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|
- Sat Oct 7 23:40:21 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352
- /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
- -subjid 0050352 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050352/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
- subjid 0050352
- 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-928 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: 66074808 63500996 2573812 1737676 0 56876712
- -/+ buffers/cache: 6624284 59450524
- 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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: 2017/10/07-21:40:21-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-928 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-6.0.0/0050352
- mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050352/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/orig/001.mgz
- mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050352/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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/UM_1/0050352/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-6.0.0/0050352/mri/orig/001.mgz...
- #--------------------------------------------
- #@# MotionCor Sat Oct 7 23:40:23 CEST 2017
- Found 1 runs
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/rawavg.mgz
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352
- mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/orig.mgz --conform
- mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/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-6.0.0/0050352/mri/orig.mgz...
- mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Sat Oct 7 23:40:32 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/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-928 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 23:40:32 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.775
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.775/nu0.mnc -odt float
- mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.775/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.775/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Sat Oct 7 23:40:34 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.775/nu0.mnc ./tmp.mri_nu_correct.mni.775/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.775/0/ -iterations 1000 -distance 50
- [ntraut@tars-928:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/] [2017-10-07 23:40:34] 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.775/0/ ./tmp.mri_nu_correct.mni.775/nu0.mnc ./tmp.mri_nu_correct.mni.775/nu1.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 38
- CV of field change: 0.00098934
-
-
-
- mri_convert ./tmp.mri_nu_correct.mni.775/nu1.mnc orig_nu.mgz --like orig.mgz --conform
- mri_convert.bin ./tmp.mri_nu_correct.mni.775/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.775/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 23:41:50 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 23:41:50 CEST 2017
- Ended at Sat Oct 7 23:42:58 CEST 2017
- talairach_avi done
- cp transforms/talairach.auto.xfm transforms/talairach.xfm
- #--------------------------------------------
- #@# Talairach Failure Detection Sat Oct 7 23:43:00 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6900, pval=0.4932 >= 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-6.0.0/0050352/mri/transforms/talairach_avi.log
- tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/transforms/talairach_avi.log
- TalAviQA: 0.97893
- z-score: 0
- #--------------------------------------------
- #@# Nu Intensity Correction Sat Oct 7 23:43:00 CEST 2017
- mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-928 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 23:43:00 CEST 2017
- Program nu_correct, built from:
- Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
- /usr/bin/bc
- tmpdir is ./tmp.mri_nu_correct.mni.1549
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1549/nu0.mnc -odt float
- mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.1549/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.1549/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Sat Oct 7 23:43:02 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.1549/nu0.mnc ./tmp.mri_nu_correct.mni.1549/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1549/0/
- [ntraut@tars-928:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/] [2017-10-07 23:43:02] running:
- /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1549/0/ ./tmp.mri_nu_correct.mni.1549/nu0.mnc ./tmp.mri_nu_correct.mni.1549/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
- Number of iterations: 33
- CV of field change: 0.000999668
-
-
- --------------------------------------------------------
- Iteration 2 Sat Oct 7 23:43:55 CEST 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.1549/nu1.mnc ./tmp.mri_nu_correct.mni.1549/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.1549/1/
- [ntraut@tars-928:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/] [2017-10-07 23:43:55] 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.1549/1/ ./tmp.mri_nu_correct.mni.1549/nu1.mnc ./tmp.mri_nu_correct.mni.1549/nu2.imp
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Processing:.................................................................Done
- Number of iterations: 13
- CV of field change: 0.000984039
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.1549/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1549/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-6.0.0/0050352/mri
- cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.1549/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1549/ones.mgz
- sysname Linux
- hostname tars-928
- machine x86_64
- user ntraut
- input ./tmp.mri_nu_correct.mni.1549/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.1549/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.1549/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1549/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1549/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.1549/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1549/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1549/input.mean.dat
- sysname Linux
- hostname tars-928
- machine x86_64
- user ntraut
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.1549/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.1549/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1549/ones.mgz --i ./tmp.mri_nu_correct.mni.1549/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1549/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1549/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.1549/ones.mgz --i ./tmp.mri_nu_correct.mni.1549/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1549/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1549/output.mean.dat
- sysname Linux
- hostname tars-928
- machine x86_64
- user ntraut
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.1549/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.1549/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.1549/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.1549/nu2.mnc ./tmp.mri_nu_correct.mni.1549/nu2.mnc mul 1.02105105068371572756
- Saving result to './tmp.mri_nu_correct.mni.1549/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.1549/nu2.mnc nu.mgz --like orig.mgz
- mri_convert.bin ./tmp.mri_nu_correct.mni.1549/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.1549/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 8 seconds.
- mapping (10, 116) to ( 3, 110)
-
-
- Sat Oct 7 23:45:18 CEST 2017
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Sat Oct 7 23:45:18 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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
- 1.00814 -0.09572 -0.06711 -112.88490;
- 0.08598 1.00471 0.13264 -170.62601;
- 0.05585 -0.04674 1.10461 -74.57378;
- 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 = 14
- Starting OpenSpline(): npoints = 14
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 110
- white matter peak found at 109
- gm peak at 76 (76), valley at 42 (42)
- csf peak at 38, setting threshold to 63
- 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 72 (72), valley at 18 (18)
- csf peak at 37, setting threshold to 60
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to T1.mgz
- 3D bias adjustment took 2 minutes and 1 seconds.
- #--------------------------------------------
- #@# Skull Stripping Sat Oct 7 23:47:20 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri
- mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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=8.0
- skull bounding box = (40, 55, 31) --> (216, 198, 230)
- using (99, 103, 131) as brain centroid...
- mean wm in atlas = 108, using box (77,85,106) --> (120, 120,155) to find MRI wm
- before smoothing, mri peak at 103
- robust fit to distribution - 102 +- 7.2
- after smoothing, mri peak at 102, scaling input intensities by 1.059
- scaling channel 0 by 1.05882
- initial log_p = -4.484
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.515277 @ (-9.091, -9.091, -27.273)
- max log p = -4.385285 @ (4.545, 4.545, 4.545)
- max log p = -4.283016 @ (6.818, -2.273, 2.273)
- max log p = -4.283016 @ (0.000, 0.000, 0.000)
- max log p = -4.283016 @ (0.000, 0.000, 0.000)
- max log p = -4.283016 @ (0.000, 0.000, 0.000)
- Found translation: (2.3, -6.8, -20.5): log p = -4.283
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.208, old_max_log_p =-4.283 (thresh=-4.3)
- 1.05669 -0.15727 0.11961 -4.45861;
- 0.13912 1.05429 0.15727 -52.62578;
- -0.13053 -0.12941 0.98296 17.06762;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.194, old_max_log_p =-4.208 (thresh=-4.2)
- 1.05669 -0.15727 0.11961 -4.45861;
- 0.14955 1.13337 0.16907 -67.23579;
- -0.13053 -0.12941 0.98296 17.06762;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 2 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.186, old_max_log_p =-4.194 (thresh=-4.2)
- 1.06717 -0.00799 0.14065 -30.68564;
- 0.01112 1.23001 0.16341 -55.36808;
- -0.13053 -0.12941 0.98296 17.06762;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.186, old_max_log_p =-4.186 (thresh=-4.2)
- 1.06717 -0.00799 0.14065 -30.68564;
- 0.01112 1.23001 0.16341 -55.36808;
- -0.13053 -0.12941 0.98296 17.06762;
- 0.00000 0.00000 0.00000 1.00000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.091, old_max_log_p =-4.186 (thresh=-4.2)
- 1.01124 -0.00386 0.10478 -17.39266;
- 0.01133 1.25308 0.16648 -59.07198;
- -0.09649 -0.13446 1.02424 9.70394;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-4.091, old_max_log_p =-4.091 (thresh=-4.1)
- 1.01124 -0.00386 0.10478 -17.39266;
- 0.01133 1.25308 0.16648 -59.07198;
- -0.09649 -0.13446 1.02424 9.70394;
- 0.00000 0.00000 0.00000 1.00000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.073, old_max_log_p =-4.091 (thresh=-4.1)
- 1.01005 -0.00385 0.10466 -16.28694;
- 0.00976 1.25217 0.18343 -61.40710;
- -0.09655 -0.15476 1.02018 12.18664;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 7 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-4.070, old_max_log_p =-4.073 (thresh=-4.1)
- 1.01199 -0.00251 0.09643 -16.12133;
- 0.00897 1.25086 0.19177 -61.73931;
- -0.08846 -0.16522 1.02066 12.58875;
- 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
- 1.01199 -0.00251 0.09643 -16.12133;
- 0.00897 1.25086 0.19177 -61.73931;
- -0.08846 -0.16522 1.02066 12.58875;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3243
- Quasinewton: input matrix
- 1.01199 -0.00251 0.09643 -16.12133;
- 0.00897 1.25086 0.19177 -61.73931;
- -0.08846 -0.16522 1.02066 12.58875;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.01199 -0.00251 0.09643 -16.12133;
- 0.00897 1.25086 0.19177 -61.73931;
- -0.08846 -0.16522 1.02066 12.58875;
- 0.00000 0.00000 0.00000 1.00000;
- pass 1, spacing 8: log(p) = -4.070 (old=-4.484)
- transform before final EM align:
- 1.01199 -0.00251 0.09643 -16.12133;
- 0.00897 1.25086 0.19177 -61.73931;
- -0.08846 -0.16522 1.02066 12.58875;
- 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
- 1.01199 -0.00251 0.09643 -16.12133;
- 0.00897 1.25086 0.19177 -61.73931;
- -0.08846 -0.16522 1.02066 12.58875;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 364799
- Quasinewton: input matrix
- 1.01199 -0.00251 0.09643 -16.12133;
- 0.00897 1.25086 0.19177 -61.73931;
- -0.08846 -0.16522 1.02066 12.58875;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 012: -log(p) = 4.5 tol 0.000000
- final transform:
- 1.01199 -0.00251 0.09643 -16.12133;
- 0.00897 1.25086 0.19177 -61.73931;
- -0.08846 -0.16522 1.02066 12.58875;
- 0.00000 0.00000 0.00000 1.00000;
- writing output transformation to transforms/talairach_with_skull.lta...
- mri_em_register utimesec 1546.076960
- mri_em_register stimesec 1.354794
- mri_em_register ru_maxrss 611716
- mri_em_register ru_ixrss 0
- mri_em_register ru_idrss 0
- mri_em_register ru_isrss 0
- mri_em_register ru_minflt 157535
- mri_em_register ru_majflt 0
- mri_em_register ru_nswap 0
- mri_em_register ru_inblock 0
- mri_em_register ru_oublock 32
- mri_em_register ru_msgsnd 0
- mri_em_register ru_msgrcv 0
- mri_em_register ru_nsignals 0
- mri_em_register ru_nvcsw 246
- mri_em_register ru_nivcsw 21665
- registration took 13 minutes and 25 seconds.
- mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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=128 y=121 z=127 r=70
- first estimation of the main basin volume: 1457595 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 17 found in the rest of the brain
- global maximum in x=109, y=109, z=93, 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=9237295665 voxels, voxel volume =1.000
- = 9237295665 mmm3 = 9237296.128 cm3
- done.
- PostAnalyze...Basin Prior
- 8 basins merged thanks to atlas
- ***** 0 basin(s) merged in 1 iteration(s)
- ***** 0 voxel(s) added to the main basin
- done.
- Weighting the input with prior template
- ****************TEMPLATE DEFORMATION****************
- second estimation of the COG coord: x=127,y=126, z=123, r=9764 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 44432
- RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1097445714
- LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1123489156
- RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1124157906
- LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1072194438
- OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1076085098
- Problem with the least square interpolation in GM_MIN calculation.
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 4, 6, 35, 64
- after analyzing : 4, 25, 35, 34
- RIGHT_CER
- before analyzing : 4, 4, 24, 76
- after analyzing : 4, 18, 25, 32
- LEFT_CER
- before analyzing : 4, 5, 34, 73
- after analyzing : 4, 24, 34, 36
- RIGHT_BRAIN
- before analyzing : 5, 8, 37, 64
- after analyzing : 5, 27, 37, 36
- LEFT_BRAIN
- before analyzing : 4, 5, 32, 64
- after analyzing : 4, 23, 32, 33
- OTHER
- before analyzing : 4, 4, 12, 91
- after analyzing : 4, 18, 25, 36
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...60 iterations
- *********************VALIDATION*********************
- curvature mean = -0.013, std = 0.008
- curvature mean = 74.943, std = 7.408
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 3.59, sigma = 5.15
- after rotation: sse = 3.59, sigma = 5.15
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 3.87, its var is 4.93
- before Erosion-Dilatation 0.74% 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...28 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1813268 voxels, voxel volume = 1.000 mm3
- = 1813268 mmm3 = 1813.268 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- mri_watershed utimesec 27.649796
- mri_watershed stimesec 0.458930
- mri_watershed ru_maxrss 821328
- mri_watershed ru_ixrss 0
- mri_watershed ru_idrss 0
- mri_watershed ru_isrss 0
- mri_watershed ru_minflt 212670
- mri_watershed ru_majflt 0
- mri_watershed ru_nswap 0
- mri_watershed ru_inblock 0
- mri_watershed ru_oublock 2848
- mri_watershed ru_msgsnd 0
- mri_watershed ru_msgrcv 0
- mri_watershed ru_nsignals 0
- mri_watershed ru_nvcsw 2251
- mri_watershed ru_nivcsw 119
- mri_watershed done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Sun Oct 8 00:01:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri
- mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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=25.0
- skull bounding box = (57, 65, 43) --> (201, 181, 215)
- using (105, 104, 129) as brain centroid...
- mean wm in atlas = 107, using box (87,90,108) --> (122, 118,150) to find MRI wm
- before smoothing, mri peak at 101
- robust fit to distribution - 102 +- 5.9
- after smoothing, mri peak at 102, scaling input intensities by 1.049
- scaling channel 0 by 1.04902
- initial log_p = -4.285
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.116086 @ (-9.091, -9.091, -9.091)
- max log p = -3.932616 @ (4.545, 4.545, -13.636)
- max log p = -3.848806 @ (2.273, -2.273, 2.273)
- max log p = -3.810682 @ (1.136, 1.136, 1.136)
- max log p = -3.810517 @ (0.568, 0.568, 0.568)
- max log p = -3.800771 @ (0.284, -0.284, 0.284)
- Found translation: (-0.3, -5.4, -18.5): log p = -3.801
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.790, old_max_log_p =-3.801 (thresh=-3.8)
- 0.91709 0.00000 0.12074 -4.71285;
- 0.00000 1.07500 0.00000 -14.74931;
- -0.13053 0.00000 0.99144 -0.82625;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.790, old_max_log_p =-3.790 (thresh=-3.8)
- 0.91709 0.00000 0.12074 -4.71285;
- 0.00000 1.07500 0.00000 -14.74931;
- -0.13053 0.00000 0.99144 -0.82625;
- 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=-3.674, old_max_log_p =-3.790 (thresh=-3.8)
- 0.95367 -0.07410 0.08683 4.08018;
- 0.05916 1.09140 0.03647 -28.82669;
- -0.10077 -0.03716 0.97485 3.95822;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.674, old_max_log_p =-3.674 (thresh=-3.7)
- 0.95367 -0.07410 0.08683 4.08018;
- 0.05916 1.09140 0.03647 -28.82669;
- -0.10077 -0.03716 0.97485 3.95822;
- 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=-3.637, old_max_log_p =-3.674 (thresh=-3.7)
- 0.95525 -0.06528 0.08710 2.73941;
- 0.05277 1.08859 0.01973 -26.09005;
- -0.09990 -0.01932 0.97646 0.95923;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.629, old_max_log_p =-3.637 (thresh=-3.6)
- 0.95413 -0.06520 0.08700 2.88472;
- 0.05271 1.08731 0.01970 -25.91927;
- -0.09979 -0.01929 0.97531 1.08168;
- 0.00000 0.00000 0.00000 1.00000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.629, old_max_log_p =-3.629 (thresh=-3.6)
- 0.95413 -0.06520 0.08700 2.88472;
- 0.05271 1.08731 0.01970 -25.91927;
- -0.09979 -0.01929 0.97531 1.08168;
- 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
- 0.95413 -0.06520 0.08700 2.88472;
- 0.05271 1.08731 0.01970 -25.91927;
- -0.09979 -0.01929 0.97531 1.08168;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2830
- Quasinewton: input matrix
- 0.95413 -0.06520 0.08700 2.88472;
- 0.05271 1.08731 0.01970 -25.91927;
- -0.09979 -0.01929 0.97531 1.08168;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 0.95413 -0.06520 0.08700 2.88472;
- 0.05271 1.08731 0.01970 -25.91927;
- -0.09979 -0.01929 0.97531 1.08168;
- 0.00000 0.00000 0.00000 1.00000;
- pass 1, spacing 8: log(p) = -3.629 (old=-4.285)
- transform before final EM align:
- 0.95413 -0.06520 0.08700 2.88472;
- 0.05271 1.08731 0.01970 -25.91927;
- -0.09979 -0.01929 0.97531 1.08168;
- 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
- 0.95413 -0.06520 0.08700 2.88472;
- 0.05271 1.08731 0.01970 -25.91927;
- -0.09979 -0.01929 0.97531 1.08168;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 315557
- Quasinewton: input matrix
- 0.95413 -0.06520 0.08700 2.88472;
- 0.05271 1.08731 0.01970 -25.91927;
- -0.09979 -0.01929 0.97531 1.08168;
- 0.00000 0.00000 0.00000 1.00000;
- outof QuasiNewtonEMA: 011: -log(p) = 4.0 tol 0.000000
- final transform:
- 0.95413 -0.06520 0.08700 2.88472;
- 0.05271 1.08731 0.01970 -25.91927;
- -0.09979 -0.01929 0.97531 1.08168;
- 0.00000 0.00000 0.00000 1.00000;
- writing output transformation to transforms/talairach.lta...
- mri_em_register utimesec 1393.353178
- mri_em_register stimesec 1.640750
- 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 163581
- 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 464
- mri_em_register ru_nivcsw 19873
- registration took 11 minutes and 57 seconds.
- #--------------------------------------
- #@# CA Normalize Sun Oct 8 00:13:08 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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=25.0
- skull bounding box = (57, 65, 43) --> (201, 181, 215)
- using (105, 104, 129) as brain centroid...
- mean wm in atlas = 107, using box (87,90,108) --> (122, 118,150) to find MRI wm
- before smoothing, mri peak at 101
- robust fit to distribution - 102 +- 5.9
- after smoothing, mri peak at 102, scaling input intensities by 1.049
- scaling channel 0 by 1.04902
- using 246344 sample points...
- INFO: compute sample coordinates transform
- 0.95413 -0.06520 0.08700 2.88472;
- 0.05271 1.08731 0.01970 -25.91927;
- -0.09979 -0.01929 0.97531 1.08168;
- 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, 63, 43) --> (198, 171, 214)
- Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0
- 1 of 910 (0.1%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (59, 64, 40) --> (129, 175, 212)
- Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0
- 1 of 1455 (0.1%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (132, 143, 66) --> (184, 180, 122)
- Left_Cerebellum_White_Matter: limiting intensities to 112.0 --> 132.0
- 3 of 10 (30.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (87, 143, 61) --> (133, 182, 120)
- Right_Cerebellum_White_Matter: limiting intensities to 117.0 --> 132.0
- 11 of 15 (73.3%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (111, 135, 101) --> (148, 199, 133)
- Brain_Stem: limiting intensities to 106.0 --> 132.0
- 0 of 12 (0.0%) samples deleted
- using 2402 total control points for intensity normalization...
- bias field = 0.954 +- 0.051
- 15 of 2386 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 39915 control points for structure...
- bounding box (123, 63, 43) --> (198, 171, 214)
- Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
- 2 of 1400 (0.1%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (59, 64, 40) --> (129, 175, 212)
- Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
- 3 of 2035 (0.1%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (132, 143, 66) --> (184, 180, 122)
- Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 15 of 72 (20.8%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (87, 143, 61) --> (133, 182, 120)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 11 of 75 (14.7%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (111, 135, 101) --> (148, 199, 133)
- Brain_Stem: limiting intensities to 88.0 --> 132.0
- 16 of 90 (17.8%) samples deleted
- using 3672 total control points for intensity normalization...
- bias field = 1.039 +- 0.062
- 11 of 3595 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 39915 control points for structure...
- bounding box (123, 63, 43) --> (198, 171, 214)
- Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
- 2 of 1492 (0.1%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 39557 control points for structure...
- bounding box (59, 64, 40) --> (129, 175, 212)
- Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
- 4 of 2098 (0.2%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3059 control points for structure...
- bounding box (132, 143, 66) --> (184, 180, 122)
- Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 71 of 133 (53.4%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2705 control points for structure...
- bounding box (87, 143, 61) --> (133, 182, 120)
- Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
- 14 of 63 (22.2%) samples deleted
- finding control points in Brain_Stem....
- found 3518 control points for structure...
- bounding box (111, 135, 101) --> (148, 199, 133)
- Brain_Stem: limiting intensities to 88.0 --> 132.0
- 65 of 186 (34.9%) samples deleted
- using 3972 total control points for intensity normalization...
- bias field = 1.040 +- 0.058
- 14 of 3738 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 1 minutes and 43 seconds.
- #--------------------------------------
- #@# CA Reg Sun Oct 8 00:14:51 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri
- mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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) = 1.03 (predicted orig area = 7.8)
- label assignment complete, 0 changed (0.00%)
- freeing gibbs priors...done.
- average std[0] = 5.0
- **************** pass 1 of 1 ************************
- enabling zero nodes
- setting smoothness coefficient to 0.039
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.823, neg=0, invalid=762
- 0001: dt=296.742586, rms=0.760 (7.589%), neg=0, invalid=762
- 0002: dt=161.210811, rms=0.751 (1.242%), neg=0, invalid=762
- 0003: dt=517.888000, rms=0.741 (1.339%), neg=0, invalid=762
- 0004: dt=131.605634, rms=0.738 (0.357%), neg=0, invalid=762
- 0005: dt=1775.616000, rms=0.728 (1.452%), neg=0, invalid=762
- 0006: dt=129.472000, rms=0.725 (0.370%), neg=0, invalid=762
- 0007: dt=517.888000, rms=0.722 (0.459%), neg=0, invalid=762
- 0008: dt=221.952000, rms=0.720 (0.187%), neg=0, invalid=762
- 0009: dt=221.952000, rms=0.719 (0.134%), neg=0, invalid=762
- 0010: dt=221.952000, rms=0.718 (0.163%), neg=0, invalid=762
- 0011: dt=221.952000, rms=0.716 (0.233%), neg=0, invalid=762
- 0012: dt=221.952000, rms=0.714 (0.337%), neg=0, invalid=762
- 0013: dt=221.952000, rms=0.712 (0.294%), neg=0, invalid=762
- 0014: dt=221.952000, rms=0.710 (0.251%), neg=0, invalid=762
- 0015: dt=221.952000, rms=0.709 (0.213%), neg=0, invalid=762
- 0016: dt=221.952000, rms=0.707 (0.255%), neg=0, invalid=762
- 0017: dt=221.952000, rms=0.705 (0.211%), neg=0, invalid=762
- 0018: dt=221.952000, rms=0.704 (0.133%), neg=0, invalid=762
- 0019: dt=221.952000, rms=0.703 (0.127%), neg=0, invalid=762
- 0020: dt=221.952000, rms=0.702 (0.197%), neg=0, invalid=762
- 0021: dt=221.952000, rms=0.701 (0.173%), neg=0, invalid=762
- 0022: dt=221.952000, rms=0.700 (0.142%), neg=0, invalid=762
- 0023: dt=221.952000, rms=0.699 (0.142%), neg=0, invalid=762
- 0024: dt=221.952000, rms=0.697 (0.214%), neg=0, invalid=762
- 0025: dt=221.952000, rms=0.696 (0.172%), neg=0, invalid=762
- 0026: dt=221.952000, rms=0.695 (0.124%), neg=0, invalid=762
- 0027: dt=221.952000, rms=0.695 (0.116%), neg=0, invalid=762
- 0028: dt=517.888000, rms=0.694 (0.098%), neg=0, invalid=762
- 0029: dt=517.888000, rms=0.694 (-0.436%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.694, neg=0, invalid=762
- 0030: dt=129.472000, rms=0.693 (0.165%), neg=0, invalid=762
- 0031: dt=443.904000, rms=0.692 (0.105%), neg=0, invalid=762
- 0032: dt=443.904000, rms=0.692 (0.113%), neg=0, invalid=762
- 0033: dt=443.904000, rms=0.691 (0.120%), neg=0, invalid=762
- 0034: dt=443.904000, rms=0.690 (0.106%), neg=0, invalid=762
- 0035: dt=443.904000, rms=0.689 (0.146%), neg=0, invalid=762
- 0036: dt=443.904000, rms=0.688 (0.132%), neg=0, invalid=762
- 0037: dt=443.904000, rms=0.688 (0.037%), neg=0, invalid=762
- 0038: dt=443.904000, rms=0.687 (0.077%), neg=0, invalid=762
- 0039: dt=443.904000, rms=0.687 (0.098%), neg=0, invalid=762
- 0040: dt=443.904000, rms=0.686 (0.031%), neg=0, invalid=762
- 0041: dt=129.472000, rms=0.686 (0.063%), neg=0, invalid=762
- 0042: dt=887.808000, rms=0.686 (0.032%), neg=0, invalid=762
- 0043: dt=887.808000, rms=0.686 (-0.138%), neg=0, invalid=762
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.693, neg=0, invalid=762
- 0044: dt=81.190083, rms=0.689 (0.507%), neg=0, invalid=762
- 0045: dt=248.832000, rms=0.680 (1.327%), neg=0, invalid=762
- 0046: dt=36.288000, rms=0.678 (0.350%), neg=0, invalid=762
- 0047: dt=145.152000, rms=0.675 (0.412%), neg=0, invalid=762
- 0048: dt=103.680000, rms=0.671 (0.581%), neg=0, invalid=762
- 0049: dt=36.288000, rms=0.670 (0.157%), neg=0, invalid=762
- 0050: dt=36.288000, rms=0.669 (0.097%), neg=0, invalid=762
- 0051: dt=36.288000, rms=0.668 (0.182%), neg=0, invalid=762
- 0052: dt=36.288000, rms=0.666 (0.271%), neg=0, invalid=762
- 0053: dt=36.288000, rms=0.664 (0.339%), neg=0, invalid=762
- 0054: dt=36.288000, rms=0.661 (0.362%), neg=0, invalid=762
- 0055: dt=36.288000, rms=0.659 (0.359%), neg=0, invalid=762
- 0056: dt=36.288000, rms=0.657 (0.350%), neg=0, invalid=762
- 0057: dt=36.288000, rms=0.654 (0.342%), neg=0, invalid=762
- 0058: dt=36.288000, rms=0.652 (0.327%), neg=0, invalid=762
- 0059: dt=36.288000, rms=0.650 (0.307%), neg=0, invalid=762
- 0060: dt=36.288000, rms=0.649 (0.279%), neg=0, invalid=762
- 0061: dt=36.288000, rms=0.647 (0.237%), neg=0, invalid=762
- 0062: dt=36.288000, rms=0.646 (0.207%), neg=0, invalid=762
- 0063: dt=36.288000, rms=0.644 (0.195%), neg=0, invalid=762
- 0064: dt=36.288000, rms=0.643 (0.192%), neg=0, invalid=762
- 0065: dt=36.288000, rms=0.642 (0.176%), neg=0, invalid=762
- 0066: dt=36.288000, rms=0.641 (0.161%), neg=0, invalid=762
- 0067: dt=36.288000, rms=0.640 (0.145%), neg=0, invalid=762
- 0068: dt=36.288000, rms=0.639 (0.144%), neg=0, invalid=762
- 0069: dt=36.288000, rms=0.638 (0.138%), neg=0, invalid=762
- 0070: dt=36.288000, rms=0.637 (0.120%), neg=0, invalid=762
- 0071: dt=36.288000, rms=0.637 (0.100%), neg=0, invalid=762
- 0072: dt=145.152000, rms=0.637 (0.028%), neg=0, invalid=762
- 0073: dt=145.152000, rms=0.637 (0.018%), neg=0, invalid=762
- 0074: dt=145.152000, rms=0.637 (-0.236%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.637, neg=0, invalid=762
- 0075: dt=67.706564, rms=0.635 (0.292%), neg=0, invalid=762
- 0076: dt=124.416000, rms=0.635 (0.122%), neg=0, invalid=762
- 0077: dt=124.416000, rms=0.635 (-0.085%), neg=0, invalid=762
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.665, neg=0, invalid=762
- 0078: dt=11.200000, rms=0.662 (0.331%), neg=0, invalid=762
- 0079: dt=9.600000, rms=0.662 (0.058%), neg=0, invalid=762
- 0080: dt=9.600000, rms=0.662 (0.025%), neg=0, invalid=762
- 0081: dt=9.600000, rms=0.662 (-0.081%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.662, neg=0, invalid=762
- 0082: dt=0.037500, rms=0.662 (0.075%), neg=0, invalid=762
- 0083: dt=0.007812, rms=0.662 (0.000%), neg=0, invalid=762
- 0084: dt=0.007812, rms=0.662 (-0.000%), neg=0, invalid=762
- setting smoothness coefficient to 2.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.725, neg=0, invalid=762
- 0085: dt=5.990338, rms=0.710 (2.032%), neg=0, invalid=762
- 0086: dt=5.333333, rms=0.708 (0.257%), neg=0, invalid=762
- 0087: dt=4.000000, rms=0.708 (0.033%), neg=0, invalid=762
- 0088: dt=4.000000, rms=0.708 (0.004%), neg=0, invalid=762
- 0089: dt=4.000000, rms=0.708 (-0.083%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.708, neg=0, invalid=762
- 0090: dt=0.000000, rms=0.708 (0.060%), neg=0, invalid=762
- 0091: dt=0.000000, rms=0.708 (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=0.756, neg=0, invalid=762
- 0092: dt=0.000000, rms=0.756 (0.053%), neg=0, invalid=762
- 0093: dt=0.000000, rms=0.756 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.756, neg=0, invalid=762
- 0094: dt=0.000000, rms=0.756 (0.053%), neg=0, invalid=762
- 0095: dt=0.000000, rms=0.756 (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=0.675, neg=0, invalid=762
- 0096: dt=0.764925, rms=0.659 (2.380%), neg=0, invalid=762
- 0097: dt=0.064000, rms=0.658 (0.093%), neg=0, invalid=762
- 0098: dt=0.064000, rms=0.658 (-0.056%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.659, neg=0, invalid=762
- 0099: dt=0.028000, rms=0.658 (0.087%), neg=0, invalid=762
- 0100: dt=0.005000, rms=0.658 (-0.001%), neg=0, invalid=762
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.10027 (20)
- mri peak = 0.06617 (27)
- Left_Lateral_Ventricle (4): linear fit = 1.33 x + 0.0 (2270 voxels, overlap=0.772)
- Left_Lateral_Ventricle (4): linear fit = 1.33 x + 0.0 (2270 voxels, peak = 26), gca=26.5
- gca peak = 0.15565 (16)
- mri peak = 0.07752 (28)
- Right_Lateral_Ventricle (43): linear fit = 1.83 x + 0.0 (1912 voxels, overlap=0.177)
- Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1912 voxels, peak = 29), gca=24.0
- gca peak = 0.26829 (96)
- mri peak = 0.09275 (96)
- Right_Pallidum (52): linear fit = 0.95 x + 0.0 (1215 voxels, overlap=0.744)
- Right_Pallidum (52): linear fit = 0.95 x + 0.0 (1215 voxels, peak = 92), gca=91.7
- gca peak = 0.20183 (93)
- mri peak = 0.08561 (92)
- Left_Pallidum (13): linear fit = 0.95 x + 0.0 (1110 voxels, overlap=1.005)
- Left_Pallidum (13): linear fit = 0.95 x + 0.0 (1110 voxels, peak = 89), gca=88.8
- gca peak = 0.21683 (55)
- mri peak = 0.05678 (65)
- Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1373 voxels, overlap=0.364)
- Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1373 voxels, peak = 62), gca=62.4
- gca peak = 0.30730 (58)
- mri peak = 0.06620 (59)
- Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (1283 voxels, overlap=0.972)
- Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (1283 voxels, peak = 64), gca=63.5
- gca peak = 0.11430 (101)
- mri peak = 0.07921 (103)
- Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (85912 voxels, overlap=0.858)
- Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (85912 voxels, peak = 104), gca=103.5
- gca peak = 0.12076 (102)
- mri peak = 0.07317 (103)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (84816 voxels, overlap=0.828)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (84816 voxels, peak = 106), gca=105.6
- gca peak = 0.14995 (59)
- mri peak = 0.03216 (71)
- Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (34054 voxels, overlap=0.285)
- Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (34054 voxels, peak = 68), gca=67.6
- gca peak = 0.15082 (58)
- mri peak = 0.03328 (72)
- Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (34337 voxels, overlap=0.050)
- Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (34337 voxels, peak = 71), gca=71.1
- gca peak = 0.14161 (67)
- mri peak = 0.06435 (72)
- Right_Caudate (50): linear fit = 1.07 x + 0.0 (1320 voxels, overlap=0.881)
- Right_Caudate (50): linear fit = 1.07 x + 0.0 (1320 voxels, peak = 71), gca=71.4
- gca peak = 0.15243 (71)
- mri peak = 0.06299 (83)
- Left_Caudate (11): linear fit = 1.08 x + 0.0 (1342 voxels, overlap=0.951)
- Left_Caudate (11): linear fit = 1.08 x + 0.0 (1342 voxels, peak = 76), gca=76.3
- gca peak = 0.13336 (57)
- mri peak = 0.04329 (64)
- Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (32035 voxels, overlap=0.745)
- Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (32035 voxels, peak = 64), gca=63.6
- gca peak = 0.13252 (56)
- mri peak = 0.04187 (67)
- Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (35082 voxels, overlap=0.310)
- Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (35082 voxels, peak = 67), gca=67.5
- gca peak = 0.18181 (84)
- mri peak = 0.06090 (85)
- Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (12496 voxels, overlap=0.929)
- Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (12496 voxels, peak = 86), gca=86.1
- gca peak = 0.20573 (83)
- mri peak = 0.05121 (87)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (10895 voxels, overlap=0.923)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (10895 voxels, peak = 86), gca=85.9
- gca peak = 0.21969 (57)
- mri peak = 0.05783 (78)
- Left_Amygdala (18): linear fit = 1.33 x + 0.0 (513 voxels, overlap=0.052)
- Left_Amygdala (18): linear fit = 1.33 x + 0.0 (513 voxels, peak = 76), gca=75.5
- gca peak = 0.39313 (56)
- mri peak = 0.09059 (70)
- Right_Amygdala (54): linear fit = 1.23 x + 0.0 (707 voxels, overlap=0.028)
- Right_Amygdala (54): linear fit = 1.23 x + 0.0 (707 voxels, peak = 69), gca=68.6
- gca peak = 0.14181 (85)
- mri peak = 0.06436 (88)
- Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (6351 voxels, overlap=0.967)
- Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (6351 voxels, peak = 86), gca=86.3
- gca peak = 0.11978 (83)
- mri peak = 0.06183 (84)
- Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (5494 voxels, overlap=0.895)
- Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (5494 voxels, peak = 86), gca=85.9
- gca peak = 0.13399 (79)
- mri peak = 0.06316 (84)
- Left_Putamen (12): linear fit = 1.04 x + 0.0 (2998 voxels, overlap=0.986)
- Left_Putamen (12): linear fit = 1.04 x + 0.0 (2998 voxels, peak = 83), gca=82.6
- gca peak = 0.14159 (79)
- mri peak = 0.06607 (82)
- Right_Putamen (51): linear fit = 1.04 x + 0.0 (3136 voxels, overlap=0.900)
- Right_Putamen (51): linear fit = 1.04 x + 0.0 (3136 voxels, peak = 83), gca=82.6
- gca peak = 0.10025 (80)
- mri peak = 0.07802 (85)
- Brain_Stem (16): linear fit = 1.10 x + 0.0 (14832 voxels, overlap=0.402)
- Brain_Stem (16): linear fit = 1.10 x + 0.0 (14832 voxels, peak = 88), gca=87.6
- gca peak = 0.13281 (86)
- mri peak = 0.07388 (87)
- Right_VentralDC (60): linear fit = 1.03 x + 0.0 (2074 voxels, overlap=0.724)
- Right_VentralDC (60): linear fit = 1.03 x + 0.0 (2074 voxels, peak = 89), gca=89.0
- gca peak = 0.12801 (89)
- mri peak = 0.06712 (86)
- Left_VentralDC (28): linear fit = 1.03 x + 0.0 (2122 voxels, overlap=0.796)
- Left_VentralDC (28): linear fit = 1.03 x + 0.0 (2122 voxels, peak = 92), gca=92.1
- gca peak = 0.20494 (23)
- mri peak = 0.10321 (18)
- gca peak = 0.15061 (21)
- mri peak = 0.07988 (13)
- Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (416 voxels, overlap=0.685)
- Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (416 voxels, peak = 17), gca=17.1
- gca peak Unknown = 0.94835 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.18056 (32)
- gca peak Left_Thalamus = 0.64095 (94)
- gca peak Third_Ventricle = 0.20494 (23)
- gca peak CSF = 0.20999 (34)
- gca peak Left_Accumbens_area = 0.39030 (62)
- gca peak Left_undetermined = 0.95280 (25)
- gca peak Left_vessel = 0.67734 (53)
- gca peak Left_choroid_plexus = 0.09433 (44)
- gca peak Right_Inf_Lat_Vent = 0.23544 (26)
- gca peak Right_Accumbens_area = 0.30312 (64)
- gca peak Right_vessel = 0.46315 (51)
- gca peak Right_choroid_plexus = 0.14086 (44)
- gca peak Fifth_Ventricle = 0.51669 (36)
- gca peak WM_hypointensities = 0.09722 (76)
- gca peak non_WM_hypointensities = 0.11899 (47)
- gca peak Optic_Chiasm = 0.39033 (72)
- label assignment complete, 0 changed (0.00%)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.19 x + 0.0
- estimating mean wm scale to be 1.03 x + 0.0
- estimating mean csf scale to be 1.21 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=0.646, neg=0, invalid=762
- 0101: dt=99.618625, rms=0.636 (1.496%), neg=0, invalid=762
- 0102: dt=295.936000, rms=0.633 (0.508%), neg=0, invalid=762
- 0103: dt=295.936000, rms=0.631 (0.327%), neg=0, invalid=762
- 0104: dt=110.976000, rms=0.630 (0.119%), neg=0, invalid=762
- 0105: dt=517.888000, rms=0.629 (0.220%), neg=0, invalid=762
- 0106: dt=92.480000, rms=0.628 (0.130%), neg=0, invalid=762
- 0107: dt=1479.680000, rms=0.626 (0.357%), neg=0, invalid=762
- 0108: dt=129.472000, rms=0.625 (0.139%), neg=0, invalid=762
- 0109: dt=295.936000, rms=0.624 (0.067%), neg=0, invalid=762
- 0110: dt=92.480000, rms=0.624 (0.036%), neg=0, invalid=762
- 0111: dt=92.480000, rms=0.624 (0.018%), neg=0, invalid=762
- 0112: dt=92.480000, rms=0.624 (0.032%), neg=0, invalid=762
- 0113: dt=92.480000, rms=0.623 (0.042%), neg=0, invalid=762
- 0114: dt=92.480000, rms=0.623 (0.055%), neg=0, invalid=762
- 0115: dt=92.480000, rms=0.623 (0.060%), neg=0, invalid=762
- 0116: dt=92.480000, rms=0.622 (0.063%), neg=0, invalid=762
- 0117: dt=92.480000, rms=0.622 (0.067%), neg=0, invalid=762
- 0118: dt=92.480000, rms=0.622 (0.068%), neg=0, invalid=762
- 0119: dt=92.480000, rms=0.621 (0.062%), neg=0, invalid=762
- 0120: dt=92.480000, rms=0.621 (0.056%), neg=0, invalid=762
- 0121: dt=92.480000, rms=0.620 (0.053%), neg=0, invalid=762
- 0122: dt=92.480000, rms=0.620 (0.053%), neg=0, invalid=762
- 0123: dt=92.480000, rms=0.620 (0.054%), neg=0, invalid=762
- 0124: dt=92.480000, rms=0.619 (0.054%), neg=0, invalid=762
- 0125: dt=92.480000, rms=0.619 (0.051%), neg=0, invalid=762
- 0126: dt=92.480000, rms=0.619 (0.046%), neg=0, invalid=762
- 0127: dt=92.480000, rms=0.619 (0.044%), neg=0, invalid=762
- 0128: dt=92.480000, rms=0.618 (0.043%), neg=0, invalid=762
- 0129: dt=92.480000, rms=0.618 (0.042%), neg=0, invalid=762
- 0130: dt=92.480000, rms=0.618 (0.042%), neg=0, invalid=762
- 0131: dt=92.480000, rms=0.618 (0.041%), neg=0, invalid=762
- 0132: dt=92.480000, rms=0.617 (0.038%), neg=0, invalid=762
- 0133: dt=92.480000, rms=0.617 (0.039%), neg=0, invalid=762
- 0134: dt=92.480000, rms=0.617 (0.036%), neg=0, invalid=762
- 0135: dt=92.480000, rms=0.617 (0.035%), neg=0, invalid=762
- 0136: dt=92.480000, rms=0.616 (0.032%), neg=0, invalid=762
- 0137: dt=92.480000, rms=0.616 (0.032%), neg=0, invalid=762
- 0138: dt=92.480000, rms=0.616 (0.030%), neg=0, invalid=762
- 0139: dt=92.480000, rms=0.616 (0.031%), neg=0, invalid=762
- 0140: dt=92.480000, rms=0.616 (0.028%), neg=0, invalid=762
- 0141: dt=92.480000, rms=0.616 (0.031%), neg=0, invalid=762
- 0142: dt=92.480000, rms=0.615 (0.025%), neg=0, invalid=762
- 0143: dt=92.480000, rms=0.615 (0.024%), neg=0, invalid=762
- 0144: dt=92.480000, rms=0.615 (0.023%), neg=0, invalid=762
- 0145: dt=5918.720000, rms=0.614 (0.117%), neg=0, invalid=762
- 0146: dt=92.480000, rms=0.614 (0.034%), neg=0, invalid=762
- 0147: dt=92.480000, rms=0.614 (0.003%), neg=0, invalid=762
- 0148: dt=92.480000, rms=0.614 (0.000%), neg=0, invalid=762
- 0149: dt=92.480000, rms=0.614 (0.002%), neg=0, invalid=762
- 0150: dt=92.480000, rms=0.614 (0.014%), neg=0, invalid=762
- 0151: dt=92.480000, rms=0.614 (0.018%), neg=0, invalid=762
- 0152: dt=92.480000, rms=0.614 (0.016%), neg=0, invalid=762
- 0153: dt=0.000000, rms=0.614 (0.001%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.614, neg=0, invalid=762
- 0154: dt=295.936000, rms=0.613 (0.186%), neg=0, invalid=762
- 0155: dt=129.472000, rms=0.613 (0.048%), neg=0, invalid=762
- 0156: dt=129.472000, rms=0.613 (0.016%), neg=0, invalid=762
- 0157: dt=129.472000, rms=0.612 (0.035%), neg=0, invalid=762
- 0158: dt=129.472000, rms=0.612 (0.042%), neg=0, invalid=762
- 0159: dt=129.472000, rms=0.612 (0.037%), neg=0, invalid=762
- 0160: dt=129.472000, rms=0.612 (0.032%), neg=0, invalid=762
- 0161: dt=129.472000, rms=0.612 (0.030%), neg=0, invalid=762
- 0162: dt=129.472000, rms=0.611 (0.025%), neg=0, invalid=762
- 0163: dt=129.472000, rms=0.611 (0.028%), neg=0, invalid=762
- 0164: dt=129.472000, rms=0.611 (0.025%), neg=0, invalid=762
- 0165: dt=129.472000, rms=0.611 (0.023%), neg=0, invalid=762
- 0166: dt=129.472000, rms=0.611 (0.023%), neg=0, invalid=762
- 0167: dt=1479.680000, rms=0.611 (0.036%), neg=0, invalid=762
- 0168: dt=110.976000, rms=0.610 (0.011%), neg=0, invalid=762
- 0169: dt=110.976000, rms=0.610 (0.006%), neg=0, invalid=762
- 0170: dt=110.976000, rms=0.610 (0.002%), neg=0, invalid=762
- 0171: dt=110.976000, rms=0.610 (0.001%), neg=0, invalid=762
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.611, neg=0, invalid=762
- 0172: dt=161.635036, rms=0.608 (0.601%), neg=0, invalid=762
- 0173: dt=181.612565, rms=0.602 (0.954%), neg=0, invalid=762
- 0174: dt=36.288000, rms=0.600 (0.385%), neg=0, invalid=762
- 0175: dt=103.680000, rms=0.598 (0.181%), neg=0, invalid=762
- 0176: dt=145.152000, rms=0.596 (0.435%), neg=0, invalid=762
- 0177: dt=36.288000, rms=0.595 (0.184%), neg=0, invalid=762
- 0178: dt=248.832000, rms=0.593 (0.360%), neg=0, invalid=762
- 0179: dt=63.806647, rms=0.591 (0.270%), neg=0, invalid=762
- 0180: dt=103.680000, rms=0.590 (0.188%), neg=0, invalid=762
- 0181: dt=36.288000, rms=0.589 (0.102%), neg=0, invalid=762
- 0182: dt=580.608000, rms=0.585 (0.772%), neg=0, invalid=762
- 0183: dt=2.268000, rms=0.585 (0.010%), neg=0, invalid=762
- 0184: dt=0.567000, rms=0.585 (0.002%), neg=0, invalid=762
- 0185: dt=0.141750, rms=0.585 (0.001%), neg=0, invalid=762
- 0186: dt=0.070875, rms=0.585 (0.000%), neg=0, invalid=762
- 0187: dt=0.035437, rms=0.585 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.585, neg=0, invalid=762
- 0188: dt=0.035437, rms=0.585 (0.083%), neg=0, invalid=762
- 0189: dt=0.000000, rms=0.585 (0.000%), neg=0, invalid=762
- 0190: dt=0.000879, rms=0.585 (0.000%), neg=0, invalid=762
- 0191: dt=0.000110, rms=0.585 (0.000%), neg=0, invalid=762
- 0192: dt=0.000055, rms=0.585 (0.000%), neg=0, invalid=762
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.589, neg=0, invalid=762
- 0193: dt=44.800000, rms=0.574 (2.528%), neg=0, invalid=762
- 0194: dt=44.800000, rms=0.565 (1.462%), neg=0, invalid=762
- 0195: dt=53.828571, rms=0.560 (0.989%), neg=0, invalid=762
- 0196: dt=24.251710, rms=0.556 (0.734%), neg=0, invalid=762
- 0197: dt=67.840000, rms=0.552 (0.652%), neg=0, invalid=762
- 0198: dt=21.136364, rms=0.549 (0.617%), neg=0, invalid=762
- 0199: dt=44.800000, rms=0.546 (0.427%), neg=0, invalid=762
- 0200: dt=44.800000, rms=0.545 (0.252%), neg=0, invalid=762
- 0201: dt=31.627907, rms=0.543 (0.315%), neg=0, invalid=762
- 0202: dt=11.200000, rms=0.543 (0.108%), neg=0, invalid=762
- 0203: dt=2.800000, rms=0.543 (0.029%), neg=0, invalid=762
- 0204: dt=1.400000, rms=0.542 (0.011%), neg=0, invalid=762
- 0205: dt=0.021875, rms=0.542 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.543, neg=0, invalid=762
- 0206: dt=91.954023, rms=0.538 (0.867%), neg=0, invalid=762
- 0207: dt=29.151335, rms=0.536 (0.360%), neg=0, invalid=762
- 0208: dt=44.800000, rms=0.535 (0.162%), neg=0, invalid=762
- 0209: dt=9.600000, rms=0.535 (0.094%), neg=0, invalid=762
- 0210: dt=0.700000, rms=0.535 (0.012%), neg=0, invalid=762
- 0211: dt=0.350000, rms=0.535 (0.001%), neg=0, invalid=762
- 0212: dt=0.175000, rms=0.535 (0.001%), neg=0, invalid=762
- 0213: dt=0.087500, rms=0.535 (0.001%), neg=0, invalid=762
- 0214: dt=0.010937, rms=0.535 (0.000%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.550, neg=0, invalid=762
- 0215: dt=6.333333, rms=0.548 (0.265%), neg=0, invalid=762
- 0216: dt=4.032000, rms=0.548 (0.068%), neg=0, invalid=762
- 0217: dt=0.864000, rms=0.548 (0.019%), neg=0, invalid=762
- 0218: dt=0.006750, rms=0.548 (0.001%), neg=0, invalid=762
- 0219: dt=0.003375, rms=0.548 (0.000%), neg=0, invalid=762
- 0220: dt=0.000422, rms=0.548 (0.000%), neg=0, invalid=762
- 0221: dt=0.000211, rms=0.548 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.548, neg=0, invalid=762
- 0222: dt=7.724138, rms=0.547 (0.197%), neg=0, invalid=762
- 0223: dt=11.200000, rms=0.547 (0.087%), neg=0, invalid=762
- 0224: dt=16.128000, rms=0.546 (0.178%), neg=0, invalid=762
- 0225: dt=4.032000, rms=0.545 (0.058%), neg=0, invalid=762
- 0226: dt=3.456000, rms=0.545 (0.049%), neg=0, invalid=762
- 0227: dt=0.108000, rms=0.545 (0.002%), neg=0, invalid=762
- 0228: dt=0.054000, rms=0.545 (0.001%), neg=0, invalid=762
- 0229: dt=0.027000, rms=0.545 (0.000%), neg=0, invalid=762
- 0230: dt=0.002813, rms=0.545 (0.000%), neg=0, invalid=762
- 0231: dt=0.000000, rms=0.545 (-0.000%), neg=0, invalid=762
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.561, neg=0, invalid=762
- 0232: dt=0.000000, rms=0.561 (0.078%), neg=0, invalid=762
- 0233: dt=0.000000, rms=0.561 (0.000%), neg=0, invalid=762
- 0234: dt=0.100000, rms=0.561 (-0.049%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.561, neg=0, invalid=762
- 0235: dt=0.000000, rms=0.561 (0.078%), neg=0, invalid=762
- 0236: dt=0.000000, rms=0.561 (0.000%), neg=0, invalid=762
- 0237: dt=0.100000, rms=0.561 (-0.034%), 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=0.535, neg=0, invalid=762
- 0238: dt=0.384000, rms=0.523 (2.160%), neg=0, invalid=762
- 0239: dt=0.384000, rms=0.520 (0.692%), neg=0, invalid=762
- 0240: dt=0.384000, rms=0.518 (0.335%), neg=0, invalid=762
- 0241: dt=0.384000, rms=0.517 (0.208%), neg=0, invalid=762
- 0242: dt=0.384000, rms=0.516 (0.143%), neg=0, invalid=762
- 0243: dt=0.384000, rms=0.515 (0.112%), neg=0, invalid=762
- 0244: dt=0.384000, rms=0.515 (0.085%), neg=0, invalid=762
- 0245: dt=0.384000, rms=0.515 (0.070%), neg=0, invalid=762
- 0246: dt=0.384000, rms=0.514 (0.058%), neg=0, invalid=762
- 0247: dt=0.384000, rms=0.514 (0.045%), neg=0, invalid=762
- 0248: dt=0.384000, rms=0.514 (0.043%), neg=0, invalid=762
- 0249: dt=0.384000, rms=0.514 (0.071%), neg=0, invalid=762
- 0250: dt=0.192000, rms=0.513 (0.017%), neg=0, invalid=762
- 0251: dt=0.192000, rms=0.513 (0.028%), neg=0, invalid=762
- 0252: dt=0.192000, rms=0.513 (0.011%), neg=0, invalid=762
- 0253: dt=0.192000, rms=0.513 (0.021%), neg=0, invalid=762
- 0254: dt=0.192000, rms=0.513 (0.027%), neg=0, invalid=762
- 0255: dt=0.192000, rms=0.513 (0.032%), neg=0, invalid=762
- 0256: dt=0.192000, rms=0.513 (0.035%), neg=0, invalid=762
- 0257: dt=0.192000, rms=0.512 (0.034%), neg=0, invalid=762
- 0258: dt=0.192000, rms=0.512 (0.002%), neg=0, invalid=762
- 0259: dt=0.192000, rms=0.512 (0.008%), neg=0, invalid=762
- 0260: dt=0.192000, rms=0.512 (0.008%), neg=0, invalid=762
- 0261: dt=0.192000, rms=0.512 (0.006%), neg=0, invalid=762
- 0262: dt=0.320000, rms=0.512 (0.003%), neg=0, invalid=762
- 0263: dt=0.320000, rms=0.512 (0.005%), neg=0, invalid=762
- 0264: dt=0.320000, rms=0.512 (0.005%), neg=0, invalid=762
- 0265: dt=0.160000, rms=0.512 (0.003%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.513, neg=0, invalid=762
- 0266: dt=0.320000, rms=0.509 (0.781%), neg=0, invalid=762
- 0267: dt=0.448000, rms=0.507 (0.352%), neg=0, invalid=762
- 0268: dt=0.448000, rms=0.507 (0.043%), neg=0, invalid=762
- 0269: dt=0.448000, rms=0.507 (0.006%), neg=0, invalid=762
- 0270: dt=0.448000, rms=0.507 (0.004%), neg=0, invalid=762
- 0271: dt=0.224000, rms=0.507 (-0.003%), neg=0, invalid=762
- label assignment complete, 0 changed (0.00%)
- ********************* ALLOWING NEGATIVE NODES IN DEFORMATION********************************
- **************** pass 1 of 1 ************************
- enabling zero nodes
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.505, neg=0, invalid=762
- 0272: dt=0.000000, rms=0.504 (0.105%), neg=0, invalid=762
- 0273: dt=0.000000, rms=0.504 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.505, neg=0, invalid=762
- 0274: dt=32.368000, rms=0.504 (0.108%), neg=0, invalid=762
- 0275: dt=73.984000, rms=0.504 (0.001%), neg=0, invalid=762
- 0276: dt=73.984000, rms=0.504 (0.007%), neg=0, invalid=762
- 0277: dt=73.984000, rms=0.504 (0.009%), neg=0, invalid=762
- 0278: dt=73.984000, rms=0.504 (0.011%), neg=0, invalid=762
- 0279: dt=73.984000, rms=0.504 (0.017%), neg=0, invalid=762
- 0280: dt=73.984000, rms=0.504 (0.015%), neg=0, invalid=762
- 0281: dt=73.984000, rms=0.504 (0.011%), neg=0, invalid=762
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.505, neg=0, invalid=762
- 0282: dt=25.920000, rms=0.504 (0.131%), neg=0, invalid=762
- 0283: dt=25.920000, rms=0.504 (0.010%), neg=0, invalid=762
- 0284: dt=25.920000, rms=0.504 (0.009%), neg=0, invalid=762
- 0285: dt=25.920000, rms=0.504 (-0.005%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.504, neg=0, invalid=762
- 0286: dt=103.680000, rms=0.502 (0.388%), neg=0, invalid=762
- 0287: dt=36.288000, rms=0.502 (0.087%), neg=0, invalid=762
- 0288: dt=36.288000, rms=0.502 (0.044%), neg=0, invalid=762
- 0289: dt=36.288000, rms=0.501 (0.075%), neg=0, invalid=762
- 0290: dt=36.288000, rms=0.501 (0.090%), neg=0, invalid=762
- 0291: dt=36.288000, rms=0.500 (0.107%), neg=0, invalid=762
- 0292: dt=36.288000, rms=0.500 (0.112%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 8 iterations, nbhd size=1, neg = 0
- 0293: dt=36.288000, rms=0.499 (0.097%), neg=0, invalid=762
- 0294: dt=36.288000, rms=0.499 (0.095%), neg=0, invalid=762
- 0295: dt=103.680000, rms=0.499 (0.018%), neg=0, invalid=762
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.500, neg=0, invalid=762
- iter 0, gcam->neg = 5
- after 10 iterations, nbhd size=1, neg = 0
- 0296: dt=32.000000, rms=0.497 (0.471%), neg=0, invalid=762
- iter 0, gcam->neg = 9
- after 11 iterations, nbhd size=1, neg = 0
- 0297: dt=73.513514, rms=0.495 (0.487%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 2 iterations, nbhd size=0, neg = 0
- 0298: dt=32.000000, rms=0.494 (0.247%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 2 iterations, nbhd size=0, neg = 0
- 0299: dt=32.000000, rms=0.492 (0.285%), neg=0, invalid=762
- iter 0, gcam->neg = 5
- after 2 iterations, nbhd size=0, neg = 0
- 0300: dt=32.000000, rms=0.491 (0.246%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 8 iterations, nbhd size=1, neg = 0
- 0301: dt=32.000000, rms=0.490 (0.197%), neg=0, invalid=762
- iter 0, gcam->neg = 5
- after 10 iterations, nbhd size=1, neg = 0
- 0302: dt=32.000000, rms=0.489 (0.194%), neg=0, invalid=762
- iter 0, gcam->neg = 21
- after 12 iterations, nbhd size=1, neg = 0
- 0303: dt=32.000000, rms=0.488 (0.164%), neg=0, invalid=762
- iter 0, gcam->neg = 18
- after 12 iterations, nbhd size=1, neg = 0
- 0304: dt=32.000000, rms=0.488 (0.109%), neg=0, invalid=762
- iter 0, gcam->neg = 12
- after 13 iterations, nbhd size=1, neg = 0
- 0305: dt=32.000000, rms=0.487 (0.127%), neg=0, invalid=762
- iter 0, gcam->neg = 16
- after 12 iterations, nbhd size=1, neg = 0
- 0306: dt=32.000000, rms=0.486 (0.119%), neg=0, invalid=762
- iter 0, gcam->neg = 6
- after 2 iterations, nbhd size=0, neg = 0
- 0307: dt=32.000000, rms=0.486 (0.143%), neg=0, invalid=762
- iter 0, gcam->neg = 10
- after 12 iterations, nbhd size=1, neg = 0
- 0308: dt=32.000000, rms=0.485 (0.120%), neg=0, invalid=762
- iter 0, gcam->neg = 5
- after 10 iterations, nbhd size=1, neg = 0
- 0309: dt=32.000000, rms=0.485 (0.131%), neg=0, invalid=762
- iter 0, gcam->neg = 8
- after 4 iterations, nbhd size=0, neg = 0
- 0310: dt=32.000000, rms=0.484 (0.093%), neg=0, invalid=762
- iter 0, gcam->neg = 11
- after 7 iterations, nbhd size=0, neg = 0
- 0311: dt=32.000000, rms=0.484 (0.088%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 1 iterations, nbhd size=0, neg = 0
- 0312: dt=38.400000, rms=0.483 (0.060%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 2 iterations, nbhd size=0, neg = 0
- 0313: dt=38.400000, rms=0.483 (-0.003%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.484, neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 2 iterations, nbhd size=0, neg = 0
- 0314: dt=53.937107, rms=0.480 (0.786%), neg=0, invalid=762
- 0315: dt=25.600000, rms=0.479 (0.262%), neg=0, invalid=762
- 0316: dt=44.800000, rms=0.478 (0.195%), neg=0, invalid=762
- 0317: dt=44.800000, rms=0.478 (0.011%), neg=0, invalid=762
- 0318: dt=44.800000, rms=0.476 (0.312%), neg=0, invalid=762
- 0319: dt=44.800000, rms=0.476 (0.013%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0320: dt=44.800000, rms=0.476 (0.183%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 2 iterations, nbhd size=0, neg = 0
- 0321: dt=44.800000, rms=0.475 (-0.086%), neg=0, invalid=762
- 0322: dt=19.200000, rms=0.475 (0.081%), neg=0, invalid=762
- 0323: dt=44.800000, rms=0.475 (0.068%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.482, neg=0, invalid=762
- 0324: dt=2.880000, rms=0.482 (0.126%), neg=0, invalid=762
- 0325: dt=0.720000, rms=0.482 (0.005%), neg=0, invalid=762
- 0326: dt=0.720000, rms=0.482 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.482, neg=0, invalid=762
- 0327: dt=6.000000, rms=0.481 (0.189%), neg=0, invalid=762
- 0328: dt=4.032000, rms=0.481 (0.026%), neg=0, invalid=762
- 0329: dt=4.032000, rms=0.481 (0.012%), neg=0, invalid=762
- 0330: dt=4.032000, rms=0.481 (-0.022%), neg=0, invalid=762
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.489, neg=0, invalid=762
- 0331: dt=0.000000, rms=0.489 (0.104%), neg=0, invalid=762
- 0332: dt=0.000000, rms=0.489 (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
- 0333: dt=1.280000, rms=0.488 (0.235%), neg=0, invalid=762
- 0334: dt=0.768000, rms=0.488 (0.029%), neg=0, invalid=762
- 0335: dt=0.768000, rms=0.488 (0.006%), neg=0, invalid=762
- 0336: dt=0.768000, rms=0.488 (-0.047%), 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=0.480, neg=0, invalid=762
- iter 0, gcam->neg = 664
- after 14 iterations, nbhd size=1, neg = 0
- 0337: dt=2.087838, rms=0.453 (5.751%), neg=0, invalid=762
- 0338: dt=0.064000, rms=0.453 (0.037%), neg=0, invalid=762
- 0339: dt=0.064000, rms=0.453 (-0.038%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.453, neg=0, invalid=762
- 0340: dt=0.080000, rms=0.452 (0.182%), neg=0, invalid=762
- 0341: dt=0.004000, rms=0.452 (0.000%), neg=0, invalid=762
- 0342: dt=0.004000, rms=0.452 (-0.000%), neg=0, invalid=762
- label assignment complete, 0 changed (0.00%)
- label assignment complete, 0 changed (0.00%)
- ***************** morphing with label term set to 0 *******************************
- **************** pass 1 of 1 ************************
- enabling zero nodes
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.438, neg=0, invalid=762
- 0343: dt=0.000000, rms=0.438 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.438, neg=0, invalid=762
- 0344: dt=6.936000, rms=0.438 (0.000%), neg=0, invalid=762
- 0345: dt=1.445000, rms=0.438 (0.000%), neg=0, invalid=762
- 0346: dt=1.445000, rms=0.438 (-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=0.439, neg=0, invalid=762
- 0347: dt=0.000000, rms=0.439 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.439, neg=0, invalid=762
- 0348: dt=36.288000, rms=0.439 (0.024%), neg=0, invalid=762
- 0349: dt=103.680000, rms=0.438 (0.026%), neg=0, invalid=762
- 0350: dt=248.832000, rms=0.438 (0.099%), neg=0, invalid=762
- 0351: dt=20.736000, rms=0.438 (0.008%), neg=0, invalid=762
- 0352: dt=20.736000, rms=0.438 (0.001%), neg=0, invalid=762
- 0353: dt=20.736000, rms=0.438 (-0.003%), neg=0, invalid=762
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.439, neg=0, invalid=762
- 0354: dt=11.200000, rms=0.438 (0.075%), neg=0, invalid=762
- 0355: dt=9.600000, rms=0.438 (0.020%), neg=0, invalid=762
- 0356: dt=9.600000, rms=0.438 (0.005%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 7 iterations, nbhd size=1, neg = 0
- 0357: dt=9.600000, rms=0.438 (-0.048%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.438, neg=0, invalid=762
- 0358: dt=61.440000, rms=0.436 (0.547%), neg=0, invalid=762
- 0359: dt=25.600000, rms=0.435 (0.235%), neg=0, invalid=762
- 0360: dt=25.600000, rms=0.434 (0.101%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0361: dt=25.600000, rms=0.434 (0.143%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 8 iterations, nbhd size=1, neg = 0
- 0362: dt=25.600000, rms=0.433 (0.192%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0363: dt=25.600000, rms=0.432 (0.179%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 6 iterations, nbhd size=1, neg = 0
- 0364: dt=25.600000, rms=0.431 (0.174%), neg=0, invalid=762
- iter 0, gcam->neg = 3
- after 2 iterations, nbhd size=0, neg = 0
- 0365: dt=25.600000, rms=0.431 (0.153%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 2 iterations, nbhd size=0, neg = 0
- 0366: dt=25.600000, rms=0.430 (0.130%), neg=0, invalid=762
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0367: dt=25.600000, rms=0.430 (0.118%), neg=0, invalid=762
- iter 0, gcam->neg = 4
- after 9 iterations, nbhd size=1, neg = 0
- 0368: dt=25.600000, rms=0.429 (0.068%), neg=0, invalid=762
- 0369: dt=38.400000, rms=0.429 (0.021%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0370: dt=38.400000, rms=0.429 (0.010%), neg=0, invalid=762
- 0371: dt=38.400000, rms=0.429 (0.021%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0372: dt=38.400000, rms=0.429 (0.012%), neg=0, invalid=762
- 0373: dt=38.400000, rms=0.429 (0.025%), neg=0, invalid=762
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0374: dt=38.400000, rms=0.429 (0.013%), neg=0, invalid=762
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.433, neg=0, invalid=762
- 0375: dt=0.000422, rms=0.433 (0.000%), neg=0, invalid=762
- 0376: dt=0.000000, rms=0.433 (0.000%), neg=0, invalid=762
- 0377: dt=0.150000, rms=0.433 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.433, neg=0, invalid=762
- 0378: dt=4.800000, rms=0.433 (0.027%), neg=0, invalid=762
- 0379: dt=4.032000, rms=0.433 (0.011%), neg=0, invalid=762
- 0380: dt=4.032000, rms=0.433 (0.007%), neg=0, invalid=762
- 0381: dt=4.032000, rms=0.433 (-0.005%), neg=0, invalid=762
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.440, neg=0, invalid=762
- 0382: dt=0.000000, rms=0.440 (0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.440, neg=0, invalid=762
- 0383: dt=0.000000, rms=0.440 (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=0.428, neg=0, invalid=762
- iter 0, gcam->neg = 480
- after 16 iterations, nbhd size=1, neg = 0
- 0384: dt=1.280000, rms=0.419 (2.022%), neg=0, invalid=762
- 0385: dt=0.000023, rms=0.419 (0.000%), neg=0, invalid=762
- 0386: dt=0.000023, rms=0.419 (-0.000%), neg=0, invalid=762
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.419, neg=0, invalid=762
- 0387: dt=0.112000, rms=0.419 (0.082%), neg=0, invalid=762
- 0388: dt=0.112000, rms=0.419 (0.033%), neg=0, invalid=762
- 0389: dt=0.112000, rms=0.419 (0.023%), neg=0, invalid=762
- 0390: dt=0.112000, rms=0.419 (-0.021%), neg=0, invalid=762
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- mri_ca_register took 2 hours, 28 minutes and 56 seconds.
- mri_ca_register utimesec 10050.217134
- mri_ca_register stimesec 9.829505
- mri_ca_register ru_maxrss 1333540
- mri_ca_register ru_ixrss 0
- mri_ca_register ru_idrss 0
- mri_ca_register ru_isrss 0
- mri_ca_register ru_minflt 4480819
- mri_ca_register ru_majflt 0
- mri_ca_register ru_nswap 0
- mri_ca_register ru_inblock 0
- mri_ca_register ru_oublock 63336
- mri_ca_register ru_msgsnd 0
- mri_ca_register ru_msgrcv 0
- mri_ca_register ru_nsignals 0
- mri_ca_register ru_nvcsw 3340
- mri_ca_register ru_nivcsw 43366
- FSRUNTIME@ mri_ca_register 2.4823 hours 2 threads
- #--------------------------------------
- #@# SubCort Seg Sun Oct 8 02:43:47 CEST 2017
- mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz
- sysname Linux
- hostname tars-928
- 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-6.0.0/0050352/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 7.80
- 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 = 0.06742 (29)
- Left_Lateral_Ventricle (4): linear fit = 1.33 x + 0.0 (2482 voxels, overlap=0.935)
- Left_Lateral_Ventricle (4): linear fit = 1.33 x + 0.0 (2482 voxels, peak = 26), gca=26.5
- gca peak = 0.17677 (13)
- mri peak = 0.08856 (28)
- Right_Lateral_Ventricle (43): linear fit = 2.08 x + 0.0 (2048 voxels, overlap=0.177)
- Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (2048 voxels, peak = 27), gca=19.5
- gca peak = 0.28129 (95)
- mri peak = 0.14358 (96)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (592 voxels, overlap=0.823)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (592 voxels, peak = 95), gca=94.5
- gca peak = 0.16930 (96)
- mri peak = 0.12101 (93)
- Left_Pallidum (13): linear fit = 0.98 x + 0.0 (593 voxels, overlap=1.011)
- Left_Pallidum (13): linear fit = 0.98 x + 0.0 (593 voxels, peak = 94), gca=93.6
- gca peak = 0.24553 (55)
- mri peak = 0.07667 (65)
- Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1352 voxels, overlap=0.367)
- Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1352 voxels, peak = 62), gca=62.4
- gca peak = 0.30264 (59)
- mri peak = 0.06650 (64)
- Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (1207 voxels, overlap=1.007)
- Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (1207 voxels, peak = 62), gca=61.7
- gca peak = 0.07580 (103)
- mri peak = 0.08078 (103)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (61203 voxels, overlap=0.784)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (61203 voxels, peak = 104), gca=103.5
- gca peak = 0.07714 (104)
- mri peak = 0.07366 (103)
- Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (61498 voxels, overlap=0.750)
- Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (61498 voxels, peak = 107), gca=106.6
- gca peak = 0.09712 (58)
- mri peak = 0.03610 (66)
- Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (39627 voxels, overlap=0.641)
- Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (39627 voxels, peak = 66), gca=65.8
- gca peak = 0.11620 (58)
- mri peak = 0.04075 (68)
- Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (40904 voxels, overlap=0.321)
- Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (40904 voxels, peak = 69), gca=69.3
- gca peak = 0.30970 (66)
- mri peak = 0.08816 (76)
- Right_Caudate (50): linear fit = 1.10 x + 0.0 (1185 voxels, overlap=0.379)
- Right_Caudate (50): linear fit = 1.10 x + 0.0 (1185 voxels, peak = 72), gca=72.3
- gca peak = 0.15280 (69)
- mri peak = 0.07814 (76)
- Left_Caudate (11): linear fit = 1.07 x + 0.0 (1200 voxels, overlap=0.853)
- Left_Caudate (11): linear fit = 1.07 x + 0.0 (1200 voxels, peak = 73), gca=73.5
- gca peak = 0.13902 (56)
- mri peak = 0.04564 (65)
- Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (31494 voxels, overlap=0.797)
- Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (31494 voxels, peak = 64), gca=63.6
- gca peak = 0.14777 (55)
- mri peak = 0.05111 (64)
- Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (32655 voxels, overlap=0.439)
- Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (32655 voxels, peak = 66), gca=65.7
- gca peak = 0.16765 (84)
- mri peak = 0.09173 (85)
- Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (7206 voxels, overlap=0.937)
- Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (7206 voxels, peak = 85), gca=85.3
- gca peak = 0.18739 (84)
- mri peak = 0.08231 (87)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6204 voxels, overlap=0.911)
- Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6204 voxels, peak = 87), gca=86.9
- gca peak = 0.29869 (57)
- mri peak = 0.06845 (78)
- Left_Amygdala (18): linear fit = 1.29 x + 0.0 (683 voxels, overlap=0.077)
- Left_Amygdala (18): linear fit = 1.29 x + 0.0 (683 voxels, peak = 74), gca=73.8
- gca peak = 0.33601 (57)
- mri peak = 0.07428 (74)
- Right_Amygdala (54): linear fit = 1.30 x + 0.0 (728 voxels, overlap=0.064)
- Right_Amygdala (54): linear fit = 1.30 x + 0.0 (728 voxels, peak = 74), gca=74.4
- gca peak = 0.11131 (90)
- mri peak = 0.07421 (88)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4999 voxels, overlap=1.000)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4999 voxels, peak = 90), gca=89.6
- gca peak = 0.11793 (83)
- mri peak = 0.07008 (86)
- Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4931 voxels, overlap=0.949)
- Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4931 voxels, peak = 85), gca=85.1
- gca peak = 0.08324 (81)
- mri peak = 0.07627 (84)
- Left_Putamen (12): linear fit = 1.02 x + 0.0 (2240 voxels, overlap=0.838)
- Left_Putamen (12): linear fit = 1.02 x + 0.0 (2240 voxels, peak = 83), gca=83.0
- gca peak = 0.10360 (77)
- mri peak = 0.08326 (83)
- Right_Putamen (51): linear fit = 1.03 x + 0.0 (2306 voxels, overlap=0.916)
- Right_Putamen (51): linear fit = 1.03 x + 0.0 (2306 voxels, peak = 80), gca=79.7
- gca peak = 0.08424 (78)
- mri peak = 0.06986 (87)
- Brain_Stem (16): linear fit = 1.11 x + 0.0 (14679 voxels, overlap=0.476)
- Brain_Stem (16): linear fit = 1.11 x + 0.0 (14679 voxels, peak = 86), gca=86.2
- gca peak = 0.12631 (89)
- mri peak = 0.07740 (90)
- Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1862 voxels, overlap=0.823)
- Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1862 voxels, peak = 92), gca=92.1
- gca peak = 0.14500 (87)
- mri peak = 0.07510 (93)
- Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1883 voxels, overlap=0.893)
- Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1883 voxels, peak = 89), gca=89.2
- gca peak = 0.14975 (24)
- mri peak = 0.11509 (18)
- gca peak = 0.19357 (14)
- mri peak = 0.09064 (13)
- Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (314 voxels, overlap=0.848)
- Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (314 voxels, peak = 14), gca=14.5
- gca peak Unknown = 0.94835 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.16825 (27)
- gca peak Left_Thalamus = 1.00000 (94)
- gca peak Third_Ventricle = 0.14975 (24)
- 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 1.19 x + 0.0
- estimating mean wm scale to be 1.01 x + 0.0
- estimating mean csf scale to be 1.29 x + 0.0
- saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.14196 (24)
- mri peak = 0.06742 (29)
- Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (2482 voxels, overlap=0.860)
- Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (2482 voxels, peak = 23), gca=23.4
- gca peak = 0.14095 (19)
- mri peak = 0.08856 (28)
- Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (2048 voxels, overlap=0.422)
- Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (2048 voxels, peak = 27), gca=26.7
- gca peak = 0.28191 (93)
- mri peak = 0.14358 (96)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (592 voxels, overlap=0.825)
- Right_Pallidum (52): linear fit = 1.00 x + 0.0 (592 voxels, peak = 93), gca=92.5
- gca peak = 0.18416 (94)
- mri peak = 0.12101 (93)
- Left_Pallidum (13): linear fit = 1.01 x + 0.0 (593 voxels, overlap=1.009)
- Left_Pallidum (13): linear fit = 1.01 x + 0.0 (593 voxels, peak = 95), gca=95.4
- gca peak = 0.26749 (63)
- mri peak = 0.07667 (65)
- Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (1352 voxels, overlap=0.999)
- Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (1352 voxels, peak = 64), gca=63.9
- gca peak = 0.27972 (59)
- mri peak = 0.06650 (64)
- Left_Hippocampus (17): linear fit = 1.03 x + 0.0 (1207 voxels, overlap=1.002)
- Left_Hippocampus (17): linear fit = 1.03 x + 0.0 (1207 voxels, peak = 61), gca=61.1
- gca peak = 0.07875 (103)
- mri peak = 0.08078 (103)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (61203 voxels, overlap=0.802)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (61203 voxels, peak = 103), gca=103.0
- gca peak = 0.07720 (107)
- mri peak = 0.07366 (103)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (61498 voxels, overlap=0.847)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (61498 voxels, peak = 106), gca=106.5
- gca peak = 0.08624 (66)
- mri peak = 0.03610 (66)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (39627 voxels, overlap=0.971)
- Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (39627 voxels, peak = 66), gca=66.0
- gca peak = 0.09981 (69)
- mri peak = 0.04075 (68)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (40904 voxels, overlap=0.963)
- Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (40904 voxels, peak = 68), gca=68.0
- gca peak = 0.25613 (73)
- mri peak = 0.08816 (76)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (1185 voxels, overlap=1.007)
- Right_Caudate (50): linear fit = 1.00 x + 0.0 (1185 voxels, peak = 73), gca=73.0
- gca peak = 0.12839 (73)
- mri peak = 0.07814 (76)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (1200 voxels, overlap=1.003)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (1200 voxels, peak = 73), gca=73.0
- gca peak = 0.12384 (63)
- mri peak = 0.04564 (65)
- Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (31494 voxels, overlap=0.999)
- Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (31494 voxels, peak = 63), gca=63.0
- gca peak = 0.12172 (66)
- mri peak = 0.05111 (64)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (32655 voxels, overlap=0.993)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (32655 voxels, peak = 65), gca=65.0
- gca peak = 0.16169 (86)
- mri peak = 0.09173 (85)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7206 voxels, overlap=0.963)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7206 voxels, peak = 86), gca=85.6
- gca peak = 0.18134 (87)
- mri peak = 0.08231 (87)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6204 voxels, overlap=0.979)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6204 voxels, peak = 87), gca=86.6
- gca peak = 0.27803 (75)
- mri peak = 0.06845 (78)
- Left_Amygdala (18): linear fit = 0.99 x + 0.0 (683 voxels, overlap=0.997)
- Left_Amygdala (18): linear fit = 0.99 x + 0.0 (683 voxels, peak = 74), gca=73.9
- gca peak = 0.31967 (74)
- mri peak = 0.07428 (74)
- Right_Amygdala (54): linear fit = 1.03 x + 0.0 (728 voxels, overlap=1.004)
- Right_Amygdala (54): linear fit = 1.03 x + 0.0 (728 voxels, peak = 77), gca=76.6
- gca peak = 0.10636 (89)
- mri peak = 0.07421 (88)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4999 voxels, overlap=0.998)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4999 voxels, peak = 89), gca=88.6
- gca peak = 0.11628 (85)
- mri peak = 0.07008 (86)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4931 voxels, overlap=0.976)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4931 voxels, peak = 85), gca=84.6
- gca peak = 0.09217 (77)
- mri peak = 0.07627 (84)
- Left_Putamen (12): linear fit = 1.01 x + 0.0 (2240 voxels, overlap=0.880)
- Left_Putamen (12): linear fit = 1.01 x + 0.0 (2240 voxels, peak = 78), gca=78.2
- gca peak = 0.10883 (78)
- mri peak = 0.08326 (83)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (2306 voxels, overlap=0.906)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (2306 voxels, peak = 78), gca=78.0
- gca peak = 0.07147 (86)
- mri peak = 0.06986 (87)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (14679 voxels, overlap=0.809)
- Brain_Stem (16): linear fit = 1.00 x + 0.0 (14679 voxels, peak = 86), gca=85.6
- gca peak = 0.12083 (87)
- mri peak = 0.07740 (90)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1862 voxels, overlap=0.868)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1862 voxels, peak = 87), gca=86.6
- gca peak = 0.14063 (89)
- mri peak = 0.07510 (93)
- Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1883 voxels, overlap=0.933)
- Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1883 voxels, peak = 88), gca=87.7
- gca peak = 0.12335 (33)
- mri peak = 0.11509 (18)
- gca peak = 0.18343 (17)
- mri peak = 0.09064 (13)
- Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (314 voxels, overlap=0.843)
- Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (314 voxels, peak = 14), gca=13.7
- gca peak Unknown = 0.94835 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.16503 (28)
- gca peak Left_Thalamus = 0.64095 (104)
- gca peak Third_Ventricle = 0.12335 (33)
- gca peak CSF = 0.20554 (47)
- gca peak Left_Accumbens_area = 0.64163 (66)
- gca peak Left_undetermined = 0.95280 (30)
- gca peak Left_vessel = 0.75997 (52)
- gca peak Left_choroid_plexus = 0.11914 (35)
- gca peak Right_Inf_Lat_Vent = 0.21972 (26)
- gca peak Right_Accumbens_area = 0.34807 (71)
- gca peak Right_vessel = 0.82168 (52)
- gca peak Right_choroid_plexus = 0.14509 (37)
- gca peak Fifth_Ventricle = 0.75707 (40)
- gca peak WM_hypointensities = 0.07483 (78)
- gca peak non_WM_hypointensities = 0.09744 (44)
- gca peak Optic_Chiasm = 0.71121 (75)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.01 x + 0.0
- estimating mean wm scale to be 1.00 x + 0.0
- estimating mean csf scale to be 1.06 x + 0.0
- saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
- saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt
- 89664 voxels changed in iteration 0 of unlikely voxel relabeling
- 444 voxels changed in iteration 1 of unlikely voxel relabeling
- 19 voxels changed in iteration 2 of unlikely voxel relabeling
- 11 voxels changed in iteration 3 of unlikely voxel relabeling
- 0 voxels changed in iteration 4 of unlikely voxel relabeling
- 76959 gm and wm labels changed (%26 to gray, %74 to white out of all changed labels)
- 497 hippocampal voxels changed.
- 0 amygdala voxels changed.
- pass 1: 87748 changed. image ll: -2.152, PF=0.500
- pass 2: 24203 changed. image ll: -2.150, PF=0.500
- pass 3: 7330 changed.
- pass 4: 2452 changed.
- 69360 voxels changed in iteration 0 of unlikely voxel relabeling
- 482 voxels changed in iteration 1 of unlikely voxel relabeling
- 11 voxels changed in iteration 2 of unlikely voxel relabeling
- 0 voxels changed in iteration 3 of unlikely voxel relabeling
- 9213 voxels changed in iteration 0 of unlikely voxel relabeling
- 203 voxels changed in iteration 1 of unlikely voxel relabeling
- 16 voxels changed in iteration 2 of unlikely voxel relabeling
- 0 voxels changed in iteration 3 of unlikely voxel relabeling
- 6597 voxels changed in iteration 0 of unlikely voxel relabeling
- 105 voxels changed in iteration 1 of unlikely voxel relabeling
- 8 voxels changed in iteration 2 of unlikely voxel relabeling
- 0 voxels changed in iteration 3 of unlikely voxel relabeling
- 6776 voxels changed in iteration 0 of unlikely voxel relabeling
- 49 voxels changed in iteration 1 of unlikely voxel relabeling
- 0 voxels changed in iteration 2 of unlikely voxel relabeling
- MRItoUCHAR: min=0, max=85
- MRItoUCHAR: converting to UCHAR
- writing labeled volume to aseg.auto_noCCseg.mgz
- mri_ca_label utimesec 4206.011589
- mri_ca_label stimesec 1.858717
- mri_ca_label ru_maxrss 2108192
- mri_ca_label ru_ixrss 0
- mri_ca_label ru_idrss 0
- mri_ca_label ru_isrss 0
- mri_ca_label ru_minflt 640551
- mri_ca_label ru_majflt 0
- mri_ca_label ru_nswap 0
- mri_ca_label ru_inblock 63328
- mri_ca_label ru_oublock 504
- mri_ca_label ru_msgsnd 0
- mri_ca_label ru_msgrcv 0
- mri_ca_label ru_nsignals 0
- mri_ca_label ru_nvcsw 352
- mri_ca_label ru_nivcsw 6784
- auto-labeling took 69 minutes and 22 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/transforms/cc_up.lta 0050352
- 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-6.0.0/0050352/mri/transforms/cc_up.lta
- reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/aseg.auto_noCCseg.mgz
- reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/norm.mgz
- 80449 voxels in left wm, 111265 in right wm, xrange [116, 134]
- searching rotation angles z=[-5 9], y=[-2 12]
-
searching scale 1 Z rot -4.9
searching scale 1 Z rot -4.7
searching scale 1 Z rot -4.4
searching scale 1 Z rot -4.2
searching scale 1 Z rot -3.9
searching scale 1 Z rot -3.7
searching scale 1 Z rot -3.4
searching scale 1 Z rot -3.2
searching scale 1 Z rot -2.9
searching scale 1 Z rot -2.7
searching scale 1 Z rot -2.4
searching scale 1 Z rot -2.2
searching scale 1 Z rot -1.9
searching scale 1 Z rot -1.7
searching scale 1 Z rot -1.4
searching scale 1 Z rot -1.2
searching scale 1 Z rot -0.9
searching scale 1 Z rot -0.7
searching scale 1 Z rot -0.4
searching scale 1 Z rot -0.2
searching scale 1 Z rot 0.1
searching scale 1 Z rot 0.3
searching scale 1 Z rot 0.6
searching scale 1 Z rot 0.8
searching scale 1 Z rot 1.1
searching scale 1 Z rot 1.3
searching scale 1 Z rot 1.6
searching scale 1 Z rot 1.8
searching scale 1 Z rot 2.1
searching scale 1 Z rot 2.3
searching scale 1 Z rot 2.6
searching scale 1 Z rot 2.8
searching scale 1 Z rot 3.1
searching scale 1 Z rot 3.3
searching scale 1 Z rot 3.6
searching scale 1 Z rot 3.8
searching scale 1 Z rot 4.1
searching scale 1 Z rot 4.3
searching scale 1 Z rot 4.6
searching scale 1 Z rot 4.8
searching scale 1 Z rot 5.1
searching scale 1 Z rot 5.3
searching scale 1 Z rot 5.6
searching scale 1 Z rot 5.8
searching scale 1 Z rot 6.1
searching scale 1 Z rot 6.3
searching scale 1 Z rot 6.6
searching scale 1 Z rot 6.8
searching scale 1 Z rot 7.1
searching scale 1 Z rot 7.3
searching scale 1 Z rot 7.6
searching scale 1 Z rot 7.8
searching scale 1 Z rot 8.1
searching scale 1 Z rot 8.3
searching scale 1 Z rot 8.6
searching scale 1 Z rot 8.8 global minimum found at slice 126.0, rotations (4.70, 2.06)
- final transformation (x=126.0, yr=4.704, zr=2.060):
- 0.99599 -0.03595 0.08195 -3.95324;
- 0.03583 0.99935 0.00295 20.18620;
- -0.08200 -0.00000 0.99663 14.75014;
- 0.00000 0.00000 0.00000 1.00000;
- updating x range to be [127, 132] in xformed coordinates
- best xformed slice 129
- cc center is found at 129 103 124
- eigenvectors:
- 0.00183 0.00166 1.00000;
- 0.01257 -0.99992 0.00164;
- 0.99992 0.01257 -0.00185;
- error in mid anterior detected - correcting...
- writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/aseg.auto.mgz...
- corpus callosum segmentation took 2.1 minutes
- #--------------------------------------
- #@# Merge ASeg Sun Oct 8 03:55:18 CEST 2017
- cp aseg.auto.mgz aseg.presurf.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Sun Oct 8 03:55:18 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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...
- 1755 control points removed
- Building bias image
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 0...
- Smoothing with sigma 8
- Applying bias correction
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 110
- white matter peak found at 109
- gm peak at 70 (70), valley at 36 (36)
- csf peak at 36, setting threshold to 58
- 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 69 (69), valley at 35 (35)
- csf peak at 35, setting threshold to 57
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to brain.mgz
- 3D bias adjustment took 3 minutes and 6 seconds.
- #--------------------------------------------
- #@# Mask BFS Sun Oct 8 03:58:26 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1774278 voxels in mask (pct= 10.58)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Sun Oct 8 03:58:27 CEST 2017
- mri_segment -mprage brain.mgz wm.seg.mgz
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- computing class statistics for intensity windows...
- WM (102.0): 102.3 +- 7.0 [79.0 --> 125.0]
- GM (72.0) : 70.3 +- 9.3 [30.0 --> 95.0]
- setting bottom of white matter range to 79.6
- setting top of gray matter range to 88.8
- 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...
- 6346 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 3553 filled
- 1511 bright non-wm voxels segmented.
- 3366 diagonally connected voxels added...
- white matter segmentation took 1.8 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 0.54 minutes
- reading wm segmentation from wm.seg.mgz...
- 232 voxels added to wm to prevent paths from MTL structures to cortex
- 3164 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 50721 voxels turned on, 45036 voxels turned off.
- propagating editing to output volume from wm.seg.mgz
- 115,126,128 old 110 new 110
- 115,126,128 old 110 new 110
- writing edited volume to wm.asegedit.mgz....
- mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
- Iteration Number : 1
- pass 1 (xy+): 26 found - 26 modified | TOTAL: 26
- pass 2 (xy+): 0 found - 26 modified | TOTAL: 26
- pass 1 (xy-): 24 found - 24 modified | TOTAL: 50
- pass 2 (xy-): 0 found - 24 modified | TOTAL: 50
- pass 1 (yz+): 24 found - 24 modified | TOTAL: 74
- pass 2 (yz+): 0 found - 24 modified | TOTAL: 74
- pass 1 (yz-): 27 found - 27 modified | TOTAL: 101
- pass 2 (yz-): 0 found - 27 modified | TOTAL: 101
- pass 1 (xz+): 19 found - 19 modified | TOTAL: 120
- pass 2 (xz+): 0 found - 19 modified | TOTAL: 120
- pass 1 (xz-): 27 found - 27 modified | TOTAL: 147
- pass 2 (xz-): 0 found - 27 modified | TOTAL: 147
- Iteration Number : 1
- pass 1 (+++): 61 found - 61 modified | TOTAL: 61
- pass 2 (+++): 0 found - 61 modified | TOTAL: 61
- pass 1 (+++): 37 found - 37 modified | TOTAL: 98
- pass 2 (+++): 0 found - 37 modified | TOTAL: 98
- pass 1 (+++): 45 found - 45 modified | TOTAL: 143
- pass 2 (+++): 0 found - 45 modified | TOTAL: 143
- pass 1 (+++): 33 found - 33 modified | TOTAL: 176
- pass 2 (+++): 0 found - 33 modified | TOTAL: 176
- Iteration Number : 1
- pass 1 (++): 110 found - 110 modified | TOTAL: 110
- pass 2 (++): 0 found - 110 modified | TOTAL: 110
- pass 1 (+-): 67 found - 67 modified | TOTAL: 177
- pass 2 (+-): 0 found - 67 modified | TOTAL: 177
- pass 1 (--): 63 found - 63 modified | TOTAL: 240
- pass 2 (--): 0 found - 63 modified | TOTAL: 240
- pass 1 (-+): 79 found - 79 modified | TOTAL: 319
- pass 2 (-+): 0 found - 79 modified | TOTAL: 319
- Iteration Number : 2
- pass 1 (xy+): 10 found - 10 modified | TOTAL: 10
- pass 2 (xy+): 0 found - 10 modified | TOTAL: 10
- pass 1 (xy-): 8 found - 8 modified | TOTAL: 18
- pass 2 (xy-): 0 found - 8 modified | TOTAL: 18
- pass 1 (yz+): 9 found - 9 modified | TOTAL: 27
- pass 2 (yz+): 0 found - 9 modified | TOTAL: 27
- pass 1 (yz-): 4 found - 4 modified | TOTAL: 31
- pass 2 (yz-): 0 found - 4 modified | TOTAL: 31
- pass 1 (xz+): 10 found - 10 modified | TOTAL: 41
- pass 2 (xz+): 0 found - 10 modified | TOTAL: 41
- pass 1 (xz-): 18 found - 18 modified | TOTAL: 59
- pass 2 (xz-): 0 found - 18 modified | TOTAL: 59
- Iteration Number : 2
- pass 1 (+++): 5 found - 5 modified | TOTAL: 5
- pass 2 (+++): 0 found - 5 modified | TOTAL: 5
- pass 1 (+++): 4 found - 4 modified | TOTAL: 9
- pass 2 (+++): 0 found - 4 modified | TOTAL: 9
- pass 1 (+++): 2 found - 2 modified | TOTAL: 11
- pass 2 (+++): 0 found - 2 modified | TOTAL: 11
- pass 1 (+++): 0 found - 0 modified | TOTAL: 11
- Iteration Number : 2
- pass 1 (++): 6 found - 6 modified | TOTAL: 6
- pass 2 (++): 0 found - 6 modified | TOTAL: 6
- pass 1 (+-): 5 found - 5 modified | TOTAL: 11
- pass 2 (+-): 0 found - 5 modified | TOTAL: 11
- pass 1 (--): 5 found - 5 modified | TOTAL: 16
- pass 2 (--): 0 found - 5 modified | TOTAL: 16
- pass 1 (-+): 9 found - 9 modified | TOTAL: 25
- pass 2 (-+): 0 found - 9 modified | TOTAL: 25
- Iteration Number : 3
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 4 found - 4 modified | TOTAL: 4
- pass 2 (yz+): 0 found - 4 modified | TOTAL: 4
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 4
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 4
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 4
- Iteration Number : 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 1 found - 1 modified | TOTAL: 1
- pass 2 (+-): 0 found - 1 modified | TOTAL: 1
- pass 1 (--): 0 found - 0 modified | TOTAL: 1
- pass 1 (-+): 2 found - 2 modified | TOTAL: 3
- pass 2 (-+): 0 found - 2 modified | TOTAL: 3
- 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 = 744 (out of 694527: 0.107123)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Sun Oct 8 04:00:52 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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
- 0.95413 -0.06520 0.08700 2.88472;
- 0.05271 1.08731 0.01970 -25.91927;
- -0.09979 -0.01929 0.97531 1.08168;
- 0.00000 0.00000 0.00000 1.00000;
- voxel to talairach voxel transform
- 0.95413 -0.06520 0.08700 2.88472;
- 0.05271 1.08731 0.01970 -25.91927;
- -0.09979 -0.01929 0.97531 1.08168;
- 0.00000 0.00000 0.00000 1.00000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 1320 (min = 350, max = 1400), aspect = 0.53 (min = 0.10, max = 0.75)
- no need to search
- using seed (127, 121, 91), TAL = (1.0, -37.0, 7.0)
- talairach voxel to voxel transform
- 1.03496 0.06040 -0.09354 -1.31879;
- -0.05207 0.91633 -0.01387 23.91576;
- 0.10486 0.02431 1.01547 -0.77087;
- 0.00000 0.00000 0.00000 1.00000;
- segmentation indicates cc at (127, 121, 91) --> (1.0, -37.0, 7.0)
- done.
- writing output to filled.mgz...
- filling took 0.7 minutes
- talairach cc position changed to (1.00, -37.00, 7.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(19.00, -37.00, 7.00) SRC: (110.29, 127.85, 106.01)
- search lh wm seed point around talairach space (-17.00, -37.00, 7.00), SRC: (147.55, 125.98, 109.78)
- 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 Sun Oct 8 04:01:36 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- Iteration Number : 1
- pass 1 (xy+): 5 found - 5 modified | TOTAL: 5
- pass 2 (xy+): 0 found - 5 modified | TOTAL: 5
- pass 1 (xy-): 4 found - 4 modified | TOTAL: 9
- pass 2 (xy-): 0 found - 4 modified | TOTAL: 9
- pass 1 (yz+): 5 found - 5 modified | TOTAL: 14
- pass 2 (yz+): 0 found - 5 modified | TOTAL: 14
- pass 1 (yz-): 3 found - 3 modified | TOTAL: 17
- pass 2 (yz-): 0 found - 3 modified | TOTAL: 17
- pass 1 (xz+): 3 found - 3 modified | TOTAL: 20
- pass 2 (xz+): 0 found - 3 modified | TOTAL: 20
- pass 1 (xz-): 4 found - 4 modified | TOTAL: 24
- pass 2 (xz-): 0 found - 4 modified | TOTAL: 24
- 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 (++): 2 found - 2 modified | TOTAL: 2
- pass 2 (++): 0 found - 2 modified | TOTAL: 2
- pass 1 (+-): 0 found - 0 modified | TOTAL: 2
- pass 1 (--): 2 found - 2 modified | TOTAL: 4
- pass 2 (--): 0 found - 2 modified | TOTAL: 4
- pass 1 (-+): 2 found - 2 modified | TOTAL: 6
- pass 2 (-+): 0 found - 2 modified | TOTAL: 6
- 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 = 30 (out of 327785: 0.009152)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
- $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
- $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
- slice 50: 908 vertices, 1007 faces
- slice 60: 6411 vertices, 6668 faces
- slice 70: 15533 vertices, 15901 faces
- slice 80: 25661 vertices, 26084 faces
- slice 90: 37638 vertices, 38060 faces
- slice 100: 49324 vertices, 49776 faces
- slice 110: 61767 vertices, 62287 faces
- slice 120: 75034 vertices, 75611 faces
- slice 130: 88695 vertices, 89288 faces
- slice 140: 102788 vertices, 103442 faces
- slice 150: 117164 vertices, 117866 faces
- slice 160: 131053 vertices, 131690 faces
- slice 170: 141710 vertices, 142296 faces
- slice 180: 151516 vertices, 152084 faces
- slice 190: 159921 vertices, 160464 faces
- slice 200: 166966 vertices, 167489 faces
- slice 210: 171723 vertices, 172108 faces
- slice 220: 172174 vertices, 172468 faces
- slice 230: 172174 vertices, 172468 faces
- slice 240: 172174 vertices, 172468 faces
- slice 250: 172174 vertices, 172468 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...
- 172174 voxel in cpt #1: X=-294 [v=172174,e=517404,f=344936] located at (-28.166349, -1.312951, 9.485765)
- For the whole surface: X=-294 [v=172174,e=517404,f=344936]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Tessellate rh Sun Oct 8 04:01:42 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
- Iteration Number : 1
- pass 1 (xy+): 9 found - 9 modified | TOTAL: 9
- pass 2 (xy+): 0 found - 9 modified | TOTAL: 9
- pass 1 (xy-): 2 found - 2 modified | TOTAL: 11
- pass 2 (xy-): 0 found - 2 modified | TOTAL: 11
- pass 1 (yz+): 2 found - 2 modified | TOTAL: 13
- pass 2 (yz+): 0 found - 2 modified | TOTAL: 13
- pass 1 (yz-): 2 found - 2 modified | TOTAL: 15
- pass 2 (yz-): 0 found - 2 modified | TOTAL: 15
- pass 1 (xz+): 2 found - 2 modified | TOTAL: 17
- pass 2 (xz+): 0 found - 2 modified | TOTAL: 17
- pass 1 (xz-): 7 found - 7 modified | TOTAL: 24
- pass 2 (xz-): 0 found - 7 modified | TOTAL: 24
- Iteration Number : 1
- pass 1 (+++): 2 found - 2 modified | TOTAL: 2
- pass 2 (+++): 0 found - 2 modified | TOTAL: 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 2
- Iteration Number : 1
- pass 1 (++): 1 found - 1 modified | TOTAL: 1
- pass 2 (++): 0 found - 1 modified | TOTAL: 1
- pass 1 (+-): 2 found - 2 modified | TOTAL: 3
- pass 2 (+-): 0 found - 2 modified | TOTAL: 3
- pass 1 (--): 2 found - 2 modified | TOTAL: 5
- pass 2 (--): 0 found - 2 modified | TOTAL: 5
- pass 1 (-+): 5 found - 5 modified | TOTAL: 10
- pass 2 (-+): 0 found - 5 modified | TOTAL: 10
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 36 (out of 342713: 0.010504)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix
- $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
- $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
- slice 50: 1463 vertices, 1596 faces
- slice 60: 8749 vertices, 9066 faces
- slice 70: 19184 vertices, 19639 faces
- slice 80: 32377 vertices, 32963 faces
- slice 90: 47305 vertices, 47862 faces
- slice 100: 60944 vertices, 61505 faces
- slice 110: 75515 vertices, 76169 faces
- slice 120: 90167 vertices, 90778 faces
- slice 130: 104430 vertices, 105108 faces
- slice 140: 119587 vertices, 120369 faces
- slice 150: 133510 vertices, 134196 faces
- slice 160: 146115 vertices, 146852 faces
- slice 170: 156195 vertices, 156838 faces
- slice 180: 165046 vertices, 165653 faces
- slice 190: 172950 vertices, 173534 faces
- slice 200: 179473 vertices, 180009 faces
- slice 210: 183407 vertices, 183819 faces
- slice 220: 183780 vertices, 184134 faces
- slice 230: 183780 vertices, 184134 faces
- slice 240: 183780 vertices, 184134 faces
- slice 250: 183780 vertices, 184134 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...
- 183780 voxel in cpt #1: X=-354 [v=183780,e=552402,f=368268] located at (30.536516, -6.303988, 8.369474)
- For the whole surface: X=-354 [v=183780,e=552402,f=368268]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Sun Oct 8 04:01:48 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- #--------------------------------------------
- #@# Smooth1 rh Sun Oct 8 04:01:48 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- Waiting for PID 16188 of (16188 16191) to complete...
- Waiting for PID 16191 of (16188 16191) 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 (16188 16191) completed and logs appended.
- #--------------------------------------------
- #@# Inflation1 lh Sun Oct 8 04:01:57 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- #--------------------------------------------
- #@# Inflation1 rh Sun Oct 8 04:01:57 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- Waiting for PID 16253 of (16253 16256) to complete...
- Waiting for PID 16256 of (16253 16256) to complete...
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- Not saving sulc
- Reading ../surf/lh.smoothwm.nofix
- avg radius = 49.1 mm, total surface area = 88904 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 0.9 minutes
-
step 000: RMS=0.173 (target=0.015)
step 005: RMS=0.136 (target=0.015)
step 010: RMS=0.111 (target=0.015)
step 015: RMS=0.099 (target=0.015)
step 020: RMS=0.092 (target=0.015)
step 025: RMS=0.085 (target=0.015)
step 030: RMS=0.080 (target=0.015)
step 035: RMS=0.077 (target=0.015)
step 040: RMS=0.074 (target=0.015)
step 045: RMS=0.072 (target=0.015)
step 050: RMS=0.071 (target=0.015)
step 055: RMS=0.070 (target=0.015)
step 060: RMS=0.070 (target=0.015)
- inflation complete.
- Not saving sulc
- mris_inflate utimesec 53.210910
- mris_inflate stimesec 0.133979
- mris_inflate ru_maxrss 252252
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 36435
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 0
- mris_inflate ru_oublock 12144
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2043
- mris_inflate ru_nivcsw 5301
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- Not saving sulc
- Reading ../surf/rh.smoothwm.nofix
- avg radius = 49.6 mm, total surface area = 94197 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 0.9 minutes
-
step 000: RMS=0.177 (target=0.015)
step 005: RMS=0.139 (target=0.015)
step 010: RMS=0.113 (target=0.015)
step 015: RMS=0.103 (target=0.015)
step 020: RMS=0.094 (target=0.015)
step 025: RMS=0.088 (target=0.015)
step 030: RMS=0.085 (target=0.015)
step 035: RMS=0.081 (target=0.015)
step 040: RMS=0.079 (target=0.015)
step 045: RMS=0.077 (target=0.015)
step 050: RMS=0.075 (target=0.015)
step 055: RMS=0.075 (target=0.015)
step 060: RMS=0.074 (target=0.015)
- inflation complete.
- Not saving sulc
- mris_inflate utimesec 55.976490
- mris_inflate stimesec 0.143978
- mris_inflate ru_maxrss 269028
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 38579
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 12944
- mris_inflate ru_oublock 12960
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 4920
- mris_inflate ru_nivcsw 4102
- PIDs (16253 16256) completed and logs appended.
- #--------------------------------------------
- #@# QSphere lh Sun Oct 8 04:02:52 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- #--------------------------------------------
- #@# QSphere rh Sun Oct 8 04:02:52 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- Waiting for PID 16310 of (16310 16314) to complete...
- Waiting for PID 16314 of (16310 16314) 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 0.89 +- 0.55 (0.00-->6.93) (max @ vno 57444 --> 57445)
- face area 0.02 +- 0.03 (-0.21-->0.70)
- == Number of threads available to mris_sphere for OpenMP = 2 ==
- scaling brain by 0.292...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.350, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.091, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.535, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.806, avgs=0
- 020/300: dt: 0.9000, rms radial error=173.977, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.090, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.171, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.235, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.292, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.345, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.399, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.455, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.515, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.580, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.649, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.723, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.802, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.886, avgs=0
- 090/300: dt: 0.9000, rms radial error=160.975, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.069, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.168, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.271, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.380, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.493, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.612, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.735, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.863, avgs=0
- 135/300: dt: 0.9000, rms radial error=152.995, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.133, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.275, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.422, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.574, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.730, avgs=0
- 165/300: dt: 0.9000, rms radial error=147.891, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.057, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.227, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.402, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.582, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.766, avgs=0
- 195/300: dt: 0.9000, rms radial error=142.955, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.148, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.346, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.548, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.755, avgs=0
- 220/300: dt: 0.9000, rms radial error=138.966, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.181, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.401, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.625, avgs=0
- 240/300: dt: 0.9000, rms radial error=135.853, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.085, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.322, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.563, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.809, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.059, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.312, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.571, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.833, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.100, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.371, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.646, avgs=0
- 300/300: dt: 0.9000, rms radial error=126.925, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 20645.08
- 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 = 3646.27
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00007
- epoch 3 (K=160.0), pass 1, starting sse = 452.69
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.04/10 = 0.00421
- epoch 4 (K=640.0), pass 1, starting sse = 54.66
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.08/12 = 0.00671
- final distance error %26.88
- writing spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.09 hours
- mris_sphere utimesec 307.246291
- mris_sphere stimesec 0.179972
- mris_sphere ru_maxrss 252452
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 36475
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 12128
- mris_sphere ru_oublock 12168
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 8235
- mris_sphere ru_nivcsw 23619
- FSRUNTIME@ mris_sphere 0.0855 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 0.87 +- 0.55 (0.00-->7.78) (max @ vno 70471 --> 70472)
- face area 0.02 +- 0.03 (-0.20-->0.56)
- == Number of threads available to mris_sphere for OpenMP = 2 ==
- scaling brain by 0.287...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.280, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.020, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.463, avgs=0
- 015/300: dt: 0.9000, rms radial error=174.731, avgs=0
- 020/300: dt: 0.9000, rms radial error=173.899, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.009, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.087, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.149, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.203, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.256, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.310, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.368, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.429, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.495, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.566, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.642, avgs=0
- 080/300: dt: 0.9000, rms radial error=162.723, avgs=0
- 085/300: dt: 0.9000, rms radial error=161.808, avgs=0
- 090/300: dt: 0.9000, rms radial error=160.899, avgs=0
- 095/300: dt: 0.9000, rms radial error=159.994, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.094, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.199, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.309, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.423, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.542, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.667, avgs=0
- 130/300: dt: 0.9000, rms radial error=153.795, avgs=0
- 135/300: dt: 0.9000, rms radial error=152.929, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.067, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.211, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.359, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.512, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.669, avgs=0
- 165/300: dt: 0.9000, rms radial error=147.831, avgs=0
- 170/300: dt: 0.9000, rms radial error=146.998, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.170, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.346, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.527, avgs=0
- 190/300: dt: 0.9000, rms radial error=143.713, avgs=0
- 195/300: dt: 0.9000, rms radial error=142.903, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.098, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.297, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.501, avgs=0
- 215/300: dt: 0.9000, rms radial error=139.709, avgs=0
- 220/300: dt: 0.9000, rms radial error=138.921, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.138, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.359, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.585, avgs=0
- 240/300: dt: 0.9000, rms radial error=135.815, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.049, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.288, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.531, avgs=0
- 260/300: dt: 0.9000, rms radial error=132.778, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.030, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.285, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.545, avgs=0
- 280/300: dt: 0.9000, rms radial error=129.810, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.078, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.350, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.626, avgs=0
- 300/300: dt: 0.9000, rms radial error=126.907, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 22174.97
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00009
- epoch 2 (K=40.0), pass 1, starting sse = 4004.38
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00002
- epoch 3 (K=160.0), pass 1, starting sse = 522.09
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.02/10 = 0.00198
- epoch 4 (K=640.0), pass 1, starting sse = 72.62
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.05/10 = 0.00478
- final distance error %26.73
- writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.09 hours
- mris_sphere utimesec 313.009415
- mris_sphere stimesec 0.192970
- mris_sphere ru_maxrss 269252
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 38634
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 12984
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 10345
- mris_sphere ru_nivcsw 22229
- FSRUNTIME@ mris_sphere 0.0865 hours 1 threads
- PIDs (16310 16314) completed and logs appended.
- #--------------------------------------------
- #@# Fix Topology Copy lh Sun Oct 8 04:08:03 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- cp ../surf/lh.orig.nofix ../surf/lh.orig
- cp ../surf/lh.inflated.nofix ../surf/lh.inflated
- #--------------------------------------------
- #@# Fix Topology Copy rh Sun Oct 8 04:08:04 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- cp ../surf/rh.orig.nofix ../surf/rh.orig
- cp ../surf/rh.inflated.nofix ../surf/rh.inflated
- #@# Fix Topology lh Sun Oct 8 04:08:04 CEST 2017
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050352 lh
- #@# Fix Topology rh Sun Oct 8 04:08:04 CEST 2017
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050352 rh
- Waiting for PID 16546 of (16546 16549) to complete...
- Waiting for PID 16549 of (16546 16549) to complete...
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050352 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=-294 (nv=172174, nf=344936, ne=517404, g=148)
- 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 7 iterations
- marking ambiguous vertices...
- 27566 ambiguous faces found in tessellation
- segmenting defects...
- 116 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 35 into 32
- -merging segment 43 into 40
- -merging segment 48 into 40
- -merging segment 42 into 41
- -merging segment 63 into 61
- -merging segment 61 into 73
- -merging segment 88 into 90
- -merging segment 104 into 101
- -merging segment 115 into 114
- 107 defects to be corrected
- 0 vertices coincident
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.2572 (-4.6286)
- -vertex loglikelihood: -6.0585 (-3.0292)
- -normal dot loglikelihood: -3.6004 (-3.6004)
- -quad curv loglikelihood: -6.5483 (-3.2742)
- Total Loglikelihood : -25.4644
- CORRECTING DEFECT 0 (vertices=29, convex hull=53, v0=2)
- After retessellation of defect 0 (v0=2), euler #=-105 (156084,463153,306964) : difference with theory (-104) = 1
- CORRECTING DEFECT 1 (vertices=48, convex hull=55, v0=23)
- After retessellation of defect 1 (v0=23), euler #=-104 (156089,463189,306996) : difference with theory (-103) = 1
- CORRECTING DEFECT 2 (vertices=42, convex hull=81, v0=229)
- After retessellation of defect 2 (v0=229), euler #=-103 (156100,463254,307051) : difference with theory (-102) = 1
- CORRECTING DEFECT 3 (vertices=766, convex hull=362, v0=378)
- After retessellation of defect 3 (v0=378), euler #=-103 (156287,464017,307627) : difference with theory (-101) = 2
- CORRECTING DEFECT 4 (vertices=6, convex hull=25, v0=668)
- After retessellation of defect 4 (v0=668), euler #=-102 (156288,464026,307636) : difference with theory (-100) = 2
- CORRECTING DEFECT 5 (vertices=118, convex hull=27, v0=848)
- After retessellation of defect 5 (v0=848), euler #=-101 (156292,464044,307651) : difference with theory (-99) = 2
- CORRECTING DEFECT 6 (vertices=50, convex hull=57, v0=1702)
- After retessellation of defect 6 (v0=1702), euler #=-100 (156303,464100,307697) : difference with theory (-98) = 2
- CORRECTING DEFECT 7 (vertices=10, convex hull=26, v0=1939)
- After retessellation of defect 7 (v0=1939), euler #=-99 (156304,464112,307709) : difference with theory (-97) = 2
- CORRECTING DEFECT 8 (vertices=21, convex hull=37, v0=2126)
- After retessellation of defect 8 (v0=2126), euler #=-98 (156309,464142,307735) : difference with theory (-96) = 2
- CORRECTING DEFECT 9 (vertices=530, convex hull=427, v0=2918)
- After retessellation of defect 9 (v0=2918), euler #=-98 (156481,464883,308304) : difference with theory (-95) = 3
- CORRECTING DEFECT 10 (vertices=13, convex hull=20, v0=3106)
- After retessellation of defect 10 (v0=3106), euler #=-97 (156482,464893,308314) : difference with theory (-94) = 3
- CORRECTING DEFECT 11 (vertices=33, convex hull=81, v0=3766)
- After retessellation of defect 11 (v0=3766), euler #=-96 (156499,464980,308385) : difference with theory (-93) = 3
- CORRECTING DEFECT 12 (vertices=62, convex hull=68, v0=5713)
- After retessellation of defect 12 (v0=5713), euler #=-95 (156522,465076,308459) : difference with theory (-92) = 3
- CORRECTING DEFECT 13 (vertices=20, convex hull=55, v0=6929)
- After retessellation of defect 13 (v0=6929), euler #=-94 (156534,465132,308504) : difference with theory (-91) = 3
- CORRECTING DEFECT 14 (vertices=10, convex hull=28, v0=7172)
- After retessellation of defect 14 (v0=7172), euler #=-93 (156535,465144,308516) : difference with theory (-90) = 3
- CORRECTING DEFECT 15 (vertices=30, convex hull=47, v0=8715)
- After retessellation of defect 15 (v0=8715), euler #=-92 (156540,465176,308544) : difference with theory (-89) = 3
- CORRECTING DEFECT 16 (vertices=33, convex hull=79, v0=8844)
- After retessellation of defect 16 (v0=8844), euler #=-91 (156557,465254,308606) : difference with theory (-88) = 3
- CORRECTING DEFECT 17 (vertices=51, convex hull=43, v0=9644)
- After retessellation of defect 17 (v0=9644), euler #=-90 (156566,465298,308642) : difference with theory (-87) = 3
- CORRECTING DEFECT 18 (vertices=157, convex hull=56, v0=13009)
- After retessellation of defect 18 (v0=13009), euler #=-89 (156583,465374,308702) : difference with theory (-86) = 3
- CORRECTING DEFECT 19 (vertices=50, convex hull=90, v0=13928)
- After retessellation of defect 19 (v0=13928), euler #=-88 (156608,465488,308792) : difference with theory (-85) = 3
- CORRECTING DEFECT 20 (vertices=6, convex hull=29, v0=14464)
- After retessellation of defect 20 (v0=14464), euler #=-87 (156608,465496,308801) : difference with theory (-84) = 3
- CORRECTING DEFECT 21 (vertices=35, convex hull=59, v0=20239)
- After retessellation of defect 21 (v0=20239), euler #=-86 (156625,465575,308864) : difference with theory (-83) = 3
- CORRECTING DEFECT 22 (vertices=74, convex hull=133, v0=20596)
- After retessellation of defect 22 (v0=20596), euler #=-85 (156676,465789,309028) : difference with theory (-82) = 3
- CORRECTING DEFECT 23 (vertices=40, convex hull=21, v0=20599)
- After retessellation of defect 23 (v0=20599), euler #=-84 (156678,465800,309038) : difference with theory (-81) = 3
- CORRECTING DEFECT 24 (vertices=33, convex hull=74, v0=22662)
- After retessellation of defect 24 (v0=22662), euler #=-83 (156696,465884,309105) : difference with theory (-80) = 3
- CORRECTING DEFECT 25 (vertices=50, convex hull=84, v0=26818)
- After retessellation of defect 25 (v0=26818), euler #=-82 (156729,466019,309208) : difference with theory (-79) = 3
- CORRECTING DEFECT 26 (vertices=26, convex hull=58, v0=27815)
- After retessellation of defect 26 (v0=27815), euler #=-81 (156741,466079,309257) : difference with theory (-78) = 3
- CORRECTING DEFECT 27 (vertices=6, convex hull=17, v0=29119)
- After retessellation of defect 27 (v0=29119), euler #=-80 (156742,466085,309263) : difference with theory (-77) = 3
- CORRECTING DEFECT 28 (vertices=50, convex hull=102, v0=35491)
- After retessellation of defect 28 (v0=35491), euler #=-79 (156769,466210,309362) : difference with theory (-76) = 3
- CORRECTING DEFECT 29 (vertices=85, convex hull=118, v0=36517)
- After retessellation of defect 29 (v0=36517), euler #=-78 (156818,466409,309513) : difference with theory (-75) = 3
- CORRECTING DEFECT 30 (vertices=40, convex hull=83, v0=39096)
- After retessellation of defect 30 (v0=39096), euler #=-77 (156843,466515,309595) : difference with theory (-74) = 3
- CORRECTING DEFECT 31 (vertices=137, convex hull=67, v0=40936)
- After retessellation of defect 31 (v0=40936), euler #=-76 (156868,466616,309672) : difference with theory (-73) = 3
- CORRECTING DEFECT 32 (vertices=881, convex hull=309, v0=42366)
- After retessellation of defect 32 (v0=42366), euler #=-75 (156978,467093,310040) : difference with theory (-72) = 3
- CORRECTING DEFECT 33 (vertices=32, convex hull=64, v0=44298)
- After retessellation of defect 33 (v0=44298), euler #=-74 (156993,467161,310094) : difference with theory (-71) = 3
- CORRECTING DEFECT 34 (vertices=26, convex hull=66, v0=44592)
- After retessellation of defect 34 (v0=44592), euler #=-73 (157007,467231,310151) : difference with theory (-70) = 3
- CORRECTING DEFECT 35 (vertices=66, convex hull=83, v0=48182)
- After retessellation of defect 35 (v0=48182), euler #=-72 (157035,467346,310239) : difference with theory (-69) = 3
- CORRECTING DEFECT 36 (vertices=91, convex hull=90, v0=50023)
- After retessellation of defect 36 (v0=50023), euler #=-71 (157077,467509,310361) : difference with theory (-68) = 3
- CORRECTING DEFECT 37 (vertices=91, convex hull=120, v0=51833)
- After retessellation of defect 37 (v0=51833), euler #=-70 (157127,467714,310517) : difference with theory (-67) = 3
- CORRECTING DEFECT 38 (vertices=27, convex hull=57, v0=52332)
- After retessellation of defect 38 (v0=52332), euler #=-69 (157139,467772,310564) : difference with theory (-66) = 3
- CORRECTING DEFECT 39 (vertices=530, convex hull=303, v0=52876)
- After retessellation of defect 39 (v0=52876), euler #=-66 (157304,468431,311061) : difference with theory (-65) = 1
- CORRECTING DEFECT 40 (vertices=527, convex hull=246, v0=55061)
- After retessellation of defect 40 (v0=55061), euler #=-64 (157332,468638,311242) : difference with theory (-64) = 0
- CORRECTING DEFECT 41 (vertices=74, convex hull=133, v0=63103)
- After retessellation of defect 41 (v0=63103), euler #=-63 (157365,468797,311369) : difference with theory (-63) = 0
- CORRECTING DEFECT 42 (vertices=18, convex hull=25, v0=63370)
- After retessellation of defect 42 (v0=63370), euler #=-62 (157368,468814,311384) : difference with theory (-62) = 0
- CORRECTING DEFECT 43 (vertices=26, convex hull=52, v0=64436)
- After retessellation of defect 43 (v0=64436), euler #=-61 (157378,468861,311422) : difference with theory (-61) = 0
- CORRECTING DEFECT 44 (vertices=118, convex hull=124, v0=68002)
- After retessellation of defect 44 (v0=68002), euler #=-60 (157437,469097,311600) : difference with theory (-60) = 0
- CORRECTING DEFECT 45 (vertices=72, convex hull=71, v0=69339)
- After retessellation of defect 45 (v0=69339), euler #=-59 (157471,469228,311698) : difference with theory (-59) = 0
- CORRECTING DEFECT 46 (vertices=245, convex hull=237, v0=70700)
- After retessellation of defect 46 (v0=70700), euler #=-58 (157523,469504,311923) : difference with theory (-58) = 0
- CORRECTING DEFECT 47 (vertices=76, convex hull=113, v0=70911)
- After retessellation of defect 47 (v0=70911), euler #=-57 (157565,469676,312054) : difference with theory (-57) = 0
- CORRECTING DEFECT 48 (vertices=16, convex hull=26, v0=73542)
- After retessellation of defect 48 (v0=73542), euler #=-56 (157567,469690,312067) : difference with theory (-56) = 0
- CORRECTING DEFECT 49 (vertices=41, convex hull=65, v0=74200)
- After retessellation of defect 49 (v0=74200), euler #=-55 (157590,469784,312139) : difference with theory (-55) = 0
- CORRECTING DEFECT 50 (vertices=27, convex hull=78, v0=82043)
- After retessellation of defect 50 (v0=82043), euler #=-54 (157605,469860,312201) : difference with theory (-54) = 0
- CORRECTING DEFECT 51 (vertices=21, convex hull=12, v0=84998)
- After retessellation of defect 51 (v0=84998), euler #=-53 (157606,469866,312207) : difference with theory (-53) = 0
- CORRECTING DEFECT 52 (vertices=661, convex hull=249, v0=85827)
- After retessellation of defect 52 (v0=85827), euler #=-54 (157640,470101,312407) : difference with theory (-52) = 2
- CORRECTING DEFECT 53 (vertices=28, convex hull=42, v0=86243)
- After retessellation of defect 53 (v0=86243), euler #=-53 (157652,470152,312447) : difference with theory (-51) = 2
- CORRECTING DEFECT 54 (vertices=248, convex hull=218, v0=87211)
- After retessellation of defect 54 (v0=87211), euler #=-52 (157724,470473,312697) : difference with theory (-50) = 2
- CORRECTING DEFECT 55 (vertices=71, convex hull=64, v0=89208)
- After retessellation of defect 55 (v0=89208), euler #=-51 (157743,470557,312763) : difference with theory (-49) = 2
- CORRECTING DEFECT 56 (vertices=49, convex hull=30, v0=89444)
- After retessellation of defect 56 (v0=89444), euler #=-50 (157750,470586,312786) : difference with theory (-48) = 2
- CORRECTING DEFECT 57 (vertices=56, convex hull=81, v0=92147)
- After retessellation of defect 57 (v0=92147), euler #=-49 (157766,470667,312852) : difference with theory (-47) = 2
- CORRECTING DEFECT 58 (vertices=40, convex hull=75, v0=95424)
- After retessellation of defect 58 (v0=95424), euler #=-48 (157787,470760,312925) : difference with theory (-46) = 2
- CORRECTING DEFECT 59 (vertices=306, convex hull=111, v0=96898)
- After retessellation of defect 59 (v0=96898), euler #=-48 (157823,470929,313058) : difference with theory (-45) = 3
- CORRECTING DEFECT 60 (vertices=37, convex hull=68, v0=97736)
- After retessellation of defect 60 (v0=97736), euler #=-47 (157848,471030,313135) : difference with theory (-44) = 3
- CORRECTING DEFECT 61 (vertices=48, convex hull=38, v0=98345)
- After retessellation of defect 61 (v0=98345), euler #=-46 (157856,471068,313166) : difference with theory (-43) = 3
- CORRECTING DEFECT 62 (vertices=9, convex hull=16, v0=101032)
- After retessellation of defect 62 (v0=101032), euler #=-45 (157856,471071,313170) : difference with theory (-42) = 3
- CORRECTING DEFECT 63 (vertices=1511, convex hull=649, v0=102420)
- XL defect detected...
- After retessellation of defect 63 (v0=102420), euler #=-44 (158282,472737,314411) : difference with theory (-41) = 3
- CORRECTING DEFECT 64 (vertices=803, convex hull=286, v0=102689)
- After retessellation of defect 64 (v0=102689), euler #=-44 (158501,473547,315002) : difference with theory (-40) = 4
- CORRECTING DEFECT 65 (vertices=132, convex hull=138, v0=102717)
- After retessellation of defect 65 (v0=102717), euler #=-43 (158542,473733,315148) : difference with theory (-39) = 4
- CORRECTING DEFECT 66 (vertices=8, convex hull=13, v0=106833)
- After retessellation of defect 66 (v0=106833), euler #=-42 (158542,473736,315152) : difference with theory (-38) = 4
- CORRECTING DEFECT 67 (vertices=237, convex hull=268, v0=107060)
- After retessellation of defect 67 (v0=107060), euler #=-39 (158656,474227,315532) : difference with theory (-37) = 2
- CORRECTING DEFECT 68 (vertices=31, convex hull=73, v0=111625)
- After retessellation of defect 68 (v0=111625), euler #=-38 (158667,474286,315581) : difference with theory (-36) = 2
- CORRECTING DEFECT 69 (vertices=504, convex hull=110, v0=114254)
- After retessellation of defect 69 (v0=114254), euler #=-37 (158683,474389,315669) : difference with theory (-35) = 2
- CORRECTING DEFECT 70 (vertices=1970, convex hull=583, v0=115182)
- XL defect detected...
- After retessellation of defect 70 (v0=115182), euler #=-36 (159002,475659,316621) : difference with theory (-34) = 2
- CORRECTING DEFECT 71 (vertices=48, convex hull=68, v0=115744)
- After retessellation of defect 71 (v0=115744), euler #=-35 (159029,475766,316702) : difference with theory (-33) = 2
- CORRECTING DEFECT 72 (vertices=48, convex hull=71, v0=116475)
- After retessellation of defect 72 (v0=116475), euler #=-34 (159038,475821,316749) : difference with theory (-32) = 2
- CORRECTING DEFECT 73 (vertices=135, convex hull=144, v0=121405)
- After retessellation of defect 73 (v0=121405), euler #=-33 (159112,476106,316961) : difference with theory (-31) = 2
- CORRECTING DEFECT 74 (vertices=35, convex hull=55, v0=123879)
- After retessellation of defect 74 (v0=123879), euler #=-32 (159130,476188,317026) : difference with theory (-30) = 2
- CORRECTING DEFECT 75 (vertices=38, convex hull=19, v0=123938)
- After retessellation of defect 75 (v0=123938), euler #=-31 (159134,476205,317040) : difference with theory (-29) = 2
- CORRECTING DEFECT 76 (vertices=352, convex hull=240, v0=123992)
- After retessellation of defect 76 (v0=123992), euler #=-30 (159168,476420,317222) : difference with theory (-28) = 2
- CORRECTING DEFECT 77 (vertices=54, convex hull=42, v0=124126)
- After retessellation of defect 77 (v0=124126), euler #=-29 (159177,476460,317254) : difference with theory (-27) = 2
- CORRECTING DEFECT 78 (vertices=319, convex hull=116, v0=124391)
- After retessellation of defect 78 (v0=124391), euler #=-28 (159198,476574,317348) : difference with theory (-26) = 2
- CORRECTING DEFECT 79 (vertices=40, convex hull=50, v0=124436)
- After retessellation of defect 79 (v0=124436), euler #=-27 (159210,476629,317392) : difference with theory (-25) = 2
- CORRECTING DEFECT 80 (vertices=353, convex hull=178, v0=128349)
- After retessellation of defect 80 (v0=128349), euler #=-26 (159310,477011,317675) : difference with theory (-24) = 2
- CORRECTING DEFECT 81 (vertices=192, convex hull=146, v0=129529)
- After retessellation of defect 81 (v0=129529), euler #=-25 (159385,477313,317903) : difference with theory (-23) = 2
- CORRECTING DEFECT 82 (vertices=24, convex hull=70, v0=133422)
- After retessellation of defect 82 (v0=133422), euler #=-24 (159401,477387,317962) : difference with theory (-22) = 2
- CORRECTING DEFECT 83 (vertices=121, convex hull=140, v0=134413)
- After retessellation of defect 83 (v0=134413), euler #=-22 (159451,477601,318128) : difference with theory (-21) = 1
- CORRECTING DEFECT 84 (vertices=189, convex hull=124, v0=137416)
- After retessellation of defect 84 (v0=137416), euler #=-21 (159469,477712,318222) : difference with theory (-20) = 1
- CORRECTING DEFECT 85 (vertices=59, convex hull=54, v0=140396)
- After retessellation of defect 85 (v0=140396), euler #=-20 (159484,477778,318274) : difference with theory (-19) = 1
- CORRECTING DEFECT 86 (vertices=412, convex hull=179, v0=143337)
- After retessellation of defect 86 (v0=143337), euler #=-19 (159581,478150,318550) : difference with theory (-18) = 1
- CORRECTING DEFECT 87 (vertices=81, convex hull=101, v0=149604)
- After retessellation of defect 87 (v0=149604), euler #=-18 (159611,478279,318650) : difference with theory (-17) = 1
- CORRECTING DEFECT 88 (vertices=72, convex hull=29, v0=152300)
- After retessellation of defect 88 (v0=152300), euler #=-17 (159613,478296,318666) : difference with theory (-16) = 1
- CORRECTING DEFECT 89 (vertices=89, convex hull=127, v0=153501)
- After retessellation of defect 89 (v0=153501), euler #=-16 (159653,478474,318805) : difference with theory (-15) = 1
- CORRECTING DEFECT 90 (vertices=49, convex hull=43, v0=154167)
- After retessellation of defect 90 (v0=154167), euler #=-15 (159661,478514,318838) : difference with theory (-14) = 1
- CORRECTING DEFECT 91 (vertices=58, convex hull=96, v0=158119)
- After retessellation of defect 91 (v0=158119), euler #=-15 (159684,478628,318929) : difference with theory (-13) = 2
- CORRECTING DEFECT 92 (vertices=40, convex hull=24, v0=158640)
- After retessellation of defect 92 (v0=158640), euler #=-14 (159687,478644,318943) : difference with theory (-12) = 2
- CORRECTING DEFECT 93 (vertices=47, convex hull=81, v0=158691)
- After retessellation of defect 93 (v0=158691), euler #=-13 (159711,478754,319030) : difference with theory (-11) = 2
- CORRECTING DEFECT 94 (vertices=31, convex hull=52, v0=159895)
- After retessellation of defect 94 (v0=159895), euler #=-11 (159712,478785,319062) : difference with theory (-10) = 1
- CORRECTING DEFECT 95 (vertices=54, convex hull=76, v0=160084)
- After retessellation of defect 95 (v0=160084), euler #=-10 (159730,478873,319133) : difference with theory (-9) = 1
- CORRECTING DEFECT 96 (vertices=48, convex hull=47, v0=161185)
- After retessellation of defect 96 (v0=161185), euler #=-9 (159736,478914,319169) : difference with theory (-8) = 1
- CORRECTING DEFECT 97 (vertices=233, convex hull=147, v0=162026)
- After retessellation of defect 97 (v0=162026), euler #=-8 (159799,479173,319366) : difference with theory (-7) = 1
- CORRECTING DEFECT 98 (vertices=69, convex hull=95, v0=165824)
- After retessellation of defect 98 (v0=165824), euler #=-7 (159834,479321,319480) : difference with theory (-6) = 1
- CORRECTING DEFECT 99 (vertices=39, convex hull=62, v0=165959)
- After retessellation of defect 99 (v0=165959), euler #=-6 (159854,479403,319543) : difference with theory (-5) = 1
- CORRECTING DEFECT 100 (vertices=52, convex hull=32, v0=166977)
- After retessellation of defect 100 (v0=166977), euler #=-5 (159856,479418,319557) : difference with theory (-4) = 1
- CORRECTING DEFECT 101 (vertices=30, convex hull=37, v0=168434)
- After retessellation of defect 101 (v0=168434), euler #=-4 (159857,479435,319574) : difference with theory (-3) = 1
- CORRECTING DEFECT 102 (vertices=36, convex hull=70, v0=168683)
- After retessellation of defect 102 (v0=168683), euler #=-3 (159868,479495,319624) : difference with theory (-2) = 1
- CORRECTING DEFECT 103 (vertices=58, convex hull=80, v0=169808)
- After retessellation of defect 103 (v0=169808), euler #=-2 (159889,479589,319698) : difference with theory (-1) = 1
- CORRECTING DEFECT 104 (vertices=14, convex hull=30, v0=169900)
- After retessellation of defect 104 (v0=169900), euler #=-1 (159890,479602,319711) : difference with theory (0) = 1
- CORRECTING DEFECT 105 (vertices=59, convex hull=65, v0=169953)
- After retessellation of defect 105 (v0=169953), euler #=0 (159909,479688,319779) : difference with theory (1) = 1
- CORRECTING DEFECT 106 (vertices=92, convex hull=77, v0=171367)
- After retessellation of defect 106 (v0=171367), euler #=2 (159921,479757,319838) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.89 +- 0.29 (0.03-->16.29) (max @ vno 105861 --> 122187)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.89 +- 0.29 (0.03-->16.29) (max @ vno 105861 --> 122187)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 290 mutations (32.2%), 611 crossovers (67.8%), 816 vertices were eliminated
- building final representation...
- 12253 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=159921, nf=319838, ne=479757, g=0)
- writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 86.6 minutes
- 0 defective edges
- removing intersecting faces
- 000: 1135 intersecting
- 001: 27 intersecting
- mris_fix_topology utimesec 5196.526007
- mris_fix_topology stimesec 0.649901
- mris_fix_topology ru_maxrss 550368
- mris_fix_topology ru_ixrss 0
- mris_fix_topology ru_idrss 0
- mris_fix_topology ru_isrss 0
- mris_fix_topology ru_minflt 65897
- mris_fix_topology ru_majflt 0
- mris_fix_topology ru_nswap 0
- mris_fix_topology ru_inblock 12128
- mris_fix_topology ru_oublock 15896
- mris_fix_topology ru_msgsnd 0
- mris_fix_topology ru_msgrcv 0
- mris_fix_topology ru_nsignals 0
- mris_fix_topology ru_nvcsw 612
- mris_fix_topology ru_nivcsw 14443
- FSRUNTIME@ mris_fix_topology lh 1.4436 hours 1 threads
- mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050352 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=-354 (nv=183780, nf=368268, ne=552402, g=178)
- 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 11 iterations
- marking ambiguous vertices...
- 41797 ambiguous faces found in tessellation
- segmenting defects...
- 106 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- -merging segment 39 into 18
- -merging segment 27 into 26
- -merging segment 38 into 37
- -merging segment 44 into 37
- 102 defects to be corrected
- 0 vertices coincident
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.1383 (-4.5692)
- -vertex loglikelihood: -5.8863 (-2.9432)
- -normal dot loglikelihood: -3.5515 (-3.5515)
- -quad curv loglikelihood: -6.0103 (-3.0052)
- Total Loglikelihood : -24.5865
- CORRECTING DEFECT 0 (vertices=37, convex hull=52, v0=0)
- After retessellation of defect 0 (v0=0), euler #=-90 (160015,473730,313625) : difference with theory (-99) = -9
- CORRECTING DEFECT 1 (vertices=39, convex hull=27, v0=49)
- After retessellation of defect 1 (v0=49), euler #=-89 (160018,473747,313640) : difference with theory (-98) = -9
- CORRECTING DEFECT 2 (vertices=126, convex hull=78, v0=54)
- After retessellation of defect 2 (v0=54), euler #=-88 (160030,473818,313700) : difference with theory (-97) = -9
- CORRECTING DEFECT 3 (vertices=72, convex hull=99, v0=312)
- After retessellation of defect 3 (v0=312), euler #=-87 (160063,473960,313810) : difference with theory (-96) = -9
- CORRECTING DEFECT 4 (vertices=203, convex hull=230, v0=504)
- After retessellation of defect 4 (v0=504), euler #=-86 (160144,474310,314080) : difference with theory (-95) = -9
- CORRECTING DEFECT 5 (vertices=34, convex hull=89, v0=550)
- After retessellation of defect 5 (v0=550), euler #=-85 (160161,474395,314149) : difference with theory (-94) = -9
- CORRECTING DEFECT 6 (vertices=124, convex hull=128, v0=658)
- After retessellation of defect 6 (v0=658), euler #=-84 (160208,474596,314304) : difference with theory (-93) = -9
- CORRECTING DEFECT 7 (vertices=43, convex hull=74, v0=924)
- After retessellation of defect 7 (v0=924), euler #=-83 (160221,474665,314361) : difference with theory (-92) = -9
- CORRECTING DEFECT 8 (vertices=723, convex hull=226, v0=1463)
- After retessellation of defect 8 (v0=1463), euler #=-82 (160329,475101,314690) : difference with theory (-91) = -9
- CORRECTING DEFECT 9 (vertices=74, convex hull=88, v0=1785)
- After retessellation of defect 9 (v0=1785), euler #=-81 (160357,475225,314787) : difference with theory (-90) = -9
- CORRECTING DEFECT 10 (vertices=25, convex hull=62, v0=2082)
- After retessellation of defect 10 (v0=2082), euler #=-80 (160369,475283,314834) : difference with theory (-89) = -9
- CORRECTING DEFECT 11 (vertices=153, convex hull=143, v0=2328)
- After retessellation of defect 11 (v0=2328), euler #=-79 (160429,475529,315021) : difference with theory (-88) = -9
- CORRECTING DEFECT 12 (vertices=274, convex hull=62, v0=2657)
- After retessellation of defect 12 (v0=2657), euler #=-78 (160445,475605,315082) : difference with theory (-87) = -9
- CORRECTING DEFECT 13 (vertices=220, convex hull=177, v0=3059)
- After retessellation of defect 13 (v0=3059), euler #=-77 (160526,475921,315318) : difference with theory (-86) = -9
- CORRECTING DEFECT 14 (vertices=58, convex hull=132, v0=3566)
- After retessellation of defect 14 (v0=3566), euler #=-76 (160558,476071,315437) : difference with theory (-85) = -9
- CORRECTING DEFECT 15 (vertices=39, convex hull=75, v0=4530)
- After retessellation of defect 15 (v0=4530), euler #=-75 (160579,476167,315513) : difference with theory (-84) = -9
- CORRECTING DEFECT 16 (vertices=14, convex hull=13, v0=6123)
- After retessellation of defect 16 (v0=6123), euler #=-74 (160579,476170,315517) : difference with theory (-83) = -9
- CORRECTING DEFECT 17 (vertices=329, convex hull=50, v0=6143)
- After retessellation of defect 17 (v0=6143), euler #=-73 (160604,476265,315588) : difference with theory (-82) = -9
- CORRECTING DEFECT 18 (vertices=5818, convex hull=1520, v0=6178)
- XL defect detected...
- After retessellation of defect 18 (v0=6178), euler #=-78 (161095,478550,317377) : difference with theory (-81) = -3
- CORRECTING DEFECT 19 (vertices=75, convex hull=87, v0=6510)
- After retessellation of defect 19 (v0=6510), euler #=-77 (161111,478632,317444) : difference with theory (-80) = -3
- CORRECTING DEFECT 20 (vertices=215, convex hull=222, v0=7492)
- After retessellation of defect 20 (v0=7492), euler #=-77 (161208,479032,317747) : difference with theory (-79) = -2
- CORRECTING DEFECT 21 (vertices=35, convex hull=67, v0=10145)
- After retessellation of defect 21 (v0=10145), euler #=-76 (161217,479087,317794) : difference with theory (-78) = -2
- CORRECTING DEFECT 22 (vertices=67, convex hull=80, v0=11171)
- After retessellation of defect 22 (v0=11171), euler #=-75 (161239,479184,317870) : difference with theory (-77) = -2
- CORRECTING DEFECT 23 (vertices=47, convex hull=87, v0=13678)
- After retessellation of defect 23 (v0=13678), euler #=-74 (161259,479284,317951) : difference with theory (-76) = -2
- CORRECTING DEFECT 24 (vertices=64, convex hull=33, v0=14984)
- After retessellation of defect 24 (v0=14984), euler #=-73 (161270,479327,317984) : difference with theory (-75) = -2
- CORRECTING DEFECT 25 (vertices=43, convex hull=107, v0=18331)
- After retessellation of defect 25 (v0=18331), euler #=-72 (161297,479458,318089) : difference with theory (-74) = -2
- CORRECTING DEFECT 26 (vertices=147, convex hull=232, v0=18468)
- After retessellation of defect 26 (v0=18468), euler #=-70 (161373,479799,318356) : difference with theory (-73) = -3
- CORRECTING DEFECT 27 (vertices=232, convex hull=306, v0=25636)
- After retessellation of defect 27 (v0=25636), euler #=-69 (161481,480278,318728) : difference with theory (-72) = -3
- CORRECTING DEFECT 28 (vertices=199, convex hull=163, v0=27626)
- After retessellation of defect 28 (v0=27626), euler #=-68 (161542,480537,318927) : difference with theory (-71) = -3
- CORRECTING DEFECT 29 (vertices=85, convex hull=103, v0=30710)
- After retessellation of defect 29 (v0=30710), euler #=-67 (161587,480721,319067) : difference with theory (-70) = -3
- CORRECTING DEFECT 30 (vertices=64, convex hull=76, v0=30737)
- After retessellation of defect 30 (v0=30737), euler #=-66 (161611,480827,319150) : difference with theory (-69) = -3
- CORRECTING DEFECT 31 (vertices=34, convex hull=75, v0=37888)
- After retessellation of defect 31 (v0=37888), euler #=-65 (161629,480908,319214) : difference with theory (-68) = -3
- CORRECTING DEFECT 32 (vertices=6, convex hull=22, v0=38071)
- After retessellation of defect 32 (v0=38071), euler #=-64 (161629,480913,319220) : difference with theory (-67) = -3
- CORRECTING DEFECT 33 (vertices=6, convex hull=17, v0=38220)
- After retessellation of defect 33 (v0=38220), euler #=-63 (161630,480920,319227) : difference with theory (-66) = -3
- CORRECTING DEFECT 34 (vertices=20, convex hull=22, v0=38369)
- After retessellation of defect 34 (v0=38369), euler #=-62 (161631,480931,319238) : difference with theory (-65) = -3
- CORRECTING DEFECT 35 (vertices=12, convex hull=21, v0=41147)
- After retessellation of defect 35 (v0=41147), euler #=-61 (161634,480946,319251) : difference with theory (-64) = -3
- CORRECTING DEFECT 36 (vertices=556, convex hull=392, v0=46035)
- After retessellation of defect 36 (v0=46035), euler #=-58 (161754,481512,319700) : difference with theory (-63) = -5
- CORRECTING DEFECT 37 (vertices=774, convex hull=205, v0=66120)
- After retessellation of defect 37 (v0=66120), euler #=-57 (161798,481738,319883) : difference with theory (-62) = -5
- CORRECTING DEFECT 38 (vertices=34, convex hull=50, v0=70793)
- After retessellation of defect 38 (v0=70793), euler #=-56 (161813,481801,319932) : difference with theory (-61) = -5
- CORRECTING DEFECT 39 (vertices=165, convex hull=168, v0=70889)
- After retessellation of defect 39 (v0=70889), euler #=-55 (161907,482165,320203) : difference with theory (-60) = -5
- CORRECTING DEFECT 40 (vertices=197, convex hull=199, v0=73834)
- After retessellation of defect 40 (v0=73834), euler #=-54 (161989,482506,320463) : difference with theory (-59) = -5
- CORRECTING DEFECT 41 (vertices=31, convex hull=57, v0=74122)
- After retessellation of defect 41 (v0=74122), euler #=-53 (162002,482574,320519) : difference with theory (-58) = -5
- CORRECTING DEFECT 42 (vertices=230, convex hull=309, v0=74758)
- After retessellation of defect 42 (v0=74758), euler #=-52 (162169,483227,321006) : difference with theory (-57) = -5
- CORRECTING DEFECT 43 (vertices=76, convex hull=94, v0=80822)
- After retessellation of defect 43 (v0=80822), euler #=-51 (162187,483326,321088) : difference with theory (-56) = -5
- CORRECTING DEFECT 44 (vertices=191, convex hull=233, v0=81364)
- After retessellation of defect 44 (v0=81364), euler #=-50 (162322,483840,321468) : difference with theory (-55) = -5
- CORRECTING DEFECT 45 (vertices=45, convex hull=69, v0=83573)
- After retessellation of defect 45 (v0=83573), euler #=-49 (162347,483943,321547) : difference with theory (-54) = -5
- CORRECTING DEFECT 46 (vertices=298, convex hull=332, v0=84908)
- After retessellation of defect 46 (v0=84908), euler #=-48 (162528,484636,322060) : difference with theory (-53) = -5
- CORRECTING DEFECT 47 (vertices=65, convex hull=31, v0=86766)
- After retessellation of defect 47 (v0=86766), euler #=-47 (162533,484666,322086) : difference with theory (-52) = -5
- CORRECTING DEFECT 48 (vertices=49, convex hull=71, v0=90673)
- After retessellation of defect 48 (v0=90673), euler #=-46 (162557,484771,322168) : difference with theory (-51) = -5
- CORRECTING DEFECT 49 (vertices=158, convex hull=142, v0=90691)
- After retessellation of defect 49 (v0=90691), euler #=-46 (162614,485014,322354) : difference with theory (-50) = -4
- CORRECTING DEFECT 50 (vertices=36, convex hull=66, v0=93452)
- After retessellation of defect 50 (v0=93452), euler #=-45 (162632,485090,322413) : difference with theory (-49) = -4
- CORRECTING DEFECT 51 (vertices=114, convex hull=105, v0=94033)
- After retessellation of defect 51 (v0=94033), euler #=-44 (162672,485256,322540) : difference with theory (-48) = -4
- CORRECTING DEFECT 52 (vertices=123, convex hull=91, v0=94392)
- After retessellation of defect 52 (v0=94392), euler #=-43 (162715,485426,322668) : difference with theory (-47) = -4
- CORRECTING DEFECT 53 (vertices=895, convex hull=146, v0=101437)
- After retessellation of defect 53 (v0=101437), euler #=-42 (162769,485657,322846) : difference with theory (-46) = -4
- CORRECTING DEFECT 54 (vertices=32, convex hull=38, v0=101458)
- After retessellation of defect 54 (v0=101458), euler #=-41 (162772,485684,322871) : difference with theory (-45) = -4
- CORRECTING DEFECT 55 (vertices=19, convex hull=29, v0=102378)
- After retessellation of defect 55 (v0=102378), euler #=-40 (162775,485700,322885) : difference with theory (-44) = -4
- CORRECTING DEFECT 56 (vertices=43, convex hull=37, v0=104074)
- After retessellation of defect 56 (v0=104074), euler #=-39 (162779,485726,322908) : difference with theory (-43) = -4
- CORRECTING DEFECT 57 (vertices=1255, convex hull=311, v0=104364)
- After retessellation of defect 57 (v0=104364), euler #=-38 (163005,486562,323519) : difference with theory (-42) = -4
- CORRECTING DEFECT 58 (vertices=32, convex hull=44, v0=105703)
- After retessellation of defect 58 (v0=105703), euler #=-37 (163021,486623,323565) : difference with theory (-41) = -4
- CORRECTING DEFECT 59 (vertices=55, convex hull=61, v0=106032)
- After retessellation of defect 59 (v0=106032), euler #=-36 (163055,486750,323659) : difference with theory (-40) = -4
- CORRECTING DEFECT 60 (vertices=35, convex hull=82, v0=106699)
- After retessellation of defect 60 (v0=106699), euler #=-35 (163070,486824,323719) : difference with theory (-39) = -4
- CORRECTING DEFECT 61 (vertices=91, convex hull=126, v0=106766)
- After retessellation of defect 61 (v0=106766), euler #=-34 (163093,486947,323820) : difference with theory (-38) = -4
- CORRECTING DEFECT 62 (vertices=10, convex hull=15, v0=108216)
- After retessellation of defect 62 (v0=108216), euler #=-33 (163094,486956,323829) : difference with theory (-37) = -4
- CORRECTING DEFECT 63 (vertices=130, convex hull=37, v0=108784)
- After retessellation of defect 63 (v0=108784), euler #=-32 (163104,486997,323861) : difference with theory (-36) = -4
- CORRECTING DEFECT 64 (vertices=25, convex hull=72, v0=109094)
- After retessellation of defect 64 (v0=109094), euler #=-31 (163118,487066,323917) : difference with theory (-35) = -4
- CORRECTING DEFECT 65 (vertices=119, convex hull=154, v0=109223)
- After retessellation of defect 65 (v0=109223), euler #=-30 (163156,487254,324068) : difference with theory (-34) = -4
- CORRECTING DEFECT 66 (vertices=1473, convex hull=583, v0=109735)
- XL defect detected...
- After retessellation of defect 66 (v0=109735), euler #=-31 (163364,488194,324799) : difference with theory (-33) = -2
- CORRECTING DEFECT 67 (vertices=20, convex hull=52, v0=115296)
- After retessellation of defect 67 (v0=115296), euler #=-30 (163374,488243,324839) : difference with theory (-32) = -2
- CORRECTING DEFECT 68 (vertices=41, convex hull=70, v0=116131)
- After retessellation of defect 68 (v0=116131), euler #=-29 (163397,488340,324914) : difference with theory (-31) = -2
- CORRECTING DEFECT 69 (vertices=82, convex hull=125, v0=121326)
- After retessellation of defect 69 (v0=121326), euler #=-28 (163439,488523,325056) : difference with theory (-30) = -2
- CORRECTING DEFECT 70 (vertices=2129, convex hull=777, v0=122199)
- XL defect detected...
- After retessellation of defect 70 (v0=122199), euler #=-29 (164084,490895,326782) : difference with theory (-29) = 0
- CORRECTING DEFECT 71 (vertices=1604, convex hull=592, v0=126769)
- XL defect detected...
- After retessellation of defect 71 (v0=126769), euler #=-28 (164516,492512,327968) : difference with theory (-28) = 0
- CORRECTING DEFECT 72 (vertices=17, convex hull=29, v0=130383)
- After retessellation of defect 72 (v0=130383), euler #=-27 (164519,492528,327982) : difference with theory (-27) = 0
- CORRECTING DEFECT 73 (vertices=649, convex hull=366, v0=130457)
- After retessellation of defect 73 (v0=130457), euler #=-26 (164628,493041,328387) : difference with theory (-26) = 0
- CORRECTING DEFECT 74 (vertices=49, convex hull=76, v0=132923)
- After retessellation of defect 74 (v0=132923), euler #=-25 (164637,493098,328436) : difference with theory (-25) = 0
- CORRECTING DEFECT 75 (vertices=48, convex hull=66, v0=134859)
- After retessellation of defect 75 (v0=134859), euler #=-24 (164655,493178,328499) : difference with theory (-24) = 0
- CORRECTING DEFECT 76 (vertices=27, convex hull=47, v0=134880)
- After retessellation of defect 76 (v0=134880), euler #=-23 (164669,493235,328543) : difference with theory (-23) = 0
- CORRECTING DEFECT 77 (vertices=46, convex hull=70, v0=141204)
- After retessellation of defect 77 (v0=141204), euler #=-22 (164692,493333,328619) : difference with theory (-22) = 0
- CORRECTING DEFECT 78 (vertices=38, convex hull=69, v0=141828)
- After retessellation of defect 78 (v0=141828), euler #=-21 (164711,493416,328684) : difference with theory (-21) = 0
- CORRECTING DEFECT 79 (vertices=37, convex hull=32, v0=144433)
- After retessellation of defect 79 (v0=144433), euler #=-20 (164720,493453,328713) : difference with theory (-20) = 0
- CORRECTING DEFECT 80 (vertices=512, convex hull=161, v0=149124)
- After retessellation of defect 80 (v0=149124), euler #=-19 (164767,493673,328887) : difference with theory (-19) = 0
- CORRECTING DEFECT 81 (vertices=54, convex hull=38, v0=149353)
- After retessellation of defect 81 (v0=149353), euler #=-18 (164775,493711,328918) : difference with theory (-18) = 0
- CORRECTING DEFECT 82 (vertices=36, convex hull=66, v0=150090)
- After retessellation of defect 82 (v0=150090), euler #=-17 (164785,493765,328963) : difference with theory (-17) = 0
- CORRECTING DEFECT 83 (vertices=31, convex hull=42, v0=151509)
- After retessellation of defect 83 (v0=151509), euler #=-16 (164799,493824,329009) : difference with theory (-16) = 0
- CORRECTING DEFECT 84 (vertices=29, convex hull=80, v0=154273)
- After retessellation of defect 84 (v0=154273), euler #=-15 (164817,493907,329075) : difference with theory (-15) = 0
- CORRECTING DEFECT 85 (vertices=35, convex hull=33, v0=157124)
- After retessellation of defect 85 (v0=157124), euler #=-14 (164819,493926,329093) : difference with theory (-14) = 0
- CORRECTING DEFECT 86 (vertices=34, convex hull=62, v0=160182)
- After retessellation of defect 86 (v0=160182), euler #=-13 (164832,493989,329144) : difference with theory (-13) = 0
- CORRECTING DEFECT 87 (vertices=46, convex hull=99, v0=161060)
- After retessellation of defect 87 (v0=161060), euler #=-12 (164859,494114,329243) : difference with theory (-12) = 0
- CORRECTING DEFECT 88 (vertices=50, convex hull=87, v0=163969)
- After retessellation of defect 88 (v0=163969), euler #=-11 (164894,494257,329352) : difference with theory (-11) = 0
- CORRECTING DEFECT 89 (vertices=48, convex hull=83, v0=165360)
- After retessellation of defect 89 (v0=165360), euler #=-10 (164924,494385,329451) : difference with theory (-10) = 0
- CORRECTING DEFECT 90 (vertices=18, convex hull=20, v0=166231)
- After retessellation of defect 90 (v0=166231), euler #=-9 (164924,494391,329458) : difference with theory (-9) = 0
- CORRECTING DEFECT 91 (vertices=48, convex hull=42, v0=168051)
- After retessellation of defect 91 (v0=168051), euler #=-8 (164927,494418,329483) : difference with theory (-8) = 0
- CORRECTING DEFECT 92 (vertices=150, convex hull=85, v0=169012)
- After retessellation of defect 92 (v0=169012), euler #=-7 (164943,494504,329554) : difference with theory (-7) = 0
- CORRECTING DEFECT 93 (vertices=58, convex hull=94, v0=171278)
- After retessellation of defect 93 (v0=171278), euler #=-6 (164970,494623,329647) : difference with theory (-6) = 0
- CORRECTING DEFECT 94 (vertices=11, convex hull=19, v0=173430)
- After retessellation of defect 94 (v0=173430), euler #=-5 (164971,494633,329657) : difference with theory (-5) = 0
- CORRECTING DEFECT 95 (vertices=42, convex hull=20, v0=174261)
- After retessellation of defect 95 (v0=174261), euler #=-4 (164973,494646,329669) : difference with theory (-4) = 0
- CORRECTING DEFECT 96 (vertices=99, convex hull=100, v0=175048)
- After retessellation of defect 96 (v0=175048), euler #=-3 (165006,494794,329785) : difference with theory (-3) = 0
- CORRECTING DEFECT 97 (vertices=104, convex hull=95, v0=176136)
- After retessellation of defect 97 (v0=176136), euler #=-2 (165045,494956,329909) : difference with theory (-2) = 0
- CORRECTING DEFECT 98 (vertices=180, convex hull=150, v0=180352)
- After retessellation of defect 98 (v0=180352), euler #=-1 (165109,495222,330112) : difference with theory (-1) = 0
- CORRECTING DEFECT 99 (vertices=172, convex hull=122, v0=180447)
- After retessellation of defect 99 (v0=180447), euler #=0 (165155,495416,330261) : difference with theory (0) = 0
- CORRECTING DEFECT 100 (vertices=42, convex hull=24, v0=180967)
- After retessellation of defect 100 (v0=180967), euler #=1 (165156,495426,330271) : difference with theory (1) = 0
- CORRECTING DEFECT 101 (vertices=52, convex hull=92, v0=183295)
- After retessellation of defect 101 (v0=183295), euler #=2 (165183,495543,330362) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.89 +- 0.32 (0.02-->28.62) (max @ vno 26853 --> 51271)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.89 +- 0.32 (0.02-->28.62) (max @ vno 26853 --> 51271)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 263 mutations (32.5%), 545 crossovers (67.5%), 2111 vertices were eliminated
- building final representation...
- 18597 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=165183, nf=330362, ne=495543, g=0)
- writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 226.2 minutes
- 0 defective edges
- removing intersecting faces
- 000: 1980 intersecting
- 001: 60 intersecting
- 002: 2 intersecting
- mris_fix_topology utimesec 13573.626495
- mris_fix_topology stimesec 0.542917
- mris_fix_topology ru_maxrss 682248
- mris_fix_topology ru_ixrss 0
- mris_fix_topology ru_idrss 0
- mris_fix_topology ru_isrss 0
- mris_fix_topology ru_minflt 71948
- mris_fix_topology ru_majflt 0
- mris_fix_topology ru_nswap 0
- mris_fix_topology ru_inblock 35984
- mris_fix_topology ru_oublock 16536
- mris_fix_topology ru_msgsnd 0
- mris_fix_topology ru_msgrcv 0
- mris_fix_topology ru_nsignals 0
- mris_fix_topology ru_nvcsw 479
- mris_fix_topology ru_nivcsw 21178
- FSRUNTIME@ mris_fix_topology rh 3.7701 hours 1 threads
- PIDs (16546 16549) completed and logs appended.
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 159921 - 479757 + 319838 = 2 --> 0 holes
- F =2V-4: 319838 = 319842-4 (0)
- 2E=3F: 959514 = 959514 (0)
- total defect index = 0
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 165183 - 495543 + 330362 = 2 --> 0 holes
- F =2V-4: 330362 = 330366-4 (0)
- 2E=3F: 991086 = 991086 (0)
- total defect index = 0
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 265 intersecting
- 001: 15 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 670 intersecting
- 001: 75 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Sun Oct 8 07:54:29 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050352 lh
- #--------------------------------------------
- #@# Make White Surf rh Sun Oct 8 07:54:29 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050352 rh
- Waiting for PID 25932 of (25932 25935) to complete...
- Waiting for PID 25935 of (25932 25935) to complete...
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050352 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-6.0.0/0050352/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
- 17660 bright wm thresholded.
- 2039 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.orig...
- computing class statistics...
- border white: 320647 voxels (1.91%)
- border gray 377071 voxels (2.25%)
- WM (94.0): 95.4 +- 7.8 [70.0 --> 110.0]
- GM (73.0) : 71.7 +- 10.6 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 58.4 (was 70)
- setting MAX_BORDER_WHITE to 106.8 (was 105)
- setting MIN_BORDER_WHITE to 69.0 (was 85)
- setting MAX_CSF to 47.9 (was 40)
- setting MAX_GRAY to 91.2 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 58.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 37.3 (was 40)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.82 +- 0.24 (0.02-->6.08) (max @ vno 56130 --> 60727)
- face area 0.28 +- 0.14 (0.00-->9.12)
- mean absolute distance = 0.68 +- 0.85
- 4499 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=99+-6.1, GM=69+-7.0
- mean inside = 91.5, mean outside = 75.7
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=81.2, 202 (202) missing vertices, mean dist 0.2 [0.6 (%40.1)->0.7 (%59.9))]
- %71 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.91 +- 0.27 (0.09-->6.24) (max @ vno 54871 --> 60605)
- face area 0.28 +- 0.14 (0.00-->9.51)
- mean absolute distance = 0.37 +- 0.66
- 5058 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3082067.2, rms=8.847
- 001: dt: 0.5000, sse=1891597.5, rms=6.396 (27.704%)
- 002: dt: 0.5000, sse=1387078.4, rms=4.957 (22.502%)
- 003: dt: 0.5000, sse=1172859.1, rms=4.201 (15.248%)
- 004: dt: 0.5000, sse=1078760.6, rms=3.809 (9.326%)
- 005: dt: 0.5000, sse=1025619.2, rms=3.573 (6.198%)
- 006: dt: 0.5000, sse=981190.0, rms=3.375 (5.544%)
- 007: dt: 0.5000, sse=958772.1, rms=3.266 (3.236%)
- 008: dt: 0.5000, sse=943257.4, rms=3.177 (2.717%)
- rms = 3.14, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=938490.4, rms=3.140 (1.182%)
- 010: dt: 0.2500, sse=795710.2, rms=2.180 (30.575%)
- 011: dt: 0.2500, sse=771011.6, rms=1.976 (9.335%)
- 012: dt: 0.2500, sse=764212.8, rms=1.923 (2.693%)
- rms = 1.89, time step reduction 2 of 3 to 0.125...
- 013: dt: 0.2500, sse=760691.6, rms=1.892 (1.598%)
- rms = 1.86, time step reduction 3 of 3 to 0.062...
- 014: dt: 0.1250, sse=756203.1, rms=1.862 (1.597%)
- positioning took 1.7 minutes
- inhibiting deformation at non-cortical midline structures...
- mean border=83.1, 248 (80) missing vertices, mean dist -0.2 [0.4 (%63.8)->0.3 (%36.2))]
- %75 local maxima, %20 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 (0.05-->6.74) (max @ vno 54871 --> 60605)
- face area 0.35 +- 0.18 (0.00-->13.17)
- mean absolute distance = 0.32 +- 0.49
- 4911 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1228946.9, rms=3.734
- 015: dt: 0.5000, sse=1016613.8, rms=2.614 (29.984%)
- 016: dt: 0.5000, sse=985590.4, rms=2.483 (5.028%)
- rms = 2.54, time step reduction 1 of 3 to 0.250...
- 017: dt: 0.2500, sse=918147.9, rms=1.964 (20.909%)
- 018: dt: 0.2500, sse=888911.6, rms=1.686 (14.136%)
- 019: dt: 0.2500, sse=895696.8, rms=1.628 (3.465%)
- rms = 1.60, time step reduction 2 of 3 to 0.125...
- 020: dt: 0.2500, sse=889456.4, rms=1.603 (1.521%)
- rms = 1.56, time step reduction 3 of 3 to 0.062...
- 021: dt: 0.1250, sse=876294.9, rms=1.561 (2.600%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=84.4, 272 (57) missing vertices, mean dist -0.1 [0.4 (%58.7)->0.2 (%41.3))]
- %80 local maxima, %15 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 0.90 +- 0.26 (0.04-->6.92) (max @ vno 60727 --> 56130)
- face area 0.34 +- 0.18 (0.00-->13.38)
- mean absolute distance = 0.31 +- 0.43
- 4211 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=980696.7, rms=2.505
- 022: dt: 0.5000, sse=930464.1, rms=2.096 (16.345%)
- rms = 2.17, time step reduction 1 of 3 to 0.250...
- 023: dt: 0.2500, sse=877605.4, rms=1.683 (19.700%)
- 024: dt: 0.2500, sse=860596.7, rms=1.496 (11.082%)
- rms = 1.45, time step reduction 2 of 3 to 0.125...
- 025: dt: 0.2500, sse=856533.9, rms=1.453 (2.862%)
- rms = 1.41, time step reduction 3 of 3 to 0.062...
- 026: dt: 0.1250, sse=850404.4, rms=1.412 (2.877%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 1 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=85.0, 264 (47) missing vertices, mean dist -0.1 [0.3 (%52.7)->0.3 (%47.3))]
- %84 local maxima, %11 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-6.0.0/0050352/surf/lh.white.preaparc...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=878171.2, rms=1.765
- 027: dt: 0.5000, sse=865516.9, rms=1.611 (8.763%)
- rms = 1.93, time step reduction 1 of 3 to 0.250...
- 028: dt: 0.2500, sse=831873.9, rms=1.282 (20.413%)
- 029: dt: 0.2500, sse=830962.7, rms=1.206 (5.948%)
- rms = 1.17, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.2500, sse=832184.2, rms=1.172 (2.816%)
- rms = 1.13, time step reduction 3 of 3 to 0.062...
- 031: dt: 0.1250, sse=817161.9, rms=1.129 (3.681%)
- positioning took 0.7 minutes
- generating cortex label...
- 12 non-cortical segments detected
- only using segment with 8687 vertices
- erasing segment 1 (vno[0] = 75424)
- erasing segment 2 (vno[0] = 93729)
- erasing segment 3 (vno[0] = 97178)
- erasing segment 4 (vno[0] = 97732)
- erasing segment 5 (vno[0] = 102244)
- erasing segment 6 (vno[0] = 104586)
- erasing segment 7 (vno[0] = 110172)
- erasing segment 8 (vno[0] = 111346)
- erasing segment 9 (vno[0] = 112461)
- erasing segment 10 (vno[0] = 112487)
- erasing segment 11 (vno[0] = 157738)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.area
- vertex spacing 0.90 +- 0.27 (0.03-->7.14) (max @ vno 56130 --> 60727)
- face area 0.34 +- 0.18 (0.00-->13.23)
- refinement took 5.8 minutes
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050352 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-6.0.0/0050352/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
- 17660 bright wm thresholded.
- 2039 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.orig...
- computing class statistics...
- border white: 320647 voxels (1.91%)
- border gray 377071 voxels (2.25%)
- WM (94.0): 95.4 +- 7.8 [70.0 --> 110.0]
- GM (73.0) : 71.7 +- 10.6 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 61.4 (was 70)
- setting MAX_BORDER_WHITE to 105.8 (was 105)
- setting MIN_BORDER_WHITE to 72.0 (was 85)
- setting MAX_CSF to 50.9 (was 40)
- setting MAX_GRAY to 90.2 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 61.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 40.3 (was 40)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.81 +- 0.25 (0.01-->6.59) (max @ vno 78197 --> 162389)
- face area 0.28 +- 0.14 (0.00-->5.58)
- mean absolute distance = 0.67 +- 0.85
- 4694 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=98+-6.1, GM=72+-6.1
- mean inside = 91.3, mean outside = 76.8
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- mean border=83.3, 281 (281) missing vertices, mean dist 0.1 [0.7 (%45.7)->0.7 (%54.3))]
- %75 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.90 +- 0.27 (0.05-->6.73) (max @ vno 108009 --> 163207)
- face area 0.28 +- 0.14 (0.00-->6.30)
- mean absolute distance = 0.39 +- 0.67
- 5920 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=2532878.8, rms=7.445
- 001: dt: 0.5000, sse=1471837.1, rms=5.038 (32.338%)
- 002: dt: 0.5000, sse=1075899.8, rms=3.608 (28.370%)
- 003: dt: 0.5000, sse=940748.9, rms=2.980 (17.415%)
- 004: dt: 0.5000, sse=900906.0, rms=2.756 (7.520%)
- 005: dt: 0.5000, sse=883643.8, rms=2.669 (3.137%)
- rms = 2.64, time step reduction 1 of 3 to 0.250...
- 006: dt: 0.5000, sse=883764.4, rms=2.645 (0.931%)
- 007: dt: 0.2500, sse=773817.1, rms=1.790 (32.303%)
- 008: dt: 0.2500, sse=757897.6, rms=1.627 (9.133%)
- rms = 1.60, time step reduction 2 of 3 to 0.125...
- 009: dt: 0.2500, sse=757189.0, rms=1.599 (1.699%)
- rms = 1.58, time step reduction 3 of 3 to 0.062...
- 010: dt: 0.1250, sse=752244.0, rms=1.575 (1.491%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- mean border=85.1, 269 (73) missing vertices, mean dist -0.2 [0.5 (%63.5)->0.3 (%36.5))]
- %79 local maxima, %17 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 +- 0.27 (0.07-->7.48) (max @ vno 108009 --> 163207)
- face area 0.34 +- 0.17 (0.00-->8.98)
- mean absolute distance = 0.33 +- 0.51
- 5228 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1178558.2, rms=3.371
- 011: dt: 0.5000, sse=982478.4, rms=2.257 (33.041%)
- 012: dt: 0.5000, sse=953683.6, rms=2.086 (7.596%)
- rms = 2.13, time step reduction 1 of 3 to 0.250...
- 013: dt: 0.2500, sse=906935.5, rms=1.704 (18.306%)
- 014: dt: 0.2500, sse=889747.2, rms=1.505 (11.657%)
- rms = 1.46, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=890636.4, rms=1.462 (2.872%)
- rms = 1.43, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=884202.3, rms=1.434 (1.918%)
- positioning took 0.8 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=86.1, 277 (46) missing vertices, mean dist -0.1 [0.4 (%57.6)->0.3 (%42.4))]
- %82 local maxima, %13 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 +- 0.27 (0.05-->8.01) (max @ vno 108009 --> 163207)
- face area 0.33 +- 0.17 (0.00-->9.26)
- mean absolute distance = 0.32 +- 0.43
- 4522 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=974259.8, rms=2.280
- 017: dt: 0.5000, sse=921469.2, rms=1.811 (20.545%)
- rms = 1.83, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=883277.1, rms=1.517 (16.252%)
- 019: dt: 0.2500, sse=872877.5, rms=1.368 (9.818%)
- rms = 1.33, time step reduction 2 of 3 to 0.125...
- 020: dt: 0.2500, sse=869855.9, rms=1.332 (2.640%)
- rms = 1.31, time step reduction 3 of 3 to 0.062...
- 021: dt: 0.1250, sse=863920.9, rms=1.307 (1.888%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 1 vertex label from ripped group
- mean border=86.7, 328 (41) missing vertices, mean dist -0.0 [0.3 (%52.3)->0.3 (%47.7))]
- %86 local maxima, %10 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-6.0.0/0050352/surf/rh.white.preaparc...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=883245.9, rms=1.585
- 022: dt: 0.5000, sse=878382.7, rms=1.314 (17.056%)
- rms = 1.65, time step reduction 1 of 3 to 0.250...
- 023: dt: 0.2500, sse=841154.0, rms=1.094 (16.745%)
- rms = 1.08, time step reduction 2 of 3 to 0.125...
- 024: dt: 0.2500, sse=855674.2, rms=1.082 (1.162%)
- rms = 1.04, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=833807.8, rms=1.038 (4.021%)
- positioning took 0.6 minutes
- generating cortex label...
- 6 non-cortical segments detected
- only using segment with 7856 vertices
- erasing segment 1 (vno[0] = 115541)
- erasing segment 2 (vno[0] = 116581)
- erasing segment 3 (vno[0] = 116654)
- erasing segment 4 (vno[0] = 117658)
- erasing segment 5 (vno[0] = 164558)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.area
- vertex spacing 0.89 +- 0.27 (0.03-->8.41) (max @ vno 108009 --> 163207)
- face area 0.33 +- 0.17 (0.00-->9.70)
- refinement took 5.3 minutes
- PIDs (25932 25935) completed and logs appended.
- #--------------------------------------------
- #@# Smooth2 lh Sun Oct 8 08:00:19 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm
- #--------------------------------------------
- #@# Smooth2 rh Sun Oct 8 08:00:19 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm
- Waiting for PID 26264 of (26264 26267) to complete...
- Waiting for PID 26267 of (26264 26267) 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 (26264 26267) completed and logs appended.
- #--------------------------------------------
- #@# Inflation2 lh Sun Oct 8 08:00:26 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated
- #--------------------------------------------
- #@# Inflation2 rh Sun Oct 8 08:00:26 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated
- Waiting for PID 26313 of (26313 26316) to complete...
- Waiting for PID 26316 of (26313 26316) to complete...
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated
- Reading ../surf/lh.smoothwm
- avg radius = 48.6 mm, total surface area = 96635 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.185 (target=0.015)
step 005: RMS=0.130 (target=0.015)
step 010: RMS=0.100 (target=0.015)
step 015: RMS=0.084 (target=0.015)
step 020: RMS=0.071 (target=0.015)
step 025: RMS=0.060 (target=0.015)
step 030: RMS=0.052 (target=0.015)
step 035: RMS=0.044 (target=0.015)
step 040: RMS=0.040 (target=0.015)
step 045: RMS=0.035 (target=0.015)
step 050: RMS=0.030 (target=0.015)
step 055: RMS=0.028 (target=0.015)
step 060: RMS=0.026 (target=0.015)
- inflation complete.
- inflation took 0.8 minutes
- mris_inflate utimesec 49.088537
- mris_inflate stimesec 0.105983
- mris_inflate ru_maxrss 234812
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 34239
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 11248
- mris_inflate ru_oublock 12528
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2264
- mris_inflate ru_nivcsw 3943
- mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated
- Reading ../surf/rh.smoothwm
- avg radius = 48.8 mm, total surface area = 97735 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.188 (target=0.015)
step 005: RMS=0.133 (target=0.015)
step 010: RMS=0.106 (target=0.015)
step 015: RMS=0.089 (target=0.015)
step 020: RMS=0.075 (target=0.015)
step 025: RMS=0.064 (target=0.015)
step 030: RMS=0.057 (target=0.015)
step 035: RMS=0.049 (target=0.015)
step 040: RMS=0.044 (target=0.015)
step 045: RMS=0.039 (target=0.015)
step 050: RMS=0.036 (target=0.015)
step 055: RMS=0.033 (target=0.015)
step 060: RMS=0.031 (target=0.015)
- inflation complete.
- inflation took 0.8 minutes
- mris_inflate utimesec 50.675296
- mris_inflate stimesec 0.115982
- mris_inflate ru_maxrss 242716
- mris_inflate ru_ixrss 0
- mris_inflate ru_idrss 0
- mris_inflate ru_isrss 0
- mris_inflate ru_minflt 35192
- mris_inflate ru_majflt 0
- mris_inflate ru_nswap 0
- mris_inflate ru_inblock 11624
- mris_inflate ru_oublock 12936
- mris_inflate ru_msgsnd 0
- mris_inflate ru_msgrcv 0
- mris_inflate ru_nsignals 0
- mris_inflate ru_nvcsw 2232
- mris_inflate ru_nivcsw 3813
- PIDs (26313 26316) completed and logs appended.
- #--------------------------------------------
- #@# Curv .H and .K lh Sun Oct 8 08:01:17 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 Sun Oct 8 08:01:17 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf
- reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 26427 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
- Waiting for PID 26430 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
- Waiting for PID 26433 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
- Waiting for PID 26436 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
- Waiting for PID 26439 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
- Waiting for PID 26442 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
- Waiting for PID 26445 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
- Waiting for PID 26448 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
- Waiting for PID 26451 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
- Waiting for PID 26454 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
- Waiting for PID 26457 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
- Waiting for PID 26460 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
- mris_curvature -w lh.white.preaparc
- total integrated curvature = 18.035*4pi (226.639) --> -17 handles
- ICI = 281.1, FI = 2023.5, variation=34940.246
- 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
- 202 vertices thresholded to be in k1 ~ [-0.34 0.79], k2 ~ [-0.12 0.08]
- total integrated curvature = 0.289*4pi (3.628) --> 1 handles
- ICI = 1.5, FI = 11.0, variation=183.930
- 139 vertices thresholded to be in [-0.01 0.02]
- writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 165 vertices thresholded to be in [-0.17 0.36]
- done.
- writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.025
- done.
- mris_curvature -w rh.white.preaparc
- total integrated curvature = 26.619*4pi (334.505) --> -26 handles
- ICI = 326.0, FI = 2252.8, variation=39306.423
- 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
- 228 vertices thresholded to be in k1 ~ [-0.47 0.96], k2 ~ [-0.15 0.08]
- total integrated curvature = 0.252*4pi (3.169) --> 1 handles
- ICI = 1.5, FI = 12.1, variation=198.815
- 178 vertices thresholded to be in [-0.04 0.02]
- writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 162 vertices thresholded to be in [-0.21 0.40]
- done.
- writing mean curvature to ./rh.inflated.H...curvature mean = -0.014, std = 0.027
- done.
- PIDs (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) completed and logs appended.
- #-----------------------------------------
- #@# Curvature Stats lh Sun Oct 8 08:02:57 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050352 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 [ 0050352/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 [ 285 ]
- Gb_filter = 0
- #-----------------------------------------
- #@# Curvature Stats rh Sun Oct 8 08:03:02 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050352 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 [ 0050352/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 [ 326 ]
- Gb_filter = 0
- WARN: S lookup min: -0.429441
- WARN: S explicit min: 0.000000 vertex = 384
- #--------------------------------------------
- #@# Sphere lh Sun Oct 8 08:03:07 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
- #--------------------------------------------
- #@# Sphere rh Sun Oct 8 08:03:07 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere
- Waiting for PID 26628 of (26628 26631) to complete...
- Waiting for PID 26631 of (26628 26631) to complete...
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0.275...
- 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 %19.95
- unfolding complete - removing small folds...
- starting distance error %19.82
- removing remaining folds...
- final distance error %19.85
- MRISunfold() return, current seed 1234
- -01: dt=0.0000, 191 negative triangles
- 265: dt=0.9900, 191 negative triangles
- 266: dt=0.9900, 111 negative triangles
- 267: dt=0.9900, 91 negative triangles
- 268: dt=0.9900, 64 negative triangles
- 269: dt=0.9900, 65 negative triangles
- 270: dt=0.9900, 62 negative triangles
- 271: dt=0.9900, 44 negative triangles
- 272: dt=0.9900, 39 negative triangles
- 273: dt=0.9900, 35 negative triangles
- 274: dt=0.9900, 22 negative triangles
- 275: dt=0.9900, 19 negative triangles
- 276: dt=0.9900, 20 negative triangles
- 277: dt=0.9900, 22 negative triangles
- 278: dt=0.9900, 16 negative triangles
- 279: dt=0.9900, 16 negative triangles
- 280: dt=0.9900, 16 negative triangles
- 281: dt=0.9900, 13 negative triangles
- 282: dt=0.9900, 14 negative triangles
- 283: dt=0.9900, 8 negative triangles
- 284: dt=0.9900, 6 negative triangles
- 285: dt=0.9900, 10 negative triangles
- 286: dt=0.9900, 5 negative triangles
- 287: dt=0.9900, 3 negative triangles
- 288: dt=0.9900, 2 negative triangles
- 289: dt=0.9900, 2 negative triangles
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 1.31 hours
- mris_sphere utimesec 4711.910680
- mris_sphere stimesec 1.819723
- mris_sphere ru_maxrss 328888
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 57908
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 11296
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 171646
- mris_sphere ru_nivcsw 378217
- FSRUNTIME@ mris_sphere 1.3070 hours 1 threads
- mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0.274...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %20.19
- pass 1: epoch 2 of 3 starting distance error %20.07
- unfolding complete - removing small folds...
- starting distance error %19.89
- removing remaining folds...
- final distance error %19.92
- MRISunfold() return, current seed 1234
- -01: dt=0.0000, 389 negative triangles
- 249: dt=0.9900, 389 negative triangles
- 250: dt=0.9900, 203 negative triangles
- 251: dt=0.9900, 157 negative triangles
- 252: dt=0.9900, 145 negative triangles
- 253: dt=0.9900, 141 negative triangles
- 254: dt=0.9900, 128 negative triangles
- 255: dt=0.9900, 133 negative triangles
- 256: dt=0.9900, 116 negative triangles
- 257: dt=0.9900, 112 negative triangles
- 258: dt=0.9900, 104 negative triangles
- 259: dt=0.9900, 105 negative triangles
- 260: dt=0.9900, 100 negative triangles
- 261: dt=0.9900, 97 negative triangles
- 262: dt=0.9900, 89 negative triangles
- 263: dt=0.9900, 82 negative triangles
- 264: dt=0.9900, 70 negative triangles
- 265: dt=0.9900, 74 negative triangles
- 266: dt=0.9900, 67 negative triangles
- 267: dt=0.9900, 62 negative triangles
- 268: dt=0.9900, 53 negative triangles
- 269: dt=0.9900, 57 negative triangles
- 270: dt=0.9900, 45 negative triangles
- 271: dt=0.9900, 40 negative triangles
- 272: dt=0.9900, 42 negative triangles
- 273: dt=0.9900, 35 negative triangles
- 274: dt=0.9900, 28 negative triangles
- 275: dt=0.9900, 23 negative triangles
- 276: dt=0.9900, 19 negative triangles
- 277: dt=0.9900, 18 negative triangles
- 278: dt=0.9900, 11 negative triangles
- 279: dt=0.9900, 8 negative triangles
- 280: dt=0.9900, 9 negative triangles
- 281: dt=0.9900, 7 negative triangles
- 282: dt=0.9900, 6 negative triangles
- 283: dt=0.9900, 3 negative triangles
- 284: dt=0.9900, 3 negative triangles
- 285: dt=0.9900, 7 negative triangles
- 286: dt=0.9900, 7 negative triangles
- 287: dt=0.9900, 1 negative triangles
- 288: dt=0.9900, 2 negative triangles
- 289: dt=0.9900, 5 negative triangles
- 290: dt=0.9900, 2 negative triangles
- 291: dt=0.9900, 1 negative triangles
- 292: dt=0.9900, 2 negative triangles
- 293: dt=0.9900, 1 negative triangles
- 294: dt=0.9900, 1 negative triangles
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 1.30 hours
- mris_sphere utimesec 4694.641306
- mris_sphere stimesec 1.756732
- mris_sphere ru_maxrss 339468
- mris_sphere ru_ixrss 0
- mris_sphere ru_idrss 0
- mris_sphere ru_isrss 0
- mris_sphere ru_minflt 59532
- mris_sphere ru_majflt 0
- mris_sphere ru_nswap 0
- mris_sphere ru_inblock 0
- mris_sphere ru_oublock 11680
- mris_sphere ru_msgsnd 0
- mris_sphere ru_msgrcv 0
- mris_sphere ru_nsignals 0
- mris_sphere ru_nvcsw 166518
- mris_sphere ru_nivcsw 377580
- FSRUNTIME@ mris_sphere 1.3044 hours 1 threads
- PIDs (26628 26631) completed and logs appended.
- #--------------------------------------------
- #@# Surf Reg lh Sun Oct 8 09:21:33 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 Sun Oct 8 09:21:33 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 29352 of (29352 29355) to complete...
- Waiting for PID 29355 of (29352 29355) to complete...
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/scripts
- cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 5.778
- curvature mean = 0.029, std = 0.820
- curvature mean = 0.017, std = 0.856
- Starting MRISrigidBodyAlignGlobal()
- d=32.00 min @ (0.00, 0.00, 8.00) sse = 345354.8, tmin=2.4124
- d=16.00 min @ (-4.00, -4.00, 0.00) sse = 325031.6, tmin=3.6389
- d=8.00 min @ (2.00, 0.00, -2.00) sse = 319974.4, tmin=4.8967
- d=4.00 min @ (-1.00, 0.00, 0.00) sse = 319718.5, tmin=6.1683
- d=2.00 min @ (0.50, 0.50, 0.50) sse = 319282.7, tmin=7.4417
- d=1.00 min @ (0.00, -0.25, 0.00) sse = 319194.3, tmin=8.6926
- 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 9.93 min
- curvature mean = -0.013, std = 0.823
- curvature mean = 0.005, std = 0.942
- curvature mean = -0.021, std = 0.831
- curvature mean = 0.002, std = 0.976
- curvature mean = -0.025, std = 0.831
- curvature mean = 0.000, std = 0.989
- 2 Reading smoothwm
- curvature mean = -0.035, std = 0.298
- curvature mean = 0.034, std = 0.244
- curvature mean = 0.069, std = 0.325
- curvature mean = 0.031, std = 0.301
- curvature mean = 0.053, std = 0.493
- curvature mean = 0.030, std = 0.325
- curvature mean = 0.032, std = 0.636
- curvature mean = 0.030, std = 0.336
- curvature mean = 0.013, std = 0.751
- MRISregister() return, current seed 0
- -01: dt=0.0000, 162 negative triangles
- 139: dt=0.9900, 162 negative triangles
- 140: dt=0.9405, 207 negative triangles
- expanding nbhd size to 1
- 141: dt=0.9900, 179 negative triangles
- 142: dt=0.9900, 145 negative triangles
- 143: dt=0.9900, 142 negative triangles
- 144: dt=0.9900, 143 negative triangles
- 145: dt=0.9900, 133 negative triangles
- 146: dt=0.9900, 130 negative triangles
- 147: dt=0.9900, 116 negative triangles
- 148: dt=0.9900, 127 negative triangles
- 149: dt=0.9900, 116 negative triangles
- 150: dt=0.9900, 108 negative triangles
- 151: dt=0.9900, 106 negative triangles
- 152: dt=0.9900, 102 negative triangles
- 153: dt=0.9900, 100 negative triangles
- 154: dt=0.9900, 95 negative triangles
- 155: dt=0.9900, 88 negative triangles
- 156: dt=0.9900, 83 negative triangles
- 157: dt=0.9900, 85 negative triangles
- 158: dt=0.9900, 74 negative triangles
- 159: dt=0.9900, 72 negative triangles
- 160: dt=0.9900, 75 negative triangles
- 161: dt=0.9900, 69 negative triangles
- 162: dt=0.9900, 62 negative triangles
- 163: dt=0.9900, 53 negative triangles
- 164: dt=0.9900, 57 negative triangles
- 165: dt=0.9900, 52 negative triangles
- 166: dt=0.9900, 47 negative triangles
- 167: dt=0.9900, 47 negative triangles
- 168: dt=0.9900, 44 negative triangles
- 169: dt=0.9900, 47 negative triangles
- 170: dt=0.9900, 43 negative triangles
- 171: dt=0.9900, 41 negative triangles
- 172: dt=0.9900, 40 negative triangles
- 173: dt=0.9900, 38 negative triangles
- 174: dt=0.9900, 35 negative triangles
- 175: dt=0.9900, 35 negative triangles
- 176: dt=0.9900, 28 negative triangles
- 177: dt=0.9900, 26 negative triangles
- 178: dt=0.9900, 17 negative triangles
- 179: dt=0.9900, 22 negative triangles
- 180: dt=0.9900, 22 negative triangles
- 181: dt=0.9900, 19 negative triangles
- 182: dt=0.9900, 16 negative triangles
- 183: dt=0.9900, 15 negative triangles
- 184: dt=0.9900, 13 negative triangles
- 185: dt=0.9900, 14 negative triangles
- 186: dt=0.9900, 12 negative triangles
- 187: dt=0.9900, 13 negative triangles
- 188: dt=0.9900, 9 negative triangles
- 189: dt=0.9900, 14 negative triangles
- 190: dt=0.9900, 11 negative triangles
- 191: dt=0.9900, 10 negative triangles
- 192: dt=0.9900, 10 negative triangles
- 193: dt=0.9900, 13 negative triangles
- 194: dt=0.9900, 8 negative triangles
- 195: dt=0.9900, 7 negative triangles
- 196: dt=0.9900, 6 negative triangles
- 197: dt=0.9900, 2 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, 3 negative triangles
- 202: dt=0.9900, 2 negative triangles
- 203: dt=0.9900, 1 negative triangles
- 204: dt=0.9900, 2 negative triangles
- writing registered surface to ../surf/lh.sphere.reg...
- registration took 1.77 hours
- mris_register utimesec 6351.960355
- mris_register stimesec 5.284196
- mris_register ru_maxrss 289340
- mris_register ru_ixrss 0
- mris_register ru_idrss 0
- mris_register ru_isrss 0
- mris_register ru_minflt 41427
- mris_register ru_majflt 0
- mris_register ru_nswap 0
- mris_register ru_inblock 0
- mris_register ru_oublock 11344
- mris_register ru_msgsnd 0
- mris_register ru_msgrcv 0
- mris_register ru_nsignals 0
- mris_register ru_nvcsw 459768
- mris_register ru_nivcsw 292004
- FSRUNTIME@ mris_register 1.7656 hours 1 threads
- mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/scripts
- cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 5.765
- curvature mean = 0.022, std = 0.803
- curvature mean = 0.020, std = 0.854
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, 0.00, 16.00) sse = 377729.0, tmin=1.2466
- d=16.00 min @ (0.00, -4.00, 0.00) sse = 355968.7, tmin=3.7840
- d=8.00 min @ (-2.00, 0.00, 0.00) sse = 355588.5, tmin=5.0671
- d=4.00 min @ (1.00, 0.00, 0.00) sse = 354644.7, tmin=6.3627
- d=2.00 min @ (0.00, 0.50, -0.50) sse = 354321.5, tmin=7.6612
- d=1.00 min @ (0.00, 0.00, 0.25) sse = 354289.4, tmin=8.9429
- d=0.50 min @ (0.00, -0.12, 0.00) sse = 354264.6, tmin=10.2319
- 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 10.23 min
- curvature mean = -0.014, std = 0.806
- curvature mean = 0.005, std = 0.942
- curvature mean = -0.021, std = 0.813
- curvature mean = 0.002, std = 0.975
- curvature mean = -0.024, std = 0.813
- curvature mean = 0.000, std = 0.989
- 2 Reading smoothwm
- curvature mean = -0.041, std = 0.359
- curvature mean = 0.029, std = 0.239
- curvature mean = 0.068, std = 0.269
- curvature mean = 0.021, std = 0.297
- curvature mean = 0.053, std = 0.406
- curvature mean = 0.020, std = 0.324
- curvature mean = 0.035, std = 0.525
- curvature mean = 0.019, std = 0.335
- curvature mean = 0.016, std = 0.632
- MRISregister() return, current seed 0
- -01: dt=0.0000, 362 negative triangles
- 137: dt=0.9900, 362 negative triangles
- expanding nbhd size to 1
- 138: dt=0.9900, 391 negative triangles
- 139: dt=0.9900, 351 negative triangles
- 140: dt=0.9900, 323 negative triangles
- 141: dt=0.9900, 325 negative triangles
- 142: dt=0.9900, 323 negative triangles
- 143: dt=0.9900, 301 negative triangles
- 144: dt=0.9900, 287 negative triangles
- 145: dt=0.9900, 275 negative triangles
- 146: dt=0.9900, 254 negative triangles
- 147: dt=0.9900, 243 negative triangles
- 148: dt=0.9900, 224 negative triangles
- 149: dt=0.9900, 218 negative triangles
- 150: dt=0.9900, 208 negative triangles
- 151: dt=0.9900, 200 negative triangles
- 152: dt=0.9900, 182 negative triangles
- 153: dt=0.9900, 184 negative triangles
- 154: dt=0.9900, 172 negative triangles
- 155: dt=0.9900, 168 negative triangles
- 156: dt=0.9900, 157 negative triangles
- 157: dt=0.9900, 142 negative triangles
- 158: dt=0.9900, 142 negative triangles
- 159: dt=0.9900, 142 negative triangles
- 160: dt=0.9900, 122 negative triangles
- 161: dt=0.9900, 114 negative triangles
- 162: dt=0.9900, 106 negative triangles
- 163: dt=0.9900, 101 negative triangles
- 164: dt=0.9900, 98 negative triangles
- 165: dt=0.9900, 91 negative triangles
- 166: dt=0.9900, 86 negative triangles
- 167: dt=0.9900, 78 negative triangles
- 168: dt=0.9900, 78 negative triangles
- 169: dt=0.9900, 71 negative triangles
- 170: dt=0.9900, 73 negative triangles
- 171: dt=0.9900, 61 negative triangles
- 172: dt=0.9900, 67 negative triangles
- 173: dt=0.9900, 64 negative triangles
- 174: dt=0.9900, 57 negative triangles
- 175: dt=0.9900, 54 negative triangles
- 176: dt=0.9900, 57 negative triangles
- 177: dt=0.9900, 51 negative triangles
- 178: dt=0.9900, 55 negative triangles
- 179: dt=0.9900, 49 negative triangles
- 180: dt=0.9900, 51 negative triangles
- 181: dt=0.9900, 46 negative triangles
- 182: dt=0.9900, 42 negative triangles
- 183: dt=0.9900, 46 negative triangles
- 184: dt=0.9900, 45 negative triangles
- 185: dt=0.9900, 46 negative triangles
- 186: dt=0.9900, 42 negative triangles
- 187: dt=0.9900, 39 negative triangles
- 188: dt=0.9900, 38 negative triangles
- 189: dt=0.9900, 38 negative triangles
- 190: dt=0.9900, 36 negative triangles
- 191: dt=0.9900, 35 negative triangles
- 192: dt=0.9900, 34 negative triangles
- 193: dt=0.9900, 32 negative triangles
- 194: dt=0.9900, 33 negative triangles
- 195: dt=0.9900, 32 negative triangles
- 196: dt=0.9900, 31 negative triangles
- 197: dt=0.9900, 31 negative triangles
- 198: dt=0.9900, 34 negative triangles
- 199: dt=0.9900, 33 negative triangles
- 200: dt=0.9900, 31 negative triangles
- 201: dt=0.9900, 30 negative triangles
- 202: dt=0.9900, 30 negative triangles
- 203: dt=0.9900, 30 negative triangles
- 204: dt=0.9900, 30 negative triangles
- 205: dt=0.9900, 29 negative triangles
- 206: dt=0.9900, 28 negative triangles
- 207: dt=0.9900, 27 negative triangles
- 208: dt=0.9900, 28 negative triangles
- 209: dt=0.9900, 28 negative triangles
- 210: dt=0.9900, 28 negative triangles
- 211: dt=0.9900, 26 negative triangles
- 212: dt=0.9900, 26 negative triangles
- 213: dt=0.9900, 26 negative triangles
- 214: dt=0.9900, 25 negative triangles
- 215: dt=0.9900, 25 negative triangles
- 216: dt=0.9900, 25 negative triangles
- 217: dt=0.9900, 27 negative triangles
- 218: dt=0.9900, 27 negative triangles
- 219: dt=0.9900, 26 negative triangles
- 220: dt=0.9900, 25 negative triangles
- 221: dt=0.9900, 25 negative triangles
- 222: dt=0.9900, 26 negative triangles
- 223: dt=0.9900, 26 negative triangles
- 224: dt=0.9405, 27 negative triangles
- 225: dt=0.9405, 24 negative triangles
- 226: dt=0.9405, 24 negative triangles
- 227: dt=0.9405, 25 negative triangles
- 228: dt=0.9405, 23 negative triangles
- 229: dt=0.9405, 23 negative triangles
- 230: dt=0.9405, 23 negative triangles
- 231: dt=0.9405, 21 negative triangles
- 232: dt=0.9405, 21 negative triangles
- 233: dt=0.9405, 21 negative triangles
- 234: dt=0.9405, 23 negative triangles
- 235: dt=0.9405, 21 negative triangles
- 236: dt=0.9405, 21 negative triangles
- 237: dt=0.9405, 22 negative triangles
- 238: dt=0.9405, 21 negative triangles
- 239: dt=0.9405, 21 negative triangles
- 240: dt=0.9405, 19 negative triangles
- 241: dt=0.9405, 20 negative triangles
- 242: dt=0.9405, 21 negative triangles
- 243: dt=0.9405, 21 negative triangles
- 244: dt=0.9405, 20 negative triangles
- 245: dt=0.9405, 19 negative triangles
- 246: dt=0.9405, 19 negative triangles
- 247: dt=0.9405, 20 negative triangles
- 248: dt=0.9405, 22 negative triangles
- 249: dt=0.9405, 19 negative triangles
- 250: dt=0.8935, 19 negative triangles
- 251: dt=0.8935, 21 negative triangles
- 252: dt=0.8935, 22 negative triangles
- 253: dt=0.8935, 19 negative triangles
- 254: dt=0.8935, 19 negative triangles
- 255: dt=0.8935, 17 negative triangles
- 256: dt=0.8935, 21 negative triangles
- 257: dt=0.8935, 20 negative triangles
- 258: dt=0.8935, 20 negative triangles
- 259: dt=0.8935, 17 negative triangles
- 260: dt=0.8935, 15 negative triangles
- 261: dt=0.8935, 15 negative triangles
- 262: dt=0.8935, 15 negative triangles
- 263: dt=0.8935, 16 negative triangles
- 264: dt=0.8935, 16 negative triangles
- 265: dt=0.8935, 16 negative triangles
- 266: dt=0.8935, 15 negative triangles
- 267: dt=0.8935, 16 negative triangles
- 268: dt=0.8935, 15 negative triangles
- 269: dt=0.8935, 15 negative triangles
- 270: dt=0.8488, 15 negative triangles
- 271: dt=0.8488, 16 negative triangles
- 272: dt=0.8488, 15 negative triangles
- 273: dt=0.8488, 15 negative triangles
- 274: dt=0.8488, 15 negative triangles
- 275: dt=0.8488, 15 negative triangles
- 276: dt=0.8488, 14 negative triangles
- 277: dt=0.8488, 14 negative triangles
- 278: dt=0.8488, 14 negative triangles
- 279: dt=0.8488, 15 negative triangles
- 280: dt=0.8488, 14 negative triangles
- 281: dt=0.8488, 13 negative triangles
- 282: dt=0.8488, 13 negative triangles
- 283: dt=0.8488, 14 negative triangles
- 284: dt=0.8488, 14 negative triangles
- 285: dt=0.8488, 13 negative triangles
- 286: dt=0.8488, 12 negative triangles
- 287: dt=0.8488, 13 negative triangles
- 288: dt=0.8488, 13 negative triangles
- 289: dt=0.8488, 12 negative triangles
- 290: dt=0.8488, 10 negative triangles
- 291: dt=0.8488, 10 negative triangles
- 292: dt=0.8488, 12 negative triangles
- 293: dt=0.8488, 10 negative triangles
- 294: dt=0.8488, 10 negative triangles
- 295: dt=0.8488, 9 negative triangles
- 296: dt=0.8488, 10 negative triangles
- 297: dt=0.8488, 10 negative triangles
- 298: dt=0.8488, 9 negative triangles
- 299: dt=0.8488, 10 negative triangles
- 300: dt=0.8488, 9 negative triangles
- 301: dt=0.8488, 9 negative triangles
- 302: dt=0.8488, 9 negative triangles
- 303: dt=0.8488, 9 negative triangles
- 304: dt=0.8488, 8 negative triangles
- 305: dt=0.8488, 8 negative triangles
- 306: dt=0.8488, 6 negative triangles
- 307: dt=0.8488, 6 negative triangles
- 308: dt=0.8488, 8 negative triangles
- 309: dt=0.8488, 5 negative triangles
- 310: dt=0.8488, 5 negative triangles
- 311: dt=0.8488, 5 negative triangles
- 312: dt=0.8488, 5 negative triangles
- 313: dt=0.8488, 6 negative triangles
- 314: dt=0.8488, 6 negative triangles
- 315: dt=0.8488, 5 negative triangles
- 316: dt=0.8488, 3 negative triangles
- 317: dt=0.8488, 3 negative triangles
- 318: dt=0.8488, 3 negative triangles
- 319: dt=0.8488, 2 negative triangles
- 320: dt=0.8488, 2 negative triangles
- 321: dt=0.8488, 2 negative triangles
- 322: dt=0.8488, 1 negative triangles
- 323: dt=0.8488, 1 negative triangles
- writing registered surface to ../surf/rh.sphere.reg...
- registration took 1.85 hours
- mris_register utimesec 6859.043266
- mris_register stimesec 5.310192
- mris_register ru_maxrss 296560
- mris_register ru_ixrss 0
- mris_register ru_idrss 0
- mris_register ru_isrss 0
- mris_register ru_minflt 41995
- mris_register ru_majflt 0
- mris_register ru_nswap 0
- mris_register ru_inblock 0
- mris_register ru_oublock 11736
- mris_register ru_msgsnd 0
- mris_register ru_msgrcv 0
- mris_register ru_nsignals 0
- mris_register ru_nvcsw 470326
- mris_register ru_nivcsw 283907
- FSRUNTIME@ mris_register 1.8520 hours 1 threads
- PIDs (29352 29355) completed and logs appended.
- #--------------------------------------------
- #@# Jacobian white lh Sun Oct 8 11:12:40 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white
- #--------------------------------------------
- #@# Jacobian white rh Sun Oct 8 11:12:40 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white
- Waiting for PID 1039 of (1039 1042) to complete...
- Waiting for PID 1042 of (1039 1042) 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 (1039 1042) completed and logs appended.
- #--------------------------------------------
- #@# AvgCurv lh Sun Oct 8 11:12:43 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 11:12:43 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 1084 of (1084 1087) to complete...
- Waiting for PID 1087 of (1084 1087) 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 (1084 1087) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc lh Sun Oct 8 11:12:45 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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 11:12:45 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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 1131 of (1131 1134) to complete...
- Waiting for PID 1134 of (1131 1134) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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...
- 1134 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3637 changed, 159921 examined...
- 001: 846 changed, 14944 examined...
- 002: 206 changed, 4666 examined...
- 003: 66 changed, 1266 examined...
- 004: 26 changed, 377 examined...
- 005: 14 changed, 160 examined...
- 006: 4 changed, 68 examined...
- 007: 4 changed, 28 examined...
- 008: 2 changed, 17 examined...
- 009: 5 changed, 14 examined...
- 010: 0 changed, 16 examined...
- 254 labels changed using aseg
- 000: 136 total segments, 88 labels (376 vertices) changed
- 001: 48 total segments, 3 labels (6 vertices) changed
- 002: 45 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 6 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 2165 vertices marked for relabeling...
- 2165 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 0 minutes and 16 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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...
- 1295 labels changed using aseg
- relabeling using gibbs priors...
- 000: 3003 changed, 165183 examined...
- 001: 719 changed, 12988 examined...
- 002: 183 changed, 4005 examined...
- 003: 58 changed, 1085 examined...
- 004: 27 changed, 371 examined...
- 005: 6 changed, 160 examined...
- 006: 2 changed, 35 examined...
- 007: 1 changed, 14 examined...
- 008: 1 changed, 7 examined...
- 009: 1 changed, 7 examined...
- 010: 1 changed, 7 examined...
- 011: 1 changed, 7 examined...
- 012: 0 changed, 7 examined...
- 169 labels changed using aseg
- 000: 104 total segments, 66 labels (298 vertices) changed
- 001: 38 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 6 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 2155 vertices marked for relabeling...
- 2155 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 0 minutes and 16 seconds.
- PIDs (1131 1134) completed and logs appended.
- #--------------------------------------------
- #@# Make Pial Surf lh Sun Oct 8 11:13:01 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050352 lh
- #--------------------------------------------
- #@# Make Pial Surf rh Sun Oct 8 11:13:01 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050352 rh
- Waiting for PID 1182 of (1182 1185) to complete...
- Waiting for PID 1185 of (1182 1185) to complete...
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050352 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-6.0.0/0050352/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
- 17660 bright wm thresholded.
- 2039 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.orig...
- computing class statistics...
- border white: 320647 voxels (1.91%)
- border gray 377071 voxels (2.25%)
- WM (94.0): 95.4 +- 7.8 [70.0 --> 110.0]
- GM (73.0) : 71.7 +- 10.6 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 58.4 (was 70)
- setting MAX_BORDER_WHITE to 106.8 (was 105)
- setting MIN_BORDER_WHITE to 69.0 (was 85)
- setting MAX_CSF to 47.9 (was 40)
- setting MAX_GRAY to 91.2 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 58.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 37.3 (was 40)
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=99+-6.1, GM=69+-7.0
- mean inside = 91.5, mean outside = 75.7
- 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 0.90 +- 0.27 (0.03-->7.14) (max @ vno 56130 --> 60727)
- face area 0.34 +- 0.18 (0.00-->13.14)
- mean absolute distance = 0.53 +- 0.83
- 4140 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 20 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- deleting segment 2 with 120 points - only 0.00% unknown
- deleting segment 4 with 90 points - only 0.00% unknown
- deleting segment 6 with 225 points - only 0.00% unknown
- deleting segment 8 with 35 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 10 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 11 with 1 points - only 0.00% unknown
- deleting segment 12 with 5 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 13 with 1 points - only 0.00% unknown
- deleting segment 14 with 123 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- mean border=81.0, 275 (275) missing vertices, mean dist 0.3 [0.6 (%22.9)->0.5 (%77.1))]
- %69 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 0
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.91 +- 0.27 (0.07-->6.86) (max @ vno 54871 --> 65504)
- face area 0.34 +- 0.18 (0.00-->12.46)
- mean absolute distance = 0.37 +- 0.65
- 4881 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1860433.5, rms=5.948
- 001: dt: 0.5000, sse=1218953.2, rms=3.797 (36.168%)
- 002: dt: 0.5000, sse=1052613.9, rms=3.018 (20.523%)
- 003: dt: 0.5000, sse=1023272.9, rms=2.873 (4.800%)
- 004: dt: 0.5000, sse=1011710.2, rms=2.778 (3.287%)
- rms = 2.85, time step reduction 1 of 3 to 0.250...
- 005: dt: 0.2500, sse=915516.4, rms=2.138 (23.035%)
- 006: dt: 0.2500, sse=882689.1, rms=1.827 (14.571%)
- 007: dt: 0.2500, sse=874442.1, rms=1.755 (3.953%)
- rms = 1.73, time step reduction 2 of 3 to 0.125...
- 008: dt: 0.2500, sse=872185.0, rms=1.732 (1.310%)
- rms = 1.70, time step reduction 3 of 3 to 0.062...
- 009: dt: 0.1250, sse=868741.6, rms=1.696 (2.044%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 17 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- deleting segment 2 with 112 points - only 0.00% unknown
- deleting segment 3 with 72 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 4 with 3 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 5 with 3 points - only 0.00% unknown
- deleting segment 6 with 74 points - only 0.00% unknown
- deleting segment 7 with 35 points - only 0.00% unknown
- deleting segment 8 with 37 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 9 with 3 points - only 0.00% unknown
- deleting segment 10 with 107 points - only 0.00% unknown
- mean border=83.1, 215 (105) missing vertices, mean dist -0.2 [0.4 (%63.9)->0.3 (%36.1))]
- %76 local maxima, %20 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 +- 0.27 (0.05-->7.03) (max @ vno 54871 --> 65504)
- face area 0.35 +- 0.19 (0.00-->13.62)
- mean absolute distance = 0.32 +- 0.49
- 5031 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1197210.9, rms=3.535
- 010: dt: 0.5000, sse=1002927.2, rms=2.429 (31.283%)
- 011: dt: 0.5000, sse=980718.8, rms=2.327 (4.183%)
- rms = 2.44, time step reduction 1 of 3 to 0.250...
- 012: dt: 0.2500, sse=913009.9, rms=1.804 (22.480%)
- 013: dt: 0.2500, sse=891020.9, rms=1.545 (14.373%)
- rms = 1.51, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=888721.8, rms=1.513 (2.045%)
- rms = 1.48, time step reduction 3 of 3 to 0.062...
- 015: dt: 0.1250, sse=882428.0, rms=1.483 (2.027%)
- positioning took 0.8 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 17 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- deleting segment 2 with 115 points - only 0.00% unknown
- deleting segment 3 with 73 points - only 0.00% unknown
- deleting segment 4 with 6 points - only 0.00% unknown
- deleting segment 5 with 166 points - only 0.00% unknown
- deleting segment 6 with 43 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- deleting segment 8 with 40 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 1 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 10 with 4 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 11 with 1 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 12 with 1 points - only 0.00% unknown
- deleting segment 13 with 105 points - only 0.00% unknown
- mean border=84.4, 236 (77) missing vertices, mean dist -0.1 [0.4 (%59.0)->0.2 (%41.0))]
- %81 local maxima, %15 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 0.90 +- 0.27 (0.04-->7.03) (max @ vno 54871 --> 65504)
- face area 0.34 +- 0.18 (0.00-->13.46)
- mean absolute distance = 0.31 +- 0.43
- 4151 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=983497.1, rms=2.471
- 016: dt: 0.5000, sse=943433.1, rms=2.062 (16.528%)
- rms = 2.14, time step reduction 1 of 3 to 0.250...
- 017: dt: 0.2500, sse=885016.3, rms=1.647 (20.141%)
- 018: dt: 0.2500, sse=890783.4, rms=1.461 (11.320%)
- rms = 1.41, time step reduction 2 of 3 to 0.125...
- 019: dt: 0.2500, sse=860965.7, rms=1.412 (3.306%)
- rms = 1.37, time step reduction 3 of 3 to 0.062...
- 020: dt: 0.1250, sse=854889.4, rms=1.375 (2.666%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 17 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 1 with 4 points - only 0.00% unknown
- deleting segment 2 with 119 points - only 0.00% unknown
- deleting segment 3 with 74 points - only 0.00% unknown
- deleting segment 4 with 9 points - only 0.00% unknown
- deleting segment 5 with 172 points - only 0.00% unknown
- deleting segment 6 with 43 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 2 points - only 0.00% unknown
- deleting segment 8 with 40 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 9 with 1 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 10 with 4 points - only 0.00% unknown
- deleting segment 11 with 5 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 12 with 1 points - only 0.00% unknown
- deleting segment 13 with 108 points - only 0.00% unknown
- mean border=85.0, 247 (64) missing vertices, mean dist -0.1 [0.3 (%52.7)->0.3 (%47.3))]
- %84 local maxima, %11 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-6.0.0/0050352/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=882570.6, rms=1.744
- 021: dt: 0.5000, sse=875049.6, rms=1.582 (9.302%)
- rms = 1.90, time step reduction 1 of 3 to 0.250...
- 022: dt: 0.2500, sse=836627.6, rms=1.242 (21.473%)
- 023: dt: 0.2500, sse=837364.1, rms=1.192 (4.035%)
- rms = 1.15, time step reduction 2 of 3 to 0.125...
- 024: dt: 0.2500, sse=827933.8, rms=1.146 (3.908%)
- rms = 1.10, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=823017.5, rms=1.099 (4.073%)
- positioning took 0.7 minutes
- generating cortex label...
- 9 non-cortical segments detected
- only using segment with 8702 vertices
- erasing segment 1 (vno[0] = 97732)
- erasing segment 2 (vno[0] = 102244)
- erasing segment 3 (vno[0] = 104586)
- erasing segment 4 (vno[0] = 107961)
- erasing segment 5 (vno[0] = 110172)
- erasing segment 6 (vno[0] = 111346)
- erasing segment 7 (vno[0] = 112461)
- erasing segment 8 (vno[0] = 112487)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.area
- vertex spacing 0.90 +- 0.27 (0.05-->6.97) (max @ vno 98357 --> 157869)
- face area 0.34 +- 0.18 (0.00-->13.04)
- 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 80 points - only 0.00% unknown
- deleting segment 1 with 13 points - only 0.00% unknown
- deleting segment 3 with 36 points - only 0.00% unknown
- deleting segment 5 with 20 points - only 0.00% unknown
- deleting segment 6 with 22 points - only 0.00% unknown
- deleting segment 7 with 25 points - only 0.00% unknown
- deleting segment 8 with 12 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 12 with 2 points - only 50.00% unknown
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from white.preaparc...
- mean border=57.5, 264 (264) missing vertices, mean dist 1.6 [1.1 (%0.0)->2.9 (%100.0))]
- %13 local maxima, %37 large gradients and %45 min vals, 692 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=25308272.0, rms=28.348
- 001: dt: 0.0500, sse=22638340.0, rms=26.761 (5.598%)
- 002: dt: 0.0500, sse=20707266.0, rms=25.552 (4.519%)
- 003: dt: 0.0500, sse=19205946.0, rms=24.570 (3.841%)
- 004: dt: 0.0500, sse=17974636.0, rms=23.735 (3.400%)
- 005: dt: 0.0500, sse=16924140.0, rms=22.998 (3.104%)
- 006: dt: 0.0500, sse=16002985.0, rms=22.332 (2.897%)
- 007: dt: 0.0500, sse=15178845.0, rms=21.719 (2.747%)
- 008: dt: 0.0500, sse=14430951.0, rms=21.146 (2.634%)
- 009: dt: 0.0500, sse=13743778.0, rms=20.607 (2.552%)
- 010: dt: 0.0500, sse=13108337.0, rms=20.095 (2.485%)
- positioning took 1.1 minutes
- mean border=57.3, 235 (154) missing vertices, mean dist 1.3 [0.5 (%0.0)->2.4 (%100.0))]
- %14 local maxima, %38 large gradients and %44 min vals, 633 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=14032075.0, rms=20.834
- 011: dt: 0.0500, sse=13433637.0, rms=20.358 (2.286%)
- 012: dt: 0.0500, sse=12874301.0, rms=19.902 (2.237%)
- 013: dt: 0.0500, sse=12349945.0, rms=19.465 (2.194%)
- 014: dt: 0.0500, sse=11857777.0, rms=19.046 (2.153%)
- 015: dt: 0.0500, sse=11395210.0, rms=18.644 (2.114%)
- 016: dt: 0.0500, sse=10960952.0, rms=18.258 (2.071%)
- 017: dt: 0.0500, sse=10553168.0, rms=17.887 (2.028%)
- 018: dt: 0.0500, sse=10170341.0, rms=17.533 (1.983%)
- 019: dt: 0.0500, sse=9810546.0, rms=17.192 (1.940%)
- 020: dt: 0.0500, sse=9472828.0, rms=16.867 (1.894%)
- positioning took 1.1 minutes
- mean border=57.2, 268 (119) missing vertices, mean dist 1.1 [0.1 (%1.4)->2.1 (%98.6))]
- %14 local maxima, %37 large gradients and %44 min vals, 602 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=9571632.0, rms=16.968
- 021: dt: 0.0500, sse=9245767.0, rms=16.649 (1.876%)
- 022: dt: 0.0500, sse=8940497.0, rms=16.345 (1.825%)
- 023: dt: 0.0500, sse=8652347.0, rms=16.053 (1.788%)
- 024: dt: 0.0500, sse=8382553.0, rms=15.775 (1.736%)
- 025: dt: 0.0500, sse=8129841.0, rms=15.509 (1.684%)
- 026: dt: 0.0500, sse=7892888.5, rms=15.256 (1.634%)
- 027: dt: 0.0500, sse=7669313.0, rms=15.012 (1.593%)
- 028: dt: 0.0500, sse=7456474.5, rms=14.777 (1.567%)
- 029: dt: 0.0500, sse=7253870.0, rms=14.550 (1.540%)
- 030: dt: 0.0500, sse=7061353.5, rms=14.330 (1.510%)
- positioning took 1.1 minutes
- mean border=57.2, 321 (99) missing vertices, mean dist 0.9 [0.1 (%11.0)->2.0 (%89.0))]
- %14 local maxima, %38 large gradients and %43 min vals, 601 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=7135658.5, rms=14.414
- 031: dt: 0.5000, sse=5781775.5, rms=12.777 (11.363%)
- 032: dt: 0.5000, sse=4890548.0, rms=11.564 (9.492%)
- 033: dt: 0.5000, sse=4245457.0, rms=10.601 (8.326%)
- 034: dt: 0.5000, sse=3765931.5, rms=9.817 (7.399%)
- 035: dt: 0.5000, sse=3374981.5, rms=9.130 (6.990%)
- 036: dt: 0.5000, sse=3036233.5, rms=8.488 (7.037%)
- 037: dt: 0.5000, sse=2733787.8, rms=7.875 (7.215%)
- 038: dt: 0.5000, sse=2472625.8, rms=7.302 (7.282%)
- 039: dt: 0.5000, sse=2252052.8, rms=6.785 (7.081%)
- 040: dt: 0.5000, sse=2083718.1, rms=6.357 (6.304%)
- 041: dt: 0.5000, sse=1957419.4, rms=6.021 (5.295%)
- 042: dt: 0.5000, sse=1878639.0, rms=5.796 (3.725%)
- 043: dt: 0.5000, sse=1823120.5, rms=5.637 (2.754%)
- 044: dt: 0.5000, sse=1789904.5, rms=5.535 (1.812%)
- 045: dt: 0.5000, sse=1765039.5, rms=5.461 (1.326%)
- rms = 5.42, time step reduction 1 of 3 to 0.250...
- 046: dt: 0.5000, sse=1753900.0, rms=5.424 (0.681%)
- 047: dt: 0.2500, sse=1666929.5, rms=5.114 (5.721%)
- 048: dt: 0.2500, sse=1642357.4, rms=5.032 (1.600%)
- rms = 5.03, time step reduction 2 of 3 to 0.125...
- 049: dt: 0.2500, sse=1641327.5, rms=5.026 (0.112%)
- 050: dt: 0.1250, sse=1623718.8, rms=4.963 (1.264%)
- rms = 4.95, time step reduction 3 of 3 to 0.062...
- 051: dt: 0.1250, sse=1620277.9, rms=4.951 (0.233%)
- positioning took 3.2 minutes
- mean border=56.3, 3115 (28) missing vertices, mean dist 0.2 [0.2 (%47.8)->0.7 (%52.2))]
- %22 local maxima, %32 large gradients and %39 min vals, 322 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=1840226.4, rms=5.043
- 052: dt: 0.5000, sse=1730001.0, rms=4.685 (7.089%)
- 053: dt: 0.5000, sse=1655061.0, rms=4.441 (5.209%)
- rms = 4.51, time step reduction 1 of 3 to 0.250...
- 054: dt: 0.2500, sse=1571264.8, rms=4.080 (8.130%)
- 055: dt: 0.2500, sse=1546017.9, rms=3.962 (2.905%)
- rms = 3.94, time step reduction 2 of 3 to 0.125...
- 056: dt: 0.2500, sse=1540530.9, rms=3.939 (0.586%)
- 057: dt: 0.1250, sse=1518452.0, rms=3.836 (2.611%)
- rms = 3.81, time step reduction 3 of 3 to 0.062...
- 058: dt: 0.1250, sse=1513212.5, rms=3.814 (0.564%)
- positioning took 1.4 minutes
- mean border=55.9, 3568 (21) missing vertices, mean dist 0.1 [0.2 (%49.2)->0.5 (%50.8))]
- %29 local maxima, %27 large gradients and %38 min vals, 403 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=1559771.0, rms=3.996
- rms = 4.20, time step reduction 1 of 3 to 0.250...
- 059: dt: 0.2500, sse=1533505.9, rms=3.882 (2.835%)
- rms = 3.84, time step reduction 2 of 3 to 0.125...
- 060: dt: 0.2500, sse=1520918.6, rms=3.835 (1.212%)
- 061: dt: 0.1250, sse=1509364.4, rms=3.781 (1.413%)
- rms = 3.76, time step reduction 3 of 3 to 0.062...
- 062: dt: 0.1250, sse=1502854.0, rms=3.755 (0.677%)
- positioning took 0.9 minutes
- mean border=55.4, 7211 (21) missing vertices, mean dist 0.1 [0.2 (%48.6)->0.4 (%51.4))]
- %33 local maxima, %22 large gradients and %36 min vals, 439 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-6.0.0/0050352/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=1530470.5, rms=3.858
- rms = 3.93, time step reduction 1 of 3 to 0.250...
- 063: dt: 0.2500, sse=1508682.0, rms=3.765 (2.412%)
- 064: dt: 0.2500, sse=1484530.5, rms=3.677 (2.330%)
- rms = 3.63, time step reduction 2 of 3 to 0.125...
- 065: dt: 0.2500, sse=1471231.2, rms=3.627 (1.356%)
- 066: dt: 0.1250, sse=1453012.9, rms=3.539 (2.421%)
- rms = 3.51, time step reduction 3 of 3 to 0.062...
- 067: dt: 0.1250, sse=1445074.5, rms=3.507 (0.911%)
- positioning took 1.2 minutes
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.area.pial
- vertex spacing 1.01 +- 0.46 (0.05-->8.40) (max @ vno 157872 --> 98357)
- face area 0.40 +- 0.34 (0.00-->9.18)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 159921 vertices processed
- 25000 of 159921 vertices processed
- 50000 of 159921 vertices processed
- 75000 of 159921 vertices processed
- 100000 of 159921 vertices processed
- 125000 of 159921 vertices processed
- 150000 of 159921 vertices processed
- 0 of 159921 vertices processed
- 25000 of 159921 vertices processed
- 50000 of 159921 vertices processed
- 75000 of 159921 vertices processed
- 100000 of 159921 vertices processed
- 125000 of 159921 vertices processed
- 150000 of 159921 vertices processed
- thickness calculation complete, 422:976 truncations.
- 33870 vertices at 0 distance
- 105995 vertices at 1 distance
- 96590 vertices at 2 distance
- 44343 vertices at 3 distance
- 15718 vertices at 4 distance
- 5428 vertices at 5 distance
- 2027 vertices at 6 distance
- 882 vertices at 7 distance
- 366 vertices at 8 distance
- 191 vertices at 9 distance
- 97 vertices at 10 distance
- 63 vertices at 11 distance
- 48 vertices at 12 distance
- 32 vertices at 13 distance
- 33 vertices at 14 distance
- 20 vertices at 15 distance
- 13 vertices at 16 distance
- 11 vertices at 17 distance
- 20 vertices at 18 distance
- 18 vertices at 19 distance
- 19 vertices at 20 distance
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.thickness
- positioning took 17.7 minutes
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050352 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-6.0.0/0050352/mri/filled.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/brain.finalsurfs.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/../mri/aseg.presurf.mgz...
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
- 17660 bright wm thresholded.
- 2039 bright non-wm voxels segmented.
- reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.orig...
- computing class statistics...
- border white: 320647 voxels (1.91%)
- border gray 377071 voxels (2.25%)
- WM (94.0): 95.4 +- 7.8 [70.0 --> 110.0]
- GM (73.0) : 71.7 +- 10.6 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 61.4 (was 70)
- setting MAX_BORDER_WHITE to 105.8 (was 105)
- setting MIN_BORDER_WHITE to 72.0 (was 85)
- setting MAX_CSF to 50.9 (was 40)
- setting MAX_GRAY to 90.2 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 61.4 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 40.3 (was 40)
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=98+-6.1, GM=72+-6.1
- mean inside = 91.3, mean outside = 76.8
- smoothing surface for 5 iterations...
- reading initial white vertex positions from white.preaparc...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.89 +- 0.27 (0.03-->8.41) (max @ vno 108009 --> 163207)
- face area 0.33 +- 0.17 (0.00-->9.65)
- mean absolute distance = 0.54 +- 0.85
- 4536 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 1 with 69 points - only 0.00% unknown
- deleting segment 2 with 14 points - only 0.00% unknown
- deleting segment 3 with 12 points - only 0.00% unknown
- deleting segment 4 with 245 points - only 0.00% unknown
- deleting segment 5 with 68 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 6 with 1 points - only 0.00% unknown
- deleting segment 7 with 6 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 8 with 1 points - only 0.00% unknown
- deleting segment 9 with 48 points - only 0.00% unknown
- mean border=83.2, 397 (395) missing vertices, mean dist 0.2 [0.6 (%24.2)->0.5 (%75.8))]
- %74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
- mom=0.00, dt=0.50
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 0.000000
- desired_rms_height 0.000000
- momentum 0.000000
- nbhd_size 0
- max_nbrs 0
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 1
- randomSeed 0
- smoothing T1 volume with sigma = 1.000
- vertex spacing 0.90 +- 0.27 (0.02-->7.79) (max @ vno 108009 --> 163207)
- face area 0.33 +- 0.17 (0.00-->9.26)
- mean absolute distance = 0.39 +- 0.67
- 5808 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1698331.2, rms=5.326
- 001: dt: 0.5000, sse=1155934.9, rms=3.366 (36.794%)
- 002: dt: 0.5000, sse=1011278.4, rms=2.639 (21.618%)
- 003: dt: 0.5000, sse=984570.6, rms=2.483 (5.904%)
- 004: dt: 0.5000, sse=971679.3, rms=2.406 (3.094%)
- rms = 2.46, time step reduction 1 of 3 to 0.250...
- 005: dt: 0.2500, sse=909869.0, rms=1.915 (20.420%)
- 006: dt: 0.2500, sse=889970.2, rms=1.674 (12.600%)
- 007: dt: 0.2500, sse=884931.4, rms=1.621 (3.136%)
- rms = 1.60, time step reduction 2 of 3 to 0.125...
- 008: dt: 0.2500, sse=880575.8, rms=1.603 (1.136%)
- rms = 1.58, time step reduction 3 of 3 to 0.062...
- 009: dt: 0.1250, sse=877829.0, rms=1.577 (1.581%)
- positioning took 1.2 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 18 points - only 0.00% unknown
- deleting segment 1 with 18 points - only 0.00% unknown
- deleting segment 2 with 11 points - only 0.00% unknown
- deleting segment 3 with 254 points - only 0.00% unknown
- deleting segment 4 with 66 points - only 0.00% unknown
- deleting segment 5 with 6 points - only 0.00% unknown
- deleting segment 6 with 48 points - only 0.00% unknown
- mean border=85.0, 324 (137) missing vertices, mean dist -0.2 [0.5 (%63.5)->0.3 (%36.5))]
- %79 local maxima, %17 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 +- 0.27 (0.06-->8.06) (max @ vno 108009 --> 163207)
- face area 0.34 +- 0.18 (0.00-->10.21)
- mean absolute distance = 0.33 +- 0.50
- 5672 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=1159586.9, rms=3.229
- 010: dt: 0.5000, sse=988661.1, rms=2.131 (34.020%)
- 011: dt: 0.5000, sse=959757.2, rms=1.974 (7.334%)
- rms = 2.07, time step reduction 1 of 3 to 0.250...
- 012: dt: 0.2500, sse=916613.5, rms=1.607 (18.625%)
- 013: dt: 0.2500, sse=903480.8, rms=1.430 (10.968%)
- rms = 1.40, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=893121.4, rms=1.405 (1.797%)
- rms = 1.38, time step reduction 3 of 3 to 0.062...
- 015: dt: 0.1250, sse=893205.6, rms=1.385 (1.400%)
- positioning took 0.8 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 45 points - only 0.00% unknown
- deleting segment 1 with 27 points - only 0.00% unknown
- deleting segment 2 with 11 points - only 0.00% unknown
- deleting segment 3 with 234 points - only 0.00% unknown
- deleting segment 4 with 58 points - only 0.00% unknown
- deleting segment 5 with 47 points - only 0.00% unknown
- mean border=86.1, 369 (93) missing vertices, mean dist -0.1 [0.4 (%57.6)->0.3 (%42.4))]
- %83 local maxima, %13 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 +- 0.27 (0.09-->8.28) (max @ vno 108009 --> 163207)
- face area 0.34 +- 0.18 (0.00-->10.30)
- mean absolute distance = 0.31 +- 0.42
- 4387 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=973929.6, rms=2.231
- 016: dt: 0.5000, sse=924500.6, rms=1.772 (20.595%)
- rms = 1.79, time step reduction 1 of 3 to 0.250...
- 017: dt: 0.2500, sse=888262.7, rms=1.475 (16.730%)
- 018: dt: 0.2500, sse=876876.8, rms=1.334 (9.564%)
- rms = 1.30, time step reduction 2 of 3 to 0.125...
- 019: dt: 0.2500, sse=877732.0, rms=1.303 (2.335%)
- rms = 1.28, time step reduction 3 of 3 to 0.062...
- 020: dt: 0.1250, sse=874149.6, rms=1.282 (1.581%)
- positioning took 0.7 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 35 points - only 0.00% unknown
- deleting segment 1 with 27 points - only 0.00% unknown
- deleting segment 2 with 12 points - only 0.00% unknown
- deleting segment 3 with 72 points - only 0.00% unknown
- deleting segment 4 with 242 points - only 0.00% unknown
- deleting segment 5 with 7 points - only 0.00% unknown
- removing 1 vertex label from ripped group
- deleting segment 6 with 1 points - only 0.00% unknown
- deleting segment 7 with 47 points - only 0.00% unknown
- mean border=86.7, 439 (77) missing vertices, mean dist -0.0 [0.3 (%52.4)->0.3 (%47.6))]
- %86 local maxima, %10 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-6.0.0/0050352/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=894350.3, rms=1.576
- 021: dt: 0.5000, sse=875687.2, rms=1.303 (17.329%)
- rms = 1.64, time step reduction 1 of 3 to 0.250...
- 022: dt: 0.2500, sse=846503.8, rms=1.085 (16.787%)
- rms = 1.07, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=845152.2, rms=1.069 (1.432%)
- rms = 1.03, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=845954.6, rms=1.031 (3.511%)
- positioning took 0.6 minutes
- generating cortex label...
- 7 non-cortical segments detected
- only using segment with 7827 vertices
- erasing segment 1 (vno[0] = 115541)
- erasing segment 2 (vno[0] = 116581)
- erasing segment 3 (vno[0] = 116654)
- erasing segment 4 (vno[0] = 117658)
- erasing segment 5 (vno[0] = 161798)
- erasing segment 6 (vno[0] = 164558)
- writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.cortex.label...
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.area
- vertex spacing 0.89 +- 0.28 (0.05-->8.65) (max @ vno 108009 --> 163207)
- face area 0.33 +- 0.18 (0.00-->10.30)
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 19 points - only 0.00% unknown
- deleting segment 2 with 27 points - only 0.00% unknown
- deleting segment 5 with 13 points - only 0.00% unknown
- deleting segment 6 with 5 points - only 0.00% unknown
- deleting segment 7 with 5 points - only 0.00% unknown
- deleting segment 8 with 29 points - only 0.00% unknown
- deleting segment 9 with 29 points - only 0.00% unknown
- smoothing surface for 5 iterations...
- reading initial pial vertex positions from white.preaparc...
- mean border=60.7, 386 (386) missing vertices, mean dist 1.5 [0.9 (%0.0)->3.2 (%100.0))]
- %13 local maxima, %31 large gradients and %52 min vals, 708 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=23544016.0, rms=26.808
- 001: dt: 0.0500, sse=21158642.0, rms=25.364 (5.387%)
- 002: dt: 0.0500, sse=19439606.0, rms=24.269 (4.314%)
- 003: dt: 0.0500, sse=18106188.0, rms=23.385 (3.643%)
- 004: dt: 0.0500, sse=17012138.0, rms=22.634 (3.213%)
- 005: dt: 0.0500, sse=16080095.0, rms=21.974 (2.918%)
- 006: dt: 0.0500, sse=15263386.0, rms=21.378 (2.710%)
- 007: dt: 0.0500, sse=14532609.0, rms=20.831 (2.561%)
- 008: dt: 0.0500, sse=13868393.0, rms=20.320 (2.450%)
- 009: dt: 0.0500, sse=13257501.0, rms=19.839 (2.367%)
- 010: dt: 0.0500, sse=12691906.0, rms=19.383 (2.299%)
- positioning took 1.1 minutes
- mean border=60.6, 399 (223) missing vertices, mean dist 1.3 [0.3 (%0.1)->2.7 (%99.9))]
- %13 local maxima, %31 large gradients and %51 min vals, 659 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=13666072.0, rms=20.157
- 011: dt: 0.0500, sse=13131304.0, rms=19.734 (2.102%)
- 012: dt: 0.0500, sse=12630489.0, rms=19.328 (2.053%)
- 013: dt: 0.0500, sse=12159891.0, rms=18.940 (2.011%)
- 014: dt: 0.0500, sse=11716678.0, rms=18.566 (1.973%)
- 015: dt: 0.0500, sse=11299747.0, rms=18.207 (1.931%)
- 016: dt: 0.0500, sse=10906847.0, rms=17.863 (1.892%)
- 017: dt: 0.0500, sse=10535416.0, rms=17.531 (1.859%)
- 018: dt: 0.0500, sse=10185154.0, rms=17.212 (1.820%)
- 019: dt: 0.0500, sse=9854004.0, rms=16.905 (1.785%)
- 020: dt: 0.0500, sse=9540912.0, rms=16.609 (1.750%)
- positioning took 1.1 minutes
- mean border=60.5, 449 (186) missing vertices, mean dist 1.1 [0.1 (%1.1)->2.4 (%98.9))]
- %14 local maxima, %31 large gradients and %51 min vals, 605 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=9662268.0, rms=16.729
- 021: dt: 0.0500, sse=9360278.0, rms=16.440 (1.723%)
- 022: dt: 0.0500, sse=9075914.0, rms=16.164 (1.680%)
- 023: dt: 0.0500, sse=8806216.0, rms=15.898 (1.649%)
- 024: dt: 0.0500, sse=8552253.0, rms=15.643 (1.605%)
- 025: dt: 0.0500, sse=8312879.0, rms=15.398 (1.563%)
- 026: dt: 0.0500, sse=8087369.5, rms=15.164 (1.520%)
- 027: dt: 0.0500, sse=7873863.0, rms=14.939 (1.484%)
- 028: dt: 0.0500, sse=7670987.0, rms=14.722 (1.453%)
- 029: dt: 0.0500, sse=7477895.0, rms=14.512 (1.425%)
- 030: dt: 0.0500, sse=7294061.0, rms=14.309 (1.396%)
- positioning took 1.1 minutes
- mean border=60.5, 495 (166) missing vertices, mean dist 1.0 [0.1 (%8.1)->2.2 (%91.9))]
- %14 local maxima, %32 large gradients and %50 min vals, 594 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=7372661.5, rms=14.396
- 031: dt: 0.5000, sse=6077852.5, rms=12.890 (10.461%)
- 032: dt: 0.5000, sse=5201354.5, rms=11.754 (8.816%)
- 033: dt: 0.5000, sse=4577101.5, rms=10.872 (7.502%)
- 034: dt: 0.5000, sse=4091796.0, rms=10.128 (6.847%)
- 035: dt: 0.5000, sse=3686014.2, rms=9.463 (6.568%)
- 036: dt: 0.5000, sse=3328144.2, rms=8.834 (6.648%)
- 037: dt: 0.5000, sse=3000743.5, rms=8.219 (6.961%)
- 038: dt: 0.5000, sse=2703600.8, rms=7.617 (7.317%)
- 039: dt: 0.5000, sse=2457405.8, rms=7.083 (7.015%)
- 040: dt: 0.5000, sse=2257831.5, rms=6.616 (6.591%)
- 041: dt: 0.5000, sse=2112330.2, rms=6.255 (5.456%)
- 042: dt: 0.5000, sse=2011447.5, rms=5.989 (4.248%)
- 043: dt: 0.5000, sse=1941394.0, rms=5.800 (3.165%)
- 044: dt: 0.5000, sse=1897147.0, rms=5.673 (2.190%)
- 045: dt: 0.5000, sse=1862829.9, rms=5.576 (1.704%)
- 046: dt: 0.5000, sse=1840550.9, rms=5.509 (1.209%)
- rms = 5.48, time step reduction 1 of 3 to 0.250...
- 047: dt: 0.5000, sse=1829233.5, rms=5.476 (0.590%)
- 048: dt: 0.2500, sse=1758783.9, rms=5.228 (4.527%)
- 049: dt: 0.2500, sse=1734882.9, rms=5.155 (1.405%)
- rms = 5.16, time step reduction 2 of 3 to 0.125...
- rms = 5.13, time step reduction 3 of 3 to 0.062...
- 050: dt: 0.1250, sse=1728468.1, rms=5.133 (0.433%)
- positioning took 3.3 minutes
- mean border=59.9, 3726 (80) missing vertices, mean dist 0.2 [0.2 (%46.7)->0.8 (%53.3))]
- %22 local maxima, %27 large gradients and %45 min vals, 326 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=1890522.4, rms=5.077
- 051: dt: 0.5000, sse=1769510.8, rms=4.696 (7.507%)
- 052: dt: 0.5000, sse=1702250.6, rms=4.490 (4.378%)
- rms = 4.54, time step reduction 1 of 3 to 0.250...
- 053: dt: 0.2500, sse=1630112.0, rms=4.191 (6.678%)
- 054: dt: 0.2500, sse=1608542.9, rms=4.094 (2.305%)
- rms = 4.08, time step reduction 2 of 3 to 0.125...
- 055: dt: 0.2500, sse=1604928.6, rms=4.081 (0.321%)
- 056: dt: 0.1250, sse=1582783.6, rms=3.984 (2.363%)
- rms = 3.96, time step reduction 3 of 3 to 0.062...
- 057: dt: 0.1250, sse=1576792.2, rms=3.961 (0.585%)
- positioning took 1.6 minutes
- mean border=59.7, 4608 (59) missing vertices, mean dist 0.1 [0.2 (%49.2)->0.6 (%50.8))]
- %27 local maxima, %22 large gradients and %44 min vals, 416 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=1617004.6, rms=4.125
- rms = 4.30, time step reduction 1 of 3 to 0.250...
- 058: dt: 0.2500, sse=1588824.6, rms=4.013 (2.723%)
- rms = 3.96, time step reduction 2 of 3 to 0.125...
- 059: dt: 0.2500, sse=1574283.1, rms=3.963 (1.241%)
- rms = 3.92, time step reduction 3 of 3 to 0.062...
- 060: dt: 0.1250, sse=1564297.1, rms=3.919 (1.116%)
- positioning took 0.8 minutes
- mean border=59.3, 8959 (57) missing vertices, mean dist 0.1 [0.2 (%47.8)->0.5 (%52.2))]
- %30 local maxima, %18 large gradients and %42 min vals, 488 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-6.0.0/0050352/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=1581459.5, rms=3.981
- rms = 4.02, time step reduction 1 of 3 to 0.250...
- 061: dt: 0.2500, sse=1556718.1, rms=3.883 (2.439%)
- 062: dt: 0.2500, sse=1528161.5, rms=3.787 (2.481%)
- rms = 3.75, time step reduction 2 of 3 to 0.125...
- 063: dt: 0.2500, sse=1515412.2, rms=3.746 (1.099%)
- 064: dt: 0.1250, sse=1496270.0, rms=3.660 (2.292%)
- rms = 3.63, time step reduction 3 of 3 to 0.062...
- 065: dt: 0.1250, sse=1487238.0, rms=3.626 (0.930%)
- positioning took 1.3 minutes
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.area.pial
- vertex spacing 0.99 +- 0.45 (0.07-->8.25) (max @ vno 111440 --> 109158)
- face area 0.39 +- 0.34 (0.00-->18.90)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 165183 vertices processed
- 25000 of 165183 vertices processed
- 50000 of 165183 vertices processed
- 75000 of 165183 vertices processed
- 100000 of 165183 vertices processed
- 125000 of 165183 vertices processed
- 150000 of 165183 vertices processed
- 0 of 165183 vertices processed
- 25000 of 165183 vertices processed
- 50000 of 165183 vertices processed
- 75000 of 165183 vertices processed
- 100000 of 165183 vertices processed
- 125000 of 165183 vertices processed
- 150000 of 165183 vertices processed
- thickness calculation complete, 583:1261 truncations.
- 32117 vertices at 0 distance
- 105552 vertices at 1 distance
- 99434 vertices at 2 distance
- 48548 vertices at 3 distance
- 18979 vertices at 4 distance
- 7284 vertices at 5 distance
- 2823 vertices at 6 distance
- 1178 vertices at 7 distance
- 547 vertices at 8 distance
- 268 vertices at 9 distance
- 165 vertices at 10 distance
- 91 vertices at 11 distance
- 60 vertices at 12 distance
- 57 vertices at 13 distance
- 43 vertices at 14 distance
- 28 vertices at 15 distance
- 27 vertices at 16 distance
- 16 vertices at 17 distance
- 28 vertices at 18 distance
- 24 vertices at 19 distance
- 43 vertices at 20 distance
- writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.thickness
- positioning took 18.4 minutes
- PIDs (1182 1185) completed and logs appended.
- #--------------------------------------------
- #@# Surf Volume lh Sun Oct 8 11:31:28 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.volume
- masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.cortex.label
- Total face volume 282813
- Total vertex volume 279572 (mask=0)
- #@# 0050352 lh 279572
-
- vertexvol Done
- #--------------------------------------------
- #@# Surf Volume rh Sun Oct 8 11:31:32 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.volume
- masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.cortex.label
- Total face volume 289365
- Total vertex volume 286560 (mask=0)
- #@# 0050352 rh 286560
-
- vertexvol Done
- #--------------------------------------------
- #@# Cortical ribbon mask Sun Oct 8 11:31:36 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352
- 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 = 466
- writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/ribbon.mgz
- mris_volmask took 14.24 minutes
- writing ribbon files
- #-----------------------------------------
- #@# Parcellation Stats lh Sun Oct 8 11:45:51 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 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 0050352 lh pial
- #-----------------------------------------
- #@# Parcellation Stats rh Sun Oct 8 11:45:51 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 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 0050352 rh pial
- Waiting for PID 2294 of (2294 2297 2300 2303) to complete...
- Waiting for PID 2297 of (2294 2297 2300 2303) to complete...
- Waiting for PID 2300 of (2294 2297 2300 2303) to complete...
- Waiting for PID 2303 of (2294 2297 2300 2303) 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 0050352 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 282813
- Total vertex volume 279572 (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) = 1712602 mm^3 (det: 1.137512 )
- lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371
- rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338
- lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115
- rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702
- SubCortGMVol 65474.000
- SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
- SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
- BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
- BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
- BrainSegVolNotVent 1346802.000
- CerebellumVol 159751.000
- VentChorVol 19992.000
- 3rd4th5thCSF 5338.000
- CSFVol 2234.000, OptChiasmVol 252.000
- MaskVol 1787646.000
- 1461 999 2374 2.693 0.525 0.112 0.026 10 1.5 bankssts
- 1379 902 2794 2.736 0.810 0.147 0.031 21 1.7 caudalanteriorcingulate
- 4942 3281 9181 2.583 0.617 0.119 0.030 45 5.8 caudalmiddlefrontal
- 2515 1686 3664 1.999 0.541 0.151 0.051 38 5.2 cuneus
- 1146 725 2011 2.411 0.784 0.172 0.085 23 4.7 entorhinal
- 5233 3572 9651 2.386 0.655 0.141 0.050 74 10.8 fusiform
- 6776 4505 12637 2.390 0.634 0.131 0.035 79 9.7 inferiorparietal
- 5852 4013 13137 2.571 0.869 0.147 0.055 121 14.8 inferiortemporal
- 1456 988 2560 2.474 0.896 0.122 0.029 18 1.5 isthmuscingulate
- 8453 5658 14533 2.213 0.722 0.149 0.050 132 17.9 lateraloccipital
- 4767 3149 9526 2.723 0.789 0.138 0.047 66 9.7 lateralorbitofrontal
- 4558 3049 6686 1.961 0.591 0.151 0.055 74 10.2 lingual
- 3190 2294 6544 2.507 0.822 0.143 0.044 49 5.8 medialorbitofrontal
- 5018 3452 11876 2.704 0.758 0.125 0.033 54 6.6 middletemporal
- 1164 708 1885 2.307 0.669 0.101 0.038 14 2.0 parahippocampal
- 2615 1677 4592 2.493 0.652 0.141 0.045 34 5.2 paracentral
- 2389 1616 4528 2.498 0.589 0.112 0.026 21 2.5 parsopercularis
- 1186 795 2454 2.524 0.911 0.151 0.057 23 2.5 parsorbitalis
- 2251 1469 4891 2.765 0.761 0.122 0.032 23 2.8 parstriangularis
- 1781 1299 2094 1.848 0.493 0.163 0.053 24 4.0 pericalcarine
- 7057 4571 10110 2.028 0.622 0.125 0.036 73 10.5 postcentral
- 2305 1584 3732 2.310 0.639 0.145 0.040 31 3.7 posteriorcingulate
- 9679 6401 16271 2.425 0.686 0.124 0.038 96 15.4 precentral
- 6234 4227 11289 2.491 0.679 0.131 0.038 73 9.4 precuneus
- 1208 848 2799 2.941 0.771 0.136 0.037 16 1.9 rostralanteriorcingulate
- 10933 7514 21687 2.588 0.656 0.149 0.049 164 21.6 rostralmiddlefrontal
- 15000 9996 29561 2.700 0.748 0.143 0.049 187 30.7 superiorfrontal
- 10890 7134 16511 2.136 0.573 0.135 0.044 133 18.9 superiorparietal
- 6865 4721 14836 2.569 0.768 0.116 0.030 67 8.5 superiortemporal
- 6047 4181 12041 2.500 0.666 0.133 0.038 85 9.4 supramarginal
- 486 316 1377 3.076 0.787 0.196 0.084 13 1.9 frontalpole
- 947 700 2618 2.783 0.919 0.172 0.066 16 2.7 temporalpole
- 939 572 1268 2.143 0.548 0.141 0.051 10 1.9 transversetemporal
- 4161 2808 7835 2.926 0.814 0.128 0.042 49 6.9 insula
- mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0050352 lh pial
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 282813
- Total vertex volume 279572 (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) = 1712602 mm^3 (det: 1.137512 )
- lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371
- rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338
- lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115
- rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702
- SubCortGMVol 65474.000
- SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
- SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
- BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
- BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
- BrainSegVolNotVent 1346802.000
- CerebellumVol 159751.000
- VentChorVol 19992.000
- 3rd4th5thCSF 5338.000
- CSFVol 2234.000, OptChiasmVol 252.000
- MaskVol 1787646.000
- 1461 817 2374 2.693 0.525 0.119 0.036 19 2.1 bankssts
- 1379 1136 2794 2.736 0.810 0.154 0.041 36 2.3 caudalanteriorcingulate
- 4942 3763 9181 2.583 0.617 0.130 0.031 63 6.9 caudalmiddlefrontal
- 2515 2035 3664 1.999 0.541 0.138 0.037 31 4.1 cuneus
- 1146 986 2011 2.411 0.784 0.200 0.127 60 8.8 entorhinal
- 5233 4387 9651 2.386 0.655 0.165 0.047 96 11.6 fusiform
- 6776 5935 12637 2.390 0.634 0.166 0.043 99 14.1 inferiorparietal
- 5852 5758 13137 2.571 0.869 0.191 0.053 97 14.9 inferiortemporal
- 1456 1189 2560 2.474 0.896 0.154 0.045 23 2.6 isthmuscingulate
- 8453 7182 14533 2.213 0.722 0.157 0.043 155 17.0 lateraloccipital
- 4767 3775 9526 2.723 0.789 0.152 0.044 77 9.3 lateralorbitofrontal
- 4558 3821 6686 1.961 0.591 0.154 0.042 77 8.7 lingual
- 3190 2917 6544 2.507 0.822 0.174 0.048 54 7.0 medialorbitofrontal
- 5018 5135 11876 2.704 0.758 0.185 0.048 65 11.5 middletemporal
- 1164 937 1885 2.307 0.669 0.146 0.039 12 2.0 parahippocampal
- 2615 2029 4592 2.493 0.652 0.143 0.039 42 4.8 paracentral
- 2389 1973 4528 2.498 0.589 0.146 0.036 35 4.0 parsopercularis
- 1186 1088 2454 2.524 0.911 0.168 0.052 200 2.8 parsorbitalis
- 2251 1966 4891 2.765 0.761 0.169 0.045 36 4.8 parstriangularis
- 1781 1088 2094 1.848 0.493 0.134 0.041 29 3.1 pericalcarine
- 7057 5457 10110 2.028 0.622 0.132 0.033 67 10.3 postcentral
- 2305 1751 3732 2.310 0.639 0.152 0.040 53 4.4 posteriorcingulate
- 9679 7020 16271 2.425 0.686 0.120 0.030 123 12.8 precentral
- 6234 4854 11289 2.491 0.679 0.147 0.044 149 12.7 precuneus
- 1208 1119 2799 2.941 0.771 0.178 0.055 54 2.7 rostralanteriorcingulate
- 10933 9038 21687 2.588 0.656 0.161 0.043 184 21.9 rostralmiddlefrontal
- 15000 11635 29561 2.700 0.748 0.143 0.042 264 27.5 superiorfrontal
- 10890 8251 16511 2.136 0.573 0.139 0.038 154 18.3 superiorparietal
- 6865 6014 14836 2.569 0.768 0.141 0.033 75 10.2 superiortemporal
- 6047 5265 12041 2.500 0.666 0.155 0.037 77 10.2 supramarginal
- 486 513 1377 3.076 0.787 0.164 0.029 6 0.8 frontalpole
- 947 1258 2618 2.783 0.919 0.218 0.051 13 2.3 temporalpole
- 939 685 1268 2.143 0.548 0.137 0.041 9 1.7 transversetemporal
- 4161 2542 7835 2.926 0.814 0.126 0.037 78 6.3 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 0050352 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 289365
- Total vertex volume 286560 (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) = 1712602 mm^3 (det: 1.137512 )
- lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371
- rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338
- lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115
- rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702
- SubCortGMVol 65474.000
- SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
- SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
- BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
- BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
- BrainSegVolNotVent 1346802.000
- CerebellumVol 159751.000
- VentChorVol 19992.000
- 3rd4th5thCSF 5338.000
- CSFVol 2234.000, OptChiasmVol 252.000
- MaskVol 1787646.000
- 1205 865 2413 2.854 0.528 0.093 0.019 6 0.9 bankssts
- 1393 920 2496 2.550 0.562 0.125 0.026 16 1.5 caudalanteriorcingulate
- 5034 3350 8709 2.558 0.589 0.128 0.049 64 10.2 caudalmiddlefrontal
- 2458 1590 3415 1.950 0.515 0.138 0.041 33 4.2 cuneus
- 862 533 1945 2.824 0.900 0.167 0.080 22 3.1 entorhinal
- 5294 3494 10625 2.667 0.776 0.134 0.046 68 10.4 fusiform
- 8832 5726 17049 2.619 0.694 0.133 0.045 115 15.7 inferiorparietal
- 6653 4352 14290 2.687 0.802 0.141 0.065 135 18.8 inferiortemporal
- 1431 944 2648 2.495 0.799 0.136 0.038 18 2.0 isthmuscingulate
- 7989 5151 12465 2.186 0.698 0.147 0.054 130 17.4 lateraloccipital
- 4793 3124 8219 2.466 0.774 0.139 0.054 75 10.9 lateralorbitofrontal
- 4841 3286 7356 2.069 0.556 0.148 0.047 68 8.8 lingual
- 3427 2254 6376 2.509 0.912 0.137 0.054 56 7.9 medialorbitofrontal
- 6429 4370 15378 2.950 0.717 0.139 0.048 87 12.5 middletemporal
- 1127 705 1893 2.400 0.727 0.105 0.026 9 1.1 parahippocampal
- 2737 1772 4181 2.259 0.624 0.130 0.053 36 6.2 paracentral
- 2415 1656 4667 2.576 0.564 0.118 0.034 25 3.2 parsopercularis
- 1903 1207 3932 2.669 0.822 0.160 0.066 40 5.1 parsorbitalis
- 2887 1940 6035 2.683 0.632 0.126 0.034 34 3.6 parstriangularis
- 2276 1563 2810 1.900 0.549 0.131 0.044 31 3.9 pericalcarine
- 6805 4389 9915 2.093 0.714 0.122 0.046 136 13.4 postcentral
- 2445 1663 4566 2.490 0.869 0.146 0.039 37 3.6 posteriorcingulate
- 9868 6484 15157 2.361 0.674 0.132 0.043 104 18.2 precentral
- 6542 4390 11989 2.512 0.668 0.131 0.037 74 9.8 precuneus
- 1058 712 2550 3.139 0.837 0.131 0.034 16 1.5 rostralanteriorcingulate
- 13658 9095 25754 2.496 0.674 0.145 0.053 201 29.4 rostralmiddlefrontal
- 14491 9415 28835 2.781 0.785 0.141 0.056 238 35.3 superiorfrontal
- 9451 6352 15822 2.289 0.659 0.137 0.046 137 19.6 superiorparietal
- 6563 4296 12078 2.546 0.692 0.130 0.054 88 15.2 superiortemporal
- 6067 3988 11430 2.673 0.619 0.131 0.042 106 11.1 supramarginal
- 507 305 1225 2.626 0.798 0.157 0.074 12 1.4 frontalpole
- 824 489 1611 2.528 0.816 0.167 0.076 17 2.8 temporalpole
- 675 420 839 2.156 0.710 0.145 0.050 11 1.4 transversetemporal
- 4096 2822 7843 3.060 0.722 0.136 0.043 50 6.7 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 0050352 rh pial
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 289365
- Total vertex volume 286560 (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) = 1712602 mm^3 (det: 1.137512 )
- lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371
- rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338
- lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115
- rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702
- SubCortGMVol 65474.000
- SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
- SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
- BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
- BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
- BrainSegVolNotVent 1346802.000
- CerebellumVol 159751.000
- VentChorVol 19992.000
- 3rd4th5thCSF 5338.000
- CSFVol 2234.000, OptChiasmVol 252.000
- MaskVol 1787646.000
- 1205 789 2413 2.854 0.528 0.108 0.026 14 1.4 bankssts
- 1393 1089 2496 2.550 0.562 0.152 0.035 41 2.4 caudalanteriorcingulate
- 5034 3475 8709 2.558 0.589 0.113 0.030 65 7.0 caudalmiddlefrontal
- 2458 2000 3415 1.950 0.515 0.146 0.038 28 4.2 cuneus
- 862 815 1945 2.824 0.900 0.164 0.046 12 1.9 entorhinal
- 5294 4360 10625 2.667 0.776 0.160 0.049 112 12.7 fusiform
- 8832 7175 17049 2.619 0.694 0.155 0.046 141 19.8 inferiorparietal
- 6653 5838 14290 2.687 0.802 0.162 0.049 350 14.7 inferiortemporal
- 1431 1139 2648 2.495 0.799 0.167 0.043 26 2.7 isthmuscingulate
- 7989 6247 12465 2.186 0.698 0.142 0.041 135 14.7 lateraloccipital
- 4793 3628 8219 2.466 0.774 0.162 0.048 81 10.8 lateralorbitofrontal
- 4841 4029 7356 2.069 0.556 0.155 0.041 68 9.0 lingual
- 3427 2939 6376 2.509 0.912 0.175 0.054 66 8.4 medialorbitofrontal
- 6429 6024 15378 2.950 0.717 0.163 0.043 114 12.5 middletemporal
- 1127 848 1893 2.400 0.727 0.135 0.034 15 1.7 parahippocampal
- 2737 1927 4181 2.259 0.624 0.129 0.033 37 4.1 paracentral
- 2415 2037 4667 2.576 0.564 0.144 0.035 27 3.7 parsopercularis
- 1903 1689 3932 2.669 0.822 0.156 0.041 25 3.4 parsorbitalis
- 2887 2570 6035 2.683 0.632 0.158 0.034 34 4.6 parstriangularis
- 2276 1479 2810 1.900 0.549 0.138 0.044 44 4.2 pericalcarine
- 6805 5214 9915 2.093 0.714 0.130 0.034 84 10.3 postcentral
- 2445 1995 4566 2.490 0.869 0.159 0.042 50 4.7 posteriorcingulate
- 9868 6535 15157 2.361 0.674 0.113 0.034 155 14.1 precentral
- 6542 5038 11989 2.512 0.668 0.147 0.039 109 11.5 precuneus
- 1058 971 2550 3.139 0.837 0.155 0.041 32 1.9 rostralanteriorcingulate
- 13658 11057 25754 2.496 0.674 0.152 0.041 267 26.1 rostralmiddlefrontal
- 14491 10927 28835 2.781 0.785 0.146 0.044 243 29.2 superiorfrontal
- 9451 7516 15822 2.289 0.659 0.144 0.040 168 17.0 superiorparietal
- 6563 5168 12078 2.546 0.692 0.145 0.039 109 11.8 superiortemporal
- 6067 4561 11430 2.673 0.619 0.143 0.039 115 11.1 supramarginal
- 507 568 1225 2.626 0.798 0.190 0.044 7 1.1 frontalpole
- 824 706 1611 2.528 0.816 0.180 0.068 34 2.3 temporalpole
- 675 410 839 2.156 0.710 0.128 0.041 10 1.1 transversetemporal
- 4096 2400 7843 3.060 0.722 0.134 0.047 87 8.6 insula
- PIDs (2294 2297 2300 2303) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc 2 lh Sun Oct 8 11:47:25 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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 11:47:25 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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 2403 of (2403 2406) to complete...
- Waiting for PID 2406 of (2403 2406) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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...
- 57 labels changed using aseg
- relabeling using gibbs priors...
- 000: 10261 changed, 159921 examined...
- 001: 2506 changed, 39819 examined...
- 002: 781 changed, 12993 examined...
- 003: 351 changed, 4484 examined...
- 004: 173 changed, 2002 examined...
- 005: 88 changed, 1017 examined...
- 006: 38 changed, 502 examined...
- 007: 11 changed, 212 examined...
- 008: 3 changed, 76 examined...
- 009: 2 changed, 16 examined...
- 010: 1 changed, 10 examined...
- 011: 0 changed, 8 examined...
- 33 labels changed using aseg
- 000: 295 total segments, 211 labels (2644 vertices) changed
- 001: 95 total segments, 12 labels (89 vertices) changed
- 002: 83 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 36 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1434 vertices marked for relabeling...
- 1434 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 0 minutes and 21 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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...
- 1 labels changed using aseg
- relabeling using gibbs priors...
- 000: 10278 changed, 165183 examined...
- 001: 2413 changed, 40284 examined...
- 002: 705 changed, 12705 examined...
- 003: 297 changed, 3968 examined...
- 004: 130 changed, 1665 examined...
- 005: 63 changed, 781 examined...
- 006: 37 changed, 350 examined...
- 007: 20 changed, 208 examined...
- 008: 7 changed, 107 examined...
- 009: 5 changed, 41 examined...
- 010: 4 changed, 25 examined...
- 011: 1 changed, 20 examined...
- 012: 0 changed, 4 examined...
- 0 labels changed using aseg
- 000: 300 total segments, 216 labels (2581 vertices) changed
- 001: 95 total segments, 11 labels (45 vertices) changed
- 002: 84 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 49 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 1584 vertices marked for relabeling...
- 1584 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 0 minutes and 22 seconds.
- PIDs (2403 2406) completed and logs appended.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Sun Oct 8 11:47:48 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 lh white
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Sun Oct 8 11:47:48 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 rh white
- Waiting for PID 2452 of (2452 2455) to complete...
- Waiting for PID 2455 of (2452 2455) 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 0050352 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 282813
- Total vertex volume 279572 (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) = 1712602 mm^3 (det: 1.137512 )
- lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371
- rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338
- lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115
- rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702
- SubCortGMVol 65474.000
- SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
- SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
- BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
- BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
- BrainSegVolNotVent 1346802.000
- CerebellumVol 159751.000
- VentChorVol 19992.000
- 3rd4th5thCSF 5338.000
- CSFVol 2234.000, OptChiasmVol 252.000
- MaskVol 1787646.000
- 1596 1066 3379 2.812 0.774 0.148 0.057 25 4.0 G&S_frontomargin
- 1680 1138 3104 2.186 0.759 0.151 0.056 26 3.9 G&S_occipital_inf
- 1818 1187 3333 2.351 0.823 0.148 0.049 26 3.9 G&S_paracentral
- 1983 1282 4103 2.573 0.623 0.130 0.035 25 2.6 G&S_subcentral
- 1011 702 3008 3.239 0.657 0.183 0.072 23 2.9 G&S_transv_frontopol
- 2810 1980 5844 2.704 0.690 0.132 0.035 31 4.3 G&S_cingul-Ant
- 1636 1110 3195 2.801 0.593 0.135 0.035 17 2.1 G&S_cingul-Mid-Ant
- 1722 1188 2617 2.264 0.582 0.131 0.035 17 2.5 G&S_cingul-Mid-Post
- 695 483 1605 2.703 0.761 0.166 0.051 14 1.4 G_cingul-Post-dorsal
- 253 180 596 2.723 0.948 0.139 0.041 3 0.3 G_cingul-Post-ventral
- 2168 1487 3545 2.049 0.642 0.158 0.059 36 5.3 G_cuneus
- 1177 782 2716 2.576 0.611 0.129 0.040 15 2.1 G_front_inf-Opercular
- 540 346 1289 2.601 0.807 0.159 0.054 10 1.3 G_front_inf-Orbital
- 1527 948 3768 2.866 0.725 0.132 0.037 20 2.1 G_front_inf-Triangul
- 6227 4146 14649 2.723 0.680 0.154 0.050 107 12.7 G_front_middle
- 10050 6575 21349 2.694 0.810 0.156 0.059 155 25.0 G_front_sup
- 794 550 1704 2.964 0.944 0.149 0.053 15 1.4 G_Ins_lg&S_cent_ins
- 827 546 2272 3.262 0.701 0.141 0.057 12 2.0 G_insular_short
- 2203 1480 5619 2.684 0.732 0.164 0.058 46 5.3 G_occipital_middle
- 1835 1137 3025 2.157 0.699 0.148 0.048 29 3.4 G_occipital_sup
- 2108 1436 4247 2.344 0.660 0.160 0.072 43 6.6 G_oc-temp_lat-fusifor
- 3455 2306 5361 1.932 0.620 0.165 0.066 67 9.5 G_oc-temp_med-Lingual
- 1984 1237 3381 2.302 0.758 0.153 0.071 38 6.7 G_oc-temp_med-Parahip
- 2893 1844 6447 2.580 0.835 0.155 0.067 61 7.8 G_orbital
- 2899 1884 6121 2.423 0.738 0.150 0.042 51 5.0 G_pariet_inf-Angular
- 3248 2190 7358 2.591 0.674 0.150 0.052 59 6.8 G_pariet_inf-Supramar
- 4691 3024 7612 2.075 0.553 0.141 0.054 68 10.2 G_parietal_sup
- 2660 1605 3913 2.072 0.633 0.132 0.045 31 4.9 G_postcentral
- 3976 2556 7278 2.423 0.731 0.133 0.048 44 8.1 G_precentral
- 3154 2136 7032 2.558 0.657 0.150 0.054 50 6.6 G_precuneus
- 1078 834 2743 2.539 0.800 0.174 0.053 29 2.3 G_rectus
- 1051 677 1598 2.399 0.968 0.129 0.052 15 2.0 G_subcallosal
- 701 414 970 2.048 0.445 0.150 0.058 10 1.5 G_temp_sup-G_T_transv
- 2223 1536 7197 3.025 0.836 0.146 0.044 34 4.0 G_temp_sup-Lateral
- 1103 802 2723 2.895 0.860 0.115 0.039 9 1.8 G_temp_sup-Plan_polar
- 1015 668 1679 2.307 0.510 0.078 0.019 5 0.8 G_temp_sup-Plan_tempo
- 3226 2202 9087 2.857 0.932 0.176 0.079 102 11.7 G_temporal_inf
- 2650 1752 7688 2.959 0.737 0.138 0.040 38 4.2 G_temporal_middle
- 292 193 354 2.150 0.544 0.112 0.023 2 0.2 Lat_Fis-ant-Horizont
- 361 266 534 2.451 0.673 0.094 0.013 2 0.2 Lat_Fis-ant-Vertical
- 1120 760 1417 2.427 0.616 0.106 0.022 6 0.9 Lat_Fis-post
- 2480 1676 4179 2.110 0.761 0.165 0.063 49 6.6 Pole_occipital
- 1767 1282 4730 2.685 0.882 0.168 0.063 30 4.9 Pole_temporal
- 2121 1497 2613 2.037 0.668 0.139 0.041 23 3.5 S_calcarine
- 3498 2419 3933 1.854 0.524 0.122 0.030 28 4.5 S_central
- 1302 899 1870 2.260 0.498 0.133 0.032 12 1.7 S_cingul-Marginalis
- 524 367 988 3.260 0.502 0.100 0.018 2 0.4 S_circular_insula_ant
- 1687 1150 2514 2.734 0.807 0.098 0.022 8 1.5 S_circular_insula_inf
- 1983 1361 3005 2.827 0.509 0.103 0.020 9 1.8 S_circular_insula_sup
- 1232 862 1899 2.469 0.618 0.117 0.028 9 1.4 S_collat_transv_ant
- 617 409 661 1.973 0.468 0.120 0.027 4 0.7 S_collat_transv_post
- 2499 1730 3547 2.206 0.489 0.119 0.033 22 3.2 S_front_inf
- 1936 1358 2894 2.425 0.590 0.131 0.033 17 2.5 S_front_middle
- 4859 3292 7788 2.588 0.528 0.113 0.030 34 5.8 S_front_sup
- 413 293 590 2.107 0.464 0.099 0.020 2 0.4 S_interm_prim-Jensen
- 3759 2525 4876 2.187 0.500 0.117 0.025 30 3.7 S_intrapariet&P_trans
- 1150 766 1371 2.011 0.405 0.119 0.028 9 1.3 S_oc_middle&Lunatus
- 1354 910 1803 2.203 0.483 0.116 0.032 9 1.7 S_oc_sup&transversal
- 805 562 1203 2.350 0.616 0.129 0.031 6 1.0 S_occipital_ant
- 1130 785 1563 2.104 0.525 0.092 0.016 5 0.7 S_oc-temp_lat
- 2117 1406 3216 2.312 0.523 0.101 0.020 13 1.5 S_oc-temp_med&Lingual
- 490 365 1202 3.246 0.770 0.165 0.047 8 1.0 S_orbital_lateral
- 726 528 908 2.022 0.605 0.119 0.027 5 0.8 S_orbital_med-olfact
- 1929 1315 3658 2.807 0.713 0.129 0.033 18 2.9 S_orbital-H_Shaped
- 2541 1703 3376 2.345 0.707 0.123 0.030 22 3.1 S_parieto_occipital
- 1415 910 1550 2.116 0.704 0.131 0.025 22 1.2 S_pericallosal
- 2719 1924 3637 2.123 0.509 0.123 0.029 23 3.2 S_postcentral
- 2570 1717 4205 2.517 0.525 0.101 0.025 22 2.8 S_precentral-inf-part
- 2005 1336 3030 2.640 0.566 0.117 0.031 15 2.8 S_precentral-sup-part
- 669 465 1198 2.656 1.044 0.124 0.026 4 0.8 S_suborbital
- 1173 802 1714 2.297 0.555 0.120 0.024 10 1.1 S_subparietal
- 2004 1377 3123 2.186 0.583 0.112 0.026 14 2.2 S_temporal_inf
- 6392 4403 10512 2.422 0.576 0.112 0.025 49 6.6 S_temporal_sup
- 519 342 758 2.390 0.467 0.130 0.031 4 0.7 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 0050352 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 289365
- Total vertex volume 286560 (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) = 1712602 mm^3 (det: 1.137512 )
- lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371
- rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338
- lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115
- rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702
- SubCortGMVol 65474.000
- SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
- SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
- BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
- BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
- BrainSegVolNotVent 1346802.000
- CerebellumVol 159751.000
- VentChorVol 19992.000
- 3rd4th5thCSF 5338.000
- CSFVol 2234.000, OptChiasmVol 252.000
- MaskVol 1787646.000
- 1308 877 2462 2.458 0.631 0.152 0.051 19 2.8 G&S_frontomargin
- 1180 763 1992 2.235 0.611 0.151 0.053 19 2.3 G&S_occipital_inf
- 1721 1107 2685 2.099 0.657 0.136 0.056 25 3.8 G&S_paracentral
- 1787 1096 3382 2.613 0.623 0.125 0.064 86 5.3 G&S_subcentral
- 1739 1112 3380 2.349 0.660 0.175 0.083 34 6.2 G&S_transv_frontopol
- 3648 2463 7363 2.828 0.807 0.129 0.039 45 5.8 G&S_cingul-Ant
- 1622 1120 3267 2.838 0.692 0.110 0.024 12 1.5 G&S_cingul-Mid-Ant
- 1898 1271 3234 2.606 0.717 0.139 0.041 21 3.1 G&S_cingul-Mid-Post
- 605 416 1788 3.016 0.993 0.170 0.059 10 1.4 G_cingul-Post-dorsal
- 316 215 682 2.512 0.878 0.137 0.055 4 0.6 G_cingul-Post-ventral
- 2328 1480 3302 1.968 0.532 0.145 0.047 41 4.5 G_cuneus
- 1417 934 3140 2.574 0.530 0.128 0.043 21 2.2 G_front_inf-Opercular
- 611 365 1262 2.501 0.562 0.152 0.066 13 1.7 G_front_inf-Orbital
- 1304 848 3441 2.891 0.662 0.144 0.044 20 2.1 G_front_inf-Triangul
- 7343 4626 15602 2.582 0.765 0.159 0.073 154 22.0 G_front_middle
- 9699 6046 20898 2.764 0.863 0.153 0.073 214 31.5 G_front_sup
- 780 542 1737 3.237 0.860 0.150 0.051 12 1.5 G_Ins_lg&S_cent_ins
- 870 560 1877 3.107 0.726 0.149 0.056 15 1.9 G_insular_short
- 2713 1750 6675 2.753 0.881 0.160 0.071 58 7.7 G_occipital_middle
- 1767 1107 3761 2.593 0.834 0.135 0.052 26 4.0 G_occipital_sup
- 2420 1518 5911 2.871 0.896 0.151 0.056 40 5.3 G_oc-temp_lat-fusifor
- 3240 2150 5426 2.088 0.577 0.152 0.052 53 6.6 G_oc-temp_med-Lingual
- 1669 1031 3592 2.753 0.840 0.148 0.069 35 4.8 G_oc-temp_med-Parahip
- 4011 2569 8341 2.495 0.819 0.164 0.075 94 12.6 G_orbital
- 3676 2289 7628 2.580 0.702 0.147 0.059 63 8.3 G_pariet_inf-Angular
- 2967 1898 6463 2.646 0.701 0.150 0.065 84 8.7 G_pariet_inf-Supramar
- 2823 1952 5095 2.124 0.618 0.156 0.067 69 8.8 G_parietal_sup
- 2396 1493 3820 2.046 0.769 0.136 0.052 32 5.2 G_postcentral
- 4059 2479 6383 2.227 0.754 0.148 0.061 62 10.9 G_precentral
- 2829 1810 6587 2.683 0.668 0.147 0.054 48 6.4 G_precuneus
- 1038 670 1995 2.189 0.822 0.148 0.061 18 2.9 G_rectus
- 616 425 1021 2.687 1.024 0.156 0.079 15 1.7 G_subcallosal
- 589 338 817 2.316 0.765 0.144 0.057 10 1.3 G_temp_sup-G_T_transv
- 2449 1525 5508 2.672 0.802 0.148 0.072 45 7.2 G_temp_sup-Lateral
- 1332 883 2304 2.457 0.681 0.157 0.071 22 4.5 G_temp_sup-Plan_polar
- 1246 843 2102 2.393 0.567 0.120 0.050 12 3.0 G_temp_sup-Plan_tempo
- 3988 2556 9713 2.704 0.872 0.162 0.086 110 15.7 G_temporal_inf
- 3794 2574 10354 2.951 0.753 0.150 0.058 64 8.5 G_temporal_middle
- 328 247 471 2.307 0.509 0.105 0.021 2 0.2 Lat_Fis-ant-Horizont
- 305 230 482 2.332 0.468 0.107 0.018 2 0.2 Lat_Fis-ant-Vertical
- 1629 1108 2401 2.663 0.600 0.120 0.026 14 1.6 Lat_Fis-post
- 3700 2373 4853 1.924 0.569 0.149 0.055 61 8.3 Pole_occipital
- 1520 981 4203 2.897 0.926 0.181 0.096 41 6.7 Pole_temporal
- 2200 1554 2806 2.015 0.618 0.129 0.036 21 3.3 S_calcarine
- 3671 2507 4165 1.987 0.600 0.118 0.031 27 4.5 S_central
- 1315 912 1855 2.131 0.522 0.097 0.021 6 1.0 S_cingul-Marginalis
- 817 548 1416 3.396 0.595 0.113 0.023 5 0.8 S_circular_insula_ant
- 1315 878 1977 2.749 0.711 0.102 0.026 9 1.5 S_circular_insula_inf
- 1657 1147 2712 2.864 0.481 0.105 0.020 8 1.4 S_circular_insula_sup
- 1265 877 2008 2.544 0.597 0.105 0.026 8 1.3 S_collat_transv_ant
- 542 389 693 2.001 0.485 0.130 0.029 5 0.7 S_collat_transv_post
- 2684 1896 4269 2.509 0.485 0.115 0.025 19 2.7 S_front_inf
- 3756 2603 5734 2.350 0.555 0.124 0.036 30 5.0 S_front_middle
- 3932 2779 6641 2.772 0.539 0.116 0.028 25 4.5 S_front_sup
- 506 342 739 2.721 0.530 0.109 0.027 3 0.5 S_interm_prim-Jensen
- 4193 2817 6009 2.407 0.629 0.121 0.029 33 5.1 S_intrapariet&P_trans
- 1117 776 1372 1.973 0.393 0.137 0.029 12 1.4 S_oc_middle&Lunatus
- 1502 1023 2088 2.271 0.451 0.118 0.027 11 1.7 S_oc_sup&transversal
- 805 555 1109 2.320 0.449 0.126 0.031 6 1.1 S_occipital_ant
- 1557 1067 2246 2.532 0.563 0.107 0.023 9 1.4 S_oc-temp_lat
- 2262 1544 2887 2.149 0.525 0.105 0.019 13 1.7 S_oc-temp_med&Lingual
- 638 447 943 2.436 0.530 0.119 0.025 4 0.6 S_orbital_lateral
- 736 512 901 1.959 0.474 0.112 0.025 5 0.7 S_orbital_med-olfact
- 1805 1198 3094 2.566 0.721 0.122 0.036 16 2.4 S_orbital-H_Shaped
- 2984 2015 4143 2.246 0.596 0.124 0.030 26 3.6 S_parieto_occipital
- 1878 1221 2192 2.290 0.777 0.135 0.022 29 1.5 S_pericallosal
- 2505 1722 3434 2.314 0.572 0.132 0.034 25 3.5 S_postcentral
- 2465 1710 4096 2.656 0.549 0.109 0.024 17 2.3 S_precentral-inf-part
- 1966 1386 2932 2.478 0.511 0.113 0.024 12 2.1 S_precentral-sup-part
- 263 176 482 2.394 0.522 0.117 0.028 2 0.4 S_suborbital
- 1288 885 2318 2.737 0.689 0.127 0.032 12 1.5 S_subparietal
- 1650 1119 2577 2.733 0.544 0.115 0.025 11 1.6 S_temporal_inf
- 6233 4213 10930 2.809 0.561 0.102 0.022 38 5.5 S_temporal_sup
- 257 184 389 2.378 0.497 0.106 0.025 1 0.3 S_temporal_transverse
- PIDs (2452 2455) completed and logs appended.
- #-----------------------------------------
- #@# Cortical Parc 3 lh Sun Oct 8 11:48:36 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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 11:48:36 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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 2525 of (2525 2528) to complete...
- Waiting for PID 2528 of (2525 2528) to complete...
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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...
- 1377 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2293 changed, 159921 examined...
- 001: 537 changed, 10466 examined...
- 002: 180 changed, 3010 examined...
- 003: 82 changed, 1028 examined...
- 004: 48 changed, 464 examined...
- 005: 38 changed, 256 examined...
- 006: 25 changed, 194 examined...
- 007: 21 changed, 124 examined...
- 008: 12 changed, 109 examined...
- 009: 11 changed, 70 examined...
- 010: 10 changed, 65 examined...
- 011: 9 changed, 63 examined...
- 012: 7 changed, 56 examined...
- 013: 2 changed, 35 examined...
- 014: 1 changed, 14 examined...
- 015: 1 changed, 7 examined...
- 016: 1 changed, 7 examined...
- 017: 1 changed, 6 examined...
- 018: 1 changed, 7 examined...
- 019: 2 changed, 6 examined...
- 020: 3 changed, 9 examined...
- 021: 2 changed, 17 examined...
- 022: 0 changed, 11 examined...
- 350 labels changed using aseg
- 000: 75 total segments, 42 labels (402 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, 8 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1017 vertices marked for relabeling...
- 1017 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas.annot...
- classification took 0 minutes and 17 seconds.
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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...
- 1236 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2187 changed, 165183 examined...
- 001: 546 changed, 10201 examined...
- 002: 164 changed, 3073 examined...
- 003: 66 changed, 1002 examined...
- 004: 32 changed, 365 examined...
- 005: 18 changed, 177 examined...
- 006: 16 changed, 99 examined...
- 007: 7 changed, 69 examined...
- 008: 2 changed, 33 examined...
- 009: 3 changed, 14 examined...
- 010: 1 changed, 20 examined...
- 011: 0 changed, 7 examined...
- 199 labels changed using aseg
- 000: 53 total segments, 20 labels (169 vertices) changed
- 001: 34 total segments, 1 labels (2 vertices) changed
- 002: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 9 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1285 vertices marked for relabeling...
- 1285 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas.annot...
- classification took 0 minutes and 17 seconds.
- PIDs (2525 2528) completed and logs appended.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Sun Oct 8 11:48:53 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 lh white
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Sun Oct 8 11:48:53 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 rh white
- Waiting for PID 2576 of (2576 2579) to complete...
- Waiting for PID 2579 of (2576 2579) 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 0050352 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 282813
- Total vertex volume 279572 (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) = 1712602 mm^3 (det: 1.137512 )
- lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371
- rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338
- lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115
- rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702
- SubCortGMVol 65474.000
- SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
- SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
- BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
- BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
- BrainSegVolNotVent 1346802.000
- CerebellumVol 159751.000
- VentChorVol 19992.000
- 3rd4th5thCSF 5338.000
- CSFVol 2234.000, OptChiasmVol 252.000
- MaskVol 1787646.000
- 1984 1295 3801 2.718 0.739 0.145 0.034 27 2.6 caudalanteriorcingulate
- 5259 3525 9733 2.591 0.605 0.120 0.029 47 6.2 caudalmiddlefrontal
- 3483 2330 5258 2.074 0.615 0.141 0.048 46 6.5 cuneus
- 1061 677 1823 2.324 0.738 0.177 0.087 24 4.2 entorhinal
- 4864 3321 8796 2.374 0.631 0.137 0.048 65 9.7 fusiform
- 7016 4674 13325 2.378 0.658 0.134 0.036 89 10.3 inferiorparietal
- 5846 3973 13327 2.616 0.887 0.146 0.057 120 15.1 inferiortemporal
- 1407 954 2554 2.540 0.879 0.124 0.029 18 1.4 isthmuscingulate
- 8406 5619 14308 2.194 0.722 0.150 0.050 130 17.7 lateraloccipital
- 5351 3524 10861 2.710 0.821 0.147 0.054 86 12.5 lateralorbitofrontal
- 4672 3130 6916 1.966 0.589 0.150 0.055 78 10.5 lingual
- 2639 1905 5501 2.473 0.873 0.144 0.044 44 4.5 medialorbitofrontal
- 6508 4486 14276 2.627 0.705 0.125 0.033 71 8.7 middletemporal
- 1229 754 1992 2.295 0.668 0.100 0.037 13 2.0 parahippocampal
- 3140 2030 5537 2.457 0.658 0.141 0.046 40 6.3 paracentral
- 2046 1397 3939 2.523 0.589 0.114 0.027 18 2.2 parsopercularis
- 1104 721 1907 2.359 0.722 0.132 0.046 16 2.0 parsorbitalis
- 2927 1916 6047 2.689 0.744 0.123 0.032 30 3.7 parstriangularis
- 1790 1289 2059 1.840 0.494 0.162 0.054 24 4.1 pericalcarine
- 8053 5247 11744 2.064 0.630 0.127 0.037 86 11.9 postcentral
- 2430 1688 3879 2.271 0.634 0.145 0.041 32 3.9 posteriorcingulate
- 9482 6253 15899 2.428 0.680 0.123 0.038 92 15.1 precentral
- 6054 4090 11174 2.500 0.678 0.134 0.040 75 9.6 precuneus
- 1909 1320 3904 2.850 0.751 0.137 0.038 24 3.0 rostralanteriorcingulate
- 8092 5512 15743 2.569 0.666 0.148 0.049 122 15.7 rostralmiddlefrontal
- 16665 11194 33950 2.701 0.747 0.145 0.050 223 35.1 superiorfrontal
- 8937 5877 13322 2.121 0.543 0.134 0.044 105 15.7 superiorparietal
- 9036 6227 19576 2.626 0.784 0.123 0.035 95 13.1 superiortemporal
- 5420 3738 10524 2.511 0.632 0.131 0.038 73 8.3 supramarginal
- 910 552 1236 2.145 0.555 0.141 0.051 10 1.8 transversetemporal
- 3105 2153 6661 3.190 0.682 0.123 0.035 31 4.4 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 0050352 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 289365
- Total vertex volume 286560 (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) = 1712602 mm^3 (det: 1.137512 )
- lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371
- rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338
- lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115
- rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702
- SubCortGMVol 65474.000
- SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
- SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
- BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
- BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
- BrainSegVolNotVent 1346802.000
- CerebellumVol 159751.000
- VentChorVol 19992.000
- 3rd4th5thCSF 5338.000
- CSFVol 2234.000, OptChiasmVol 252.000
- MaskVol 1787646.000
- 1542 1014 2786 2.549 0.572 0.125 0.026 18 1.6 caudalanteriorcingulate
- 5126 3420 8908 2.552 0.593 0.129 0.049 65 10.4 caudalmiddlefrontal
- 3021 1961 4084 1.971 0.522 0.138 0.041 42 4.9 cuneus
- 701 435 1756 3.006 0.836 0.162 0.076 19 2.2 entorhinal
- 4849 3201 9621 2.674 0.781 0.130 0.043 58 8.2 fusiform
- 8875 5746 17133 2.614 0.696 0.133 0.046 115 16.0 inferiorparietal
- 7063 4640 15203 2.663 0.803 0.143 0.067 143 21.1 inferiortemporal
- 1450 956 2652 2.481 0.792 0.135 0.039 18 2.1 isthmuscingulate
- 8041 5170 12610 2.195 0.705 0.149 0.056 134 18.4 lateraloccipital
- 5995 3862 10502 2.429 0.747 0.145 0.059 102 14.8 lateralorbitofrontal
- 4755 3235 7255 2.071 0.555 0.149 0.047 68 8.7 lingual
- 2512 1678 4773 2.448 0.939 0.138 0.054 40 5.5 medialorbitofrontal
- 7430 5066 17004 2.927 0.686 0.133 0.044 93 13.3 middletemporal
- 1239 770 2018 2.378 0.739 0.111 0.032 12 1.6 parahippocampal
- 2979 1920 4703 2.274 0.638 0.137 0.061 43 8.4 paracentral
- 2907 2000 5650 2.566 0.544 0.118 0.035 30 3.8 parsopercularis
- 1435 916 2556 2.655 0.766 0.147 0.059 27 3.5 parsorbitalis
- 2812 1882 5636 2.662 0.640 0.132 0.034 34 3.5 parstriangularis
- 2241 1554 2803 1.911 0.546 0.130 0.041 27 3.8 pericalcarine
- 7477 4868 10805 2.094 0.701 0.124 0.044 140 14.3 postcentral
- 2486 1700 4588 2.495 0.866 0.149 0.040 38 3.8 posteriorcingulate
- 9396 6125 14482 2.384 0.675 0.132 0.045 103 17.9 precentral
- 6753 4500 12606 2.505 0.681 0.131 0.039 80 10.4 precuneus
- 1525 1028 3561 3.105 0.885 0.131 0.040 21 2.5 rostralanteriorcingulate
- 9844 6566 19487 2.597 0.700 0.143 0.050 146 19.7 rostralmiddlefrontal
- 18652 12191 35936 2.671 0.777 0.141 0.056 299 44.0 superiorfrontal
- 7905 5343 13406 2.298 0.650 0.137 0.046 116 16.1 superiorparietal
- 8248 5407 15580 2.577 0.718 0.134 0.055 115 19.6 superiortemporal
- 5691 3740 10782 2.687 0.621 0.129 0.042 101 10.4 supramarginal
- 703 428 857 2.158 0.707 0.146 0.050 11 1.4 transversetemporal
- 3391 2322 6818 3.180 0.678 0.130 0.036 36 4.6 insula
- PIDs (2576 2579) completed and logs appended.
- #-----------------------------------------
- #@# WM/GM Contrast lh Sun Oct 8 11:49:40 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- pctsurfcon --s 0050352 --lh-only
- #-----------------------------------------
- #@# WM/GM Contrast rh Sun Oct 8 11:49:40 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts
- pctsurfcon --s 0050352 --rh-only
- Waiting for PID 2645 of (2645 2656) to complete...
- Waiting for PID 2656 of (2645 2656) to complete...
- pctsurfcon --s 0050352 --lh-only
- Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts/pctsurfcon.log
- Sun Oct 8 11:49:40 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-6.0.0/0050352/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-928 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-6.0.0/0050352/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2645/lh.wm.mgh --regheader 0050352 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 -0.00002;
- 0.00000 0.00000 1.00000 -0.00001;
- 0.00000 -1.00000 0.00000 0.00003;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 76153
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2645/lh.wm.mgh
- Dim: 159921 1 1
- mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2645/lh.gm.mgh --projfrac 0.3 --regheader 0050352 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 -0.00002;
- 0.00000 0.00000 1.00000 -0.00001;
- 0.00000 -1.00000 0.00000 0.00003;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white
- Done reading source surface
- Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 88661
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2645/lh.gm.mgh
- Dim: 159921 1 1
- mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2645/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2645/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/lh.w-g.pct.mgh
- mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.w-g.pct.mgh --annot 0050352 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/lh.w-g.pct.mgh --annot 0050352 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/stats/lh.w-g.pct.stats --snr
- sysname Linux
- hostname tars-928
- machine x86_64
- user ntraut
- UseRobust 0
- Constructing seg from annotation
- Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/lh.w-g.pct.mgh
- Vertex Area is 0.673795 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 0050352 --rh-only
- Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts/pctsurfcon.log
- Sun Oct 8 11:49:40 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-6.0.0/0050352/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-928 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-6.0.0/0050352/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2656/rh.wm.mgh --regheader 0050352 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 -0.00002;
- 0.00000 0.00000 1.00000 -0.00001;
- 0.00000 -1.00000 0.00000 0.00003;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 76979
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2656/rh.wm.mgh
- Dim: 165183 1 1
- mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2656/rh.gm.mgh --projfrac 0.3 --regheader 0050352 --cortex
- srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/mri/orig.mgz as target reference.
- -------- original matrix -----------
- 1.00000 0.00000 0.00000 -0.00002;
- 0.00000 0.00000 1.00000 -0.00001;
- 0.00000 -1.00000 0.00000 0.00003;
- 0.00000 0.00000 0.00000 1.00000;
- -------- original matrix -----------
- Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.cortex.label
- Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white
- Done reading source surface
- Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 90051
- Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.cortex.label
- Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2656/rh.gm.mgh
- Dim: 165183 1 1
- mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2656/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2656/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/rh.w-g.pct.mgh
- mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.w-g.pct.mgh --annot 0050352 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/rh.w-g.pct.mgh --annot 0050352 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/stats/rh.w-g.pct.stats --snr
- sysname Linux
- hostname tars-928
- machine x86_64
- user ntraut
- UseRobust 0
- Constructing seg from annotation
- Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/rh.w-g.pct.mgh
- Vertex Area is 0.661551 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 (2645 2656) completed and logs appended.
- #-----------------------------------------
- #@# Relabel Hypointensities Sun Oct 8 11:49:47 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri
- mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz
- reading input surface ../surf/lh.white...
- relabeling lh hypointensities...
- 3168 voxels changed to hypointensity...
- reading input surface ../surf/rh.white...
- relabeling rh hypointensities...
- 4008 voxels changed to hypointensity...
- 7379 hypointense voxels neighboring cortex changed
- #-----------------------------------------
- #@# AParc-to-ASeg aparc Sun Oct 8 11:50:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352
- mri_aparc2aseg --s 0050352 --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 11:50:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352
- mri_aparc2aseg --s 0050352 --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 11:50:11 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352
- mri_aparc2aseg --s 0050352 --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 2839 of (2839 2842 2845) to complete...
- Waiting for PID 2842 of (2839 2842 2845) to complete...
- Waiting for PID 2845 of (2839 2842 2845) to complete...
- mri_aparc2aseg --s 0050352 --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 0050352
- outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/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-6.0.0/0050352/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 7.80
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 106
- rescaling Left_Cerebral_Cortex from 61 --> 66
- rescaling Left_Lateral_Ventricle from 13 --> 23
- rescaling Left_Inf_Lat_Vent from 34 --> 29
- rescaling Left_Cerebellum_White_Matter from 86 --> 86
- rescaling Left_Cerebellum_Cortex from 60 --> 63
- rescaling Left_Thalamus from 94 --> 105
- rescaling Left_Thalamus_Proper from 84 --> 89
- rescaling Left_Caudate from 75 --> 73
- rescaling Left_Putamen from 80 --> 78
- rescaling Left_Pallidum from 98 --> 95
- rescaling Third_Ventricle from 25 --> 35
- rescaling Fourth_Ventricle from 22 --> 14
- rescaling Brain_Stem from 81 --> 86
- rescaling Left_Hippocampus from 57 --> 61
- rescaling Left_Amygdala from 56 --> 74
- rescaling CSF from 32 --> 50
- rescaling Left_Accumbens_area from 62 --> 66
- rescaling Left_VentralDC from 87 --> 88
- rescaling Right_Cerebral_White_Matter from 105 --> 103
- rescaling Right_Cerebral_Cortex from 58 --> 68
- rescaling Right_Lateral_Ventricle from 13 --> 27
- rescaling Right_Inf_Lat_Vent from 25 --> 26
- rescaling Right_Cerebellum_White_Matter from 87 --> 87
- rescaling Right_Cerebellum_Cortex from 59 --> 65
- rescaling Right_Thalamus_Proper from 85 --> 85
- rescaling Right_Caudate from 62 --> 73
- rescaling Right_Putamen from 80 --> 78
- rescaling Right_Pallidum from 97 --> 93
- rescaling Right_Hippocampus from 53 --> 64
- rescaling Right_Amygdala from 55 --> 77
- rescaling Right_Accumbens_area from 65 --> 71
- rescaling Right_VentralDC from 86 --> 87
- rescaling Fifth_Ventricle from 40 --> 42
- 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 = 558621
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 159 changed.
- pass 2: 14 changed.
- pass 3: 0 changed.
- nchanged = 0
- Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/aparc+aseg.mgz
- mri_aparc2aseg --s 0050352 --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 0050352
- outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/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-6.0.0/0050352/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 7.80
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 106
- rescaling Left_Cerebral_Cortex from 61 --> 66
- rescaling Left_Lateral_Ventricle from 13 --> 23
- rescaling Left_Inf_Lat_Vent from 34 --> 29
- rescaling Left_Cerebellum_White_Matter from 86 --> 86
- rescaling Left_Cerebellum_Cortex from 60 --> 63
- rescaling Left_Thalamus from 94 --> 105
- rescaling Left_Thalamus_Proper from 84 --> 89
- rescaling Left_Caudate from 75 --> 73
- rescaling Left_Putamen from 80 --> 78
- rescaling Left_Pallidum from 98 --> 95
- rescaling Third_Ventricle from 25 --> 35
- rescaling Fourth_Ventricle from 22 --> 14
- rescaling Brain_Stem from 81 --> 86
- rescaling Left_Hippocampus from 57 --> 61
- rescaling Left_Amygdala from 56 --> 74
- rescaling CSF from 32 --> 50
- rescaling Left_Accumbens_area from 62 --> 66
- rescaling Left_VentralDC from 87 --> 88
- rescaling Right_Cerebral_White_Matter from 105 --> 103
- rescaling Right_Cerebral_Cortex from 58 --> 68
- rescaling Right_Lateral_Ventricle from 13 --> 27
- rescaling Right_Inf_Lat_Vent from 25 --> 26
- rescaling Right_Cerebellum_White_Matter from 87 --> 87
- rescaling Right_Cerebellum_Cortex from 59 --> 65
- rescaling Right_Thalamus_Proper from 85 --> 85
- rescaling Right_Caudate from 62 --> 73
- rescaling Right_Putamen from 80 --> 78
- rescaling Right_Pallidum from 97 --> 93
- rescaling Right_Hippocampus from 53 --> 64
- rescaling Right_Amygdala from 55 --> 77
- rescaling Right_Accumbens_area from 65 --> 71
- rescaling Right_VentralDC from 86 --> 87
- rescaling Fifth_Ventricle from 40 --> 42
- 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 = 558598
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 159 changed.
- pass 2: 14 changed.
- pass 3: 0 changed.
- nchanged = 0
- Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/aparc.a2009s+aseg.mgz
- mri_aparc2aseg --s 0050352 --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 0050352
- outvol mri/aparc.DKTatlas+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/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-6.0.0/0050352/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 7.80
- reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
- rescaling Left_Cerebral_White_Matter from 107 --> 106
- rescaling Left_Cerebral_Cortex from 61 --> 66
- rescaling Left_Lateral_Ventricle from 13 --> 23
- rescaling Left_Inf_Lat_Vent from 34 --> 29
- rescaling Left_Cerebellum_White_Matter from 86 --> 86
- rescaling Left_Cerebellum_Cortex from 60 --> 63
- rescaling Left_Thalamus from 94 --> 105
- rescaling Left_Thalamus_Proper from 84 --> 89
- rescaling Left_Caudate from 75 --> 73
- rescaling Left_Putamen from 80 --> 78
- rescaling Left_Pallidum from 98 --> 95
- rescaling Third_Ventricle from 25 --> 35
- rescaling Fourth_Ventricle from 22 --> 14
- rescaling Brain_Stem from 81 --> 86
- rescaling Left_Hippocampus from 57 --> 61
- rescaling Left_Amygdala from 56 --> 74
- rescaling CSF from 32 --> 50
- rescaling Left_Accumbens_area from 62 --> 66
- rescaling Left_VentralDC from 87 --> 88
- rescaling Right_Cerebral_White_Matter from 105 --> 103
- rescaling Right_Cerebral_Cortex from 58 --> 68
- rescaling Right_Lateral_Ventricle from 13 --> 27
- rescaling Right_Inf_Lat_Vent from 25 --> 26
- rescaling Right_Cerebellum_White_Matter from 87 --> 87
- rescaling Right_Cerebellum_Cortex from 59 --> 65
- rescaling Right_Thalamus_Proper from 85 --> 85
- rescaling Right_Caudate from 62 --> 73
- rescaling Right_Putamen from 80 --> 78
- rescaling Right_Pallidum from 97 --> 93
- rescaling Right_Hippocampus from 53 --> 64
- rescaling Right_Amygdala from 55 --> 77
- rescaling Right_Accumbens_area from 65 --> 71
- rescaling Right_VentralDC from 86 --> 87
- rescaling Fifth_Ventricle from 40 --> 42
- 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 = 558598
- Used brute-force search on 0 voxels
- relabeling unlikely voxels in interior of white matter
- average std[0] = 7.3
- pass 1: 159 changed.
- pass 2: 14 changed.
- pass 3: 0 changed.
- nchanged = 0
- Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
- PIDs (2839 2842 2845) completed and logs appended.
- #-----------------------------------------
- #@# APas-to-ASeg Sun Oct 8 11:57:31 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri
- apas2aseg --i aparc+aseg.mgz --o aseg.mgz
- Sun Oct 8 11:57:31 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-6.0.0/0050352/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-928 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-6.0.0/0050352/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-928
- 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 11:57:31 CEST 2017
- Ended at Sun Oct 8 11:57:38 CEST 2017
- Apas2aseg-Run-Time-Sec 7
-
- apas2aseg Done
- #--------------------------------------------
- #@# ASeg Stats Sun Oct 8 11:57:38 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352
- 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 0050352
- $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 0050352
- sysname Linux
- hostname tars-928
- machine x86_64
- user ntraut
- UseRobust 0
- atlas_icv (eTIV) = 1712602 mm^3 (det: 1.137512 )
- Computing euler number
- orig.nofix lheno = -294, rheno = -354
- orig.nofix lhholes = 148, rhholes = 178
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371
- rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338
- lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115
- rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702
- SubCortGMVol 65474.000
- SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
- SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
- BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
- BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
- BrainSegVolNotVent 1346802.000
- CerebellumVol 159751.000
- VentChorVol 19992.000
- 3rd4th5thCSF 5338.000
- CSFVol 2234.000, OptChiasmVol 252.000
- MaskVol 1787646.000
- 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 11:59:27 CEST 2017
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352
- mri_aparc2aseg --s 0050352 --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 0050352
- 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-6.0.0/0050352/mri/aparc+aseg.mgz
- Reading lh white surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white
- Reading lh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial
- Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/rh.white
- Reading rh pial surface
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial
- Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/mri/ribbon.mgz
- Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/ribbon.mgz
- Ripping vertices labeled as unkown
- Ripped 9038 vertices from left hemi
- Ripped 8147 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-6.0.0/0050352/mri/aseg.mgz
- Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 1119622
- Used brute-force search on 711 voxels
- Fixing Parahip LH WM
- Found 6 clusters
- 0 k 2.000000
- 1 k 4.000000
- 2 k 1.000000
- 3 k 1.000000
- 4 k 1.000000
- 5 k 1561.000000
- Fixing Parahip RH WM
- Found 8 clusters
- 0 k 1.000000
- 1 k 1.000000
- 2 k 2.000000
- 3 k 2.000000
- 4 k 1.000000
- 5 k 1.000000
- 6 k 1.000000
- 7 k 1734.000000
- 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 0050352 --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 0050352 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv
- sysname Linux
- hostname tars-928
- machine x86_64
- user ntraut
- UseRobust 0
- atlas_icv (eTIV) = 1712602 mm^3 (det: 1.137512 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371
- rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338
- lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115
- rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702
- SubCortGMVol 65474.000
- SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
- SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
- BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
- BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
- BrainSegVolNotVent 1346802.000
- CerebellumVol 159751.000
- VentChorVol 19992.000
- 3rd4th5thCSF 5338.000
- CSFVol 2234.000, OptChiasmVol 252.000
- MaskVol 1787646.000
- 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-6.0.0/0050352/label
- #--------------------------------------------
- #@# BA_exvivo Labels lh Sun Oct 8 12:08:55 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 3670 of (3670 3675 3682 3687 3694) to complete...
- Waiting for PID 3675 of (3670 3675 3682 3687 3694) to complete...
- Waiting for PID 3682 of (3670 3675 3682 3687 3694) to complete...
- Waiting for PID 3687 of (3670 3675 3682 3687 3694) to complete...
- Waiting for PID 3694 of (3670 3675 3682 3687 3694) 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 429
- Checking for and removing duplicates
- Writing label file ./lh.BA1_exvivo.label 4558
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 632
- Checking for and removing duplicates
- Writing label file ./lh.BA2_exvivo.label 8541
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 263
- Checking for and removing duplicates
- Writing label file ./lh.BA3a_exvivo.label 4340
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 450
- Checking for and removing duplicates
- Writing label file ./lh.BA3b_exvivo.label 6433
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 1000
- Checking for and removing duplicates
- Writing label file ./lh.BA4a_exvivo.label 6784
- mri_label2label: Done
- PIDs (3670 3675 3682 3687 3694) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 3755 of (3755 3761 3767 3772) to complete...
- Waiting for PID 3761 of (3755 3761 3767 3772) to complete...
- Waiting for PID 3767 of (3755 3761 3767 3772) to complete...
- Waiting for PID 3772 of (3755 3761 3767 3772) 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 465
- Checking for and removing duplicates
- Writing label file ./lh.BA4p_exvivo.label 4535
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 4184
- Checking for and removing duplicates
- Writing label file ./lh.BA6_exvivo.label 17773
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 609
- Checking for and removing duplicates
- Writing label file ./lh.BA44_exvivo.label 4790
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 1134
- Checking for and removing duplicates
- Writing label file ./lh.BA45_exvivo.label 4556
- mri_label2label: Done
- PIDs (3755 3761 3767 3772) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface
- Waiting for PID 3814 of (3814 3820 3826 3832 3838) to complete...
- Waiting for PID 3820 of (3814 3820 3826 3832 3838) to complete...
- Waiting for PID 3826 of (3814 3820 3826 3832 3838) to complete...
- Waiting for PID 3832 of (3814 3820 3826 3832 3838) to complete...
- Waiting for PID 3838 of (3814 3820 3826 3832 3838) 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 1579
- Checking for and removing duplicates
- Writing label file ./lh.V1_exvivo.label 6220
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 3361
- Checking for and removing duplicates
- Writing label file ./lh.V2_exvivo.label 11475
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 565
- Checking for and removing duplicates
- Writing label file ./lh.MT_exvivo.label 2583
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 603
- Checking for and removing duplicates
- Writing label file ./lh.entorhinal_exvivo.label 1893
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 549
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal_exvivo.label 1748
- mri_label2label: Done
- PIDs (3814 3820 3826 3832 3838) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 3919 of (3919 3925 3931 3937 3943) to complete...
- Waiting for PID 3925 of (3919 3925 3931 3937 3943) to complete...
- Waiting for PID 3931 of (3919 3925 3931 3937 3943) to complete...
- Waiting for PID 3937 of (3919 3925 3931 3937 3943) to complete...
- Waiting for PID 3943 of (3919 3925 3931 3937 3943) 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 104
- Checking for and removing duplicates
- Writing label file ./lh.BA1_exvivo.thresh.label 1118
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 179
- Checking for and removing duplicates
- Writing label file ./lh.BA2_exvivo.thresh.label 2271
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 112
- Checking for and removing duplicates
- Writing label file ./lh.BA3a_exvivo.thresh.label 1616
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 188
- Checking for and removing duplicates
- Writing label file ./lh.BA3b_exvivo.thresh.label 2184
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 365
- Checking for and removing duplicates
- Writing label file ./lh.BA4a_exvivo.thresh.label 2684
- mri_label2label: Done
- PIDs (3919 3925 3931 3937 3943) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 3988 of (3988 3994 4000 4005) to complete...
- Waiting for PID 3994 of (3988 3994 4000 4005) to complete...
- Waiting for PID 4000 of (3988 3994 4000 4005) to complete...
- Waiting for PID 4005 of (3988 3994 4000 4005) 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 90
- Checking for and removing duplicates
- Writing label file ./lh.BA4p_exvivo.thresh.label 1639
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 1882
- Checking for and removing duplicates
- Writing label file ./lh.BA6_exvivo.thresh.label 8917
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 163
- Checking for and removing duplicates
- Writing label file ./lh.BA44_exvivo.thresh.label 2075
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 527
- Checking for and removing duplicates
- Writing label file ./lh.BA45_exvivo.thresh.label 1678
- mri_label2label: Done
- PIDs (3988 3994 4000 4005) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface
- Waiting for PID 4052 of (4052 4058 4064 4069 4074) to complete...
- Waiting for PID 4058 of (4052 4058 4064 4069 4074) to complete...
- Waiting for PID 4064 of (4052 4058 4064 4069 4074) to complete...
- Waiting for PID 4069 of (4052 4058 4064 4069 4074) to complete...
- Waiting for PID 4074 of (4052 4058 4064 4069 4074) 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 1170
- Checking for and removing duplicates
- Writing label file ./lh.V1_exvivo.thresh.label 4575
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 1483
- Checking for and removing duplicates
- Writing label file ./lh.V2_exvivo.thresh.label 4817
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 131
- Checking for and removing duplicates
- Writing label file ./lh.MT_exvivo.thresh.label 644
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 262
- Checking for and removing duplicates
- Writing label file ./lh.entorhinal_exvivo.thresh.label 732
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/lh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
- Number of reverse mapping hits = 264
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal_exvivo.thresh.label 714
- mri_label2label: Done
- PIDs (4052 4058 4064 4069 4074) completed and logs appended.
- mris_label2annot --s 0050352 --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-6.0.0/0050352/label
- cmdline mris_label2annot --s 0050352 --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-928
- machine x86_64
- user ntraut
- subject 0050352
- 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-6.0.0/0050352/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 110687 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.BA_exvivo.annot
- mris_label2annot --s 0050352 --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-6.0.0/0050352/label
- cmdline mris_label2annot --s 0050352 --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-928
- machine x86_64
- user ntraut
- subject 0050352
- 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-6.0.0/0050352/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 131466 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 lh white
- computing statistics for each annotation in ./lh.BA_exvivo.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 282813
- Total vertex volume 279572 (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) = 1712602 mm^3 (det: 1.137512 )
- lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371
- rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338
- lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115
- rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702
- SubCortGMVol 65474.000
- SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
- SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
- BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
- BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
- BrainSegVolNotVent 1346802.000
- CerebellumVol 159751.000
- VentChorVol 19992.000
- 3rd4th5thCSF 5338.000
- CSFVol 2234.000, OptChiasmVol 252.000
- MaskVol 1787646.000
- 1264 762 2039 2.137 0.690 0.140 0.046 16 2.2 BA1_exvivo
- 4066 2764 6269 2.202 0.598 0.133 0.038 46 6.5 BA2_exvivo
- 1185 811 1341 1.896 0.575 0.141 0.038 13 1.8 BA3a_exvivo
- 2625 1746 3897 1.899 0.706 0.125 0.036 28 3.8 BA3b_exvivo
- 2093 1292 3153 2.281 0.709 0.137 0.045 26 4.3 BA4a_exvivo
- 1515 1056 2241 2.232 0.677 0.132 0.038 12 2.5 BA4p_exvivo
- 13908 9155 24122 2.471 0.692 0.136 0.048 169 28.3 BA6_exvivo
- 2336 1562 4233 2.432 0.586 0.111 0.027 20 2.7 BA44_exvivo
- 3687 2465 7665 2.579 0.732 0.132 0.038 45 6.0 BA45_exvivo
- 3460 2497 4797 1.865 0.568 0.170 0.063 62 9.3 V1_exvivo
- 8815 5767 13023 2.027 0.647 0.149 0.053 138 19.1 V2_exvivo
- 2297 1555 4609 2.492 0.767 0.144 0.042 34 4.0 MT_exvivo
- 929 549 1365 2.249 0.681 0.153 0.073 18 3.3 perirhinal_exvivo
- 1054 744 2325 2.670 0.821 0.164 0.073 21 3.6 entorhinal_exvivo
- mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0050352 lh white
- computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 282813
- Total vertex volume 279572 (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) = 1712602 mm^3 (det: 1.137512 )
- lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371
- rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338
- lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115
- rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702
- SubCortGMVol 65474.000
- SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
- SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
- BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
- BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
- BrainSegVolNotVent 1346802.000
- CerebellumVol 159751.000
- VentChorVol 19992.000
- 3rd4th5thCSF 5338.000
- CSFVol 2234.000, OptChiasmVol 252.000
- MaskVol 1787646.000
- 803 454 1195 2.064 0.669 0.143 0.048 11 1.6 BA1_exvivo
- 1570 1039 2454 2.229 0.559 0.124 0.039 17 2.6 BA2_exvivo
- 1036 703 1028 1.855 0.510 0.146 0.040 12 1.7 BA3a_exvivo
- 1640 1114 1795 1.578 0.348 0.110 0.028 11 1.9 BA3b_exvivo
- 2004 1270 2973 2.227 0.720 0.138 0.049 24 4.4 BA4a_exvivo
- 1150 835 1635 2.193 0.658 0.136 0.037 9 1.9 BA4p_exvivo
- 7478 4950 12444 2.388 0.692 0.140 0.050 85 16.6 BA6_exvivo
- 1403 947 2439 2.326 0.543 0.123 0.035 15 2.1 BA44_exvivo
- 1584 1014 3841 2.812 0.739 0.126 0.037 19 2.2 BA45_exvivo
- 3740 2654 5176 1.882 0.575 0.168 0.064 66 10.2 V1_exvivo
- 4349 2917 6614 2.028 0.654 0.159 0.056 78 9.8 V2_exvivo
- 577 389 1083 2.470 0.700 0.133 0.038 8 0.9 MT_exvivo
- 485 307 711 2.241 0.701 0.158 0.083 9 1.9 perirhinal_exvivo
- 636 410 1250 2.459 0.742 0.179 0.092 16 2.9 entorhinal_exvivo
- #--------------------------------------------
- #@# BA_exvivo Labels rh Sun Oct 8 12:12:21 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 4207 of (4207 4213 4219 4225 4231) to complete...
- Waiting for PID 4213 of (4207 4213 4219 4225 4231) to complete...
- Waiting for PID 4219 of (4207 4213 4219 4225 4231) to complete...
- Waiting for PID 4225 of (4207 4213 4219 4225 4231) to complete...
- Waiting for PID 4231 of (4207 4213 4219 4225 4231) 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 501
- Checking for and removing duplicates
- Writing label file ./rh.BA1_exvivo.label 4463
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 690
- Checking for and removing duplicates
- Writing label file ./rh.BA2_exvivo.label 7377
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 326
- Checking for and removing duplicates
- Writing label file ./rh.BA3a_exvivo.label 4306
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 585
- Checking for and removing duplicates
- Writing label file ./rh.BA3b_exvivo.label 5107
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 1317
- Checking for and removing duplicates
- Writing label file ./rh.BA4a_exvivo.label 7064
- mri_label2label: Done
- PIDs (4207 4213 4219 4225 4231) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 4284 of (4284 4290 4296 4302) to complete...
- Waiting for PID 4290 of (4284 4290 4296 4302) to complete...
- Waiting for PID 4296 of (4284 4290 4296 4302) to complete...
- Waiting for PID 4302 of (4284 4290 4296 4302) 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 588
- Checking for and removing duplicates
- Writing label file ./rh.BA4p_exvivo.label 5061
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 3560
- Checking for and removing duplicates
- Writing label file ./rh.BA6_exvivo.label 15816
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 1684
- Checking for and removing duplicates
- Writing label file ./rh.BA44_exvivo.label 8596
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 1882
- Checking for and removing duplicates
- Writing label file ./rh.BA45_exvivo.label 7237
- mri_label2label: Done
- PIDs (4284 4290 4296 4302) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface
- Waiting for PID 4358 of (4358 4364 4370 4375 4382) to complete...
- Waiting for PID 4364 of (4358 4364 4370 4375 4382) to complete...
- Waiting for PID 4370 of (4358 4364 4370 4375 4382) to complete...
- Waiting for PID 4375 of (4358 4364 4370 4375 4382) to complete...
- Waiting for PID 4382 of (4358 4364 4370 4375 4382) 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 1904
- Checking for and removing duplicates
- Writing label file ./rh.V1_exvivo.label 6631
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 3270
- Checking for and removing duplicates
- Writing label file ./rh.V2_exvivo.label 11286
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 615
- Checking for and removing duplicates
- Writing label file ./rh.MT_exvivo.label 2547
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 295
- Checking for and removing duplicates
- Writing label file ./rh.entorhinal_exvivo.label 1333
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 190
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal_exvivo.label 942
- mri_label2label: Done
- PIDs (4358 4364 4370 4375 4382) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 4434 of (4434 4440 4446 4452 4458) to complete...
- Waiting for PID 4440 of (4434 4440 4446 4452 4458) to complete...
- Waiting for PID 4446 of (4434 4440 4446 4452 4458) to complete...
- Waiting for PID 4452 of (4434 4440 4446 4452 4458) to complete...
- Waiting for PID 4458 of (4434 4440 4446 4452 4458) 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 126
- Checking for and removing duplicates
- Writing label file ./rh.BA1_exvivo.thresh.label 1002
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 147
- Checking for and removing duplicates
- Writing label file ./rh.BA2_exvivo.thresh.label 2835
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 99
- Checking for and removing duplicates
- Writing label file ./rh.BA3a_exvivo.thresh.label 1797
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 282
- Checking for and removing duplicates
- Writing label file ./rh.BA3b_exvivo.thresh.label 2465
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 271
- Checking for and removing duplicates
- Writing label file ./rh.BA4a_exvivo.thresh.label 1659
- mri_label2label: Done
- PIDs (4434 4440 4446 4452 4458) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 4504 of (4504 4510 4516 4521) to complete...
- Waiting for PID 4510 of (4504 4510 4516 4521) to complete...
- Waiting for PID 4516 of (4504 4510 4516 4521) to complete...
- Waiting for PID 4521 of (4504 4510 4516 4521) 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 279
- Checking for and removing duplicates
- Writing label file ./rh.BA4p_exvivo.thresh.label 1768
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 2018
- Checking for and removing duplicates
- Writing label file ./rh.BA6_exvivo.thresh.label 8977
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 251
- Checking for and removing duplicates
- Writing label file ./rh.BA44_exvivo.thresh.label 1263
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 396
- Checking for and removing duplicates
- Writing label file ./rh.BA45_exvivo.thresh.label 1574
- mri_label2label: Done
- PIDs (4504 4510 4516 4521) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface
- Waiting for PID 4579 of (4579 4585 4591 4596 4602) to complete...
- Waiting for PID 4585 of (4579 4585 4591 4596 4602) to complete...
- Waiting for PID 4591 of (4579 4585 4591 4596 4602) to complete...
- Waiting for PID 4596 of (4579 4585 4591 4596 4602) to complete...
- Waiting for PID 4602 of (4579 4585 4591 4596 4602) 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 1188
- Checking for and removing duplicates
- Writing label file ./rh.V1_exvivo.thresh.label 4420
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 1581
- Checking for and removing duplicates
- Writing label file ./rh.V2_exvivo.thresh.label 5018
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 95
- Checking for and removing duplicates
- Writing label file ./rh.MT_exvivo.thresh.label 363
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 195
- Checking for and removing duplicates
- Writing label file ./rh.entorhinal_exvivo.thresh.label 889
- 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 0050352 --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 = 0050352
- 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-6.0.0/0050352/surf/rh.white
- Reading target registration
- /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
- Number of reverse mapping hits = 79
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal_exvivo.thresh.label 370
- mri_label2label: Done
- PIDs (4579 4585 4591 4596 4602) completed and logs appended.
- mris_label2annot --s 0050352 --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-6.0.0/0050352/label
- cmdline mris_label2annot --s 0050352 --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-928
- machine x86_64
- user ntraut
- subject 0050352
- 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-6.0.0/0050352/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 115506 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.BA_exvivo.annot
- mris_label2annot --s 0050352 --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-6.0.0/0050352/label
- cmdline mris_label2annot --s 0050352 --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-928
- machine x86_64
- user ntraut
- subject 0050352
- 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-6.0.0/0050352/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 137244 unhit vertices
- Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 rh white
- computing statistics for each annotation in ./rh.BA_exvivo.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 289365
- Total vertex volume 286560 (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) = 1712602 mm^3 (det: 1.137512 )
- lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371
- rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338
- lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115
- rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702
- SubCortGMVol 65474.000
- SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
- SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
- BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
- BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
- BrainSegVolNotVent 1346802.000
- CerebellumVol 159751.000
- VentChorVol 19992.000
- 3rd4th5thCSF 5338.000
- CSFVol 2234.000, OptChiasmVol 252.000
- MaskVol 1787646.000
- 1113 655 1936 2.206 0.833 0.149 0.062 17 2.7 BA1_exvivo
- 3341 2188 5246 2.300 0.605 0.135 0.044 40 6.5 BA2_exvivo
- 1215 867 1244 1.971 0.495 0.142 0.037 12 1.7 BA3a_exvivo
- 2286 1513 2760 1.659 0.569 0.112 0.051 82 5.7 BA3b_exvivo
- 2018 1228 3158 2.363 0.654 0.127 0.059 25 5.1 BA4a_exvivo
- 1587 1070 2117 2.243 0.660 0.132 0.046 15 2.8 BA4p_exvivo
- 12072 7760 20645 2.501 0.779 0.138 0.052 158 28.2 BA6_exvivo
- 4478 2988 8571 2.621 0.572 0.118 0.034 46 5.8 BA44_exvivo
- 5432 3676 10839 2.634 0.653 0.139 0.041 76 8.3 BA45_exvivo
- 4068 2739 5413 1.875 0.549 0.141 0.049 61 8.0 V1_exvivo
- 8541 5588 12255 2.060 0.615 0.150 0.050 134 17.7 V2_exvivo
- 2316 1556 4345 2.513 0.723 0.141 0.042 32 3.4 MT_exvivo
- 789 485 1866 2.910 0.952 0.159 0.070 15 2.8 perirhinal_exvivo
- 421 279 808 2.436 0.677 0.157 0.073 9 1.4 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 0050352 rh white
- computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
- reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
- reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white...
- reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial...
- reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white...
- INFO: using TH3 volume calc
- INFO: assuming MGZ format for volumes.
- Using TH3 vertex volume calc
- Total face volume 289365
- Total vertex volume 286560 (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) = 1712602 mm^3 (det: 1.137512 )
- lhCtxGM: 276583.918 275557.000 diff= 1026.9 pctdiff= 0.371
- rhCtxGM: 282762.460 281806.000 diff= 956.5 pctdiff= 0.338
- lhCtxWM: 279774.026 280096.000 diff= -322.0 pctdiff=-0.115
- rhCtxWM: 281871.829 283851.000 diff=-1979.2 pctdiff=-0.702
- SubCortGMVol 65474.000
- SupraTentVol 1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
- SupraTentVolNotVent 1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
- BrainSegVol 1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
- BrainSegVolNotVent 1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
- BrainSegVolNotVent 1346802.000
- CerebellumVol 159751.000
- VentChorVol 19992.000
- 3rd4th5thCSF 5338.000
- CSFVol 2234.000, OptChiasmVol 252.000
- MaskVol 1787646.000
- 747 464 1190 1.948 0.739 0.152 0.058 11 1.8 BA1_exvivo
- 1766 1123 2907 2.394 0.631 0.116 0.038 16 2.6 BA2_exvivo
- 1101 778 1048 1.941 0.489 0.143 0.036 11 1.6 BA3a_exvivo
- 1768 1211 1826 1.522 0.386 0.096 0.022 10 1.5 BA3b_exvivo
- 1256 782 2056 2.289 0.710 0.140 0.070 20 3.9 BA4a_exvivo
- 1395 937 1948 2.362 0.654 0.132 0.049 13 2.7 BA4p_exvivo
- 7774 4988 12516 2.373 0.769 0.143 0.054 105 19.3 BA6_exvivo
- 1094 750 2301 2.670 0.552 0.114 0.034 11 1.4 BA44_exvivo
- 1445 956 3617 2.784 0.654 0.151 0.049 24 2.7 BA45_exvivo
- 3840 2590 5064 1.874 0.546 0.139 0.049 57 7.5 V1_exvivo
- 4616 3027 6524 1.985 0.594 0.151 0.050 69 9.2 V2_exvivo
- 340 225 783 2.675 0.725 0.156 0.047 6 0.6 MT_exvivo
- 486 294 1063 2.891 0.950 0.161 0.075 10 1.8 perirhinal_exvivo
- 311 198 629 2.409 0.929 0.188 0.095 10 1.4 entorhinal_exvivo
- Started at Sat Oct 7 23:40:21 CEST 2017
- Ended at Sun Oct 8 12:15:48 CEST 2017
- #@#%# recon-all-run-time-hours 12.591
- recon-all -s 0050352 finished without error at Sun Oct 8 12:15:48 CEST 2017
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