3.96, time step reduction 2 of 3 to 0.125...
- 048: dt: 0.1250, sse=1178114.8, rms=3.877 (1.682%)
- 049: dt: 0.1250, sse=1161202.0, rms=3.789 (2.261%)
- rms = 3.77, time step reduction 3 of 3 to 0.062...
- 050: dt: 0.1250, sse=1158307.2, rms=3.773 (0.429%)
- positioning took 3.0 minutes
- mean border=68.8, 2917 (16) missing vertices, mean dist 0.1 [0.2 (%43.9)->0.5 (%56.1))]
- %28 local maxima, %25 large gradients and %41 min vals, 123 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=1416592.2, rms=4.166
- rms = 4.27, time step reduction 1 of 3 to 0.250...
- 051: dt: 0.2500, sse=1318414.9, rms=3.689 (11.467%)
- 052: dt: 0.2500, sse=1256609.0, rms=3.355 (9.047%)
- 053: dt: 0.2500, sse=1245166.8, rms=3.298 (1.709%)
- 054: dt: 0.2500, sse=1230992.2, rms=3.224 (2.241%)
- rms = 3.20, time step reduction 2 of 3 to 0.125...
- 055: dt: 0.2500, sse=1226442.9, rms=3.202 (0.682%)
- 056: dt: 0.1250, sse=1184414.6, rms=2.937 (8.271%)
- rms = 2.89, time step reduction 3 of 3 to 0.062...
- 057: dt: 0.1250, sse=1176263.1, rms=2.888 (1.680%)
- positioning took 1.4 minutes
- mean border=68.3, 3222 (9) missing vertices, mean dist 0.1 [0.2 (%44.0)->0.3 (%56.0))]
- %38 local maxima, %15 large gradients and %41 min vals, 119 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=1203516.4, rms=3.068
- rms = 3.60, time step reduction 1 of 3 to 0.250...
- 058: dt: 0.2500, sse=1176896.6, rms=2.899 (5.508%)
- rms = 2.88, time step reduction 2 of 3 to 0.125...
- 059: dt: 0.2500, sse=1171498.1, rms=2.876 (0.826%)
- 060: dt: 0.1250, sse=1162856.6, rms=2.814 (2.131%)
- rms = 2.79, time step reduction 3 of 3 to 0.062...
- 061: dt: 0.1250, sse=1158066.8, rms=2.787 (0.971%)
- positioning took 0.9 minutes
- mean border=67.8, 6310 (8) missing vertices, mean dist 0.0 [0.2 (%46.1)->0.3 (%53.9))]
- %40 local maxima, %12 large gradients and %39 min vals, 113 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-6.0.0/0050669/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=1173548.0, rms=2.865
- rms = 3.25, time step reduction 1 of 3 to 0.250...
- 062: dt: 0.2500, sse=1159729.2, rms=2.774 (3.173%)
- rms = 2.74, time step reduction 2 of 3 to 0.125...
- 063: dt: 0.2500, sse=1151469.4, rms=2.739 (1.233%)
- 064: dt: 0.1250, sse=1143879.5, rms=2.683 (2.051%)
- rms = 2.65, time step reduction 3 of 3 to 0.062...
- 065: dt: 0.1250, sse=1138718.5, rms=2.654 (1.091%)
- positioning took 0.9 minutes
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.area.pial
- vertex spacing 1.00 +- 0.44 (0.05-->7.40) (max @ vno 58886 --> 60006)
- face area 0.39 +- 0.32 (0.00-->5.70)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 143612 vertices processed
- 25000 of 143612 vertices processed
- 50000 of 143612 vertices processed
- 75000 of 143612 vertices processed
- 100000 of 143612 vertices processed
- 125000 of 143612 vertices processed
- 0 of 143612 vertices processed
- 25000 of 143612 vertices processed
- 50000 of 143612 vertices processed
- 75000 of 143612 vertices processed
- 100000 of 143612 vertices processed
- 125000 of 143612 vertices processed
- thickness calculation complete, 299:965 truncations.
- 30470 vertices at 0 distance
- 99126 vertices at 1 distance
- 87946 vertices at 2 distance
- 37670 vertices at 3 distance
- 12767 vertices at 4 distance
- 4267 vertices at 5 distance
- 1266 vertices at 6 distance
- 449 vertices at 7 distance
- 156 vertices at 8 distance
- 65 vertices at 9 distance
- 36 vertices at 10 distance
- 37 vertices at 11 distance
- 29 vertices at 12 distance
- 26 vertices at 13 distance
- 26 vertices at 14 distance
- 21 vertices at 15 distance
- 23 vertices at 16 distance
- 24 vertices at 17 distance
- 10 vertices at 18 distance
- 8 vertices at 19 distance
- 10 vertices at 20 distance
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.thickness
- positioning took 16.3 minutes
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050669 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-6.0.0/0050669/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/wm.mgz...
- 37330 bright wm thresholded.
- 2468 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.orig...
- computing class statistics...
- border white: 295606 voxels (1.76%)
- border gray 303578 voxels (1.81%)
- WM (103.0): 103.2 +- 5.8 [70.0 --> 110.0]
- GM (85.0) : 83.8 +- 10.2 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 71.8 (was 70)
- setting MAX_BORDER_WHITE to 111.8 (was 105)
- setting MIN_BORDER_WHITE to 82.0 (was 85)
- setting MAX_CSF to 61.6 (was 40)
- setting MAX_GRAY to 100.2 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 71.8 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 51.3 (was 40)
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=106+-5.2, GM=82+-7.0
- mean inside = 99.9, mean outside = 87.3
- 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 +- 0.25 (0.05-->5.54) (max @ vno 55103 --> 55122)
- face area 0.33 +- 0.16 (0.00-->4.98)
- mean absolute distance = 0.72 +- 0.96
- 3428 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 17 points - only 0.00% unknown
- deleting segment 4 with 37 points - only 0.00% unknown
- deleting segment 5 with 47 points - only 0.00% unknown
- deleting segment 6 with 33 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 7 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 8 with 2 points - only 0.00% unknown
- deleting segment 9 with 47 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- mean border=90.0, 161 (161) missing vertices, mean dist 0.4 [1.1 (%15.4)->0.6 (%84.6))]
- %67 local maxima, %28 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 0.91 +- 0.27 (0.04-->5.28) (max @ vno 58640 --> 57453)
- face area 0.33 +- 0.17 (0.00-->4.62)
- mean absolute distance = 0.41 +- 0.65
- 4360 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1552393.5, rms=5.599
- 001: dt: 0.5000, sse=1009855.4, rms=3.374 (39.733%)
- 002: dt: 0.5000, sse=842305.2, rms=2.386 (29.272%)
- 003: dt: 0.5000, sse=800896.4, rms=2.084 (12.682%)
- 004: dt: 0.5000, sse=787866.8, rms=1.949 (6.455%)
- rms = 1.95, time step reduction 1 of 3 to 0.250...
- 005: dt: 0.5000, sse=789384.8, rms=1.946 (0.171%)
- 006: dt: 0.2500, sse=754443.1, rms=1.538 (20.944%)
- 007: dt: 0.2500, sse=750984.0, rms=1.474 (4.211%)
- rms = 1.46, time step reduction 2 of 3 to 0.125...
- 008: dt: 0.2500, sse=749632.9, rms=1.462 (0.820%)
- rms = 1.44, time step reduction 3 of 3 to 0.062...
- 009: dt: 0.1250, sse=748345.9, rms=1.445 (1.160%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 16 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 2 with 30 points - only 0.00% unknown
- deleting segment 3 with 28 points - only 0.00% unknown
- deleting segment 4 with 38 points - only 0.00% unknown
- deleting segment 5 with 21 points - only 0.00% unknown
- mean border=91.9, 71 (19) missing vertices, mean dist -0.2 [0.5 (%67.2)->0.3 (%32.8))]
- %80 local maxima, %16 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 0.90 +- 0.26 (0.07-->5.32) (max @ vno 55122 --> 55103)
- face area 0.35 +- 0.17 (0.00-->5.05)
- mean absolute distance = 0.33 +- 0.43
- 5011 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=995335.2, rms=3.094
- 010: dt: 0.5000, sse=847112.9, rms=1.945 (37.147%)
- 011: dt: 0.5000, sse=803676.6, rms=1.655 (14.899%)
- rms = 1.65, time step reduction 1 of 3 to 0.250...
- 012: dt: 0.5000, sse=801415.0, rms=1.652 (0.189%)
- 013: dt: 0.2500, sse=776113.4, rms=1.281 (22.467%)
- rms = 1.25, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=772142.6, rms=1.245 (2.796%)
- rms = 1.23, time step reduction 3 of 3 to 0.062...
- 015: dt: 0.1250, sse=771083.2, rms=1.233 (0.989%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 16 points - only 0.00% unknown
- deleting segment 1 with 34 points - only 0.00% unknown
- deleting segment 2 with 30 points - only 0.00% unknown
- deleting segment 3 with 35 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 4 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 6 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- mean border=93.6, 60 (11) missing vertices, mean dist -0.2 [0.4 (%70.8)->0.3 (%29.2))]
- %90 local maxima, % 6 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 (0.10-->5.38) (max @ vno 55122 --> 55103)
- face area 0.34 +- 0.17 (0.00-->4.98)
- mean absolute distance = 0.26 +- 0.35
- 4228 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=887528.6, rms=2.568
- 016: dt: 0.5000, sse=783545.9, rms=1.631 (36.496%)
- 017: dt: 0.5000, sse=769948.8, rms=1.525 (6.525%)
- rms = 1.60, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=750450.9, rms=1.270 (16.696%)
- 019: dt: 0.2500, sse=743278.8, rms=1.156 (8.991%)
- rms = 1.15, time step reduction 2 of 3 to 0.125...
- 020: dt: 0.2500, sse=742311.9, rms=1.147 (0.753%)
- rms = 1.14, time step reduction 3 of 3 to 0.062...
- 021: dt: 0.1250, sse=742009.1, rms=1.136 (0.939%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 17 points - only 0.00% unknown
- deleting segment 1 with 32 points - only 0.00% unknown
- deleting segment 2 with 33 points - only 0.00% unknown
- deleting segment 3 with 35 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 4 with 1 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 5 with 2 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 2 points - only 0.00% unknown
- mean border=94.2, 83 (8) missing vertices, mean dist -0.1 [0.3 (%57.4)->0.2 (%42.6))]
- %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-6.0.0/0050669/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=748380.0, rms=1.404
- 022: dt: 0.5000, sse=719576.0, rms=0.993 (29.302%)
- rms = 1.34, time step reduction 1 of 3 to 0.250...
- 023: dt: 0.2500, sse=712971.7, rms=0.893 (10.011%)
- rms = 0.93, time step reduction 2 of 3 to 0.125...
- rms = 0.89, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=712237.2, rms=0.885 (0.900%)
- positioning took 0.5 minutes
- generating cortex label...
- 10 non-cortical segments detected
- only using segment with 7438 vertices
- erasing segment 1 (vno[0] = 61109)
- erasing segment 2 (vno[0] = 91907)
- erasing segment 3 (vno[0] = 93970)
- erasing segment 4 (vno[0] = 100454)
- erasing segment 5 (vno[0] = 104050)
- erasing segment 6 (vno[0] = 105847)
- erasing segment 7 (vno[0] = 108685)
- erasing segment 8 (vno[0] = 114324)
- erasing segment 9 (vno[0] = 116722)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/label/rh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.area
- vertex spacing 0.89 +- 0.26 (0.07-->5.44) (max @ vno 143304 --> 143321)
- face area 0.33 +- 0.17 (0.00-->4.89)
- 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 50 points - only 0.00% unknown
- deleting segment 2 with 15 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- removing 1 vertex label from ripped group
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from white.preaparc...
- mean border=70.3, 183 (183) missing vertices, mean dist 1.5 [0.0 (%0.0)->3.1 (%100.0))]
- %13 local maxima, %33 large gradients and %50 min vals, 149 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=17503290.0, rms=24.697
- 001: dt: 0.0500, sse=15843734.0, rms=23.447 (5.063%)
- 002: dt: 0.0500, sse=14644516.0, rms=22.500 (4.039%)
- 003: dt: 0.0500, sse=13724802.0, rms=21.745 (3.353%)
- 004: dt: 0.0500, sse=12982586.0, rms=21.117 (2.891%)
- 005: dt: 0.0500, sse=12359033.0, rms=20.574 (2.572%)
- 006: dt: 0.0500, sse=11821138.0, rms=20.093 (2.335%)
- 007: dt: 0.0500, sse=11346176.0, rms=19.659 (2.160%)
- 008: dt: 0.0500, sse=10919982.0, rms=19.261 (2.024%)
- 009: dt: 0.0500, sse=10532982.0, rms=18.893 (1.914%)
- 010: dt: 0.0500, sse=10178078.0, rms=18.548 (1.824%)
- positioning took 1.1 minutes
- mean border=70.2, 131 (84) missing vertices, mean dist 1.3 [0.1 (%0.1)->2.6 (%99.9))]
- %14 local maxima, %33 large gradients and %49 min vals, 144 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=10996505.0, rms=19.333
- 011: dt: 0.0500, sse=10666304.0, rms=19.020 (1.618%)
- 012: dt: 0.0500, sse=10359424.0, rms=18.725 (1.553%)
- 013: dt: 0.0500, sse=10072792.0, rms=18.445 (1.497%)
- 014: dt: 0.0500, sse=9804124.0, rms=18.178 (1.446%)
- 015: dt: 0.0500, sse=9551781.0, rms=17.924 (1.398%)
- 016: dt: 0.0500, sse=9313760.0, rms=17.681 (1.357%)
- 017: dt: 0.0500, sse=9088526.0, rms=17.447 (1.320%)
- 018: dt: 0.0500, sse=8874758.0, rms=17.223 (1.286%)
- 019: dt: 0.0500, sse=8671087.0, rms=17.006 (1.258%)
- 020: dt: 0.0500, sse=8476539.0, rms=16.797 (1.233%)
- positioning took 1.0 minutes
- mean border=70.1, 141 (51) missing vertices, mean dist 1.1 [0.1 (%0.3)->2.3 (%99.7))]
- %15 local maxima, %33 large gradients and %48 min vals, 146 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=8576129.0, rms=16.909
- 021: dt: 0.0500, sse=8386468.5, rms=16.704 (1.216%)
- 022: dt: 0.0500, sse=8204572.0, rms=16.504 (1.195%)
- 023: dt: 0.0500, sse=8029128.5, rms=16.309 (1.181%)
- 024: dt: 0.0500, sse=7859949.5, rms=16.119 (1.167%)
- 025: dt: 0.0500, sse=7696106.0, rms=15.932 (1.157%)
- 026: dt: 0.0500, sse=7537047.0, rms=15.749 (1.150%)
- 027: dt: 0.0500, sse=7381528.5, rms=15.568 (1.151%)
- 028: dt: 0.0500, sse=7229462.5, rms=15.388 (1.153%)
- 029: dt: 0.0500, sse=7080084.0, rms=15.210 (1.159%)
- 030: dt: 0.0500, sse=6933434.5, rms=15.033 (1.165%)
- positioning took 1.1 minutes
- mean border=70.0, 195 (45) missing vertices, mean dist 1.0 [0.1 (%2.1)->2.0 (%97.9))]
- %15 local maxima, %33 large gradients and %48 min vals, 119 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=7003964.5, rms=15.120
- 031: dt: 0.5000, sse=5886311.0, rms=13.703 (9.373%)
- 032: dt: 0.5000, sse=4947366.0, rms=12.383 (9.632%)
- 033: dt: 0.5000, sse=4161232.5, rms=11.160 (9.872%)
- 034: dt: 0.5000, sse=3505712.8, rms=10.025 (10.174%)
- 035: dt: 0.5000, sse=2976468.5, rms=9.006 (10.161%)
- 036: dt: 0.5000, sse=2516398.0, rms=8.014 (11.016%)
- 037: dt: 0.5000, sse=2157531.8, rms=7.149 (10.797%)
- 038: dt: 0.5000, sse=1878954.6, rms=6.393 (10.568%)
- 039: dt: 0.5000, sse=1702859.6, rms=5.869 (8.204%)
- 040: dt: 0.5000, sse=1571300.9, rms=5.439 (7.327%)
- 041: dt: 0.5000, sse=1499908.4, rms=5.193 (4.513%)
- 042: dt: 0.5000, sse=1441714.9, rms=4.980 (4.105%)
- 043: dt: 0.5000, sse=1419970.0, rms=4.900 (1.605%)
- 044: dt: 0.5000, sse=1391476.6, rms=4.788 (2.289%)
- rms = 4.77, time step reduction 1 of 3 to 0.250...
- 045: dt: 0.5000, sse=1386268.8, rms=4.770 (0.372%)
- 046: dt: 0.2500, sse=1256183.9, rms=4.188 (12.216%)
- 047: dt: 0.2500, sse=1220668.4, rms=4.029 (3.796%)
- rms = 4.03, time step reduction 2 of 3 to 0.125...
- 048: dt: 0.1250, sse=1207350.4, rms=3.964 (1.602%)
- 049: dt: 0.1250, sse=1189553.4, rms=3.875 (2.252%)
- rms = 3.86, time step reduction 3 of 3 to 0.062...
- 050: dt: 0.1250, sse=1186354.4, rms=3.857 (0.446%)
- positioning took 3.1 minutes
- mean border=69.1, 3250 (10) missing vertices, mean dist 0.1 [0.2 (%44.6)->0.5 (%55.4))]
- %26 local maxima, %24 large gradients and %43 min vals, 87 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=1438655.2, rms=4.228
- rms = 4.29, time step reduction 1 of 3 to 0.250...
- 051: dt: 0.2500, sse=1342805.0, rms=3.772 (10.776%)
- 052: dt: 0.2500, sse=1278154.4, rms=3.435 (8.950%)
- 053: dt: 0.2500, sse=1263900.5, rms=3.364 (2.070%)
- 054: dt: 0.2500, sse=1250507.8, rms=3.297 (1.990%)
- rms = 3.27, time step reduction 2 of 3 to 0.125...
- 055: dt: 0.2500, sse=1245721.2, rms=3.274 (0.675%)
- 056: dt: 0.1250, sse=1204027.4, rms=3.020 (7.774%)
- rms = 2.97, time step reduction 3 of 3 to 0.062...
- 057: dt: 0.1250, sse=1195724.1, rms=2.971 (1.607%)
- positioning took 1.4 minutes
- mean border=68.6, 3693 (7) missing vertices, mean dist 0.1 [0.1 (%44.1)->0.4 (%55.9))]
- %36 local maxima, %14 large gradients and %43 min vals, 100 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=1219435.5, rms=3.124
- rms = 3.62, time step reduction 1 of 3 to 0.250...
- 058: dt: 0.2500, sse=1194166.1, rms=2.968 (4.996%)
- rms = 2.96, time step reduction 2 of 3 to 0.125...
- 059: dt: 0.2500, sse=1190494.2, rms=2.955 (0.434%)
- 060: dt: 0.1250, sse=1181480.8, rms=2.893 (2.089%)
- rms = 2.87, time step reduction 3 of 3 to 0.062...
- 061: dt: 0.1250, sse=1176998.6, rms=2.870 (0.826%)
- positioning took 0.9 minutes
- mean border=68.2, 6871 (6) missing vertices, mean dist 0.0 [0.1 (%46.1)->0.3 (%53.9))]
- %38 local maxima, %12 large gradients and %41 min vals, 104 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-6.0.0/0050669/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=1191759.9, rms=2.941
- rms = 3.30, time step reduction 1 of 3 to 0.250...
- 062: dt: 0.2500, sse=1178925.8, rms=2.859 (2.763%)
- rms = 2.83, time step reduction 2 of 3 to 0.125...
- 063: dt: 0.2500, sse=1170773.8, rms=2.828 (1.105%)
- 064: dt: 0.1250, sse=1161834.8, rms=2.764 (2.248%)
- rms = 2.73, time step reduction 3 of 3 to 0.062...
- 065: dt: 0.1250, sse=1155725.2, rms=2.729 (1.268%)
- positioning took 1.0 minutes
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.area.pial
- vertex spacing 1.00 +- 0.45 (0.07-->7.06) (max @ vno 104226 --> 103210)
- face area 0.39 +- 0.32 (0.00-->6.14)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 144204 vertices processed
- 25000 of 144204 vertices processed
- 50000 of 144204 vertices processed
- 75000 of 144204 vertices processed
- 100000 of 144204 vertices processed
- 125000 of 144204 vertices processed
- 0 of 144204 vertices processed
- 25000 of 144204 vertices processed
- 50000 of 144204 vertices processed
- 75000 of 144204 vertices processed
- 100000 of 144204 vertices processed
- 125000 of 144204 vertices processed
- thickness calculation complete, 290:840 truncations.
- 31675 vertices at 0 distance
- 99927 vertices at 1 distance
- 87753 vertices at 2 distance
- 37342 vertices at 3 distance
- 12988 vertices at 4 distance
- 4156 vertices at 5 distance
- 1274 vertices at 6 distance
- 402 vertices at 7 distance
- 179 vertices at 8 distance
- 95 vertices at 9 distance
- 78 vertices at 10 distance
- 74 vertices at 11 distance
- 40 vertices at 12 distance
- 29 vertices at 13 distance
- 31 vertices at 14 distance
- 18 vertices at 15 distance
- 18 vertices at 16 distance
- 14 vertices at 17 distance
- 10 vertices at 18 distance
- 5 vertices at 19 distance
- 12 vertices at 20 distance
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.thickness
- positioning took 16.6 minutes
- PIDs (30739 30742) completed and logs appended.
- #--------------------------------------------
- #@# Surf Volume lh Sun Oct 8 00:48:23 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 0050669 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.volume
- masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/label/lh.cortex.label
- Total face volume 261182
- Total vertex volume 257709 (mask=0)
- #@# 0050669 lh 257709
-
- vertexvol Done
- #--------------------------------------------
- #@# Surf Volume rh Sun Oct 8 00:48:27 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 0050669 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.volume
- masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/label/rh.cortex.label
- Total face volume 262717
- Total vertex volume 259281 (mask=0)
- #@# 0050669 rh 259281
-
- vertexvol Done
- #--------------------------------------------
- #@# Cortical ribbon mask Sun Oct 8 00:48:31 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 0050669
- 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 = 82
- writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/ribbon.mgz
- mris_volmask took 14.77 minutes
- writing ribbon files
- #-----------------------------------------
- #@# Parcellation Stats lh Sun Oct 8 01:03:17 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 0050669 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 0050669 lh pial
- #-----------------------------------------
- #@# Parcellation Stats rh Sun Oct 8 01:03:17 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 0050669 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 0050669 rh pial
- Waiting for PID 541 of (541 544 547 550) to complete...
- Waiting for PID 544 of (541 544 547 550) to complete...
- Waiting for PID 547 of (541 544 547 550) to complete...
- Waiting for PID 550 of (541 544 547 550) 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 0050669 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 261182
- Total vertex volume 257709 (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) = 1621644 mm^3 (det: 1.201315 )
- lhCtxGM: 255870.833 255358.000 diff= 512.8 pctdiff= 0.200
- rhCtxGM: 258074.617 257348.000 diff= 726.6 pctdiff= 0.282
- lhCtxWM: 245180.163 245240.000 diff= -59.8 pctdiff=-0.024
- rhCtxWM: 249181.729 250251.000 diff=-1069.3 pctdiff=-0.429
- SubCortGMVol 61757.000
- SupraTentVol 1086642.342 (1082895.000) diff=3747.342 pctdiff=0.345
- SupraTentVolNotVent 1073724.342 (1069977.000) diff=3747.342 pctdiff=0.349
- BrainSegVol 1252935.000 (1250314.000) diff=2621.000 pctdiff=0.209
- BrainSegVolNotVent 1236271.000 (1236310.342) diff=-39.342 pctdiff=-0.003
- BrainSegVolNotVent 1236271.000
- CerebellumVol 166223.000
- VentChorVol 12918.000
- 3rd4th5thCSF 3746.000
- CSFVol 1125.000, OptChiasmVol 71.000
- MaskVol 1689719.000
- 1193 866 2117 2.584 0.339 0.101 0.017 6 0.9 bankssts
- 964 645 1849 2.870 0.577 0.155 0.031 20 1.1 caudalanteriorcingulate
- 3675 2403 6972 2.722 0.446 0.123 0.033 41 4.9 caudalmiddlefrontal
- 2624 1674 3312 1.914 0.519 0.135 0.030 37 3.4 cuneus
- 830 571 3307 3.914 0.720 0.121 0.038 13 1.4 entorhinal
- 5052 3429 10781 2.822 0.523 0.132 0.033 71 6.6 fusiform
- 6230 4233 12034 2.573 0.449 0.136 0.032 98 7.9 inferiorparietal
- 5521 3767 12764 2.779 0.740 0.136 0.036 92 8.1 inferiortemporal
- 1307 807 2107 2.489 0.735 0.131 0.040 22 1.6 isthmuscingulate
- 9105 5716 13353 2.137 0.556 0.140 0.036 141 13.6 lateraloccipital
- 4062 2703 8398 2.823 0.686 0.141 0.043 71 7.6 lateralorbitofrontal
- 4556 3045 5945 1.886 0.560 0.140 0.037 65 6.8 lingual
- 3057 2029 5813 2.508 0.692 0.133 0.042 69 5.4 medialorbitofrontal
- 4900 3426 12096 2.936 0.589 0.145 0.035 95 7.4 middletemporal
- 1053 727 2284 2.795 0.673 0.107 0.029 9 1.2 parahippocampal
- 2328 1424 3485 2.340 0.439 0.111 0.029 22 2.8 paracentral
- 2927 1954 5890 2.726 0.418 0.117 0.025 34 3.0 parsopercularis
- 1165 789 3093 3.020 0.570 0.157 0.040 22 2.3 parsorbitalis
- 2426 1670 5071 2.605 0.478 0.128 0.028 31 2.8 parstriangularis
- 2508 1537 2261 1.738 0.550 0.139 0.040 32 4.1 pericalcarine
- 6330 3873 9442 2.182 0.614 0.109 0.029 62 7.7 postcentral
- 1635 1090 2883 2.573 0.530 0.143 0.029 29 1.9 posteriorcingulate
- 7363 4556 12389 2.515 0.611 0.117 0.034 70 10.4 precentral
- 5278 3545 9582 2.513 0.443 0.125 0.028 60 6.0 precuneus
- 1380 898 3116 3.020 0.719 0.135 0.038 27 2.0 rostralanteriorcingulate
- 9366 6424 18094 2.529 0.504 0.136 0.032 145 12.7 rostralmiddlefrontal
- 11095 7549 24295 2.826 0.506 0.126 0.030 125 13.6 superiorfrontal
- 8772 5748 14834 2.354 0.423 0.129 0.028 109 9.8 superiorparietal
- 6022 4001 13647 2.879 0.624 0.113 0.026 62 6.5 superiortemporal
- 6969 4621 13418 2.666 0.501 0.121 0.030 108 9.4 supramarginal
- 334 243 1160 3.116 0.651 0.175 0.052 8 0.7 frontalpole
- 838 588 2953 3.490 0.740 0.134 0.039 11 1.4 temporalpole
- 910 535 1416 2.334 0.444 0.118 0.038 10 1.5 transversetemporal
- 3583 2346 7509 3.054 0.861 0.129 0.077 56 6.6 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 0050669 lh pial
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.pial...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 261182
- Total vertex volume 257709 (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) = 1621644 mm^3 (det: 1.201315 )
- lhCtxGM: 255870.833 255358.000 diff= 512.8 pctdiff= 0.200
- rhCtxGM: 258074.617 257348.000 diff= 726.6 pctdiff= 0.282
- lhCtxWM: 245180.163 245240.000 diff= -59.8 pctdiff=-0.024
- rhCtxWM: 249181.729 250251.000 diff=-1069.3 pctdiff=-0.429
- SubCortGMVol 61757.000
- SupraTentVol 1086642.342 (1082895.000) diff=3747.342 pctdiff=0.345
- SupraTentVolNotVent 1073724.342 (1069977.000) diff=3747.342 pctdiff=0.349
- BrainSegVol 1252935.000 (1250314.000) diff=2621.000 pctdiff=0.209
- BrainSegVolNotVent 1236271.000 (1236310.342) diff=-39.342 pctdiff=-0.003
- BrainSegVolNotVent 1236271.000
- CerebellumVol 166223.000
- VentChorVol 12918.000
- 3rd4th5thCSF 3746.000
- CSFVol 1125.000, OptChiasmVol 71.000
- MaskVol 1689719.000
- 1193 759 2117 2.584 0.339 0.103 0.026 14 1.4 bankssts
- 964 734 1849 2.870 0.577 0.134 0.032 19 1.1 caudalanteriorcingulate
- 3675 2686 6972 2.722 0.446 0.116 0.035 67 4.5 caudalmiddlefrontal
- 2624 1908 3312 1.914 0.519 0.124 0.027 34 3.3 cuneus
- 830 1133 3307 3.914 0.720 0.201 0.046 11 1.8 entorhinal
- 5052 4174 10781 2.822 0.523 0.146 0.036 90 8.1 fusiform
- 6230 5060 12034 2.573 0.449 0.142 0.032 91 8.9 inferiorparietal
- 5521 5107 12764 2.779 0.740 0.153 0.035 86 8.6 inferiortemporal
- 1307 906 2107 2.489 0.735 0.140 0.043 32 2.2 isthmuscingulate
- 9105 6907 13353 2.137 0.556 0.124 0.029 123 11.9 lateraloccipital
- 4062 3119 8398 2.823 0.686 0.137 0.034 69 6.1 lateralorbitofrontal
- 4556 3420 5945 1.886 0.560 0.132 0.034 86 6.7 lingual
- 3057 2523 5813 2.508 0.692 0.150 0.039 58 5.3 medialorbitofrontal
- 4900 4613 12096 2.936 0.589 0.155 0.034 92 7.8 middletemporal
- 1053 963 2284 2.795 0.673 0.160 0.038 12 2.0 parahippocampal
- 2328 1573 3485 2.340 0.439 0.117 0.058 122 8.6 paracentral
- 2927 2337 5890 2.726 0.418 0.129 0.028 32 3.6 parsopercularis
- 1165 1232 3093 3.020 0.570 0.184 0.043 18 2.4 parsorbitalis
- 2426 2144 5071 2.605 0.478 0.146 0.029 32 3.2 parstriangularis
- 2508 1188 2261 1.738 0.550 0.100 0.030 43 2.9 pericalcarine
- 6330 4702 9442 2.182 0.614 0.110 0.022 52 6.2 postcentral
- 1635 1201 2883 2.573 0.530 0.146 0.039 37 2.4 posteriorcingulate
- 7363 5186 12389 2.515 0.611 0.103 0.024 114 7.7 precentral
- 5278 3948 9582 2.513 0.443 0.135 0.032 95 7.6 precuneus
- 1380 1231 3116 3.020 0.719 0.160 0.039 28 2.2 rostralanteriorcingulate
- 9366 7597 18094 2.529 0.504 0.146 0.031 159 13.3 rostralmiddlefrontal
- 11095 9214 24295 2.826 0.506 0.134 0.029 140 13.5 superiorfrontal
- 8772 6675 14834 2.354 0.423 0.132 0.029 115 10.8 superiorparietal
- 6022 5031 13647 2.879 0.624 0.136 0.031 87 8.6 superiortemporal
- 6969 5344 13418 2.666 0.501 0.125 0.030 102 8.4 supramarginal
- 334 475 1160 3.116 0.651 0.263 0.046 6 0.8 frontalpole
- 838 1116 2953 3.490 0.740 0.223 0.047 13 1.8 temporalpole
- 910 714 1416 2.334 0.444 0.116 0.028 5 1.1 transversetemporal
- 3583 2353 7509 3.054 0.861 0.143 0.047 88 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 0050669 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 262717
- Total vertex volume 259281 (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) = 1621644 mm^3 (det: 1.201315 )
- lhCtxGM: 255870.833 255358.000 diff= 512.8 pctdiff= 0.200
- rhCtxGM: 258074.617 257348.000 diff= 726.6 pctdiff= 0.282
- lhCtxWM: 245180.163 245240.000 diff= -59.8 pctdiff=-0.024
- rhCtxWM: 249181.729 250251.000 diff=-1069.3 pctdiff=-0.429
- SubCortGMVol 61757.000
- SupraTentVol 1086642.342 (1082895.000) diff=3747.342 pctdiff=0.345
- SupraTentVolNotVent 1073724.342 (1069977.000) diff=3747.342 pctdiff=0.349
- BrainSegVol 1252935.000 (1250314.000) diff=2621.000 pctdiff=0.209
- BrainSegVolNotVent 1236271.000 (1236310.342) diff=-39.342 pctdiff=-0.003
- BrainSegVolNotVent 1236271.000
- CerebellumVol 166223.000
- VentChorVol 12918.000
- 3rd4th5thCSF 3746.000
- CSFVol 1125.000, OptChiasmVol 71.000
- MaskVol 1689719.000
- 1449 1026 2460 2.554 0.421 0.108 0.020 10 1.3 bankssts
- 1218 789 2360 2.553 0.709 0.138 0.025 21 1.1 caudalanteriorcingulate
- 3608 2402 7282 2.737 0.558 0.130 0.032 41 4.7 caudalmiddlefrontal
- 2850 1796 3485 1.856 0.486 0.151 0.041 48 4.9 cuneus
- 577 383 2299 3.855 0.798 0.110 0.034 8 0.7 entorhinal
- 4492 3052 9236 2.782 0.587 0.133 0.032 62 6.2 fusiform
- 7354 5009 14726 2.618 0.500 0.130 0.027 110 8.0 inferiorparietal
- 5215 3445 11208 2.734 0.775 0.134 0.039 95 8.5 inferiortemporal
- 1374 886 2318 2.286 0.900 0.138 0.044 26 1.8 isthmuscingulate
- 9196 5956 14449 2.233 0.525 0.144 0.036 140 13.4 lateraloccipital
- 4053 2780 8067 2.708 0.640 0.147 0.042 72 7.2 lateralorbitofrontal
- 5432 3562 7362 1.937 0.629 0.141 0.042 82 9.2 lingual
- 2977 1970 5642 2.589 0.653 0.127 0.038 55 4.7 medialorbitofrontal
- 5798 3999 14085 2.908 0.535 0.131 0.032 90 7.8 middletemporal
- 1039 707 2230 2.819 0.791 0.105 0.026 8 1.0 parahippocampal
- 2502 1493 3832 2.443 0.458 0.124 0.034 26 3.5 paracentral
- 2168 1495 4444 2.788 0.429 0.120 0.028 23 2.5 parsopercularis
- 1165 791 2991 3.032 0.548 0.158 0.046 23 2.0 parsorbitalis
- 2384 1673 5214 2.753 0.571 0.137 0.033 36 3.3 parstriangularis
- 2556 1746 2401 1.575 0.451 0.142 0.042 31 4.2 pericalcarine
- 6886 4231 9997 2.173 0.640 0.110 0.029 61 8.2 postcentral
- 1771 1181 3315 2.574 0.557 0.151 0.034 33 2.5 posteriorcingulate
- 8286 5111 13924 2.533 0.635 0.112 0.030 73 10.2 precentral
- 5583 3698 9395 2.512 0.464 0.127 0.029 66 6.3 precuneus
- 1107 740 2952 3.141 0.519 0.140 0.033 19 1.6 rostralanteriorcingulate
- 8432 5782 16917 2.574 0.504 0.139 0.037 132 13.3 rostralmiddlefrontal
- 10522 7124 22735 2.841 0.512 0.131 0.032 120 13.3 superiorfrontal
- 8522 5564 14394 2.340 0.429 0.122 0.026 96 8.9 superiorparietal
- 6221 4131 14603 3.071 0.597 0.106 0.024 58 6.0 superiortemporal
- 5992 4019 11788 2.762 0.493 0.126 0.028 73 6.4 supramarginal
- 459 297 1382 3.224 0.490 0.187 0.053 13 1.1 frontalpole
- 711 517 3017 3.737 0.720 0.144 0.047 11 1.5 temporalpole
- 703 393 1200 2.535 0.478 0.110 0.037 6 1.0 transversetemporal
- 3603 2344 7534 3.033 0.854 0.126 0.045 44 5.8 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 0050669 rh pial
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.pial...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 262717
- Total vertex volume 259281 (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) = 1621644 mm^3 (det: 1.201315 )
- lhCtxGM: 255870.833 255358.000 diff= 512.8 pctdiff= 0.200
- rhCtxGM: 258074.617 257348.000 diff= 726.6 pctdiff= 0.282
- lhCtxWM: 245180.163 245240.000 diff= -59.8 pctdiff=-0.024
- rhCtxWM: 249181.729 250251.000 diff=-1069.3 pctdiff=-0.429
- SubCortGMVol 61757.000
- SupraTentVol 1086642.342 (1082895.000) diff=3747.342 pctdiff=0.345
- SupraTentVolNotVent 1073724.342 (1069977.000) diff=3747.342 pctdiff=0.349
- BrainSegVol 1252935.000 (1250314.000) diff=2621.000 pctdiff=0.209
- BrainSegVolNotVent 1236271.000 (1236310.342) diff=-39.342 pctdiff=-0.003
- BrainSegVolNotVent 1236271.000
- CerebellumVol 166223.000
- VentChorVol 12918.000
- 3rd4th5thCSF 3746.000
- CSFVol 1125.000, OptChiasmVol 71.000
- MaskVol 1689719.000
- 1449 872 2460 2.554 0.421 0.108 0.030 24 1.7 bankssts
- 1218 976 2360 2.553 0.709 0.159 0.041 44 1.8 caudalanteriorcingulate
- 3608 2782 7282 2.737 0.558 0.130 0.030 52 4.5 caudalmiddlefrontal
- 2850 2047 3485 1.856 0.486 0.129 0.031 34 3.8 cuneus
- 577 816 2299 3.855 0.798 0.174 0.038 5 0.9 entorhinal
- 4492 3535 9236 2.782 0.587 0.142 0.037 76 7.4 fusiform
- 7354 6099 14726 2.618 0.500 0.134 0.027 86 9.2 inferiorparietal
- 5215 4463 11208 2.734 0.775 0.140 0.032 80 7.9 inferiortemporal
- 1374 1080 2318 2.286 0.900 0.155 0.050 77 2.8 isthmuscingulate
- 9196 7058 14449 2.233 0.525 0.126 0.030 143 11.9 lateraloccipital
- 4053 3227 8067 2.708 0.640 0.143 0.036 66 5.9 lateralorbitofrontal
- 5432 4095 7362 1.937 0.629 0.126 0.032 93 7.5 lingual
- 2977 2368 5642 2.589 0.653 0.142 0.037 51 5.2 medialorbitofrontal
- 5798 5511 14085 2.908 0.535 0.149 0.029 68 8.2 middletemporal
- 1039 853 2230 2.819 0.791 0.132 0.032 13 1.4 parahippocampal
- 2502 1633 3832 2.443 0.458 0.108 0.026 23 2.8 paracentral
- 2168 1642 4444 2.788 0.429 0.133 0.032 32 3.1 parsopercularis
- 1165 1099 2991 3.032 0.548 0.149 0.031 13 1.6 parsorbitalis
- 2384 2112 5214 2.753 0.571 0.149 0.030 29 3.3 parstriangularis
- 2556 1413 2401 1.575 0.451 0.100 0.030 44 2.5 pericalcarine
- 6886 4953 9997 2.173 0.640 0.109 0.023 57 6.9 postcentral
- 1771 1361 3315 2.574 0.557 0.148 0.035 38 2.5 posteriorcingulate
- 8286 5739 13924 2.533 0.635 0.104 0.043 377 21.7 precentral
- 5583 3794 9395 2.512 0.464 0.120 0.030 85 6.9 precuneus
- 1107 1139 2952 3.141 0.519 0.163 0.033 12 1.7 rostralanteriorcingulate
- 8432 7168 16917 2.574 0.504 0.154 0.033 134 12.9 rostralmiddlefrontal
- 10522 8521 22735 2.841 0.512 0.135 0.030 148 13.1 superiorfrontal
- 8522 6637 14394 2.340 0.429 0.126 0.026 103 9.0 superiorparietal
- 6221 5264 14603 3.071 0.597 0.128 0.026 66 7.3 superiortemporal
- 5992 4451 11788 2.762 0.493 0.124 0.029 72 7.2 supramarginal
- 459 530 1382 3.224 0.490 0.189 0.032 4 0.7 frontalpole
- 711 1020 3017 3.737 0.720 0.212 0.042 8 1.4 temporalpole
- 703 541 1200 2.535 0.478 0.102 0.025 4 0.8 transversetemporal
- 3603 2419 7534 3.033 0.854 0.151 0.055 114 7.4 insula
- PIDs (541 544 547 550) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc 2 lh Sun Oct 8 01:04:48 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050669 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 01:04:48 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050669 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 649 of (649 652) to complete...
- Waiting for PID 652 of (649 652) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050669 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...
- 44 labels changed using aseg
- relabeling using gibbs priors...
- 000: 9359 changed, 143612 examined...
- 001: 2151 changed, 36497 examined...
- 002: 593 changed, 11307 examined...
- 003: 222 changed, 3364 examined...
- 004: 107 changed, 1258 examined...
- 005: 58 changed, 593 examined...
- 006: 22 changed, 324 examined...
- 007: 7 changed, 114 examined...
- 008: 3 changed, 39 examined...
- 009: 3 changed, 15 examined...
- 010: 4 changed, 18 examined...
- 011: 1 changed, 18 examined...
- 012: 0 changed, 5 examined...
- 22 labels changed using aseg
- 000: 279 total segments, 195 labels (2412 vertices) changed
- 001: 93 total segments, 10 labels (563 vertices) changed
- 002: 83 total segments, 1 labels (170 vertices) changed
- 003: 82 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 37 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1044 vertices marked for relabeling...
- 1044 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 0 minutes and 22 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050669 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...
- 2 labels changed using aseg
- relabeling using gibbs priors...
- 000: 9217 changed, 144204 examined...
- 001: 2130 changed, 36182 examined...
- 002: 586 changed, 11292 examined...
- 003: 252 changed, 3323 examined...
- 004: 116 changed, 1376 examined...
- 005: 41 changed, 653 examined...
- 006: 18 changed, 219 examined...
- 007: 11 changed, 116 examined...
- 008: 5 changed, 69 examined...
- 009: 3 changed, 29 examined...
- 010: 4 changed, 17 examined...
- 011: 1 changed, 15 examined...
- 012: 0 changed, 10 examined...
- 1 labels changed using aseg
- 000: 241 total segments, 154 labels (2313 vertices) changed
- 001: 95 total segments, 9 labels (74 vertices) changed
- 002: 86 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 38 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1058 vertices marked for relabeling...
- 1058 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 0 minutes and 20 seconds.
- PIDs (649 652) completed and logs appended.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Sun Oct 8 01:05:10 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 0050669 lh white
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Sun Oct 8 01:05:10 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 0050669 rh white
- Waiting for PID 707 of (707 710) to complete...
- Waiting for PID 710 of (707 710) 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 0050669 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 261182
- Total vertex volume 257709 (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) = 1621644 mm^3 (det: 1.201315 )
- lhCtxGM: 255870.833 255358.000 diff= 512.8 pctdiff= 0.200
- rhCtxGM: 258074.617 257348.000 diff= 726.6 pctdiff= 0.282
- lhCtxWM: 245180.163 245240.000 diff= -59.8 pctdiff=-0.024
- rhCtxWM: 249181.729 250251.000 diff=-1069.3 pctdiff=-0.429
- SubCortGMVol 61757.000
- SupraTentVol 1086642.342 (1082895.000) diff=3747.342 pctdiff=0.345
- SupraTentVolNotVent 1073724.342 (1069977.000) diff=3747.342 pctdiff=0.349
- BrainSegVol 1252935.000 (1250314.000) diff=2621.000 pctdiff=0.209
- BrainSegVolNotVent 1236271.000 (1236310.342) diff=-39.342 pctdiff=-0.003
- BrainSegVolNotVent 1236271.000
- CerebellumVol 166223.000
- VentChorVol 12918.000
- 3rd4th5thCSF 3746.000
- CSFVol 1125.000, OptChiasmVol 71.000
- MaskVol 1689719.000
- 1083 786 2245 2.503 0.628 0.141 0.029 17 1.4 G&S_frontomargin
- 1987 1308 3469 2.213 0.573 0.136 0.035 28 2.8 G&S_occipital_inf
- 1802 1038 2851 2.296 0.521 0.119 0.033 20 2.5 G&S_paracentral
- 1609 1058 3298 2.689 0.484 0.135 0.042 23 2.7 G&S_subcentral
- 763 529 1975 2.834 0.548 0.166 0.055 18 1.8 G&S_transv_frontopol
- 2427 1620 4949 2.878 0.521 0.136 0.035 39 3.5 G&S_cingul-Ant
- 1390 969 2451 2.613 0.428 0.126 0.022 16 1.1 G&S_cingul-Mid-Ant
- 1477 1017 2746 2.589 0.423 0.126 0.026 17 1.5 G&S_cingul-Mid-Post
- 483 332 1259 2.970 0.602 0.165 0.050 11 0.9 G_cingul-Post-dorsal
- 304 186 612 2.667 0.651 0.114 0.036 5 0.2 G_cingul-Post-ventral
- 2582 1603 3307 1.847 0.539 0.141 0.036 38 4.0 G_cuneus
- 1583 1047 3880 2.867 0.428 0.121 0.029 23 1.9 G_front_inf-Opercular
- 438 273 1209 3.161 0.438 0.155 0.038 8 0.6 G_front_inf-Orbital
- 1652 1119 4079 2.796 0.426 0.143 0.034 30 2.3 G_front_inf-Triangul
- 5443 3516 11929 2.719 0.528 0.144 0.040 101 8.8 G_front_middle
- 7773 5162 18704 2.892 0.531 0.135 0.035 115 11.2 G_front_sup
- 904 594 2163 3.147 0.992 0.142 0.190 29 2.3 G_Ins_lg&S_cent_ins
- 763 471 2402 3.624 0.831 0.142 0.053 12 1.7 G_insular_short
- 2786 1780 5745 2.597 0.511 0.147 0.036 52 4.1 G_occipital_middle
- 1776 1129 2932 2.251 0.587 0.142 0.033 27 2.3 G_occipital_sup
- 2157 1424 5319 2.989 0.488 0.146 0.040 42 3.4 G_oc-temp_lat-fusifor
- 3180 2034 4253 1.851 0.592 0.154 0.047 58 6.0 G_oc-temp_med-Lingual
- 1448 1001 4454 3.439 0.839 0.112 0.030 16 1.8 G_oc-temp_med-Parahip
- 2621 1741 6898 2.940 0.766 0.166 0.055 68 6.9 G_orbital
- 2953 1952 6644 2.681 0.502 0.149 0.037 62 4.1 G_pariet_inf-Angular
- 3373 2254 8115 2.873 0.493 0.137 0.036 56 5.1 G_pariet_inf-Supramar
- 3155 2056 6566 2.471 0.443 0.139 0.033 55 4.0 G_parietal_sup
- 2400 1286 3819 2.299 0.597 0.108 0.031 27 3.0 G_postcentral
- 2768 1560 5400 2.723 0.581 0.116 0.039 29 4.6 G_precentral
- 2400 1606 5365 2.598 0.473 0.140 0.032 41 3.1 G_precuneus
- 875 574 2108 2.439 0.866 0.175 0.075 36 3.2 G_rectus
- 768 474 1286 2.640 1.014 0.083 0.033 8 0.9 G_subcallosal
- 804 474 1444 2.448 0.408 0.114 0.036 8 1.3 G_temp_sup-G_T_transv
- 1986 1304 6364 3.167 0.648 0.145 0.038 35 3.0 G_temp_sup-Lateral
- 830 600 2376 3.351 0.815 0.091 0.018 4 0.7 G_temp_sup-Plan_polar
- 1062 740 2134 2.611 0.547 0.093 0.040 33 2.7 G_temp_sup-Plan_tempo
- 2976 1950 7665 2.850 0.801 0.150 0.045 68 5.4 G_temporal_inf
- 2849 1990 8252 3.134 0.596 0.162 0.042 73 5.3 G_temporal_middle
- 358 246 493 2.224 0.291 0.108 0.017 2 0.3 Lat_Fis-ant-Horizont
- 222 160 381 2.545 0.375 0.098 0.014 1 0.1 Lat_Fis-ant-Vertical
- 1302 842 1720 2.616 0.434 0.124 0.027 11 1.5 Lat_Fis-post
- 2691 1512 3017 1.880 0.520 0.139 0.041 47 4.6 Pole_occipital
- 1852 1316 6737 3.347 0.731 0.147 0.042 35 3.3 Pole_temporal
- 2927 1904 3062 1.886 0.627 0.126 0.034 30 3.9 S_calcarine
- 2908 1925 2948 1.768 0.521 0.119 0.030 23 3.6 S_central
- 1160 766 1577 2.371 0.333 0.105 0.019 8 0.9 S_cingul-Marginalis
- 636 420 993 2.724 0.495 0.091 0.022 3 0.5 S_circular_insula_ant
- 1444 933 2159 2.731 0.585 0.093 0.021 7 1.3 S_circular_insula_inf
- 1739 1169 2474 2.639 0.405 0.110 0.022 10 1.6 S_circular_insula_sup
- 911 632 1369 2.726 0.357 0.106 0.022 4 0.8 S_collat_transv_ant
- 551 375 614 2.042 0.527 0.146 0.035 6 0.8 S_collat_transv_post
- 2874 1990 4576 2.454 0.397 0.117 0.023 25 2.7 S_front_inf
- 1756 1242 3253 2.471 0.459 0.127 0.030 25 2.3 S_front_middle
- 3078 2152 5029 2.507 0.331 0.103 0.020 17 2.6 S_front_sup
- 360 243 459 2.536 0.290 0.135 0.025 3 0.4 S_interm_prim-Jensen
- 3250 2203 4591 2.303 0.328 0.105 0.018 22 2.4 S_intrapariet&P_trans
- 1115 746 1284 2.103 0.398 0.139 0.033 14 1.5 S_oc_middle&Lunatus
- 1386 937 1812 2.204 0.401 0.131 0.029 13 1.7 S_oc_sup&transversal
- 546 375 704 2.321 0.336 0.136 0.036 6 0.8 S_occipital_ant
- 1065 720 1773 2.558 0.472 0.123 0.028 12 1.3 S_oc-temp_lat
- 2417 1708 3767 2.358 0.436 0.113 0.022 17 2.2 S_oc-temp_med&Lingual
- 450 314 663 2.257 0.327 0.117 0.025 3 0.5 S_orbital_lateral
- 675 462 946 2.487 0.511 0.107 0.019 4 0.4 S_orbital_med-olfact
- 1452 989 2931 2.973 0.593 0.137 0.035 18 2.1 S_orbital-H_Shaped
- 2409 1599 3624 2.483 0.417 0.116 0.026 19 2.6 S_parieto_occipital
- 1072 624 1108 2.525 0.946 0.146 0.034 25 1.2 S_pericallosal
- 3346 2187 4414 2.198 0.364 0.100 0.019 23 2.7 S_postcentral
- 1692 1132 2520 2.611 0.422 0.104 0.026 12 1.6 S_precentral-inf-part
- 1264 885 1961 2.488 0.335 0.107 0.019 8 1.1 S_precentral-sup-part
- 679 492 1042 2.459 0.584 0.124 0.020 6 0.5 S_suborbital
- 879 602 1257 2.391 0.367 0.113 0.017 6 0.6 S_subparietal
- 1820 1283 3016 2.554 0.498 0.120 0.025 15 1.8 S_temporal_inf
- 4977 3476 8161 2.586 0.357 0.113 0.023 40 4.6 S_temporal_sup
- 507 340 604 2.073 0.407 0.111 0.020 4 0.4 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 0050669 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 262717
- Total vertex volume 259281 (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) = 1621644 mm^3 (det: 1.201315 )
- lhCtxGM: 255870.833 255358.000 diff= 512.8 pctdiff= 0.200
- rhCtxGM: 258074.617 257348.000 diff= 726.6 pctdiff= 0.282
- lhCtxWM: 245180.163 245240.000 diff= -59.8 pctdiff=-0.024
- rhCtxWM: 249181.729 250251.000 diff=-1069.3 pctdiff=-0.429
- SubCortGMVol 61757.000
- SupraTentVol 1086642.342 (1082895.000) diff=3747.342 pctdiff=0.345
- SupraTentVolNotVent 1073724.342 (1069977.000) diff=3747.342 pctdiff=0.349
- BrainSegVol 1252935.000 (1250314.000) diff=2621.000 pctdiff=0.209
- BrainSegVolNotVent 1236271.000 (1236310.342) diff=-39.342 pctdiff=-0.003
- BrainSegVolNotVent 1236271.000
- CerebellumVol 166223.000
- VentChorVol 12918.000
- 3rd4th5thCSF 3746.000
- CSFVol 1125.000, OptChiasmVol 71.000
- MaskVol 1689719.000
- 872 593 1873 2.630 0.593 0.159 0.046 19 1.8 G&S_frontomargin
- 1534 1013 2862 2.364 0.551 0.125 0.027 20 1.6 G&S_occipital_inf
- 1509 818 2233 2.325 0.488 0.124 0.036 19 2.2 G&S_paracentral
- 1457 958 3248 2.996 0.478 0.125 0.030 17 1.6 G&S_subcentral
- 1068 710 2620 2.889 0.563 0.173 0.064 29 2.6 G&S_transv_frontopol
- 2897 1984 6090 2.793 0.517 0.117 0.025 32 3.1 G&S_cingul-Ant
- 1478 1001 2940 2.803 0.431 0.136 0.031 20 1.8 G&S_cingul-Mid-Ant
- 1425 994 2665 2.636 0.430 0.126 0.028 15 1.6 G&S_cingul-Mid-Post
- 527 342 1416 3.081 0.523 0.171 0.044 12 1.0 G_cingul-Post-dorsal
- 323 202 760 2.655 0.745 0.133 0.046 5 0.4 G_cingul-Post-ventral
- 2701 1695 3300 1.802 0.531 0.146 0.042 44 4.5 G_cuneus
- 1330 916 3705 2.955 0.372 0.128 0.037 22 2.0 G_front_inf-Opercular
- 335 221 954 3.118 0.360 0.155 0.046 6 0.6 G_front_inf-Orbital
- 1125 784 2991 3.031 0.489 0.165 0.045 26 2.1 G_front_inf-Triangul
- 4177 2781 11016 2.914 0.526 0.154 0.045 83 7.5 G_front_middle
- 7238 4746 17691 2.965 0.530 0.142 0.039 104 11.1 G_front_sup
- 607 397 1548 3.253 0.940 0.140 0.048 10 1.1 G_Ins_lg&S_cent_ins
- 1221 736 3102 3.031 1.082 0.131 0.064 20 2.5 G_insular_short
- 2612 1725 5796 2.727 0.531 0.164 0.040 60 4.0 G_occipital_middle
- 2063 1289 3567 2.313 0.468 0.143 0.033 30 2.8 G_occipital_sup
- 1961 1297 4539 2.768 0.579 0.146 0.040 37 3.3 G_oc-temp_lat-fusifor
- 3493 2190 4885 1.889 0.659 0.145 0.049 60 6.5 G_oc-temp_med-Lingual
- 1109 754 3601 3.407 0.861 0.124 0.042 16 1.5 G_oc-temp_med-Parahip
- 2972 2030 7540 2.867 0.731 0.166 0.056 76 7.0 G_orbital
- 2868 1881 6511 2.692 0.517 0.141 0.034 58 4.0 G_pariet_inf-Angular
- 2910 1935 7250 3.016 0.492 0.143 0.037 51 4.4 G_pariet_inf-Supramar
- 2538 1656 5212 2.441 0.495 0.131 0.031 38 3.2 G_parietal_sup
- 2710 1472 4032 2.213 0.596 0.117 0.038 30 4.3 G_postcentral
- 3320 1851 6421 2.659 0.734 0.112 0.035 34 4.9 G_precentral
- 2362 1590 4766 2.477 0.443 0.132 0.032 36 2.8 G_precuneus
- 896 571 1981 2.366 0.854 0.150 0.054 24 2.4 G_rectus
- 377 228 755 3.090 0.632 0.117 0.065 13 0.7 G_subcallosal
- 623 357 1219 2.641 0.491 0.120 0.039 7 0.9 G_temp_sup-G_T_transv
- 2052 1367 6414 3.386 0.593 0.138 0.035 34 2.9 G_temp_sup-Lateral
- 939 632 2296 3.313 0.656 0.080 0.022 4 0.8 G_temp_sup-Plan_polar
- 777 548 1659 2.675 0.485 0.078 0.013 3 0.4 G_temp_sup-Plan_tempo
- 3027 1947 7395 2.770 0.849 0.155 0.055 83 6.9 G_temporal_inf
- 3554 2492 10077 3.053 0.543 0.153 0.041 75 6.2 G_temporal_middle
- 356 250 456 2.098 0.411 0.107 0.018 2 0.3 Lat_Fis-ant-Horizont
- 363 258 529 2.260 0.321 0.101 0.020 2 0.3 Lat_Fis-ant-Vertical
- 1504 982 2221 2.708 0.438 0.110 0.022 10 1.3 Lat_Fis-post
- 4389 2665 5471 1.929 0.543 0.150 0.045 72 8.3 Pole_occipital
- 1723 1219 6570 3.517 0.779 0.141 0.039 27 2.9 Pole_temporal
- 2377 1726 2706 1.852 0.583 0.141 0.035 28 3.4 S_calcarine
- 2924 1985 3067 1.835 0.510 0.111 0.028 19 3.3 S_central
- 1175 799 1638 2.329 0.373 0.126 0.030 14 1.5 S_cingul-Marginalis
- 507 365 856 3.000 0.526 0.111 0.021 2 0.5 S_circular_insula_ant
- 1245 815 1920 2.960 0.573 0.083 0.016 5 0.8 S_circular_insula_inf
- 1341 895 1951 2.699 0.457 0.111 0.024 7 1.5 S_circular_insula_sup
- 1219 831 2085 2.769 0.530 0.098 0.016 6 0.9 S_collat_transv_ant
- 637 453 714 2.026 0.346 0.143 0.036 7 0.9 S_collat_transv_post
- 2304 1571 3511 2.393 0.306 0.104 0.019 16 1.7 S_front_inf
- 2215 1593 3668 2.394 0.366 0.128 0.027 21 2.7 S_front_middle
- 2953 2045 4707 2.510 0.341 0.115 0.021 21 2.9 S_front_sup
- 598 398 720 2.403 0.286 0.114 0.017 4 0.4 S_interm_prim-Jensen
- 3219 2154 4539 2.243 0.339 0.098 0.018 21 2.4 S_intrapariet&P_trans
- 1007 689 1240 2.079 0.301 0.114 0.022 7 0.9 S_oc_middle&Lunatus
- 1610 1080 2275 2.327 0.404 0.125 0.024 15 1.5 S_oc_sup&transversal
- 882 588 1189 2.350 0.319 0.123 0.026 8 0.9 S_occipital_ant
- 865 610 1390 2.738 0.419 0.123 0.023 6 1.1 S_oc-temp_lat
- 2339 1638 3581 2.499 0.551 0.111 0.019 17 1.9 S_oc-temp_med&Lingual
- 409 288 587 2.524 0.537 0.131 0.026 3 0.5 S_orbital_lateral
- 749 528 1064 2.439 0.535 0.112 0.018 5 0.6 S_orbital_med-olfact
- 1518 1032 2733 2.743 0.553 0.138 0.032 18 2.1 S_orbital-H_Shaped
- 2821 1856 3934 2.407 0.515 0.122 0.026 27 3.0 S_parieto_occipital
- 1576 962 1467 2.011 0.753 0.134 0.028 29 1.1 S_pericallosal
- 2979 1994 3729 2.188 0.385 0.110 0.020 23 2.4 S_postcentral
- 2286 1511 3530 2.634 0.403 0.104 0.019 15 1.9 S_precentral-inf-part
- 1508 995 2033 2.447 0.373 0.106 0.020 8 1.3 S_precentral-sup-part
- 390 270 635 2.605 0.516 0.129 0.023 4 0.4 S_suborbital
- 849 577 1279 2.446 0.442 0.141 0.029 10 1.1 S_subparietal
- 1317 907 2008 2.467 0.374 0.113 0.019 10 1.1 S_temporal_inf
- 6693 4609 11853 2.652 0.451 0.106 0.019 53 5.3 S_temporal_sup
- 373 253 498 2.507 0.299 0.114 0.017 2 0.2 S_temporal_transverse
- PIDs (707 710) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc 3 lh Sun Oct 8 01:05:56 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050669 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 01:05:56 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050669 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 775 of (775 778) to complete...
- Waiting for PID 778 of (775 778) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050669 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...
- 1625 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2029 changed, 143612 examined...
- 001: 495 changed, 9360 examined...
- 002: 152 changed, 2777 examined...
- 003: 56 changed, 898 examined...
- 004: 25 changed, 344 examined...
- 005: 16 changed, 162 examined...
- 006: 6 changed, 94 examined...
- 007: 5 changed, 40 examined...
- 008: 4 changed, 22 examined...
- 009: 2 changed, 27 examined...
- 010: 2 changed, 13 examined...
- 011: 1 changed, 13 examined...
- 012: 2 changed, 8 examined...
- 013: 4 changed, 13 examined...
- 014: 3 changed, 18 examined...
- 015: 5 changed, 19 examined...
- 016: 3 changed, 23 examined...
- 017: 0 changed, 17 examined...
- 267 labels changed using aseg
- 000: 54 total segments, 21 labels (151 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 10 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 622 vertices marked for relabeling...
- 622 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas.annot...
- classification took 0 minutes and 16 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050669 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...
- 1503 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2108 changed, 144204 examined...
- 001: 487 changed, 9759 examined...
- 002: 144 changed, 2750 examined...
- 003: 68 changed, 861 examined...
- 004: 28 changed, 367 examined...
- 005: 22 changed, 162 examined...
- 006: 10 changed, 104 examined...
- 007: 3 changed, 62 examined...
- 008: 2 changed, 17 examined...
- 009: 0 changed, 8 examined...
- 254 labels changed using aseg
- 000: 50 total segments, 17 labels (139 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, 12 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 725 vertices marked for relabeling...
- 725 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas.annot...
- classification took 0 minutes and 17 seconds.
- PIDs (775 778) completed and logs appended.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Sun Oct 8 01:06:13 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 0050669 lh white
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Sun Oct 8 01:06:13 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 0050669 rh white
- Waiting for PID 830 of (830 833) to complete...
- Waiting for PID 833 of (830 833) 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 0050669 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 261182
- Total vertex volume 257709 (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) = 1621644 mm^3 (det: 1.201315 )
- lhCtxGM: 255870.833 255358.000 diff= 512.8 pctdiff= 0.200
- rhCtxGM: 258074.617 257348.000 diff= 726.6 pctdiff= 0.282
- lhCtxWM: 245180.163 245240.000 diff= -59.8 pctdiff=-0.024
- rhCtxWM: 249181.729 250251.000 diff=-1069.3 pctdiff=-0.429
- SubCortGMVol 61757.000
- SupraTentVol 1086642.342 (1082895.000) diff=3747.342 pctdiff=0.345
- SupraTentVolNotVent 1073724.342 (1069977.000) diff=3747.342 pctdiff=0.349
- BrainSegVol 1252935.000 (1250314.000) diff=2621.000 pctdiff=0.209
- BrainSegVolNotVent 1236271.000 (1236310.342) diff=-39.342 pctdiff=-0.003
- BrainSegVolNotVent 1236271.000
- CerebellumVol 166223.000
- VentChorVol 12918.000
- 3rd4th5thCSF 3746.000
- CSFVol 1125.000, OptChiasmVol 71.000
- MaskVol 1689719.000
- 1624 1092 3219 2.851 0.523 0.143 0.030 28 1.8 caudalanteriorcingulate
- 3923 2577 7446 2.716 0.449 0.123 0.033 44 5.1 caudalmiddlefrontal
- 3606 2267 4765 2.060 0.543 0.135 0.031 48 4.8 cuneus
- 763 528 2904 3.891 0.747 0.114 0.033 9 1.0 entorhinal
- 4642 3168 9608 2.768 0.515 0.131 0.032 63 5.9 fusiform
- 6556 4441 12572 2.566 0.446 0.136 0.031 103 8.1 inferiorparietal
- 5566 3764 13103 2.828 0.757 0.137 0.037 94 8.4 inferiortemporal
- 1332 824 2132 2.501 0.719 0.129 0.038 21 1.7 isthmuscingulate
- 8992 5644 13270 2.147 0.555 0.141 0.036 141 13.3 lateraloccipital
- 4419 2972 9882 2.942 0.772 0.148 0.047 86 9.3 lateralorbitofrontal
- 4722 3138 6041 1.868 0.553 0.141 0.038 68 7.2 lingual
- 2524 1677 5051 2.508 0.750 0.137 0.045 63 4.9 medialorbitofrontal
- 6319 4414 14864 2.875 0.583 0.140 0.035 111 9.1 middletemporal
- 1146 794 2510 2.804 0.685 0.109 0.029 11 1.3 parahippocampal
- 2684 1660 4449 2.415 0.466 0.114 0.030 26 3.3 paracentral
- 2607 1746 5364 2.753 0.417 0.115 0.026 29 2.7 parsopercularis
- 1232 800 2755 2.819 0.528 0.133 0.032 17 1.8 parsorbitalis
- 3173 2173 6113 2.554 0.449 0.132 0.028 42 3.7 parstriangularis
- 2487 1526 2243 1.742 0.545 0.138 0.039 31 4.0 pericalcarine
- 7173 4408 10582 2.202 0.606 0.113 0.030 73 8.9 postcentral
- 1843 1230 3356 2.579 0.539 0.143 0.030 32 2.2 posteriorcingulate
- 7302 4508 12229 2.518 0.610 0.118 0.034 71 10.5 precentral
- 5230 3525 9826 2.502 0.442 0.122 0.027 62 5.7 precuneus
- 1791 1171 3740 2.925 0.693 0.136 0.036 33 2.5 rostralanteriorcingulate
- 6954 4742 13757 2.550 0.502 0.136 0.032 105 9.3 rostralmiddlefrontal
- 11929 8152 25625 2.776 0.528 0.128 0.031 145 15.4 superiorfrontal
- 6878 4564 11969 2.371 0.431 0.126 0.027 81 7.4 superiorparietal
- 7741 5240 18037 2.889 0.662 0.115 0.027 80 8.9 superiortemporal
- 6371 4226 12367 2.662 0.507 0.120 0.031 101 8.7 supramarginal
- 875 512 1365 2.351 0.434 0.118 0.039 9 1.5 transversetemporal
- 2996 1973 6563 3.061 0.816 0.125 0.078 48 5.0 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 0050669 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 262717
- Total vertex volume 259281 (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) = 1621644 mm^3 (det: 1.201315 )
- lhCtxGM: 255870.833 255358.000 diff= 512.8 pctdiff= 0.200
- rhCtxGM: 258074.617 257348.000 diff= 726.6 pctdiff= 0.282
- lhCtxWM: 245180.163 245240.000 diff= -59.8 pctdiff=-0.024
- rhCtxWM: 249181.729 250251.000 diff=-1069.3 pctdiff=-0.429
- SubCortGMVol 61757.000
- SupraTentVol 1086642.342 (1082895.000) diff=3747.342 pctdiff=0.345
- SupraTentVolNotVent 1073724.342 (1069977.000) diff=3747.342 pctdiff=0.349
- BrainSegVol 1252935.000 (1250314.000) diff=2621.000 pctdiff=0.209
- BrainSegVolNotVent 1236271.000 (1236310.342) diff=-39.342 pctdiff=-0.003
- BrainSegVolNotVent 1236271.000
- CerebellumVol 166223.000
- VentChorVol 12918.000
- 3rd4th5thCSF 3746.000
- CSFVol 1125.000, OptChiasmVol 71.000
- MaskVol 1689719.000
- 1351 884 2643 2.546 0.709 0.141 0.027 24 1.3 caudalanteriorcingulate
- 3722 2481 7588 2.749 0.565 0.129 0.033 43 4.8 caudalmiddlefrontal
- 3508 2212 4393 1.911 0.505 0.148 0.040 57 5.9 cuneus
- 489 330 1891 3.816 0.797 0.110 0.034 7 0.5 entorhinal
- 4106 2791 8063 2.733 0.558 0.135 0.032 56 5.8 fusiform
- 7383 5009 14586 2.611 0.495 0.130 0.027 110 8.2 inferiorparietal
- 5585 3717 12562 2.783 0.788 0.134 0.039 102 8.9 inferiortemporal
- 1357 874 2259 2.289 0.898 0.136 0.043 26 1.8 isthmuscingulate
- 9297 6001 14444 2.222 0.528 0.143 0.036 140 13.3 lateraloccipital
- 4804 3240 9832 2.719 0.718 0.153 0.050 95 9.9 lateralorbitofrontal
- 5303 3492 7188 1.945 0.621 0.141 0.042 80 9.0 lingual
- 2256 1490 4543 2.578 0.748 0.130 0.043 48 4.0 medialorbitofrontal
- 6986 4821 16154 2.862 0.543 0.130 0.031 101 9.2 middletemporal
- 1099 751 2399 2.833 0.780 0.105 0.027 9 1.1 parahippocampal
- 2685 1606 4241 2.470 0.461 0.124 0.034 28 3.8 paracentral
- 2405 1672 4944 2.742 0.442 0.118 0.028 25 2.7 parsopercularis
- 998 678 2439 2.900 0.568 0.140 0.043 15 1.7 parsorbitalis
- 2340 1635 4926 2.734 0.563 0.137 0.033 34 3.2 parstriangularis
- 2562 1734 2379 1.569 0.442 0.139 0.041 31 4.1 pericalcarine
- 7482 4639 10966 2.188 0.640 0.111 0.028 66 8.7 postcentral
- 1774 1189 3336 2.585 0.546 0.150 0.034 32 2.5 posteriorcingulate
- 8063 4947 13614 2.541 0.638 0.112 0.030 72 10.1 precentral
- 5879 3881 10080 2.504 0.453 0.127 0.030 73 6.8 precuneus
- 1381 921 3312 3.052 0.525 0.134 0.031 21 1.8 rostralanteriorcingulate
- 6218 4274 12801 2.580 0.478 0.139 0.035 95 9.1 rostralmiddlefrontal
- 13138 8890 27571 2.791 0.521 0.133 0.033 164 17.4 superiorfrontal
- 6793 4470 11864 2.368 0.430 0.121 0.025 75 6.8 superiorparietal
- 7845 5291 19276 3.068 0.665 0.109 0.026 76 8.3 superiortemporal
- 5704 3814 11166 2.765 0.483 0.125 0.028 69 6.2 supramarginal
- 692 389 1175 2.538 0.475 0.114 0.037 6 1.0 transversetemporal
- 3002 1973 6645 3.183 0.767 0.124 0.037 34 4.4 insula
- PIDs (830 833) completed and logs appended.
- #-----------------------------------------
- #@# WM/GM Contrast lh Sun Oct 8 01:06:55 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- pctsurfcon --s 0050669 --lh-only
- #-----------------------------------------
- #@# WM/GM Contrast rh Sun Oct 8 01:06:55 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts
- pctsurfcon --s 0050669 --rh-only
- Waiting for PID 891 of (891 903) to complete...
- Waiting for PID 903 of (891 903) to complete...
- pctsurfcon --s 0050669 --lh-only
- Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts/pctsurfcon.log
- Sun Oct 8 01:06:55 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-6.0.0/0050669/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-385 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-6.0.0/0050669/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/tmp.pctsurfcon.891/lh.wm.mgh --regheader 0050669 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/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-6.0.0/0050669/label/lh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 = 78274
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/label/lh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/tmp.pctsurfcon.891/lh.wm.mgh
- Dim: 143612 1 1
- mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/tmp.pctsurfcon.891/lh.gm.mgh --projfrac 0.3 --regheader 0050669 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/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-6.0.0/0050669/label/lh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.white
- Done reading source surface
- Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 = 93785
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/label/lh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/tmp.pctsurfcon.891/lh.gm.mgh
- Dim: 143612 1 1
- mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/tmp.pctsurfcon.891/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/tmp.pctsurfcon.891/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/surf/lh.w-g.pct.mgh
- mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.w-g.pct.mgh --annot 0050669 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/surf/lh.w-g.pct.mgh --annot 0050669 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/stats/lh.w-g.pct.stats --snr
- sysname Linux
- hostname tars-385
- machine x86_64
- user ntraut
- UseRobust 0
- Constructing seg from annotation
- Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/surf/lh.w-g.pct.mgh
- Vertex Area is 0.66136 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 0050669 --rh-only
- Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/scripts/pctsurfcon.log
- Sun Oct 8 01:06:55 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-6.0.0/0050669/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-385 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-6.0.0/0050669/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/tmp.pctsurfcon.903/rh.wm.mgh --regheader 0050669 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/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-6.0.0/0050669/label/rh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 = 78884
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/label/rh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/tmp.pctsurfcon.903/rh.wm.mgh
- Dim: 144204 1 1
- mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/tmp.pctsurfcon.903/rh.gm.mgh --projfrac 0.3 --regheader 0050669 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/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-6.0.0/0050669/label/rh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.white
- Done reading source surface
- Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 = 93989
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/label/rh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/tmp.pctsurfcon.903/rh.gm.mgh
- Dim: 144204 1 1
- mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/tmp.pctsurfcon.903/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/tmp.pctsurfcon.903/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/surf/rh.w-g.pct.mgh
- mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.w-g.pct.mgh --annot 0050669 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/surf/rh.w-g.pct.mgh --annot 0050669 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/stats/rh.w-g.pct.stats --snr
- sysname Linux
- hostname tars-385
- machine x86_64
- user ntraut
- UseRobust 0
- Constructing seg from annotation
- Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/surf/rh.w-g.pct.mgh
- Vertex Area is 0.663046 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 (891 903) completed and logs appended.
- #-----------------------------------------
- #@# Relabel Hypointensities Sun Oct 8 01:07:03 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri
- mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz
- reading input surface ../surf/lh.white...
- relabeling lh hypointensities...
- 2853 voxels changed to hypointensity...
- reading input surface ../surf/rh.white...
- relabeling rh hypointensities...
- 2594 voxels changed to hypointensity...
- 5448 hypointense voxels neighboring cortex changed
- #-----------------------------------------
- #@# AParc-to-ASeg aparc Sun Oct 8 01:07:27 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669
- mri_aparc2aseg --s 0050669 --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 01:07:27 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669
- mri_aparc2aseg --s 0050669 --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 01:07:27 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669
- mri_aparc2aseg --s 0050669 --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 1061 of (1061 1064 1067) to complete...
- Waiting for PID 1064 of (1061 1064 1067) to complete...
- Waiting for PID 1067 of (1061 1064 1067) to complete...
- mri_aparc2aseg --s 0050669 --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 0050669
- outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/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-6.0.0/0050669/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 7.18
- 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 --> 77
- rescaling Left_Lateral_Ventricle from 13 --> 34
- rescaling Left_Inf_Lat_Vent from 34 --> 34
- rescaling Left_Cerebellum_White_Matter from 86 --> 91
- rescaling Left_Cerebellum_Cortex from 60 --> 73
- rescaling Left_Thalamus from 94 --> 103
- rescaling Left_Thalamus_Proper from 84 --> 96
- rescaling Left_Caudate from 75 --> 90
- rescaling Left_Putamen from 80 --> 89
- rescaling Left_Pallidum from 98 --> 102
- rescaling Third_Ventricle from 25 --> 50
- rescaling Fourth_Ventricle from 22 --> 32
- rescaling Brain_Stem from 81 --> 85
- rescaling Left_Hippocampus from 57 --> 72
- rescaling Left_Amygdala from 56 --> 73
- rescaling CSF from 32 --> 72
- rescaling Left_Accumbens_area from 62 --> 73
- rescaling Left_VentralDC from 87 --> 93
- rescaling Right_Cerebral_White_Matter from 105 --> 103
- 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 --> 90
- rescaling Right_Cerebellum_Cortex from 59 --> 72
- rescaling Right_Thalamus_Proper from 85 --> 90
- rescaling Right_Caudate from 62 --> 84
- rescaling Right_Putamen from 80 --> 92
- rescaling Right_Pallidum from 97 --> 99
- rescaling Right_Hippocampus from 53 --> 71
- rescaling Right_Amygdala from 55 --> 72
- rescaling Right_Accumbens_area from 65 --> 83
- rescaling Right_VentralDC from 86 --> 92
- rescaling Fifth_Ventricle from 40 --> 60
- rescaling WM_hypointensities from 78 --> 78
- rescaling non_WM_hypointensities from 40 --> 44
- 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
- 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39
- 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
- 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79
- 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
- 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119
- 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139
- 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159
- 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
- 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
- 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219
- 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239
- 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 512832
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 110 changed.
- pass 2: 9 changed.
- pass 3: 0 changed.
- nchanged = 0
- Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/aparc+aseg.mgz
- mri_aparc2aseg --s 0050669 --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 0050669
- outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/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-6.0.0/0050669/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 7.18
- 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 --> 77
- rescaling Left_Lateral_Ventricle from 13 --> 34
- rescaling Left_Inf_Lat_Vent from 34 --> 34
- rescaling Left_Cerebellum_White_Matter from 86 --> 91
- rescaling Left_Cerebellum_Cortex from 60 --> 73
- rescaling Left_Thalamus from 94 --> 103
- rescaling Left_Thalamus_Proper from 84 --> 96
- rescaling Left_Caudate from 75 --> 90
- rescaling Left_Putamen from 80 --> 89
- rescaling Left_Pallidum from 98 --> 102
- rescaling Third_Ventricle from 25 --> 50
- rescaling Fourth_Ventricle from 22 --> 32
- rescaling Brain_Stem from 81 --> 85
- rescaling Left_Hippocampus from 57 --> 72
- rescaling Left_Amygdala from 56 --> 73
- rescaling CSF from 32 --> 72
- rescaling Left_Accumbens_area from 62 --> 73
- rescaling Left_VentralDC from 87 --> 93
- rescaling Right_Cerebral_White_Matter from 105 --> 103
- 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 --> 90
- rescaling Right_Cerebellum_Cortex from 59 --> 72
- rescaling Right_Thalamus_Proper from 85 --> 90
- rescaling Right_Caudate from 62 --> 84
- rescaling Right_Putamen from 80 --> 92
- rescaling Right_Pallidum from 97 --> 99
- rescaling Right_Hippocampus from 53 --> 71
- rescaling Right_Amygdala from 55 --> 72
- rescaling Right_Accumbens_area from 65 --> 83
- rescaling Right_VentralDC from 86 --> 92
- rescaling Fifth_Ventricle from 40 --> 60
- rescaling WM_hypointensities from 78 --> 78
- rescaling non_WM_hypointensities from 40 --> 44
- 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
- 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39
- 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
- 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79
- 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
- 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119
- 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139
- 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159
- 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
- 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
- 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219
- 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239
- 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 512831
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 110 changed.
- pass 2: 9 changed.
- pass 3: 0 changed.
- nchanged = 0
- Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/aparc.a2009s+aseg.mgz
- mri_aparc2aseg --s 0050669 --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 0050669
- outvol mri/aparc.DKTatlas+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/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-6.0.0/0050669/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 7.18
- 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 --> 77
- rescaling Left_Lateral_Ventricle from 13 --> 34
- rescaling Left_Inf_Lat_Vent from 34 --> 34
- rescaling Left_Cerebellum_White_Matter from 86 --> 91
- rescaling Left_Cerebellum_Cortex from 60 --> 73
- rescaling Left_Thalamus from 94 --> 103
- rescaling Left_Thalamus_Proper from 84 --> 96
- rescaling Left_Caudate from 75 --> 90
- rescaling Left_Putamen from 80 --> 89
- rescaling Left_Pallidum from 98 --> 102
- rescaling Third_Ventricle from 25 --> 50
- rescaling Fourth_Ventricle from 22 --> 32
- rescaling Brain_Stem from 81 --> 85
- rescaling Left_Hippocampus from 57 --> 72
- rescaling Left_Amygdala from 56 --> 73
- rescaling CSF from 32 --> 72
- rescaling Left_Accumbens_area from 62 --> 73
- rescaling Left_VentralDC from 87 --> 93
- rescaling Right_Cerebral_White_Matter from 105 --> 103
- 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 --> 90
- rescaling Right_Cerebellum_Cortex from 59 --> 72
- rescaling Right_Thalamus_Proper from 85 --> 90
- rescaling Right_Caudate from 62 --> 84
- rescaling Right_Putamen from 80 --> 92
- rescaling Right_Pallidum from 97 --> 99
- rescaling Right_Hippocampus from 53 --> 71
- rescaling Right_Amygdala from 55 --> 72
- rescaling Right_Accumbens_area from 65 --> 83
- rescaling Right_VentralDC from 86 --> 92
- rescaling Fifth_Ventricle from 40 --> 60
- rescaling WM_hypointensities from 78 --> 78
- rescaling non_WM_hypointensities from 40 --> 44
- 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
- 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39
- 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
- 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79
- 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
- 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119
- 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139
- 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159
- 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
- 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
- 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219
- 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239
- 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 512831
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 110 changed.
- pass 2: 9 changed.
- pass 3: 0 changed.
- nchanged = 0
- Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
- PIDs (1061 1064 1067) completed and logs appended.
- #-----------------------------------------
- #@# APas-to-ASeg Sun Oct 8 01:14:55 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri
- apas2aseg --i aparc+aseg.mgz --o aseg.mgz
- Sun Oct 8 01:14:55 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-6.0.0/0050669/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-385 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-6.0.0/0050669/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-385
- 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 01:14:55 CEST 2017
- Ended at Sun Oct 8 01:15:02 CEST 2017
- Apas2aseg-Run-Time-Sec 7
-
- apas2aseg Done
- #--------------------------------------------
- #@# ASeg Stats Sun Oct 8 01:15:02 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669
- 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 0050669
- $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 0050669
- sysname Linux
- hostname tars-385
- machine x86_64
- user ntraut
- UseRobust 0
- atlas_icv (eTIV) = 1621644 mm^3 (det: 1.201315 )
- Computing euler number
- orig.nofix lheno = -110, rheno = -114
- orig.nofix lhholes = 56, rhholes = 58
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 255870.833 255358.000 diff= 512.8 pctdiff= 0.200
- rhCtxGM: 258074.617 257348.000 diff= 726.6 pctdiff= 0.282
- lhCtxWM: 245180.163 245240.000 diff= -59.8 pctdiff=-0.024
- rhCtxWM: 249181.729 250251.000 diff=-1069.3 pctdiff=-0.429
- SubCortGMVol 61757.000
- SupraTentVol 1086642.342 (1082895.000) diff=3747.342 pctdiff=0.345
- SupraTentVolNotVent 1073724.342 (1069977.000) diff=3747.342 pctdiff=0.349
- BrainSegVol 1252935.000 (1250314.000) diff=2621.000 pctdiff=0.209
- BrainSegVolNotVent 1236271.000 (1236310.342) diff=-39.342 pctdiff=-0.003
- BrainSegVolNotVent 1236271.000
- CerebellumVol 166223.000
- VentChorVol 12918.000
- 3rd4th5thCSF 3746.000
- CSFVol 1125.000, OptChiasmVol 71.000
- MaskVol 1689719.000
- 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 01:17:16 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669
- mri_aparc2aseg --s 0050669 --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 0050669
- 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-6.0.0/0050669/mri/aparc+aseg.mgz
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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-6.0.0/0050669/mri/ribbon.mgz
- Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/ribbon.mgz
- Ripping vertices labeled as unkown
- Ripped 8254 vertices from left hemi
- Ripped 7999 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-6.0.0/0050669/mri/aseg.mgz
- Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 = 1005209
- Used brute-force search on 97 voxels
- Fixing Parahip LH WM
- Found 11 clusters
- 0 k 2.000000
- 1 k 3.000000
- 2 k 1.000000
- 3 k 1.000000
- 4 k 1.000000
- 5 k 1.000000
- 6 k 3.000000
- 7 k 1.000000
- 8 k 1.000000
- 9 k 54.000000
- 10 k 1724.000000
- Fixing Parahip RH WM
- Found 10 clusters
- 0 k 1.000000
- 1 k 1878.000000
- 2 k 1.000000
- 3 k 2.000000
- 4 k 3.000000
- 5 k 1.000000
- 6 k 1.000000
- 7 k 1.000000
- 8 k 1.000000
- 9 k 42.000000
- 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 0050669 --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 0050669 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv
- sysname Linux
- hostname tars-385
- machine x86_64
- user ntraut
- UseRobust 0
- atlas_icv (eTIV) = 1621644 mm^3 (det: 1.201315 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 255870.833 255358.000 diff= 512.8 pctdiff= 0.200
- rhCtxGM: 258074.617 257348.000 diff= 726.6 pctdiff= 0.282
- lhCtxWM: 245180.163 245240.000 diff= -59.8 pctdiff=-0.024
- rhCtxWM: 249181.729 250251.000 diff=-1069.3 pctdiff=-0.429
- SubCortGMVol 61757.000
- SupraTentVol 1086642.342 (1082895.000) diff=3747.342 pctdiff=0.345
- SupraTentVolNotVent 1073724.342 (1069977.000) diff=3747.342 pctdiff=0.349
- BrainSegVol 1252935.000 (1250314.000) diff=2621.000 pctdiff=0.209
- BrainSegVolNotVent 1236271.000 (1236310.342) diff=-39.342 pctdiff=-0.003
- BrainSegVolNotVent 1236271.000
- CerebellumVol 166223.000
- VentChorVol 12918.000
- 3rd4th5thCSF 3746.000
- CSFVol 1125.000, OptChiasmVol 71.000
- MaskVol 1689719.000
- 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-6.0.0/0050669/label
- #--------------------------------------------
- #@# BA_exvivo Labels lh Sun Oct 8 01:26:54 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 0050669 --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 0050669 --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 0050669 --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 0050669 --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 0050669 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 1846 of (1846 1852 1858 1864 1867) to complete...
- Waiting for PID 1852 of (1846 1852 1858 1864 1867) to complete...
- Waiting for PID 1858 of (1846 1852 1858 1864 1867) to complete...
- Waiting for PID 1864 of (1846 1852 1858 1864 1867) to complete...
- Waiting for PID 1867 of (1846 1852 1858 1864 1867) 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 331
- Checking for and removing duplicates
- Writing label file ./lh.BA1_exvivo.label 4460
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 605
- Checking for and removing duplicates
- Writing label file ./lh.BA2_exvivo.label 8514
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 167
- Checking for and removing duplicates
- Writing label file ./lh.BA3a_exvivo.label 4244
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 281
- Checking for and removing duplicates
- Writing label file ./lh.BA3b_exvivo.label 6264
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 529
- Checking for and removing duplicates
- Writing label file ./lh.BA4a_exvivo.label 6313
- mri_label2label: Done
- PIDs (1846 1852 1858 1864 1867) 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 0050669 --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 0050669 --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 0050669 --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 0050669 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 1923 of (1923 1929 1935 1941) to complete...
- Waiting for PID 1929 of (1923 1929 1935 1941) to complete...
- Waiting for PID 1935 of (1923 1929 1935 1941) to complete...
- Waiting for PID 1941 of (1923 1929 1935 1941) 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 254
- Checking for and removing duplicates
- Writing label file ./lh.BA4p_exvivo.label 4324
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 1540
- Checking for and removing duplicates
- Writing label file ./lh.BA6_exvivo.label 15129
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 557
- Checking for and removing duplicates
- Writing label file ./lh.BA44_exvivo.label 4738
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 1493
- Checking for and removing duplicates
- Writing label file ./lh.BA45_exvivo.label 4915
- mri_label2label: Done
- PIDs (1923 1929 1935 1941) 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 0050669 --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 0050669 --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 0050669 --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 0050669 --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 0050669 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 1987 of (1987 1993 1999 2005 2011) to complete...
- Waiting for PID 1993 of (1987 1993 1999 2005 2011) to complete...
- Waiting for PID 1999 of (1987 1993 1999 2005 2011) to complete...
- Waiting for PID 2005 of (1987 1993 1999 2005 2011) to complete...
- Waiting for PID 2011 of (1987 1993 1999 2005 2011) 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 2028
- Checking for and removing duplicates
- Writing label file ./lh.V1_exvivo.label 6669
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 3645
- Checking for and removing duplicates
- Writing label file ./lh.V2_exvivo.label 11759
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 570
- Checking for and removing duplicates
- Writing label file ./lh.MT_exvivo.label 2588
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 156
- Checking for and removing duplicates
- Writing label file ./lh.entorhinal_exvivo.label 1446
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 162
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal_exvivo.label 1361
- mri_label2label: Done
- PIDs (1987 1993 1999 2005 2011) 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 0050669 --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 0050669 --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 0050669 --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 0050669 --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 0050669 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 2066 of (2066 2072 2078 2084 2089) to complete...
- Waiting for PID 2072 of (2066 2072 2078 2084 2089) to complete...
- Waiting for PID 2078 of (2066 2072 2078 2084 2089) to complete...
- Waiting for PID 2084 of (2066 2072 2078 2084 2089) to complete...
- Waiting for PID 2089 of (2066 2072 2078 2084 2089) 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 71
- Checking for and removing duplicates
- Writing label file ./lh.BA1_exvivo.thresh.label 1085
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 188
- Checking for and removing duplicates
- Writing label file ./lh.BA2_exvivo.thresh.label 2280
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 44
- Checking for and removing duplicates
- Writing label file ./lh.BA3a_exvivo.thresh.label 1548
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 90
- Checking for and removing duplicates
- Writing label file ./lh.BA3b_exvivo.thresh.label 2086
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 172
- Checking for and removing duplicates
- Writing label file ./lh.BA4a_exvivo.thresh.label 2491
- mri_label2label: Done
- PIDs (2066 2072 2078 2084 2089) 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 0050669 --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 0050669 --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 0050669 --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 0050669 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 2139 of (2139 2145 2151 2157) to complete...
- Waiting for PID 2145 of (2139 2145 2151 2157) to complete...
- Waiting for PID 2151 of (2139 2145 2151 2157) to complete...
- Waiting for PID 2157 of (2139 2145 2151 2157) 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 113
- Checking for and removing duplicates
- Writing label file ./lh.BA4p_exvivo.thresh.label 1662
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 717
- Checking for and removing duplicates
- Writing label file ./lh.BA6_exvivo.thresh.label 7752
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 234
- Checking for and removing duplicates
- Writing label file ./lh.BA44_exvivo.thresh.label 2146
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 623
- Checking for and removing duplicates
- Writing label file ./lh.BA45_exvivo.thresh.label 1774
- mri_label2label: Done
- PIDs (2139 2145 2151 2157) 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 0050669 --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 0050669 --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 0050669 --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 0050669 --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 0050669 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 2197 of (2197 2203 2209 2215 2221) to complete...
- Waiting for PID 2203 of (2197 2203 2209 2215 2221) to complete...
- Waiting for PID 2209 of (2197 2203 2209 2215 2221) to complete...
- Waiting for PID 2215 of (2197 2203 2209 2215 2221) to complete...
- Waiting for PID 2221 of (2197 2203 2209 2215 2221) 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 1466
- Checking for and removing duplicates
- Writing label file ./lh.V1_exvivo.thresh.label 4871
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 1646
- Checking for and removing duplicates
- Writing label file ./lh.V2_exvivo.thresh.label 4980
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 144
- Checking for and removing duplicates
- Writing label file ./lh.MT_exvivo.thresh.label 657
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 76
- Checking for and removing duplicates
- Writing label file ./lh.entorhinal_exvivo.thresh.label 546
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 143612
- Number of reverse mapping hits = 59
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal_exvivo.thresh.label 509
- mri_label2label: Done
- PIDs (2197 2203 2209 2215 2221) completed and logs appended.
- mris_label2annot --s 0050669 --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-6.0.0/0050669/label
- cmdline mris_label2annot --s 0050669 --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-385
- machine x86_64
- user ntraut
- subject 0050669
- 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-6.0.0/0050669/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 98450 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/label/lh.BA_exvivo.annot
- mris_label2annot --s 0050669 --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-6.0.0/0050669/label
- cmdline mris_label2annot --s 0050669 --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-385
- machine x86_64
- user ntraut
- subject 0050669
- 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-6.0.0/0050669/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 117039 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 0050669 lh white
- computing statistics for each annotation in ./lh.BA_exvivo.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 261182
- Total vertex volume 257709 (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) = 1621644 mm^3 (det: 1.201315 )
- lhCtxGM: 255870.833 255358.000 diff= 512.8 pctdiff= 0.200
- rhCtxGM: 258074.617 257348.000 diff= 726.6 pctdiff= 0.282
- lhCtxWM: 245180.163 245240.000 diff= -59.8 pctdiff=-0.024
- rhCtxWM: 249181.729 250251.000 diff=-1069.3 pctdiff=-0.429
- SubCortGMVol 61757.000
- SupraTentVol 1086642.342 (1082895.000) diff=3747.342 pctdiff=0.345
- SupraTentVolNotVent 1073724.342 (1069977.000) diff=3747.342 pctdiff=0.349
- BrainSegVol 1252935.000 (1250314.000) diff=2621.000 pctdiff=0.209
- BrainSegVolNotVent 1236271.000 (1236310.342) diff=-39.342 pctdiff=-0.003
- BrainSegVolNotVent 1236271.000
- CerebellumVol 166223.000
- VentChorVol 12918.000
- 3rd4th5thCSF 3746.000
- CSFVol 1125.000, OptChiasmVol 71.000
- MaskVol 1689719.000
- 1181 581 1930 2.392 0.607 0.118 0.036 19 1.6 BA1_exvivo
- 4316 2732 6645 2.330 0.480 0.105 0.023 35 4.1 BA2_exvivo
- 943 624 899 1.784 0.504 0.142 0.034 11 1.2 BA3a_exvivo
- 2157 1385 2975 1.990 0.697 0.119 0.034 22 3.1 BA3b_exvivo
- 1776 1020 2628 2.333 0.591 0.113 0.037 16 2.8 BA4a_exvivo
- 1241 779 1547 2.108 0.694 0.123 0.040 10 2.2 BA4p_exvivo
- 9908 6423 20069 2.742 0.472 0.118 0.030 102 12.0 BA6_exvivo
- 2486 1652 5194 2.828 0.447 0.118 0.031 27 2.9 BA44_exvivo
- 4073 2777 7959 2.551 0.452 0.130 0.029 55 5.0 BA45_exvivo
- 4283 2617 4115 1.682 0.529 0.132 0.038 56 6.9 V1_exvivo
- 9226 5836 11833 1.946 0.541 0.147 0.040 148 14.8 V2_exvivo
- 2169 1462 4199 2.499 0.514 0.137 0.034 36 2.6 MT_exvivo
- 663 457 2246 3.752 0.753 0.111 0.030 7 0.8 perirhinal_exvivo
- 740 516 2461 3.359 0.719 0.121 0.037 11 1.3 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 0050669 lh white
- computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/lh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 261182
- Total vertex volume 257709 (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) = 1621644 mm^3 (det: 1.201315 )
- lhCtxGM: 255870.833 255358.000 diff= 512.8 pctdiff= 0.200
- rhCtxGM: 258074.617 257348.000 diff= 726.6 pctdiff= 0.282
- lhCtxWM: 245180.163 245240.000 diff= -59.8 pctdiff=-0.024
- rhCtxWM: 249181.729 250251.000 diff=-1069.3 pctdiff=-0.429
- SubCortGMVol 61757.000
- SupraTentVol 1086642.342 (1082895.000) diff=3747.342 pctdiff=0.345
- SupraTentVolNotVent 1073724.342 (1069977.000) diff=3747.342 pctdiff=0.349
- BrainSegVol 1252935.000 (1250314.000) diff=2621.000 pctdiff=0.209
- BrainSegVolNotVent 1236271.000 (1236310.342) diff=-39.342 pctdiff=-0.003
- BrainSegVolNotVent 1236271.000
- CerebellumVol 166223.000
- VentChorVol 12918.000
- 3rd4th5thCSF 3746.000
- CSFVol 1125.000, OptChiasmVol 71.000
- MaskVol 1689719.000
- 731 358 1345 2.528 0.621 0.118 0.034 10 1.0 BA1_exvivo
- 1684 1035 2447 2.207 0.424 0.098 0.023 13 1.7 BA2_exvivo
- 792 517 675 1.701 0.461 0.143 0.034 10 1.0 BA3a_exvivo
- 1330 857 1381 1.608 0.400 0.108 0.033 11 2.0 BA3b_exvivo
- 1639 944 2398 2.348 0.630 0.108 0.034 13 2.5 BA4a_exvivo
- 1059 668 1232 2.013 0.643 0.125 0.041 9 1.8 BA4p_exvivo
- 5491 3490 10712 2.694 0.453 0.116 0.031 54 7.1 BA6_exvivo
- 1660 1079 3468 2.808 0.484 0.121 0.036 22 2.1 BA44_exvivo
- 1688 1168 3943 2.703 0.456 0.136 0.031 28 2.2 BA45_exvivo
- 4493 2756 4380 1.690 0.534 0.129 0.037 57 7.1 V1_exvivo
- 4675 2925 5503 1.824 0.523 0.158 0.043 85 8.4 V2_exvivo
- 585 388 1199 2.551 0.501 0.136 0.028 11 0.7 MT_exvivo
- 330 236 1243 3.894 0.681 0.094 0.019 3 0.3 perirhinal_exvivo
- 416 272 1400 3.412 0.549 0.119 0.039 6 0.8 entorhinal_exvivo
- #--------------------------------------------
- #@# BA_exvivo Labels rh Sun Oct 8 01:30:19 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 0050669 --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 0050669 --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 0050669 --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 0050669 --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 0050669 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 2360 of (2360 2366 2372 2378 2384) to complete...
- Waiting for PID 2366 of (2360 2366 2372 2378 2384) to complete...
- Waiting for PID 2372 of (2360 2366 2372 2378 2384) to complete...
- Waiting for PID 2378 of (2360 2366 2372 2378 2384) to complete...
- Waiting for PID 2384 of (2360 2366 2372 2378 2384) 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 525
- Checking for and removing duplicates
- Writing label file ./rh.BA1_exvivo.label 4487
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 748
- Checking for and removing duplicates
- Writing label file ./rh.BA2_exvivo.label 7435
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 148
- Checking for and removing duplicates
- Writing label file ./rh.BA3a_exvivo.label 4128
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 251
- Checking for and removing duplicates
- Writing label file ./rh.BA3b_exvivo.label 4773
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 705
- Checking for and removing duplicates
- Writing label file ./rh.BA4a_exvivo.label 6452
- mri_label2label: Done
- PIDs (2360 2366 2372 2378 2384) 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 0050669 --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 0050669 --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 0050669 --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 0050669 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 2435 of (2435 2441 2447 2452) to complete...
- Waiting for PID 2441 of (2435 2441 2447 2452) to complete...
- Waiting for PID 2447 of (2435 2441 2447 2452) to complete...
- Waiting for PID 2452 of (2435 2441 2447 2452) 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 244
- Checking for and removing duplicates
- Writing label file ./rh.BA4p_exvivo.label 4717
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 1583
- Checking for and removing duplicates
- Writing label file ./rh.BA6_exvivo.label 13839
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 1233
- Checking for and removing duplicates
- Writing label file ./rh.BA44_exvivo.label 8145
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 990
- Checking for and removing duplicates
- Writing label file ./rh.BA45_exvivo.label 6345
- mri_label2label: Done
- PIDs (2435 2441 2447 2452) 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 0050669 --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 0050669 --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 0050669 --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 0050669 --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 0050669 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 2503 of (2503 2509 2515 2520 2525) to complete...
- Waiting for PID 2509 of (2503 2509 2515 2520 2525) to complete...
- Waiting for PID 2515 of (2503 2509 2515 2520 2525) to complete...
- Waiting for PID 2520 of (2503 2509 2515 2520 2525) to complete...
- Waiting for PID 2525 of (2503 2509 2515 2520 2525) 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 2446
- Checking for and removing duplicates
- Writing label file ./rh.V1_exvivo.label 7173
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 4335
- Checking for and removing duplicates
- Writing label file ./rh.V2_exvivo.label 12351
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 525
- Checking for and removing duplicates
- Writing label file ./rh.MT_exvivo.label 2457
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 109
- Checking for and removing duplicates
- Writing label file ./rh.entorhinal_exvivo.label 1147
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 90
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal_exvivo.label 842
- mri_label2label: Done
- PIDs (2503 2509 2515 2520 2525) 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 0050669 --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 0050669 --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 0050669 --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 0050669 --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 0050669 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 2637 of (2637 2643 2649 2655 2661) to complete...
- Waiting for PID 2643 of (2637 2643 2649 2655 2661) to complete...
- Waiting for PID 2649 of (2637 2643 2649 2655 2661) to complete...
- Waiting for PID 2655 of (2637 2643 2649 2655 2661) to complete...
- Waiting for PID 2661 of (2637 2643 2649 2655 2661) 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 157
- Checking for and removing duplicates
- Writing label file ./rh.BA1_exvivo.thresh.label 1033
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 387
- Checking for and removing duplicates
- Writing label file ./rh.BA2_exvivo.thresh.label 3075
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 43
- Checking for and removing duplicates
- Writing label file ./rh.BA3a_exvivo.thresh.label 1741
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 94
- Checking for and removing duplicates
- Writing label file ./rh.BA3b_exvivo.thresh.label 2277
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 212
- Checking for and removing duplicates
- Writing label file ./rh.BA4a_exvivo.thresh.label 1600
- mri_label2label: Done
- PIDs (2637 2643 2649 2655 2661) 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 0050669 --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 0050669 --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 0050669 --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 0050669 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 2703 of (2703 2709 2715 2720) to complete...
- Waiting for PID 2709 of (2703 2709 2715 2720) to complete...
- Waiting for PID 2715 of (2703 2709 2715 2720) to complete...
- Waiting for PID 2720 of (2703 2709 2715 2720) 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 81
- Checking for and removing duplicates
- Writing label file ./rh.BA4p_exvivo.thresh.label 1570
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 710
- Checking for and removing duplicates
- Writing label file ./rh.BA6_exvivo.thresh.label 7669
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 174
- Checking for and removing duplicates
- Writing label file ./rh.BA44_exvivo.thresh.label 1186
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 241
- Checking for and removing duplicates
- Writing label file ./rh.BA45_exvivo.thresh.label 1419
- mri_label2label: Done
- PIDs (2703 2709 2715 2720) 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 0050669 --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 0050669 --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 0050669 --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 0050669 --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 0050669 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 2766 of (2766 2772 2778 2782 2788) to complete...
- Waiting for PID 2772 of (2766 2772 2778 2782 2788) to complete...
- Waiting for PID 2778 of (2766 2772 2778 2782 2788) to complete...
- Waiting for PID 2782 of (2766 2772 2778 2782 2788) to complete...
- Waiting for PID 2788 of (2766 2772 2778 2782 2788) 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 1637
- Checking for and removing duplicates
- Writing label file ./rh.V1_exvivo.thresh.label 4869
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 2005
- Checking for and removing duplicates
- Writing label file ./rh.V2_exvivo.thresh.label 5442
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 66
- Checking for and removing duplicates
- Writing label file ./rh.MT_exvivo.thresh.label 334
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 75
- Checking for and removing duplicates
- Writing label file ./rh.entorhinal_exvivo.thresh.label 769
- 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 0050669 --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 = 0050669
- 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-6.0.0/0050669/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 144204
- Number of reverse mapping hits = 43
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal_exvivo.thresh.label 334
- mri_label2label: Done
- PIDs (2766 2772 2778 2782 2788) completed and logs appended.
- mris_label2annot --s 0050669 --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-6.0.0/0050669/label
- cmdline mris_label2annot --s 0050669 --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-385
- machine x86_64
- user ntraut
- subject 0050669
- 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-6.0.0/0050669/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 97778 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/label/rh.BA_exvivo.annot
- mris_label2annot --s 0050669 --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-6.0.0/0050669/label
- cmdline mris_label2annot --s 0050669 --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-385
- machine x86_64
- user ntraut
- subject 0050669
- 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-6.0.0/0050669/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 118029 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/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 0050669 rh white
- computing statistics for each annotation in ./rh.BA_exvivo.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 262717
- Total vertex volume 259281 (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) = 1621644 mm^3 (det: 1.201315 )
- lhCtxGM: 255870.833 255358.000 diff= 512.8 pctdiff= 0.200
- rhCtxGM: 258074.617 257348.000 diff= 726.6 pctdiff= 0.282
- lhCtxWM: 245180.163 245240.000 diff= -59.8 pctdiff=-0.024
- rhCtxWM: 249181.729 250251.000 diff=-1069.3 pctdiff=-0.429
- SubCortGMVol 61757.000
- SupraTentVol 1086642.342 (1082895.000) diff=3747.342 pctdiff=0.345
- SupraTentVolNotVent 1073724.342 (1069977.000) diff=3747.342 pctdiff=0.349
- BrainSegVol 1252935.000 (1250314.000) diff=2621.000 pctdiff=0.209
- BrainSegVolNotVent 1236271.000 (1236310.342) diff=-39.342 pctdiff=-0.003
- BrainSegVolNotVent 1236271.000
- CerebellumVol 166223.000
- VentChorVol 12918.000
- 3rd4th5thCSF 3746.000
- CSFVol 1125.000, OptChiasmVol 71.000
- MaskVol 1689719.000
- 1079 573 1710 2.311 0.638 0.123 0.043 13 2.2 BA1_exvivo
- 4000 2526 5874 2.272 0.451 0.111 0.026 37 3.9 BA2_exvivo
- 1029 699 938 1.781 0.437 0.133 0.034 10 1.3 BA3a_exvivo
- 1972 1226 2251 1.753 0.535 0.112 0.027 18 2.3 BA3b_exvivo
- 1798 1047 2661 2.336 0.567 0.120 0.036 18 2.9 BA4a_exvivo
- 1282 819 1655 2.147 0.530 0.107 0.030 8 1.6 BA4p_exvivo
- 9077 5695 18576 2.823 0.571 0.118 0.032 86 11.5 BA6_exvivo
- 4202 2825 8462 2.777 0.424 0.115 0.025 44 4.4 BA44_exvivo
- 4391 3050 9596 2.716 0.568 0.141 0.036 66 6.3 BA45_exvivo
- 4703 3017 5106 1.658 0.503 0.139 0.042 64 8.3 V1_exvivo
- 9743 6247 12951 2.001 0.549 0.149 0.042 154 16.4 V2_exvivo
- 2177 1474 3531 2.395 0.388 0.127 0.026 28 2.2 MT_exvivo
- 589 398 2328 3.962 0.668 0.108 0.029 7 0.6 perirhinal_exvivo
- 384 257 1183 3.390 0.678 0.142 0.044 6 0.8 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 0050669 rh white
- computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050669/surf/rh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 262717
- Total vertex volume 259281 (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) = 1621644 mm^3 (det: 1.201315 )
- lhCtxGM: 255870.833 255358.000 diff= 512.8 pctdiff= 0.200
- rhCtxGM: 258074.617 257348.000 diff= 726.6 pctdiff= 0.282
- lhCtxWM: 245180.163 245240.000 diff= -59.8 pctdiff=-0.024
- rhCtxWM: 249181.729 250251.000 diff=-1069.3 pctdiff=-0.429
- SubCortGMVol 61757.000
- SupraTentVol 1086642.342 (1082895.000) diff=3747.342 pctdiff=0.345
- SupraTentVolNotVent 1073724.342 (1069977.000) diff=3747.342 pctdiff=0.349
- BrainSegVol 1252935.000 (1250314.000) diff=2621.000 pctdiff=0.209
- BrainSegVolNotVent 1236271.000 (1236310.342) diff=-39.342 pctdiff=-0.003
- BrainSegVolNotVent 1236271.000
- CerebellumVol 166223.000
- VentChorVol 12918.000
- 3rd4th5thCSF 3746.000
- CSFVol 1125.000, OptChiasmVol 71.000
- MaskVol 1689719.000
- 795 405 1148 2.177 0.599 0.121 0.045 9 1.6 BA1_exvivo
- 2421 1472 3622 2.292 0.472 0.104 0.026 20 2.5 BA2_exvivo
- 931 620 749 1.728 0.382 0.136 0.033 9 1.2 BA3a_exvivo
- 1487 987 1502 1.576 0.377 0.103 0.022 9 1.4 BA3b_exvivo
- 1179 629 1801 2.527 0.504 0.127 0.041 13 2.0 BA4a_exvivo
- 1012 683 1339 2.143 0.575 0.107 0.033 6 1.3 BA4p_exvivo
- 5636 3509 11365 2.780 0.571 0.117 0.032 53 7.0 BA6_exvivo
- 975 677 2393 2.897 0.375 0.126 0.033 14 1.3 BA44_exvivo
- 1210 866 3117 2.932 0.572 0.156 0.042 24 2.1 BA45_exvivo
- 4452 2884 4774 1.661 0.513 0.137 0.041 56 8.0 V1_exvivo
- 5162 3224 6316 1.870 0.544 0.153 0.047 90 9.5 V2_exvivo
- 298 218 674 2.617 0.401 0.139 0.035 7 0.4 MT_exvivo
- 354 241 1486 4.090 0.590 0.093 0.021 3 0.3 perirhinal_exvivo
- 263 169 731 3.269 0.628 0.149 0.052 5 0.6 entorhinal_exvivo
- Started at Sat Oct 7 16:15:11 CEST 2017
- Ended at Sun Oct 8 01:33:38 CEST 2017
- #@#%# recon-all-run-time-hours 9.307
- recon-all -s 0050669 finished without error at Sun Oct 8 01:33:38 CEST 2017
|
