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|
- Sat Jan 14 08:35:50 UTC 2017
- /data/out/sub-02
- /opt/freesurfer/bin/recon-all
- -subjid sub-02 -sd /data/out -i /data/in/sub-02/anat/sub-02_T1w.nii.gz -autorecon-all -openmp 1
- subjid sub-02
- setenv SUBJECTS_DIR /data/out
- FREESURFER_HOME /opt/freesurfer
- Actual FREESURFER_HOME /opt/freesurfer
- build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP
- Linux 3dcbcfbafa99 3.13.0-105-generic #152-Ubuntu SMP Fri Dec 2 15:37:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
- cputime unlimited
- filesize unlimited
- datasize unlimited
- stacksize 8192 kbytes
- coredumpsize 0 kbytes
- memoryuse unlimited
- vmemoryuse unlimited
- descriptors 524288
- memorylocked 64 kbytes
- maxproc 524288
- maxlocks unlimited
- maxsignal 62147
- maxmessage 819200
- maxnice 0
- maxrtprio 0
- maxrttime unlimited
- total used free shared buffers cached
- Mem: 7982312 508032 7474280 660 34248 313044
- -/+ buffers/cache: 160740 7821572
- Swap: 0 0 0
- ########################################
- program versions used
- $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
- $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
- mri_convert -all-info
- ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:50-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- FLIRT version 5.5
- $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
- mri_convert --version
- stable5
- ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:50-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- Program nu_correct, built from:
- Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
- ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:50-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:51-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:51-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:51-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:51-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:51-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:51-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:51-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:51-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:51-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:51-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:52-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:52-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:52-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:52-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:52-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:52-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:52-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:52-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:52-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:52-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:52-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:52-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/14-08:35:53-GMT BuildTimeStamp: Feb 1 2014 05:44:06 CVS: $Id: mris_make_surfaces.c,v 1.147 2014/01/29 20:42:02 fischl Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:53-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:53-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:53-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:53-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:53-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:53-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
- ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:53-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
- ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:53-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:53-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:53-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:54-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/01/14-08:35:54-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: root Machine: 3dcbcfbafa99 Platform: Linux PlatformVersion: 3.13.0-105-generic CompilerName: GCC CompilerVersion: 30400
- #######################################
- GCADIR /opt/freesurfer/average
- GCA RB_all_2008-03-26.gca
- GCASkull RB_all_withskull_2008-03-26.gca
- AvgCurvTif average.curvature.filled.buckner40.tif
- GCSDIR /opt/freesurfer/average
- GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
- #######################################
- /data/out/sub-02
- mri_convert /data/in/sub-02/anat/sub-02_T1w.nii.gz /data/out/sub-02/mri/orig/001.mgz
- mri_convert /data/in/sub-02/anat/sub-02_T1w.nii.gz /data/out/sub-02/mri/orig/001.mgz
- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
- reading from /data/in/sub-02/anat/sub-02_T1w.nii.gz...
- TR=9.62, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (0.999775, 0.00988981, 0.0187681)
- j_ras = (-0.00988811, 0.999951, -0.000183108)
- k_ras = (-0.018769, 0, 0.999824)
- writing to /data/out/sub-02/mri/orig/001.mgz...
- #--------------------------------------------
- #@# MotionCor Sat Jan 14 08:35:59 UTC 2017
- Found 1 runs
- /data/out/sub-02/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 /data/out/sub-02/mri/orig/001.mgz /data/out/sub-02/mri/rawavg.mgz
- /data/out/sub-02
- mri_convert /data/out/sub-02/mri/rawavg.mgz /data/out/sub-02/mri/orig.mgz --conform
- mri_convert /data/out/sub-02/mri/rawavg.mgz /data/out/sub-02/mri/orig.mgz --conform
- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
- reading from /data/out/sub-02/mri/rawavg.mgz...
- TR=9.62, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (0.999775, 0.00988981, 0.0187681)
- j_ras = (-0.00988811, 0.999951, -0.000183108)
- k_ras = (-0.018769, 0, 0.999824)
- Original Data has (1.2993, 1, 1) mm size and (156, 256, 256) voxels.
- Data is conformed to 1 mm size and 256 voxels for all directions
- changing data type from float to uchar (noscale = 0)...
- MRIchangeType: Building histogram
- Reslicing using trilinear interpolation
- writing to /data/out/sub-02/mri/orig.mgz...
- mri_add_xform_to_header -c /data/out/sub-02/mri/transforms/talairach.xfm /data/out/sub-02/mri/orig.mgz /data/out/sub-02/mri/orig.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Talairach Sat Jan 14 08:36:08 UTC 2017
- /data/out/sub-02/mri
- mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
- talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
- cp transforms/talairach.auto.xfm transforms/talairach.xfm
- #--------------------------------------------
- #@# Talairach Failure Detection Sat Jan 14 08:37:15 UTC 2017
- /data/out/sub-02/mri
- talairach_afd -T 0.005 -xfm transforms/talairach.xfm
- talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7605, pval=0.6675 >= threshold=0.0050)
- awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /data/out/sub-02/mri/transforms/talairach_avi.log
- tal_QC_AZS /data/out/sub-02/mri/transforms/talairach_avi.log
- TalAviQA: 0.97637
- z-score: 0
- #--------------------------------------------
- #@# Nu Intensity Correction Sat Jan 14 08:37:16 UTC 2017
- mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
- /data/out/sub-02/mri
- /opt/freesurfer/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 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
- Linux 3dcbcfbafa99 3.13.0-105-generic #152-Ubuntu SMP Fri Dec 2 15:37:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
- Sat Jan 14 08:37:16 UTC 2017
- Program nu_correct, built from:
- Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
- tmpdir is ./tmp.mri_nu_correct.mni.716
- /data/out/sub-02/mri
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.716/nu0.mnc -odt float
- mri_convert orig.mgz ./tmp.mri_nu_correct.mni.716/nu0.mnc -odt float
- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
- reading from orig.mgz...
- TR=9.62, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 0, -1.86265e-09)
- j_ras = (1.86265e-09, 1.45519e-11, -1)
- k_ras = (-3.11857e-10, 1, 6.13909e-12)
- changing data type from uchar to float (noscale = 0)...
- writing to ./tmp.mri_nu_correct.mni.716/nu0.mnc...
-
- --------------------------------------------------------
- Iteration 1 Sat Jan 14 08:37:18 UTC 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.716/nu0.mnc ./tmp.mri_nu_correct.mni.716/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.716/0/
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 165.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 170.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 211.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1051.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1054.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1449.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1455.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1457.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1481.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1631.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1633.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1635.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1637.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1639.
- (Maybe you should just omit the defined()?)
- [root@3dcbcfbafa99:/data/out/sub-02/mri/] [2017-01-14 08:37:18] running:
- /opt/freesurfer/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 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.716/0/ ./tmp.mri_nu_correct.mni.716/nu0.mnc ./tmp.mri_nu_correct.mni.716/nu1.imp
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Number of iterations: 18
- CV of field change: 0.000964001
- [root@3dcbcfbafa99:/data/out/sub-02/mri/] [2017-01-14 08:37:30] running:
- /opt/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.716/nu0.mnc ./tmp.mri_nu_correct.mni.716/0//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
- --------------------------------------------------------
- Iteration 2 Sat Jan 14 08:37:34 UTC 2017
- nu_correct -clobber ./tmp.mri_nu_correct.mni.716/nu1.mnc ./tmp.mri_nu_correct.mni.716/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.716/1/
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 165.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 170.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 211.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1051.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1054.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1449.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1455.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1457.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1481.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1631.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1633.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1635.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1637.
- (Maybe you should just omit the defined()?)
- defined(@array) is deprecated at /opt/freesurfer/mni/bin/nu_estimate_np_and_em line 1639.
- (Maybe you should just omit the defined()?)
- [root@3dcbcfbafa99:/data/out/sub-02/mri/] [2017-01-14 08:37:34] running:
- /opt/freesurfer/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 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.716/1/ ./tmp.mri_nu_correct.mni.716/nu1.mnc ./tmp.mri_nu_correct.mni.716/nu2.imp
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/mni/bin/sharpen_volume line 153.
- Processing:.................................................................Done
- Number of iterations: 16
- CV of field change: 0.0009728
- [root@3dcbcfbafa99:/data/out/sub-02/mri/] [2017-01-14 08:37:44] running:
- /opt/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.716/nu1.mnc ./tmp.mri_nu_correct.mni.716/1//template.mnc
- Transforming slices:......................................................................................Done
- Transforming slices:................................................................................................................................................................................................................................................................Done
-
-
-
- mri_binarize --i ./tmp.mri_nu_correct.mni.716/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.716/ones.mgz
- $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
- cwd /data/out/sub-02/mri
- cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.716/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.716/ones.mgz
- sysname Linux
- hostname 3dcbcfbafa99
- machine x86_64
- user root
- input ./tmp.mri_nu_correct.mni.716/nu2.mnc
- frame 0
- nErode3d 0
- nErode2d 0
- output ./tmp.mri_nu_correct.mni.716/ones.mgz
- Binarizing based on threshold
- min -1
- max +infinity
- binval 1
- binvalnot 0
- Found 16777216 values in range
- Counting number of voxels
- Found 16777216 voxels in final mask
- mri_binarize done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.716/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.716/sum.junk --avgwf ./tmp.mri_nu_correct.mni.716/input.mean.dat
- $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
- cwd
- cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.716/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.716/sum.junk --avgwf ./tmp.mri_nu_correct.mni.716/input.mean.dat
- sysname Linux
- hostname 3dcbcfbafa99
- machine x86_64
- user root
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.716/ones.mgz
- Loading orig.mgz
- Voxel Volume is 1 mm^3
- Generating list of segmentation ids
- Found 1 segmentations
- Computing statistics for each segmentation
- 0 1 16777216 16777216.000
- Reporting on 1 segmentations
- Computing spatial average of each frame
- 0
- Writing to ./tmp.mri_nu_correct.mni.716/input.mean.dat
- mri_segstats done
- mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.716/ones.mgz --i ./tmp.mri_nu_correct.mni.716/nu2.mnc --sum ./tmp.mri_nu_correct.mni.716/sum.junk --avgwf ./tmp.mri_nu_correct.mni.716/output.mean.dat
- $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
- cwd
- cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.716/ones.mgz --i ./tmp.mri_nu_correct.mni.716/nu2.mnc --sum ./tmp.mri_nu_correct.mni.716/sum.junk --avgwf ./tmp.mri_nu_correct.mni.716/output.mean.dat
- sysname Linux
- hostname 3dcbcfbafa99
- machine x86_64
- user root
- UseRobust 0
- Loading ./tmp.mri_nu_correct.mni.716/ones.mgz
- Loading ./tmp.mri_nu_correct.mni.716/nu2.mnc
- Voxel Volume is 1 mm^3
- Generating list of segmentation ids
- Found 1 segmentations
- Computing statistics for each segmentation
- 0 1 16777216 16777216.000
- Reporting on 1 segmentations
- Computing spatial average of each frame
- 0
- Writing to ./tmp.mri_nu_correct.mni.716/output.mean.dat
- mri_segstats done
- mris_calc -o ./tmp.mri_nu_correct.mni.716/nu2.mnc ./tmp.mri_nu_correct.mni.716/nu2.mnc mul 1.10275123692108037959
- Saving result to './tmp.mri_nu_correct.mni.716/nu2.mnc' (type = MINC ) [ ok ]
- mri_convert ./tmp.mri_nu_correct.mni.716/nu2.mnc nu.mgz --like orig.mgz
- mri_convert ./tmp.mri_nu_correct.mni.716/nu2.mnc nu.mgz --like orig.mgz
- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
- reading from ./tmp.mri_nu_correct.mni.716/nu2.mnc...
- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
- i_ras = (-1, 0, -1.86265e-09)
- j_ras = (1.86264e-09, 1.45519e-11, -1)
- k_ras = (-3.11857e-10, 1, 6.13909e-12)
- 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 6 seconds.
- mapping ( 7, 90) to ( 3, 110)
-
-
- Sat Jan 14 08:38:17 UTC 2017
- mri_nu_correct.mni done
- mri_add_xform_to_header -c /data/out/sub-02/mri/transforms/talairach.xfm nu.mgz nu.mgz
- INFO: extension is mgz
- #--------------------------------------------
- #@# Intensity Normalization Sat Jan 14 08:38:18 UTC 2017
- /data/out/sub-02/mri
- mri_normalize -g 1 nu.mgz T1.mgz
- using max gradient = 1.000
- reading from nu.mgz...
- normalizing image...
- talairach transform
- 1.097 -0.007 -0.038 3.369;
- 0.052 1.105 0.062 -44.826;
- 0.036 -0.003 1.168 -0.165;
- 0.000 0.000 0.000 1.000;
- processing without aseg, no1d=0
- MRInormInit():
- INFO: Modifying talairach volume c_(r,a,s) based on average_305
- MRInormalize():
- MRIsplineNormalize(): npeaks = 13
- Starting OpenSpline(): npoints = 13
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Iterating 2 times
- ---------------------------------
- 3d normalization pass 1 of 2
- white matter peak found at 111
- white matter peak found at 109
- gm peak at 56 (56), valley at 30 (30)
- csf peak at 28, setting threshold to 46
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 111
- white matter peak found at 110
- gm peak at 56 (56), valley at 28 (28)
- csf peak at 28, setting threshold to 46
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to T1.mgz
- 3D bias adjustment took 1 minutes and 38 seconds.
- #--------------------------------------------
- #@# Skull Stripping Sat Jan 14 08:39:56 UTC 2017
- /data/out/sub-02/mri
- mri_em_register -skull nu.mgz /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta
- aligning to atlas containing skull, setting unknown_nbr_spacing = 5
- reading 1 input volumes...
- logging results to talairach_with_skull.log
- reading '/opt/freesurfer/average/RB_all_withskull_2008-03-26.gca'...
- average std = 23.1 using min determinant for regularization = 53.4
- 0 singular and 5702 ill-conditioned covariance matrices regularized
- reading 'nu.mgz'...
- freeing gibbs priors...done.
- bounding unknown intensity as < 20.2 or > 943.7
- total sample mean = 92.0 (1443 zeros)
- ************************************************
- spacing=8, using 3481 sample points, tol=1.00e-05...
- ************************************************
- register_mri: find_optimal_transform
- find_optimal_transform: nsamples 3481, passno 0, spacing 8
- resetting wm mean[0]: 117 --> 126
- resetting gm mean[0]: 74 --> 74
- input volume #1 is the most T1-like
- using real data threshold=7.0
- skull bounding box = (48, 33, 34) --> (209, 216, 231)
- using (102, 94, 133) as brain centroid...
- mean wm in atlas = 126, using box (82,71,109) --> (121, 116,157) to find MRI wm
- before smoothing, mri peak at 106
- after smoothing, mri peak at 106, scaling input intensities by 1.189
- scaling channel 0 by 1.18868
- initial log_p = -4.9
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -4.626143 @ (-9.091, 9.091, -27.273)
- max log p = -4.550845 @ (4.545, -4.545, 13.636)
- max log p = -4.508931 @ (2.273, 2.273, -6.818)
- max log p = -4.508931 @ (0.000, 0.000, 0.000)
- max log p = -4.504515 @ (0.568, 0.568, -0.568)
- max log p = -4.504515 @ (0.000, 0.000, 0.000)
- Found translation: (-1.7, 7.4, -21.0): log p = -4.505
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.5 (thresh=-4.5)
- 1.150 0.000 0.000 -20.824;
- 0.000 1.236 0.000 -19.481;
- 0.000 0.000 1.150 -40.082;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.236 0.000 0.000 -31.818;
- 0.000 1.329 0.000 -30.026;
- 0.000 0.000 1.150 -40.082;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 2 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
- 1.236 0.000 0.000 -31.818;
- 0.000 1.329 0.000 -30.026;
- 0.000 0.000 1.150 -40.082;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0)
- 1.189 -0.042 -0.001 -22.795;
- 0.040 1.302 0.037 -38.543;
- 0.000 -0.041 1.086 -25.346;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 4 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.189 -0.042 -0.001 -22.795;
- 0.040 1.302 0.037 -38.543;
- 0.000 -0.041 1.086 -25.346;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.193 -0.042 -0.001 -23.318;
- 0.040 1.304 0.028 -37.648;
- 0.000 -0.030 1.087 -27.272;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.195 -0.042 -0.001 -23.492;
- 0.040 1.304 0.028 -37.648;
- 0.000 -0.030 1.087 -27.272;
- 0.000 0.000 0.000 1.000;
- min search scale 0.025000 reached
- ***********************************************
- Computing MAP estimate using 3481 samples...
- ***********************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-05
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.19483 -0.04203 -0.00119 -23.49222;
- 0.03971 1.30354 0.02803 -37.64787;
- 0.00032 -0.03045 1.08707 -27.27153;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.19483 -0.04203 -0.00119 -23.49222;
- 0.03971 1.30354 0.02803 -37.64787;
- 0.00032 -0.03045 1.08707 -27.27153;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.195 -0.042 -0.001 -23.492;
- 0.040 1.304 0.028 -37.648;
- 0.000 -0.030 1.087 -27.272;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.9 (old=-4.9)
- transform before final EM align:
- 1.195 -0.042 -0.001 -23.492;
- 0.040 1.304 0.028 -37.648;
- 0.000 -0.030 1.087 -27.272;
- 0.000 0.000 0.000 1.000;
- **************************************************
- EM alignment process ...
- Computing final MAP estimate using 382743 samples.
- **************************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-07
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.19483 -0.04203 -0.00119 -23.49222;
- 0.03971 1.30354 0.02803 -37.64787;
- 0.00032 -0.03045 1.08707 -27.27153;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.19483 -0.04203 -0.00119 -23.49222;
- 0.03971 1.30354 0.02803 -37.64787;
- 0.00032 -0.03045 1.08707 -27.27153;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 4.3 tol 0.000000
- final transform:
- 1.195 -0.042 -0.001 -23.492;
- 0.040 1.304 0.028 -37.648;
- 0.000 -0.030 1.087 -27.272;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull.lta...
- registration took 24 minutes and 22 seconds.
- mri_watershed -T1 -brain_atlas /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
- Mode: T1 normalized volume
- Mode: Use the information of atlas (default parms, --help for details)
- *********************************************************
- The input file is T1.mgz
- The output file is brainmask.auto.mgz
- Weighting the input with atlas information before watershed
- *************************WATERSHED**************************
- Sorting...
- first estimation of the COG coord: x=129 y=104 z=133 r=76
- first estimation of the main basin volume: 1856434 voxels
- Looking for seedpoints
- 2 found in the cerebellum
- 12 found in the rest of the brain
- global maximum in x=146, y=92, z=97, Imax=255
- CSF=21, WM_intensity=110, WM_VARIANCE=5
- WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110
- preflooding height equal to 10 percent
- done.
- Analyze...
- main basin size=9195722540 voxels, voxel volume =1.000
- = 9195722540 mmm3 = 9195722.752 cm3
- done.
- PostAnalyze...Basin Prior
- 5 basins merged thanks to atlas
- ***** 0 basin(s) merged in 1 iteration(s)
- ***** 0 voxel(s) added to the main basin
- done.
- Weighting the input with prior template
- ****************TEMPLATE DEFORMATION****************
- second estimation of the COG coord: x=128,y=114, z=125, r=9058 iterations
- ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
- GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=32 , nb = 45738
- RIGHT_CER CSF_MIN=0, CSF_intensity=5, CSF_MAX=22 , nb = 3366
- LEFT_CER CSF_MIN=0, CSF_intensity=7, CSF_MAX=24 , nb = 3132
- RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=35 , nb = 19170
- LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=34 , nb = 19350
- OTHER CSF_MIN=0, CSF_intensity=5, CSF_MAX=18 , nb = 720
-
- CSF_MAX TRANSITION GM_MIN GM
- GLOBAL
- before analyzing : 32, 27, 22, 50
- after analyzing : 22, 27, 27, 32
- RIGHT_CER
- before analyzing : 22, 23, 26, 52
- after analyzing : 22, 25, 26, 31
- LEFT_CER
- before analyzing : 24, 23, 22, 50
- after analyzing : 23, 24, 25, 30
- RIGHT_BRAIN
- before analyzing : 35, 28, 21, 50
- after analyzing : 22, 28, 28, 33
- LEFT_BRAIN
- before analyzing : 34, 27, 21, 50
- after analyzing : 22, 27, 27, 32
- OTHER
- before analyzing : 18, 19, 22, 50
- after analyzing : 18, 23, 25, 29
- mri_strip_skull: done peeling brain
- highly tesselated surface with 10242 vertices
- matching...73 iterations
- *********************VALIDATION*********************
- curvature mean = -0.014, std = 0.011
- curvature mean = 67.361, std = 7.088
- No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
- before rotation: sse = 5.32, sigma = 8.12
- after rotation: sse = 5.32, sigma = 8.12
- Localization of inacurate regions: Erosion-Dilation steps
- the sse mean is 5.63, its var is 6.92
- before Erosion-Dilatation 2.47% of inacurate vertices
- after Erosion-Dilatation 2.41% 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...32 iterations
- mri_strip_skull: done peeling brain
- Brain Size = 1429370 voxels, voxel volume = 1.000 mm3
- = 1429370 mmm3 = 1429.370 cm3
- ******************************
- Saving brainmask.auto.mgz
- done
- cp brainmask.auto.mgz brainmask.mgz
- #-------------------------------------
- #@# EM Registration Sat Jan 14 09:04:38 UTC 2017
- /data/out/sub-02/mri
- mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta
- aligning to atlas containing skull, setting unknown_nbr_spacing = 3
- using MR volume brainmask.mgz to mask input volume...
- reading 1 input volumes...
- logging results to talairach.log
- reading '/opt/freesurfer/average/RB_all_2008-03-26.gca'...
- average std = 6.9 using min determinant for regularization = 4.7
- 0 singular and 1812 ill-conditioned covariance matrices regularized
- reading 'nu.mgz'...
- freeing gibbs priors...done.
- bounding unknown intensity as < 14.9 or > 790.2
- total sample mean = 84.4 (994 zeros)
- ************************************************
- spacing=8, using 2772 sample points, tol=1.00e-05...
- ************************************************
- register_mri: find_optimal_transform
- find_optimal_transform: nsamples 2772, passno 0, spacing 8
- resetting wm mean[0]: 102 --> 107
- resetting gm mean[0]: 64 --> 64
- input volume #1 is the most T1-like
- using real data threshold=17.0
- skull bounding box = (62, 52, 49) --> (195, 163, 210)
- using (106, 89, 130) as brain centroid...
- mean wm in atlas = 107, using box (90,75,110) --> (122, 102,149) to find MRI wm
- before smoothing, mri peak at 106
- after smoothing, mri peak at 107, scaling input intensities by 1.000
- scaling channel 0 by 1
- initial log_p = -4.4
- ************************************************
- First Search limited to translation only.
- ************************************************
- max log p = -3.947873 @ (-9.091, 9.091, -27.273)
- max log p = -3.866553 @ (4.545, -4.545, 4.545)
- max log p = -3.851453 @ (2.273, -2.273, 2.273)
- max log p = -3.851453 @ (0.000, 0.000, 0.000)
- max log p = -3.839586 @ (0.568, 6.250, 0.568)
- max log p = -3.839586 @ (0.000, 0.000, 0.000)
- Found translation: (-1.7, 8.5, -19.9): log p = -3.840
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.8 (thresh=-3.8)
- 1.150 0.000 0.000 -20.982;
- 0.000 1.150 0.000 -8.028;
- 0.000 0.000 1.064 -27.869;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
- 1.150 0.000 0.000 -20.982;
- 0.000 1.150 0.000 -8.028;
- 0.000 0.000 1.064 -27.869;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 2 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.4 (thresh=-3.4)
- 1.106 0.000 0.032 -21.282;
- 0.000 1.215 0.000 -19.076;
- -0.040 0.000 1.083 -25.172;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
- 1.106 0.000 0.032 -21.282;
- 0.000 1.215 0.000 -19.076;
- -0.040 0.000 1.083 -25.172;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 4 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
- 1.105 -0.040 0.014 -14.369;
- 0.036 1.216 0.009 -24.562;
- -0.022 -0.010 1.080 -26.882;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.3 (thresh=-3.3)
- 1.105 -0.040 0.014 -14.369;
- 0.036 1.215 0.009 -24.394;
- -0.022 -0.010 1.078 -26.727;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 6 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
- 1.105 -0.040 0.014 -14.369;
- 0.036 1.212 0.009 -24.058;
- -0.022 -0.010 1.078 -26.727;
- 0.000 0.000 0.000 1.000;
- min search scale 0.025000 reached
- ***********************************************
- Computing MAP estimate using 2772 samples...
- ***********************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-05
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.10498 -0.03972 0.01445 -14.36920;
- 0.03595 1.21195 0.00927 -24.05831;
- -0.02185 -0.00994 1.07830 -26.72696;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 2772
- Quasinewton: input matrix
- 1.10498 -0.03972 0.01445 -14.36920;
- 0.03595 1.21195 0.00927 -24.05831;
- -0.02185 -0.00994 1.07830 -26.72696;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.105 -0.040 0.014 -14.369;
- 0.036 1.212 0.009 -24.058;
- -0.022 -0.010 1.078 -26.727;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.2 (old=-4.4)
- transform before final EM align:
- 1.105 -0.040 0.014 -14.369;
- 0.036 1.212 0.009 -24.058;
- -0.022 -0.010 1.078 -26.727;
- 0.000 0.000 0.000 1.000;
- **************************************************
- EM alignment process ...
- Computing final MAP estimate using 312841 samples.
- **************************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-07
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.10498 -0.03972 0.01445 -14.36920;
- 0.03595 1.21195 0.00927 -24.05831;
- -0.02185 -0.00994 1.07830 -26.72696;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 312841
- Quasinewton: input matrix
- 1.10498 -0.03972 0.01445 -14.36920;
- 0.03595 1.21195 0.00927 -24.05831;
- -0.02185 -0.00994 1.07830 -26.72696;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 3.8 tol 0.000000
- final transform:
- 1.105 -0.040 0.014 -14.369;
- 0.036 1.212 0.009 -24.058;
- -0.022 -0.010 1.078 -26.727;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach.lta...
- registration took 18 minutes and 58 seconds.
- #--------------------------------------
- #@# CA Normalize Sat Jan 14 09:23:36 UTC 2017
- /data/out/sub-02/mri
- mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2008-03-26.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 '/opt/freesurfer/average/RB_all_2008-03-26.gca'...
- reading transform from 'transforms/talairach.lta'...
- reading input volume from nu.mgz...
- resetting wm mean[0]: 102 --> 107
- resetting gm mean[0]: 64 --> 64
- input volume #1 is the most T1-like
- using real data threshold=17.0
- skull bounding box = (62, 52, 49) --> (195, 163, 210)
- using (106, 89, 130) as brain centroid...
- mean wm in atlas = 107, using box (90,75,110) --> (122, 102,149) to find MRI wm
- before smoothing, mri peak at 106
- after smoothing, mri peak at 107, scaling input intensities by 1.000
- scaling channel 0 by 1
- using 244171 sample points...
- INFO: compute sample coordinates transform
- 1.105 -0.040 0.014 -14.369;
- 0.036 1.212 0.009 -24.058;
- -0.022 -0.010 1.078 -26.727;
- 0.000 0.000 0.000 1.000;
- INFO: transform used
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (129, 58, 53) --> (190, 154, 209)
- Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 172.0
- 0 of 272 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (71, 58, 52) --> (130, 156, 208)
- Right_Cerebral_White_Matter: limiting intensities to 100.0 --> 172.0
- 0 of 168 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (132, 126, 74) --> (177, 162, 124)
- Left_Cerebellum_White_Matter: limiting intensities to 79.0 --> 172.0
- 0 of 8 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (90, 126, 71) --> (131, 163, 123)
- Right_Cerebellum_White_Matter: limiting intensities to 81.0 --> 172.0
- 0 of 10 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (116, 122, 105) --> (145, 179, 135)
- Brain_Stem: limiting intensities to 83.0 --> 172.0
- 8 of 11 (72.7%) samples deleted
- using 469 total control points for intensity normalization...
- bias field = 0.987 +- 0.041
- 0 of 461 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (129, 58, 53) --> (190, 154, 209)
- Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 170.0
- 0 of 318 (0.0%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (71, 58, 52) --> (130, 156, 208)
- Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 170.0
- 0 of 258 (0.0%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (132, 126, 74) --> (177, 162, 124)
- Left_Cerebellum_White_Matter: limiting intensities to 75.0 --> 170.0
- 0 of 60 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (90, 126, 71) --> (131, 163, 123)
- Right_Cerebellum_White_Matter: limiting intensities to 76.0 --> 170.0
- 0 of 54 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (116, 122, 105) --> (145, 179, 135)
- Brain_Stem: limiting intensities to 65.0 --> 170.0
- 5 of 73 (6.8%) samples deleted
- using 763 total control points for intensity normalization...
- bias field = 1.018 +- 0.054
- 4 of 758 control points discarded
- finding control points in Left_Cerebral_White_Matter....
- found 41584 control points for structure...
- bounding box (129, 58, 53) --> (190, 154, 209)
- Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 179.0
- 1 of 371 (0.3%) samples deleted
- finding control points in Right_Cerebral_White_Matter....
- found 40735 control points for structure...
- bounding box (71, 58, 52) --> (130, 156, 208)
- Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 179.0
- 1 of 351 (0.3%) samples deleted
- finding control points in Left_Cerebellum_White_Matter....
- found 3012 control points for structure...
- bounding box (132, 126, 74) --> (177, 162, 124)
- Left_Cerebellum_White_Matter: limiting intensities to 77.0 --> 179.0
- 0 of 91 (0.0%) samples deleted
- finding control points in Right_Cerebellum_White_Matter....
- found 2764 control points for structure...
- bounding box (90, 126, 71) --> (131, 163, 123)
- Right_Cerebellum_White_Matter: limiting intensities to 79.0 --> 179.0
- 0 of 66 (0.0%) samples deleted
- finding control points in Brain_Stem....
- found 3520 control points for structure...
- bounding box (116, 122, 105) --> (145, 179, 135)
- Brain_Stem: limiting intensities to 58.0 --> 179.0
- 0 of 141 (0.0%) samples deleted
- using 1020 total control points for intensity normalization...
- bias field = 1.011 +- 0.058
- 0 of 1018 control points discarded
- writing normalized volume to norm.mgz...
- writing control points to ctrl_pts.mgz
- freeing GCA...done.
- normalization took 1 minutes and 23 seconds.
- #--------------------------------------
- #@# CA Reg Sat Jan 14 09:24:59 UTC 2017
- /data/out/sub-02/mri
- mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/average/RB_all_2008-03-26.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...
- reading 1 input volumes...
- logging results to talairach.log
- reading input volume 'norm.mgz'...
- reading GCA '/opt/freesurfer/average/RB_all_2008-03-26.gca'...
- label assignment complete, 0 changed (0.00%)
- det(m_affine) = 1.45 (predicted orig area = 5.5)
- label assignment complete, 0 changed (0.00%)
- freeing gibbs priors...done.
- average std[0] = 5.0
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.039
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.861, neg=0, invalid=96777
- 0001: dt=129.472000, rms=0.799 (7.220%), neg=0, invalid=96777
- 0002: dt=92.480000, rms=0.791 (0.981%), neg=0, invalid=96777
- 0003: dt=295.936000, rms=0.777 (1.803%), neg=0, invalid=96777
- 0004: dt=73.984000, rms=0.772 (0.600%), neg=0, invalid=96777
- 0005: dt=517.888000, rms=0.758 (1.807%), neg=0, invalid=96777
- 0006: dt=32.368000, rms=0.757 (0.179%), neg=0, invalid=96777
- 0007: dt=32.368000, rms=0.756 (0.080%), neg=0, invalid=96777
- 0008: dt=32.368000, rms=0.756 (0.063%), neg=0, invalid=96777
- 0009: dt=32.368000, rms=0.755 (0.078%), neg=0, invalid=96777
- 0010: dt=32.368000, rms=0.753 (0.208%), neg=0, invalid=96777
- 0011: dt=32.368000, rms=0.751 (0.342%), neg=0, invalid=96777
- 0012: dt=32.368000, rms=0.748 (0.360%), neg=0, invalid=96777
- 0013: dt=32.368000, rms=0.746 (0.315%), neg=0, invalid=96777
- 0014: dt=32.368000, rms=0.744 (0.295%), neg=0, invalid=96777
- 0015: dt=32.368000, rms=0.741 (0.295%), neg=0, invalid=96777
- 0016: dt=32.368000, rms=0.740 (0.248%), neg=0, invalid=96777
- 0017: dt=32.368000, rms=0.738 (0.205%), neg=0, invalid=96777
- 0018: dt=32.368000, rms=0.737 (0.212%), neg=0, invalid=96777
- 0019: dt=32.368000, rms=0.735 (0.271%), neg=0, invalid=96777
- 0020: dt=32.368000, rms=0.732 (0.316%), neg=0, invalid=96777
- 0021: dt=32.368000, rms=0.730 (0.292%), neg=0, invalid=96777
- 0022: dt=32.368000, rms=0.728 (0.253%), neg=0, invalid=96777
- 0023: dt=32.368000, rms=0.727 (0.234%), neg=0, invalid=96777
- 0024: dt=32.368000, rms=0.725 (0.212%), neg=0, invalid=96777
- 0025: dt=32.368000, rms=0.724 (0.175%), neg=0, invalid=96777
- 0026: dt=32.368000, rms=0.723 (0.157%), neg=0, invalid=96777
- 0027: dt=32.368000, rms=0.721 (0.187%), neg=0, invalid=96777
- 0028: dt=32.368000, rms=0.720 (0.215%), neg=0, invalid=96777
- 0029: dt=32.368000, rms=0.718 (0.212%), neg=0, invalid=96777
- 0030: dt=32.368000, rms=0.717 (0.199%), neg=0, invalid=96777
- 0031: dt=32.368000, rms=0.715 (0.186%), neg=0, invalid=96777
- 0032: dt=32.368000, rms=0.714 (0.171%), neg=0, invalid=96777
- 0033: dt=32.368000, rms=0.713 (0.158%), neg=0, invalid=96777
- 0034: dt=32.368000, rms=0.712 (0.149%), neg=0, invalid=96777
- 0035: dt=32.368000, rms=0.711 (0.155%), neg=0, invalid=96777
- 0036: dt=32.368000, rms=0.710 (0.163%), neg=0, invalid=96777
- 0037: dt=32.368000, rms=0.709 (0.146%), neg=0, invalid=96777
- 0038: dt=32.368000, rms=0.708 (0.142%), neg=0, invalid=96777
- 0039: dt=32.368000, rms=0.707 (0.121%), neg=0, invalid=96777
- 0040: dt=32.368000, rms=0.706 (0.107%), neg=0, invalid=96777
- 0041: dt=32.368000, rms=0.706 (0.001%), neg=0, invalid=96777
- 0042: dt=32.368000, rms=0.706 (0.010%), neg=0, invalid=96777
- 0043: dt=32.368000, rms=0.706 (0.016%), neg=0, invalid=96777
- 0044: dt=32.368000, rms=0.706 (0.017%), neg=0, invalid=96777
- 0045: dt=32.368000, rms=0.706 (0.027%), neg=0, invalid=96777
- 0046: dt=32.368000, rms=0.705 (0.042%), neg=0, invalid=96777
- 0047: dt=32.368000, rms=0.705 (0.055%), neg=0, invalid=96777
- 0048: dt=32.368000, rms=0.704 (0.057%), neg=0, invalid=96777
- 0049: dt=32.368000, rms=0.704 (0.057%), neg=0, invalid=96777
- 0050: dt=32.368000, rms=0.704 (0.057%), neg=0, invalid=96777
- 0051: dt=32.368000, rms=0.703 (0.050%), neg=0, invalid=96777
- 0052: dt=32.368000, rms=0.703 (0.056%), neg=0, invalid=96777
- 0053: dt=32.368000, rms=0.702 (0.066%), neg=0, invalid=96777
- 0054: dt=32.368000, rms=0.702 (0.072%), neg=0, invalid=96777
- 0055: dt=32.368000, rms=0.701 (0.068%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.701, neg=0, invalid=96777
- 0056: dt=129.472000, rms=0.701 (0.096%), neg=0, invalid=96777
- 0057: dt=369.920000, rms=0.698 (0.346%), neg=0, invalid=96777
- 0058: dt=27.744000, rms=0.698 (0.023%), neg=0, invalid=96777
- 0059: dt=27.744000, rms=0.698 (-0.002%), neg=0, invalid=96777
- setting smoothness coefficient to 0.154
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.703, neg=0, invalid=96777
- 0060: dt=103.680000, rms=0.694 (1.284%), neg=0, invalid=96777
- 0061: dt=62.208000, rms=0.683 (1.663%), neg=0, invalid=96777
- 0062: dt=15.552000, rms=0.680 (0.332%), neg=0, invalid=96777
- 0063: dt=145.152000, rms=0.674 (0.891%), neg=0, invalid=96777
- 0064: dt=36.288000, rms=0.665 (1.373%), neg=0, invalid=96777
- 0065: dt=9.072000, rms=0.665 (0.093%), neg=0, invalid=96777
- 0066: dt=9.072000, rms=0.664 (0.073%), neg=0, invalid=96777
- 0067: dt=9.072000, rms=0.663 (0.093%), neg=0, invalid=96777
- 0068: dt=9.072000, rms=0.663 (0.126%), neg=0, invalid=96777
- 0069: dt=9.072000, rms=0.661 (0.206%), neg=0, invalid=96777
- 0070: dt=9.072000, rms=0.659 (0.303%), neg=0, invalid=96777
- 0071: dt=9.072000, rms=0.657 (0.374%), neg=0, invalid=96777
- 0072: dt=9.072000, rms=0.654 (0.401%), neg=0, invalid=96777
- 0073: dt=9.072000, rms=0.652 (0.391%), neg=0, invalid=96777
- 0074: dt=9.072000, rms=0.649 (0.359%), neg=0, invalid=96777
- 0075: dt=9.072000, rms=0.647 (0.333%), neg=0, invalid=96777
- 0076: dt=9.072000, rms=0.645 (0.308%), neg=0, invalid=96777
- 0077: dt=9.072000, rms=0.643 (0.285%), neg=0, invalid=96777
- 0078: dt=9.072000, rms=0.641 (0.281%), neg=0, invalid=96777
- 0079: dt=9.072000, rms=0.640 (0.278%), neg=0, invalid=96777
- 0080: dt=9.072000, rms=0.638 (0.283%), neg=0, invalid=96777
- 0081: dt=9.072000, rms=0.636 (0.284%), neg=0, invalid=96777
- 0082: dt=9.072000, rms=0.634 (0.271%), neg=0, invalid=96777
- 0083: dt=9.072000, rms=0.633 (0.248%), neg=0, invalid=96777
- 0084: dt=9.072000, rms=0.631 (0.209%), neg=0, invalid=96777
- 0085: dt=9.072000, rms=0.630 (0.197%), neg=0, invalid=96777
- 0086: dt=9.072000, rms=0.629 (0.170%), neg=0, invalid=96777
- 0087: dt=9.072000, rms=0.628 (0.164%), neg=0, invalid=96777
- 0088: dt=9.072000, rms=0.627 (0.153%), neg=0, invalid=96777
- 0089: dt=9.072000, rms=0.626 (0.159%), neg=0, invalid=96777
- 0090: dt=9.072000, rms=0.625 (0.154%), neg=0, invalid=96777
- 0091: dt=9.072000, rms=0.624 (0.142%), neg=0, invalid=96777
- 0092: dt=9.072000, rms=0.623 (0.135%), neg=0, invalid=96777
- 0093: dt=9.072000, rms=0.623 (0.119%), neg=0, invalid=96777
- 0094: dt=9.072000, rms=0.622 (0.101%), neg=0, invalid=96777
- 0095: dt=0.000000, rms=0.622 (-0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.622, neg=0, invalid=96777
- 0096: dt=36.288000, rms=0.621 (0.112%), neg=0, invalid=96777
- 0097: dt=103.680000, rms=0.620 (0.197%), neg=0, invalid=96777
- 0098: dt=2.268000, rms=0.620 (-0.008%), neg=0, invalid=96777
- setting smoothness coefficient to 0.588
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.644, neg=0, invalid=96777
- 0099: dt=8.645161, rms=0.643 (0.159%), neg=0, invalid=96777
- 0100: dt=8.000000, rms=0.643 (0.082%), neg=0, invalid=96777
- 0101: dt=8.000000, rms=0.643 (-0.004%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.643, neg=0, invalid=96777
- 0102: dt=0.000000, rms=0.643 (0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 2.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.704, neg=0, invalid=96777
- 0103: dt=5.246637, rms=0.692 (1.676%), neg=0, invalid=96777
- 0104: dt=1.008000, rms=0.692 (0.015%), neg=0, invalid=96777
- 0105: dt=1.008000, rms=0.692 (0.003%), neg=0, invalid=96777
- 0106: dt=1.008000, rms=0.692 (-0.045%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.692, neg=0, invalid=96777
- 0107: dt=0.000000, rms=0.692 (0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 5.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.765, neg=0, invalid=96777
- 0108: dt=0.676471, rms=0.763 (0.259%), neg=0, invalid=96777
- 0109: dt=1.450292, rms=0.760 (0.366%), neg=0, invalid=96777
- 0110: dt=2.077778, rms=0.757 (0.400%), neg=0, invalid=96777
- 0111: dt=0.448000, rms=0.757 (0.029%), neg=0, invalid=96777
- 0112: dt=0.448000, rms=0.757 (0.020%), neg=0, invalid=96777
- 0113: dt=0.448000, rms=0.756 (0.021%), neg=0, invalid=96777
- 0114: dt=0.448000, rms=0.756 (-0.005%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.756, neg=0, invalid=96777
- 0115: dt=1.536000, rms=0.755 (0.172%), neg=0, invalid=96777
- 0116: dt=0.000000, rms=0.755 (-0.000%), neg=0, invalid=96777
- resetting metric properties...
- setting smoothness coefficient to 10.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.704, neg=0, invalid=96777
- 0117: dt=0.159286, rms=0.695 (1.227%), neg=0, invalid=96777
- 0118: dt=0.000000, rms=0.695 (0.002%), neg=0, invalid=96777
- 0119: dt=0.050000, rms=0.695 (-0.014%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.695, neg=0, invalid=96777
- 0120: dt=0.265560, rms=0.693 (0.289%), neg=0, invalid=96777
- 0121: dt=0.112000, rms=0.692 (0.193%), neg=0, invalid=96777
- 0122: dt=0.112000, rms=0.691 (0.046%), neg=0, invalid=96777
- 0123: dt=0.112000, rms=0.691 (0.085%), neg=0, invalid=96777
- 0124: dt=0.112000, rms=0.690 (0.161%), neg=0, invalid=96777
- 0125: dt=0.112000, rms=0.688 (0.162%), neg=0, invalid=96777
- 0126: dt=0.112000, rms=0.687 (0.144%), neg=0, invalid=96777
- 0127: dt=0.112000, rms=0.687 (0.113%), neg=0, invalid=96777
- 0128: dt=0.112000, rms=0.686 (0.106%), neg=0, invalid=96777
- 0129: dt=0.096000, rms=0.686 (0.010%), neg=0, invalid=96777
- 0130: dt=0.096000, rms=0.686 (-0.012%), neg=0, invalid=96777
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.11725 (24)
- mri peak = 0.12953 ( 6)
- Left_Lateral_Ventricle (4): linear fit = 0.20 x + 0.0 (1084 voxels, overlap=0.006)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1084 voxels, peak = 5), gca=9.6
- gca peak = 0.14022 (22)
- mri peak = 0.13506 ( 9)
- Right_Lateral_Ventricle (43): linear fit = 0.28 x + 0.0 (771 voxels, overlap=0.007)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (771 voxels, peak = 6), gca=8.8
- gca peak = 0.24234 (100)
- mri peak = 0.10257 (90)
- Right_Pallidum (52): linear fit = 0.93 x + 0.0 (361 voxels, overlap=0.552)
- Right_Pallidum (52): linear fit = 0.93 x + 0.0 (361 voxels, peak = 92), gca=92.5
- gca peak = 0.19192 (97)
- mri peak = 0.09108 (90)
- Left_Pallidum (13): linear fit = 0.92 x + 0.0 (273 voxels, overlap=0.467)
- Left_Pallidum (13): linear fit = 0.92 x + 0.0 (273 voxels, peak = 89), gca=88.8
- gca peak = 0.24007 (63)
- mri peak = 0.06591 (45)
- Right_Hippocampus (53): linear fit = 0.70 x + 0.0 (648 voxels, overlap=0.039)
- Right_Hippocampus (53): linear fit = 0.70 x + 0.0 (648 voxels, peak = 44), gca=44.4
- gca peak = 0.29892 (64)
- mri peak = 0.08540 (44)
- Left_Hippocampus (17): linear fit = 0.65 x + 0.0 (741 voxels, overlap=0.023)
- Left_Hippocampus (17): linear fit = 0.65 x + 0.0 (741 voxels, peak = 42), gca=41.9
- gca peak = 0.12541 (104)
- mri peak = 0.07593 (107)
- Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (57702 voxels, overlap=0.760)
- Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (57702 voxels, peak = 109), gca=108.7
- gca peak = 0.13686 (104)
- mri peak = 0.07903 (108)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (58038 voxels, overlap=0.713)
- Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (58038 voxels, peak = 109), gca=108.7
- gca peak = 0.11691 (63)
- mri peak = 0.03587 (51)
- Left_Cerebral_Cortex (3): linear fit = 0.77 x + 0.0 (18769 voxels, overlap=0.186)
- Left_Cerebral_Cortex (3): linear fit = 0.77 x + 0.0 (18769 voxels, peak = 49), gca=48.8
- gca peak = 0.13270 (63)
- mri peak = 0.04065 (42)
- Right_Cerebral_Cortex (42): linear fit = 0.75 x + 0.0 (20578 voxels, overlap=0.014)
- Right_Cerebral_Cortex (42): linear fit = 0.75 x + 0.0 (20578 voxels, peak = 47), gca=46.9
- gca peak = 0.15182 (70)
- mri peak = 0.08443 (56)
- Right_Caudate (50): linear fit = 0.79 x + 0.0 (370 voxels, overlap=0.015)
- Right_Caudate (50): linear fit = 0.79 x + 0.0 (370 voxels, peak = 55), gca=55.0
- gca peak = 0.14251 (76)
- mri peak = 0.04575 (60)
- Left_Caudate (11): linear fit = 0.89 x + 0.0 (582 voxels, overlap=0.125)
- Left_Caudate (11): linear fit = 0.89 x + 0.0 (582 voxels, peak = 68), gca=68.0
- gca peak = 0.12116 (60)
- mri peak = 0.04234 (57)
- Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (20684 voxels, overlap=0.981)
- Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (20684 voxels, peak = 56), gca=56.1
- gca peak = 0.12723 (61)
- mri peak = 0.03992 (57)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (23872 voxels, overlap=0.925)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (23872 voxels, peak = 59), gca=58.9
- gca peak = 0.22684 (88)
- mri peak = 0.07432 (94)
- Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (6429 voxels, overlap=0.582)
- Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (6429 voxels, peak = 95), gca=95.5
- gca peak = 0.21067 (87)
- mri peak = 0.07069 (93)
- Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5765 voxels, overlap=0.618)
- Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5765 voxels, peak = 94), gca=93.5
- gca peak = 0.25455 (62)
- mri peak = 0.22086 (51)
- Left_Amygdala: unreasonable value (49.3/51.0), not in range [50, 90] - rejecting
- gca peak = 0.39668 (62)
- mri peak = 0.18750 (51)
- Right_Amygdala: unreasonable value (49.9/51.0), not in range [50, 90] - rejecting
- gca peak = 0.10129 (93)
- mri peak = 0.05432 (88)
- Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (4614 voxels, overlap=0.752)
- Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (4614 voxels, peak = 89), gca=88.8
- gca peak = 0.12071 (89)
- mri peak = 0.06928 (83)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3438 voxels, overlap=0.909)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3438 voxels, peak = 89), gca=88.6
- gca peak = 0.13716 (82)
- mri peak = 0.06124 (74)
- Left_Putamen (12): linear fit = 0.88 x + 0.0 (2084 voxels, overlap=0.361)
- Left_Putamen (12): linear fit = 0.88 x + 0.0 (2084 voxels, peak = 73), gca=72.6
- gca peak = 0.15214 (84)
- mri peak = 0.05301 (62)
- Right_Putamen (51): linear fit = 0.80 x + 0.0 (2006 voxels, overlap=0.375)
- Right_Putamen (51): linear fit = 0.80 x + 0.0 (2006 voxels, peak = 67), gca=66.8
- gca peak = 0.08983 (85)
- mri peak = 0.08005 (80)
- Brain_Stem (16): linear fit = 1.02 x + 0.0 (10320 voxels, overlap=0.777)
- Brain_Stem (16): linear fit = 1.02 x + 0.0 (10320 voxels, peak = 87), gca=87.1
- gca peak = 0.11809 (92)
- mri peak = 0.06852 (100)
- Right_VentralDC (60): linear fit = 1.04 x + 0.0 (729 voxels, overlap=0.857)
- Right_VentralDC (60): linear fit = 1.04 x + 0.0 (729 voxels, peak = 96), gca=96.1
- gca peak = 0.12914 (94)
- mri peak = 0.07143 (87)
- Left_VentralDC (28): linear fit = 0.98 x + 0.0 (974 voxels, overlap=0.911)
- Left_VentralDC (28): linear fit = 0.98 x + 0.0 (974 voxels, peak = 92), gca=91.7
- gca peak = 0.21100 (36)
- mri peak = 0.18790 (48)
- gca peak = 0.13542 (27)
- mri peak = 0.17001 ( 8)
- Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (234 voxels, overlap=0.015)
- Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (234 voxels, peak = 6), gca=6.1
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.21802 (40)
- gca peak Third_Ventricle = 0.21100 (36)
- gca peak Fourth_Ventricle = 0.13542 (27)
- gca peak Left_Hippocampus = 0.29892 (64)
- gca peak Left_Amygdala = 0.25455 (62)
- gca peak CSF = 0.17123 (45)
- gca peak Left_Accumbens_area = 0.25875 (69)
- gca peak Left_undetermined = 0.96240 (36)
- gca peak Left_vessel = 0.33262 (65)
- gca peak Left_choroid_plexus = 0.09846 (46)
- gca peak Right_Inf_Lat_Vent = 0.28113 (34)
- gca peak Right_Amygdala = 0.39668 (62)
- gca peak Right_Accumbens_area = 0.27120 (72)
- gca peak Right_vessel = 0.61915 (60)
- gca peak Right_choroid_plexus = 0.12775 (51)
- gca peak Fifth_Ventricle = 0.45329 (44)
- gca peak WM_hypointensities = 0.11729 (81)
- gca peak non_WM_hypointensities = 0.10912 (56)
- gca peak Optic_Chiasm = 0.33287 (75)
- label assignment complete, 0 changed (0.00%)
- not using caudate to estimate GM means
- setting label Left_Hippocampus based on Right_Hippocampus = 0.70 x + 0: 44
- estimating mean gm scale to be 0.73 x + 0.0
- estimating mean wm scale to be 1.04 x + 0.0
- estimating mean csf scale to be 0.40 x + 0.0
- saving intensity scales to talairach.label_intensities.txt
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.735, neg=0, invalid=96777
- 0131: dt=129.472000, rms=0.728 (0.963%), neg=0, invalid=96777
- 0132: dt=110.976000, rms=0.725 (0.408%), neg=0, invalid=96777
- 0133: dt=73.984000, rms=0.723 (0.237%), neg=0, invalid=96777
- 0134: dt=129.472000, rms=0.721 (0.255%), neg=0, invalid=96777
- 0135: dt=92.480000, rms=0.720 (0.148%), neg=0, invalid=96777
- 0136: dt=129.472000, rms=0.719 (0.182%), neg=0, invalid=96777
- 0137: dt=73.984000, rms=0.718 (0.123%), neg=0, invalid=96777
- 0138: dt=129.472000, rms=0.717 (0.162%), neg=0, invalid=96777
- 0139: dt=73.984000, rms=0.716 (0.077%), neg=0, invalid=96777
- 0140: dt=129.472000, rms=0.715 (0.138%), neg=0, invalid=96777
- 0141: dt=110.976000, rms=0.715 (0.068%), neg=0, invalid=96777
- 0142: dt=92.480000, rms=0.714 (0.106%), neg=0, invalid=96777
- 0143: dt=73.984000, rms=0.714 (0.046%), neg=0, invalid=96777
- 0144: dt=73.984000, rms=0.713 (0.076%), neg=0, invalid=96777
- 0145: dt=73.984000, rms=0.713 (0.091%), neg=0, invalid=96777
- 0146: dt=73.984000, rms=0.712 (0.130%), neg=0, invalid=96777
- 0147: dt=73.984000, rms=0.711 (0.123%), neg=0, invalid=96777
- 0148: dt=73.984000, rms=0.710 (0.156%), neg=0, invalid=96777
- 0149: dt=73.984000, rms=0.709 (0.148%), neg=0, invalid=96777
- 0150: dt=73.984000, rms=0.708 (0.140%), neg=0, invalid=96777
- 0151: dt=73.984000, rms=0.707 (0.136%), neg=0, invalid=96777
- 0152: dt=73.984000, rms=0.706 (0.117%), neg=0, invalid=96777
- 0153: dt=73.984000, rms=0.705 (0.123%), neg=0, invalid=96777
- 0154: dt=73.984000, rms=0.704 (0.112%), neg=0, invalid=96777
- 0155: dt=73.984000, rms=0.703 (0.105%), neg=0, invalid=96777
- 0156: dt=73.984000, rms=0.703 (0.094%), neg=0, invalid=96777
- 0157: dt=73.984000, rms=0.702 (0.083%), neg=0, invalid=96777
- 0158: dt=73.984000, rms=0.702 (0.091%), neg=0, invalid=96777
- 0159: dt=73.984000, rms=0.701 (0.080%), neg=0, invalid=96777
- 0160: dt=73.984000, rms=0.700 (0.088%), neg=0, invalid=96777
- 0161: dt=73.984000, rms=0.700 (0.083%), neg=0, invalid=96777
- 0162: dt=73.984000, rms=0.699 (0.076%), neg=0, invalid=96777
- 0163: dt=73.984000, rms=0.699 (0.081%), neg=0, invalid=96777
- 0164: dt=73.984000, rms=0.698 (0.073%), neg=0, invalid=96777
- 0165: dt=73.984000, rms=0.698 (0.077%), neg=0, invalid=96777
- 0166: dt=73.984000, rms=0.697 (0.066%), neg=0, invalid=96777
- 0167: dt=73.984000, rms=0.697 (0.067%), neg=0, invalid=96777
- 0168: dt=73.984000, rms=0.696 (0.056%), neg=0, invalid=96777
- 0169: dt=73.984000, rms=0.696 (0.053%), neg=0, invalid=96777
- 0170: dt=73.984000, rms=0.696 (0.053%), neg=0, invalid=96777
- 0171: dt=73.984000, rms=0.695 (0.056%), neg=0, invalid=96777
- 0172: dt=73.984000, rms=0.695 (0.069%), neg=0, invalid=96777
- 0173: dt=73.984000, rms=0.694 (0.064%), neg=0, invalid=96777
- 0174: dt=73.984000, rms=0.694 (0.056%), neg=0, invalid=96777
- 0175: dt=73.984000, rms=0.693 (0.055%), neg=0, invalid=96777
- 0176: dt=73.984000, rms=0.693 (0.059%), neg=0, invalid=96777
- 0177: dt=73.984000, rms=0.693 (0.057%), neg=0, invalid=96777
- 0178: dt=73.984000, rms=0.692 (0.051%), neg=0, invalid=96777
- 0179: dt=73.984000, rms=0.692 (0.042%), neg=0, invalid=96777
- 0180: dt=73.984000, rms=0.692 (0.048%), neg=0, invalid=96777
- 0181: dt=73.984000, rms=0.691 (0.044%), neg=0, invalid=96777
- 0182: dt=73.984000, rms=0.691 (0.043%), neg=0, invalid=96777
- 0183: dt=73.984000, rms=0.691 (0.043%), neg=0, invalid=96777
- 0184: dt=73.984000, rms=0.690 (0.044%), neg=0, invalid=96777
- 0185: dt=73.984000, rms=0.690 (0.052%), neg=0, invalid=96777
- 0186: dt=73.984000, rms=0.690 (0.048%), neg=0, invalid=96777
- 0187: dt=73.984000, rms=0.689 (0.042%), neg=0, invalid=96777
- 0188: dt=73.984000, rms=0.689 (0.032%), neg=0, invalid=96777
- 0189: dt=73.984000, rms=0.689 (0.034%), neg=0, invalid=96777
- 0190: dt=73.984000, rms=0.689 (0.033%), neg=0, invalid=96777
- 0191: dt=73.984000, rms=0.689 (0.036%), neg=0, invalid=96777
- 0192: dt=73.984000, rms=0.688 (0.036%), neg=0, invalid=96777
- 0193: dt=73.984000, rms=0.688 (0.032%), neg=0, invalid=96777
- 0194: dt=73.984000, rms=0.688 (0.029%), neg=0, invalid=96777
- 0195: dt=73.984000, rms=0.688 (0.030%), neg=0, invalid=96777
- 0196: dt=73.984000, rms=0.687 (0.032%), neg=0, invalid=96777
- 0197: dt=73.984000, rms=0.687 (0.024%), neg=0, invalid=96777
- 0198: dt=73.984000, rms=0.687 (0.026%), neg=0, invalid=96777
- 0199: dt=73.984000, rms=0.687 (0.029%), neg=0, invalid=96777
- 0200: dt=73.984000, rms=0.687 (0.029%), neg=0, invalid=96777
- 0201: dt=73.984000, rms=0.687 (0.028%), neg=0, invalid=96777
- 0202: dt=73.984000, rms=0.686 (0.025%), neg=0, invalid=96777
- 0203: dt=73.984000, rms=0.686 (0.023%), neg=0, invalid=96777
- 0204: dt=73.984000, rms=0.686 (0.023%), neg=0, invalid=96777
- 0205: dt=517.888000, rms=0.686 (0.023%), neg=0, invalid=96777
- 0206: dt=32.368000, rms=0.686 (0.003%), neg=0, invalid=96777
- 0207: dt=32.368000, rms=0.686 (0.001%), neg=0, invalid=96777
- 0208: dt=32.368000, rms=0.686 (0.001%), neg=0, invalid=96777
- 0209: dt=32.368000, rms=0.686 (-0.002%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.686, neg=0, invalid=96777
- 0210: dt=129.472000, rms=0.685 (0.091%), neg=0, invalid=96777
- 0211: dt=295.936000, rms=0.684 (0.135%), neg=0, invalid=96777
- 0212: dt=32.368000, rms=0.684 (0.050%), neg=0, invalid=96777
- 0213: dt=32.368000, rms=0.684 (0.006%), neg=0, invalid=96777
- 0214: dt=32.368000, rms=0.684 (-0.009%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.685, neg=0, invalid=96777
- 0215: dt=145.152000, rms=0.676 (1.227%), neg=0, invalid=96777
- 0216: dt=82.944000, rms=0.671 (0.809%), neg=0, invalid=96777
- 0217: dt=20.736000, rms=0.668 (0.401%), neg=0, invalid=96777
- 0218: dt=248.832000, rms=0.661 (1.096%), neg=0, invalid=96777
- 0219: dt=20.736000, rms=0.657 (0.562%), neg=0, invalid=96777
- 0220: dt=103.680000, rms=0.654 (0.456%), neg=0, invalid=96777
- 0221: dt=25.920000, rms=0.653 (0.188%), neg=0, invalid=96777
- 0222: dt=82.944000, rms=0.651 (0.329%), neg=0, invalid=96777
- 0223: dt=15.552000, rms=0.650 (0.114%), neg=0, invalid=96777
- 0224: dt=124.416000, rms=0.649 (0.231%), neg=0, invalid=96777
- 0225: dt=31.104000, rms=0.646 (0.328%), neg=0, invalid=96777
- 0226: dt=20.736000, rms=0.646 (0.054%), neg=0, invalid=96777
- 0227: dt=580.608000, rms=0.637 (1.412%), neg=0, invalid=96777
- 0228: dt=20.736000, rms=0.636 (0.144%), neg=0, invalid=96777
- 0229: dt=124.416000, rms=0.634 (0.358%), neg=0, invalid=96777
- 0230: dt=20.736000, rms=0.633 (0.071%), neg=0, invalid=96777
- 0231: dt=82.944000, rms=0.633 (0.107%), neg=0, invalid=96777
- 0232: dt=62.208000, rms=0.632 (0.093%), neg=0, invalid=96777
- 0233: dt=36.288000, rms=0.631 (0.124%), neg=0, invalid=96777
- 0234: dt=25.920000, rms=0.631 (0.026%), neg=0, invalid=96777
- 0235: dt=25.920000, rms=0.631 (0.063%), neg=0, invalid=96777
- 0236: dt=25.920000, rms=0.630 (0.080%), neg=0, invalid=96777
- 0237: dt=25.920000, rms=0.629 (0.120%), neg=0, invalid=96777
- 0238: dt=25.920000, rms=0.629 (0.137%), neg=0, invalid=96777
- 0239: dt=25.920000, rms=0.628 (0.164%), neg=0, invalid=96777
- 0240: dt=25.920000, rms=0.626 (0.186%), neg=0, invalid=96777
- 0241: dt=25.920000, rms=0.625 (0.192%), neg=0, invalid=96777
- 0242: dt=25.920000, rms=0.624 (0.197%), neg=0, invalid=96777
- 0243: dt=25.920000, rms=0.623 (0.199%), neg=0, invalid=96777
- 0244: dt=25.920000, rms=0.621 (0.210%), neg=0, invalid=96777
- 0245: dt=25.920000, rms=0.620 (0.201%), neg=0, invalid=96777
- 0246: dt=25.920000, rms=0.619 (0.207%), neg=0, invalid=96777
- 0247: dt=25.920000, rms=0.618 (0.190%), neg=0, invalid=96777
- 0248: dt=25.920000, rms=0.616 (0.189%), neg=0, invalid=96777
- 0249: dt=25.920000, rms=0.615 (0.183%), neg=0, invalid=96777
- 0250: dt=25.920000, rms=0.614 (0.181%), neg=0, invalid=96777
- 0251: dt=25.920000, rms=0.613 (0.169%), neg=0, invalid=96777
- 0252: dt=25.920000, rms=0.612 (0.164%), neg=0, invalid=96777
- 0253: dt=25.920000, rms=0.611 (0.147%), neg=0, invalid=96777
- 0254: dt=25.920000, rms=0.610 (0.141%), neg=0, invalid=96777
- 0255: dt=25.920000, rms=0.610 (0.143%), neg=0, invalid=96777
- 0256: dt=25.920000, rms=0.609 (0.139%), neg=0, invalid=96777
- 0257: dt=25.920000, rms=0.608 (0.136%), neg=0, invalid=96777
- 0258: dt=25.920000, rms=0.607 (0.126%), neg=0, invalid=96777
- 0259: dt=25.920000, rms=0.606 (0.116%), neg=0, invalid=96777
- 0260: dt=25.920000, rms=0.606 (0.109%), neg=0, invalid=96777
- 0261: dt=25.920000, rms=0.605 (0.108%), neg=0, invalid=96777
- 0262: dt=25.920000, rms=0.604 (0.103%), neg=0, invalid=96777
- 0263: dt=25.920000, rms=0.604 (0.098%), neg=0, invalid=96777
- 0264: dt=25.920000, rms=0.603 (0.097%), neg=0, invalid=96777
- 0265: dt=25.920000, rms=0.603 (0.091%), neg=0, invalid=96777
- 0266: dt=25.920000, rms=0.602 (0.087%), neg=0, invalid=96777
- 0267: dt=25.920000, rms=0.602 (0.084%), neg=0, invalid=96777
- 0268: dt=25.920000, rms=0.601 (0.082%), neg=0, invalid=96777
- 0269: dt=25.920000, rms=0.601 (0.082%), neg=0, invalid=96777
- 0270: dt=25.920000, rms=0.600 (0.081%), neg=0, invalid=96777
- 0271: dt=25.920000, rms=0.600 (0.079%), neg=0, invalid=96777
- 0272: dt=25.920000, rms=0.599 (0.076%), neg=0, invalid=96777
- 0273: dt=25.920000, rms=0.599 (0.068%), neg=0, invalid=96777
- 0274: dt=25.920000, rms=0.599 (0.065%), neg=0, invalid=96777
- 0275: dt=25.920000, rms=0.598 (0.074%), neg=0, invalid=96777
- 0276: dt=25.920000, rms=0.598 (0.073%), neg=0, invalid=96777
- 0277: dt=25.920000, rms=0.597 (0.063%), neg=0, invalid=96777
- 0278: dt=25.920000, rms=0.597 (0.062%), neg=0, invalid=96777
- 0279: dt=25.920000, rms=0.597 (0.056%), neg=0, invalid=96777
- 0280: dt=25.920000, rms=0.596 (0.063%), neg=0, invalid=96777
- 0281: dt=25.920000, rms=0.596 (0.063%), neg=0, invalid=96777
- 0282: dt=25.920000, rms=0.596 (0.050%), neg=0, invalid=96777
- 0283: dt=25.920000, rms=0.595 (0.045%), neg=0, invalid=96777
- 0284: dt=25.920000, rms=0.595 (0.049%), neg=0, invalid=96777
- 0285: dt=25.920000, rms=0.595 (0.063%), neg=0, invalid=96777
- 0286: dt=25.920000, rms=0.594 (0.050%), neg=0, invalid=96777
- 0287: dt=25.920000, rms=0.594 (0.046%), neg=0, invalid=96777
- 0288: dt=25.920000, rms=0.594 (0.042%), neg=0, invalid=96777
- 0289: dt=25.920000, rms=0.593 (0.048%), neg=0, invalid=96777
- 0290: dt=25.920000, rms=0.593 (0.051%), neg=0, invalid=96777
- 0291: dt=25.920000, rms=0.593 (0.041%), neg=0, invalid=96777
- 0292: dt=25.920000, rms=0.593 (0.034%), neg=0, invalid=96777
- 0293: dt=25.920000, rms=0.593 (0.038%), neg=0, invalid=96777
- 0294: dt=25.920000, rms=0.592 (0.043%), neg=0, invalid=96777
- 0295: dt=25.920000, rms=0.592 (0.047%), neg=0, invalid=96777
- 0296: dt=25.920000, rms=0.592 (0.033%), neg=0, invalid=96777
- 0297: dt=25.920000, rms=0.592 (0.028%), neg=0, invalid=96777
- 0298: dt=25.920000, rms=0.591 (0.037%), neg=0, invalid=96777
- 0299: dt=25.920000, rms=0.591 (0.045%), neg=0, invalid=96777
- 0300: dt=25.920000, rms=0.591 (0.038%), neg=0, invalid=96777
- 0301: dt=25.920000, rms=0.591 (0.029%), neg=0, invalid=96777
- 0302: dt=25.920000, rms=0.591 (0.027%), neg=0, invalid=96777
- 0303: dt=25.920000, rms=0.590 (0.032%), neg=0, invalid=96777
- 0304: dt=25.920000, rms=0.590 (0.039%), neg=0, invalid=96777
- 0305: dt=25.920000, rms=0.590 (0.034%), neg=0, invalid=96777
- 0306: dt=25.920000, rms=0.590 (0.028%), neg=0, invalid=96777
- 0307: dt=25.920000, rms=0.590 (0.025%), neg=0, invalid=96777
- 0308: dt=25.920000, rms=0.590 (0.023%), neg=0, invalid=96777
- 0309: dt=82.944000, rms=0.589 (0.022%), neg=0, invalid=96777
- 0310: dt=82.944000, rms=0.589 (-0.231%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.589, neg=0, invalid=96777
- 0311: dt=36.288000, rms=0.588 (0.171%), neg=0, invalid=96777
- 0312: dt=82.944000, rms=0.587 (0.275%), neg=0, invalid=96777
- 0313: dt=15.552000, rms=0.587 (0.049%), neg=0, invalid=96777
- 0314: dt=15.552000, rms=0.586 (0.028%), neg=0, invalid=96777
- 0315: dt=15.552000, rms=0.586 (0.036%), neg=0, invalid=96777
- 0316: dt=15.552000, rms=0.586 (0.051%), neg=0, invalid=96777
- 0317: dt=15.552000, rms=0.585 (0.067%), neg=0, invalid=96777
- 0318: dt=15.552000, rms=0.585 (0.076%), neg=0, invalid=96777
- 0319: dt=15.552000, rms=0.585 (0.067%), neg=0, invalid=96777
- 0320: dt=15.552000, rms=0.584 (0.055%), neg=0, invalid=96777
- 0321: dt=15.552000, rms=0.584 (0.050%), neg=0, invalid=96777
- 0322: dt=15.552000, rms=0.584 (0.040%), neg=0, invalid=96777
- 0323: dt=15.552000, rms=0.584 (0.041%), neg=0, invalid=96777
- 0324: dt=15.552000, rms=0.583 (0.048%), neg=0, invalid=96777
- 0325: dt=15.552000, rms=0.583 (0.043%), neg=0, invalid=96777
- 0326: dt=15.552000, rms=0.583 (0.034%), neg=0, invalid=96777
- 0327: dt=15.552000, rms=0.583 (0.027%), neg=0, invalid=96777
- 0328: dt=15.552000, rms=0.582 (0.026%), neg=0, invalid=96777
- 0329: dt=15.552000, rms=0.582 (0.025%), neg=0, invalid=96777
- 0330: dt=15.552000, rms=0.582 (0.029%), neg=0, invalid=96777
- 0331: dt=15.552000, rms=0.582 (0.029%), neg=0, invalid=96777
- 0332: dt=15.552000, rms=0.582 (0.026%), neg=0, invalid=96777
- 0333: dt=15.552000, rms=0.582 (0.029%), neg=0, invalid=96777
- 0334: dt=15.552000, rms=0.582 (0.021%), neg=0, invalid=96777
- 0335: dt=15.552000, rms=0.581 (0.025%), neg=0, invalid=96777
- 0336: dt=15.552000, rms=0.581 (0.024%), neg=0, invalid=96777
- 0337: dt=15.552000, rms=0.581 (0.025%), neg=0, invalid=96777
- 0338: dt=15.552000, rms=0.581 (0.029%), neg=0, invalid=96777
- 0339: dt=15.552000, rms=0.581 (0.024%), neg=0, invalid=96777
- 0340: dt=15.552000, rms=0.581 (0.028%), neg=0, invalid=96777
- 0341: dt=15.552000, rms=0.581 (0.021%), neg=0, invalid=96777
- 0342: dt=15.552000, rms=0.580 (0.026%), neg=0, invalid=96777
- 0343: dt=15.552000, rms=0.580 (0.025%), neg=0, invalid=96777
- 0344: dt=15.552000, rms=0.580 (0.025%), neg=0, invalid=96777
- 0345: dt=15.552000, rms=0.580 (0.020%), neg=0, invalid=96777
- 0346: dt=145.152000, rms=0.580 (0.009%), neg=0, invalid=96777
- 0347: dt=145.152000, rms=0.580 (-0.157%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.588, neg=0, invalid=96777
- 0348: dt=32.000000, rms=0.586 (0.407%), neg=0, invalid=96777
- 0349: dt=11.200000, rms=0.585 (0.232%), neg=0, invalid=96777
- 0350: dt=32.000000, rms=0.582 (0.366%), neg=0, invalid=96777
- 0351: dt=6.450867, rms=0.581 (0.303%), neg=0, invalid=96777
- 0352: dt=44.800000, rms=0.577 (0.667%), neg=0, invalid=96777
- 0353: dt=6.909091, rms=0.576 (0.136%), neg=0, invalid=96777
- 0354: dt=76.800000, rms=0.573 (0.467%), neg=0, invalid=96777
- 0355: dt=9.403509, rms=0.570 (0.509%), neg=0, invalid=96777
- 0356: dt=11.200000, rms=0.569 (0.221%), neg=0, invalid=96777
- 0357: dt=25.600000, rms=0.568 (0.234%), neg=0, invalid=96777
- 0358: dt=5.556886, rms=0.567 (0.109%), neg=0, invalid=96777
- 0359: dt=153.600000, rms=0.561 (1.044%), neg=0, invalid=96777
- 0360: dt=9.968254, rms=0.560 (0.254%), neg=0, invalid=96777
- 0361: dt=11.200000, rms=0.559 (0.132%), neg=0, invalid=96777
- 0362: dt=11.200000, rms=0.559 (0.053%), neg=0, invalid=96777
- 0363: dt=19.200000, rms=0.558 (0.100%), neg=0, invalid=96777
- 0364: dt=6.400000, rms=0.558 (0.052%), neg=0, invalid=96777
- 0365: dt=179.200000, rms=0.554 (0.732%), neg=0, invalid=96777
- 0366: dt=8.000000, rms=0.553 (0.166%), neg=0, invalid=96777
- 0367: dt=25.600000, rms=0.553 (0.066%), neg=0, invalid=96777
- 0368: dt=8.000000, rms=0.552 (0.068%), neg=0, invalid=96777
- 0369: dt=25.600000, rms=0.552 (0.037%), neg=0, invalid=96777
- 0370: dt=12.800000, rms=0.552 (0.065%), neg=0, invalid=96777
- 0371: dt=12.800000, rms=0.551 (0.107%), neg=0, invalid=96777
- 0372: dt=12.800000, rms=0.551 (0.080%), neg=0, invalid=96777
- 0373: dt=12.800000, rms=0.550 (0.169%), neg=0, invalid=96777
- 0374: dt=12.800000, rms=0.549 (0.147%), neg=0, invalid=96777
- 0375: dt=12.800000, rms=0.548 (0.217%), neg=0, invalid=96777
- 0376: dt=12.800000, rms=0.547 (0.157%), neg=0, invalid=96777
- 0377: dt=12.800000, rms=0.546 (0.227%), neg=0, invalid=96777
- 0378: dt=12.800000, rms=0.545 (0.178%), neg=0, invalid=96777
- 0379: dt=12.800000, rms=0.543 (0.228%), neg=0, invalid=96777
- 0380: dt=12.800000, rms=0.542 (0.171%), neg=0, invalid=96777
- 0381: dt=12.800000, rms=0.541 (0.210%), neg=0, invalid=96777
- 0382: dt=12.800000, rms=0.540 (0.176%), neg=0, invalid=96777
- 0383: dt=12.800000, rms=0.539 (0.168%), neg=0, invalid=96777
- 0384: dt=12.800000, rms=0.539 (0.153%), neg=0, invalid=96777
- 0385: dt=12.800000, rms=0.538 (0.170%), neg=0, invalid=96777
- 0386: dt=12.800000, rms=0.537 (0.148%), neg=0, invalid=96777
- 0387: dt=12.800000, rms=0.536 (0.132%), neg=0, invalid=96777
- 0388: dt=12.800000, rms=0.535 (0.150%), neg=0, invalid=96777
- 0389: dt=12.800000, rms=0.535 (0.106%), neg=0, invalid=96777
- 0390: dt=12.800000, rms=0.534 (0.106%), neg=0, invalid=96777
- 0391: dt=12.800000, rms=0.534 (0.080%), neg=0, invalid=96777
- 0392: dt=12.800000, rms=0.533 (0.121%), neg=0, invalid=96777
- 0393: dt=12.800000, rms=0.533 (0.093%), neg=0, invalid=96777
- 0394: dt=12.800000, rms=0.532 (0.100%), neg=0, invalid=96777
- 0395: dt=12.800000, rms=0.532 (0.067%), neg=0, invalid=96777
- 0396: dt=12.800000, rms=0.531 (0.087%), neg=0, invalid=96777
- 0397: dt=12.800000, rms=0.531 (0.089%), neg=0, invalid=96777
- 0398: dt=12.800000, rms=0.531 (0.052%), neg=0, invalid=96777
- 0399: dt=12.800000, rms=0.530 (0.069%), neg=0, invalid=96777
- 0400: dt=12.800000, rms=0.530 (0.068%), neg=0, invalid=96777
- 0401: dt=12.800000, rms=0.529 (0.061%), neg=0, invalid=96777
- 0402: dt=12.800000, rms=0.529 (0.041%), neg=0, invalid=96777
- 0403: dt=12.800000, rms=0.529 (0.075%), neg=0, invalid=96777
- 0404: dt=12.800000, rms=0.529 (0.067%), neg=0, invalid=96777
- 0405: dt=12.800000, rms=0.528 (0.062%), neg=0, invalid=96777
- 0406: dt=12.800000, rms=0.528 (0.034%), neg=0, invalid=96777
- 0407: dt=12.800000, rms=0.528 (0.042%), neg=0, invalid=96777
- 0408: dt=12.800000, rms=0.528 (0.043%), neg=0, invalid=96777
- 0409: dt=12.800000, rms=0.527 (0.037%), neg=0, invalid=96777
- 0410: dt=12.800000, rms=0.527 (0.043%), neg=0, invalid=96777
- 0411: dt=12.800000, rms=0.527 (0.048%), neg=0, invalid=96777
- 0412: dt=12.800000, rms=0.527 (0.043%), neg=0, invalid=96777
- 0413: dt=12.800000, rms=0.527 (0.029%), neg=0, invalid=96777
- 0414: dt=12.800000, rms=0.526 (0.028%), neg=0, invalid=96777
- 0415: dt=12.800000, rms=0.526 (0.033%), neg=0, invalid=96777
- 0416: dt=12.800000, rms=0.526 (0.038%), neg=0, invalid=96777
- 0417: dt=12.800000, rms=0.526 (0.030%), neg=0, invalid=96777
- 0418: dt=12.800000, rms=0.526 (0.040%), neg=0, invalid=96777
- 0419: dt=12.800000, rms=0.525 (0.033%), neg=0, invalid=96777
- 0420: dt=12.800000, rms=0.525 (0.020%), neg=0, invalid=96777
- 0421: dt=12.800000, rms=0.525 (0.030%), neg=0, invalid=96777
- 0422: dt=12.800000, rms=0.525 (0.033%), neg=0, invalid=96777
- 0423: dt=12.800000, rms=0.525 (0.046%), neg=0, invalid=96777
- 0424: dt=12.800000, rms=0.525 (0.021%), neg=0, invalid=96777
- 0425: dt=12.800000, rms=0.525 (0.006%), neg=0, invalid=96777
- 0426: dt=32.000000, rms=0.524 (0.041%), neg=0, invalid=96777
- 0427: dt=0.000000, rms=0.524 (-0.009%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.524, neg=0, invalid=96777
- 0428: dt=11.200000, rms=0.524 (0.142%), neg=0, invalid=96777
- 0429: dt=25.600000, rms=0.522 (0.263%), neg=0, invalid=96777
- 0430: dt=5.000000, rms=0.522 (0.042%), neg=0, invalid=96777
- 0431: dt=5.000000, rms=0.522 (0.027%), neg=0, invalid=96777
- 0432: dt=5.000000, rms=0.522 (0.031%), neg=0, invalid=96777
- 0433: dt=5.000000, rms=0.522 (0.040%), neg=0, invalid=96777
- 0434: dt=5.000000, rms=0.521 (0.060%), neg=0, invalid=96777
- 0435: dt=5.000000, rms=0.521 (0.047%), neg=0, invalid=96777
- 0436: dt=5.000000, rms=0.521 (0.033%), neg=0, invalid=96777
- 0437: dt=5.000000, rms=0.521 (0.015%), neg=0, invalid=96777
- 0438: dt=5.000000, rms=0.521 (0.005%), neg=0, invalid=96777
- 0439: dt=38.400000, rms=0.521 (0.038%), neg=0, invalid=96777
- 0440: dt=2.400000, rms=0.521 (-0.003%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.546, neg=0, invalid=96777
- 0441: dt=0.000000, rms=0.546 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.546, neg=0, invalid=96777
- 0442: dt=0.000000, rms=0.546 (0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.597, neg=0, invalid=96777
- 0443: dt=1.415704, rms=0.590 (1.142%), neg=0, invalid=96777
- 0444: dt=0.448000, rms=0.590 (0.052%), neg=0, invalid=96777
- 0445: dt=0.048000, rms=0.590 (-0.005%), neg=0, invalid=96777
- 0446: dt=0.048000, rms=0.590 (0.001%), neg=0, invalid=96777
- 0447: dt=0.048000, rms=0.590 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.590, neg=0, invalid=96777
- 0448: dt=0.500000, rms=0.589 (0.067%), neg=0, invalid=96777
- 0449: dt=0.192000, rms=0.589 (0.003%), neg=0, invalid=96777
- 0450: dt=0.192000, rms=0.589 (0.001%), neg=0, invalid=96777
- 0451: dt=0.192000, rms=0.589 (-0.033%), neg=0, invalid=96777
- resetting metric properties...
- setting smoothness coefficient to 2.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.540, neg=0, invalid=96777
- 0452: dt=0.173000, rms=0.532 (1.438%), neg=0, invalid=96777
- 0453: dt=0.141906, rms=0.528 (0.802%), neg=0, invalid=96777
- 0454: dt=0.384000, rms=0.519 (1.614%), neg=0, invalid=96777
- 0455: dt=0.006000, rms=0.519 (0.010%), neg=0, invalid=96777
- 0456: dt=0.003000, rms=0.519 (0.003%), neg=0, invalid=96777
- 0457: dt=0.003000, rms=0.519 (0.010%), neg=0, invalid=96777
- 0458: dt=0.003000, rms=0.519 (0.005%), neg=0, invalid=96777
- 0459: dt=0.003000, rms=0.519 (0.008%), neg=0, invalid=96777
- 0460: dt=0.003000, rms=0.519 (0.012%), neg=0, invalid=96777
- 0461: dt=0.003000, rms=0.519 (0.017%), neg=0, invalid=96777
- 0462: dt=0.003000, rms=0.519 (0.022%), neg=0, invalid=96777
- 0463: dt=0.003000, rms=0.519 (0.021%), neg=0, invalid=96777
- 0464: dt=0.112000, rms=0.518 (0.172%), neg=0, invalid=96777
- 0465: dt=0.112000, rms=0.517 (0.155%), neg=0, invalid=96777
- 0466: dt=0.112000, rms=0.516 (0.132%), neg=0, invalid=96777
- 0467: dt=0.112000, rms=0.516 (0.119%), neg=0, invalid=96777
- 0468: dt=0.028000, rms=0.516 (0.027%), neg=0, invalid=96777
- 0469: dt=0.028000, rms=0.515 (0.030%), neg=0, invalid=96777
- 0470: dt=0.028000, rms=0.515 (0.048%), neg=0, invalid=96777
- 0471: dt=0.028000, rms=0.515 (0.066%), neg=0, invalid=96777
- 0472: dt=0.028000, rms=0.514 (0.088%), neg=0, invalid=96777
- 0473: dt=0.028000, rms=0.514 (0.020%), neg=0, invalid=96777
- 0474: dt=0.028000, rms=0.514 (0.037%), neg=0, invalid=96777
- 0475: dt=0.028000, rms=0.514 (0.059%), neg=0, invalid=96777
- 0476: dt=0.028000, rms=0.513 (0.063%), neg=0, invalid=96777
- 0477: dt=0.028000, rms=0.513 (0.078%), neg=0, invalid=96777
- 0478: dt=0.028000, rms=0.513 (0.084%), neg=0, invalid=96777
- 0479: dt=0.028000, rms=0.512 (0.093%), neg=0, invalid=96777
- 0480: dt=0.028000, rms=0.512 (0.091%), neg=0, invalid=96777
- 0481: dt=0.028000, rms=0.511 (0.091%), neg=0, invalid=96777
- 0482: dt=0.028000, rms=0.511 (0.088%), neg=0, invalid=96777
- 0483: dt=0.028000, rms=0.510 (0.086%), neg=0, invalid=96777
- 0484: dt=0.028000, rms=0.510 (0.084%), neg=0, invalid=96777
- 0485: dt=0.028000, rms=0.509 (0.078%), neg=0, invalid=96777
- 0486: dt=0.028000, rms=0.509 (0.001%), neg=0, invalid=96777
- 0487: dt=0.028000, rms=0.509 (0.007%), neg=0, invalid=96777
- 0488: dt=0.028000, rms=0.509 (0.009%), neg=0, invalid=96777
- 0489: dt=0.028000, rms=0.509 (0.010%), neg=0, invalid=96777
- 0490: dt=0.028000, rms=0.509 (0.015%), neg=0, invalid=96777
- 0491: dt=0.028000, rms=0.509 (0.014%), neg=0, invalid=96777
- 0492: dt=0.028000, rms=0.509 (0.004%), neg=0, invalid=96777
- 0493: dt=0.028000, rms=0.509 (0.003%), neg=0, invalid=96777
- 0494: dt=0.028000, rms=0.509 (0.004%), neg=0, invalid=96777
- 0495: dt=0.028000, rms=0.509 (0.006%), neg=0, invalid=96777
- 0496: dt=0.028000, rms=0.509 (0.015%), neg=0, invalid=96777
- 0497: dt=0.028000, rms=0.509 (0.015%), neg=0, invalid=96777
- 0498: dt=0.028000, rms=0.509 (0.002%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.509, neg=0, invalid=96777
- 0499: dt=0.080000, rms=0.508 (0.161%), neg=0, invalid=96777
- 0500: dt=0.028000, rms=0.508 (0.052%), neg=0, invalid=96777
- 0501: dt=0.112000, rms=0.507 (0.176%), neg=0, invalid=96777
- 0502: dt=0.024000, rms=0.507 (0.025%), neg=0, invalid=96777
- 0503: dt=0.006000, rms=0.507 (0.009%), neg=0, invalid=96777
- 0504: dt=0.006000, rms=0.507 (0.013%), neg=0, invalid=96777
- 0505: dt=0.006000, rms=0.507 (0.017%), neg=0, invalid=96777
- 0506: dt=0.006000, rms=0.507 (0.021%), neg=0, invalid=96777
- 0507: dt=0.006000, rms=0.506 (0.024%), neg=0, invalid=96777
- 0508: dt=0.006000, rms=0.506 (0.030%), neg=0, invalid=96777
- 0509: dt=0.006000, rms=0.506 (0.032%), neg=0, invalid=96777
- 0510: dt=0.006000, rms=0.506 (0.036%), neg=0, invalid=96777
- 0511: dt=0.006000, rms=0.506 (0.034%), neg=0, invalid=96777
- 0512: dt=0.006000, rms=0.506 (0.036%), neg=0, invalid=96777
- 0513: dt=0.006000, rms=0.505 (0.032%), neg=0, invalid=96777
- 0514: dt=0.006000, rms=0.505 (0.038%), neg=0, invalid=96777
- 0515: dt=0.006000, rms=0.505 (0.034%), neg=0, invalid=96777
- 0516: dt=0.006000, rms=0.505 (0.028%), neg=0, invalid=96777
- 0517: dt=0.006000, rms=0.505 (0.032%), neg=0, invalid=96777
- 0518: dt=0.006000, rms=0.505 (0.028%), neg=0, invalid=96777
- 0519: dt=0.006000, rms=0.504 (0.027%), neg=0, invalid=96777
- 0520: dt=0.006000, rms=0.504 (0.028%), neg=0, invalid=96777
- 0521: dt=0.006000, rms=0.504 (0.025%), neg=0, invalid=96777
- 0522: dt=0.006000, rms=0.504 (0.023%), neg=0, invalid=96777
- 0523: dt=0.112000, rms=0.504 (0.005%), neg=0, invalid=96777
- 0524: dt=0.014000, rms=0.504 (-0.006%), neg=0, invalid=96777
- label assignment complete, 0 changed (0.00%)
- *********************************************************************************************
- *********************************************************************************************
- *********************************************************************************************
- ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ********************************
- *********************************************************************************************
- *********************************************************************************************
- *********************************************************************************************
- **************** pass 1 of 1 ************************
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.502, neg=0, invalid=96777
- 0525: dt=0.867000, rms=0.502 (0.000%), neg=0, invalid=96777
- 0526: dt=0.867000, rms=0.502 (0.000%), neg=0, invalid=96777
- 0527: dt=0.867000, rms=0.502 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.502, neg=0, invalid=96777
- 0528: dt=129.472000, rms=0.501 (0.097%), neg=0, invalid=96777
- 0529: dt=110.976000, rms=0.501 (0.053%), neg=0, invalid=96777
- 0530: dt=110.976000, rms=0.501 (-0.030%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.501, neg=0, invalid=96777
- 0531: dt=36.288000, rms=0.501 (0.100%), neg=0, invalid=96777
- 0532: dt=36.288000, rms=0.500 (0.121%), neg=0, invalid=96777
- 0533: dt=36.288000, rms=0.500 (0.036%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0534: dt=36.288000, rms=0.500 (0.079%), neg=0, invalid=96777
- 0535: dt=36.288000, rms=0.499 (0.058%), neg=0, invalid=96777
- 0536: dt=36.288000, rms=0.499 (0.008%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.499, neg=0, invalid=96777
- 0537: dt=82.944000, rms=0.497 (0.492%), neg=0, invalid=96777
- 0538: dt=15.552000, rms=0.496 (0.102%), neg=0, invalid=96777
- 0539: dt=15.552000, rms=0.496 (0.038%), neg=0, invalid=96777
- 0540: dt=15.552000, rms=0.496 (0.075%), neg=0, invalid=96777
- 0541: dt=15.552000, rms=0.495 (0.080%), neg=0, invalid=96777
- 0542: dt=15.552000, rms=0.495 (0.073%), neg=0, invalid=96777
- 0543: dt=15.552000, rms=0.495 (0.086%), neg=0, invalid=96777
- 0544: dt=15.552000, rms=0.494 (0.085%), neg=0, invalid=96777
- 0545: dt=124.416000, rms=0.494 (0.066%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.494, neg=0, invalid=96777
- iter 0, gcam->neg = 47
- after 21 iterations, nbhd size=2, neg = 0
- 0546: dt=32.000000, rms=0.491 (0.565%), neg=0, invalid=96777
- 0547: dt=9.680672, rms=0.490 (0.256%), neg=0, invalid=96777
- 0548: dt=11.200000, rms=0.489 (0.182%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0549: dt=11.200000, rms=0.488 (0.208%), neg=0, invalid=96777
- iter 0, gcam->neg = 5
- after 16 iterations, nbhd size=2, neg = 0
- 0550: dt=11.200000, rms=0.487 (0.305%), neg=0, invalid=96777
- iter 0, gcam->neg = 9
- after 25 iterations, nbhd size=3, neg = 0
- 0551: dt=11.200000, rms=0.485 (0.262%), neg=0, invalid=96777
- iter 0, gcam->neg = 9
- after 18 iterations, nbhd size=2, neg = 0
- 0552: dt=11.200000, rms=0.484 (0.323%), neg=0, invalid=96777
- iter 0, gcam->neg = 10
- after 31 iterations, nbhd size=3, neg = 0
- 0553: dt=11.200000, rms=0.482 (0.249%), neg=0, invalid=96777
- iter 0, gcam->neg = 6
- after 31 iterations, nbhd size=4, neg = 0
- 0554: dt=11.200000, rms=0.482 (0.175%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 7 iterations, nbhd size=1, neg = 0
- 0555: dt=11.200000, rms=0.481 (0.111%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 14 iterations, nbhd size=2, neg = 0
- 0556: dt=11.200000, rms=0.480 (0.227%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 13 iterations, nbhd size=2, neg = 0
- 0557: dt=11.200000, rms=0.479 (0.232%), neg=0, invalid=96777
- 0558: dt=11.200000, rms=0.478 (0.238%), neg=0, invalid=96777
- 0559: dt=11.200000, rms=0.477 (0.194%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0560: dt=11.200000, rms=0.476 (0.243%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0561: dt=11.200000, rms=0.475 (0.174%), neg=0, invalid=96777
- 0562: dt=11.200000, rms=0.474 (0.123%), neg=0, invalid=96777
- iter 0, gcam->neg = 5
- after 25 iterations, nbhd size=3, neg = 0
- 0563: dt=11.200000, rms=0.474 (0.066%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 12 iterations, nbhd size=2, neg = 0
- 0564: dt=11.200000, rms=0.473 (0.114%), neg=0, invalid=96777
- 0565: dt=11.200000, rms=0.473 (0.031%), neg=0, invalid=96777
- 0566: dt=11.200000, rms=0.473 (0.063%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 24 iterations, nbhd size=3, neg = 0
- 0567: dt=11.200000, rms=0.473 (0.041%), neg=0, invalid=96777
- iter 0, gcam->neg = 4
- after 23 iterations, nbhd size=3, neg = 0
- 0568: dt=11.200000, rms=0.473 (0.042%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 27 iterations, nbhd size=4, neg = 0
- 0569: dt=11.200000, rms=0.472 (0.021%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.472, neg=0, invalid=96777
- iter 0, gcam->neg = 4
- after 1 iterations, nbhd size=0, neg = 0
- 0570: dt=38.400000, rms=0.470 (0.548%), neg=0, invalid=96777
- 0571: dt=8.000000, rms=0.469 (0.170%), neg=0, invalid=96777
- 0572: dt=8.000000, rms=0.469 (0.124%), neg=0, invalid=96777
- 0573: dt=8.000000, rms=0.468 (0.124%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0574: dt=8.000000, rms=0.467 (0.116%), neg=0, invalid=96777
- iter 0, gcam->neg = 5
- after 25 iterations, nbhd size=3, neg = 0
- 0575: dt=8.000000, rms=0.467 (0.062%), neg=0, invalid=96777
- 0576: dt=11.200000, rms=0.467 (0.093%), neg=0, invalid=96777
- 0577: dt=6.400000, rms=0.467 (-0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.473, neg=0, invalid=96777
- iter 0, gcam->neg = 9
- after 17 iterations, nbhd size=2, neg = 0
- 0578: dt=4.032000, rms=0.473 (0.107%), neg=0, invalid=96777
- iter 0, gcam->neg = 13
- after 15 iterations, nbhd size=1, neg = 0
- 0579: dt=4.032000, rms=0.472 (0.078%), neg=0, invalid=96777
- iter 0, gcam->neg = 78
- after 34 iterations, nbhd size=3, neg = 0
- 0580: dt=4.032000, rms=0.472 (-0.037%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.472, neg=0, invalid=96777
- iter 0, gcam->neg = 26
- after 22 iterations, nbhd size=2, neg = 0
- 0581: dt=1.866667, rms=0.472 (0.070%), neg=0, invalid=96777
- iter 0, gcam->neg = 48
- after 18 iterations, nbhd size=1, neg = 0
- 0582: dt=4.032000, rms=0.471 (0.154%), neg=0, invalid=96777
- iter 0, gcam->neg = 28
- after 13 iterations, nbhd size=1, neg = 0
- 0583: dt=7.652174, rms=0.471 (0.147%), neg=0, invalid=96777
- iter 0, gcam->neg = 137
- after 15 iterations, nbhd size=1, neg = 0
- 0584: dt=7.652174, rms=0.470 (0.094%), neg=0, invalid=96777
- iter 0, gcam->neg = 237
- after 22 iterations, nbhd size=1, neg = 0
- 0585: dt=7.652174, rms=0.470 (0.024%), neg=0, invalid=96777
- iter 0, gcam->neg = 148
- after 16 iterations, nbhd size=1, neg = 0
- 0586: dt=7.652174, rms=0.470 (0.049%), neg=0, invalid=96777
- iter 0, gcam->neg = 121
- after 15 iterations, nbhd size=1, neg = 0
- 0587: dt=7.652174, rms=0.468 (0.291%), neg=0, invalid=96777
- iter 0, gcam->neg = 187
- after 16 iterations, nbhd size=1, neg = 0
- 0588: dt=7.652174, rms=0.466 (0.578%), neg=0, invalid=96777
- iter 0, gcam->neg = 204
- after 26 iterations, nbhd size=2, neg = 0
- 0589: dt=7.652174, rms=0.463 (0.531%), neg=0, invalid=96777
- iter 0, gcam->neg = 296
- after 27 iterations, nbhd size=2, neg = 0
- 0590: dt=7.652174, rms=0.461 (0.403%), neg=0, invalid=96777
- iter 0, gcam->neg = 265
- after 33 iterations, nbhd size=2, neg = 0
- 0591: dt=7.652174, rms=0.460 (0.358%), neg=0, invalid=96777
- iter 0, gcam->neg = 270
- after 44 iterations, nbhd size=2, neg = 0
- 0592: dt=7.652174, rms=0.459 (0.184%), neg=0, invalid=96777
- iter 0, gcam->neg = 274
- after 47 iterations, nbhd size=3, neg = 0
- 0593: dt=7.652174, rms=0.459 (0.004%), neg=0, invalid=96777
- iter 0, gcam->neg = 258
- after 49 iterations, nbhd size=4, neg = 0
- 0594: dt=7.652174, rms=0.459 (-0.057%), neg=0, invalid=96777
- iter 0, gcam->neg = 10
- after 17 iterations, nbhd size=2, neg = 0
- 0595: dt=4.769231, rms=0.458 (0.127%), neg=0, invalid=96777
- iter 0, gcam->neg = 22
- after 22 iterations, nbhd size=2, neg = 0
- 0596: dt=4.032000, rms=0.458 (0.087%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.464, neg=0, invalid=96777
- 0597: dt=0.000000, rms=0.464 (-0.003%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.464, neg=0, invalid=96777
- 0598: dt=0.000000, rms=0.464 (0.000%), neg=0, invalid=96777
- resetting metric properties...
- setting smoothness coefficient to 2.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.453, neg=0, invalid=96777
- iter 0, gcam->neg = 922
- after 48 iterations, nbhd size=1, neg = 0
- 0599: dt=1.792000, rms=0.416 (8.190%), neg=0, invalid=96777
- 0600: dt=0.000313, rms=0.416 (0.007%), neg=0, invalid=96777
- 0601: dt=0.000313, rms=0.416 (-0.001%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.416, neg=0, invalid=96777
- 0602: dt=0.000016, rms=0.416 (0.000%), neg=0, invalid=96777
- 0603: dt=0.000016, rms=0.416 (-0.000%), neg=0, invalid=96777
- 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 ************************
- setting smoothness coefficient to 0.008
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.403, neg=0, invalid=96777
- 0604: dt=8.092000, rms=0.404 (-0.399%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.404, neg=0, invalid=96777
- 0605: dt=23.120000, rms=0.404 (0.006%), neg=0, invalid=96777
- 0606: dt=0.000000, rms=0.404 (0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 0.031
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.404, neg=0, invalid=96777
- 0607: dt=2.268000, rms=0.404 (0.001%), neg=0, invalid=96777
- 0608: dt=0.324000, rms=0.404 (0.000%), neg=0, invalid=96777
- 0609: dt=0.324000, rms=0.404 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.404, neg=0, invalid=96777
- 0610: dt=9.072000, rms=0.404 (0.006%), neg=0, invalid=96777
- 0611: dt=3.888000, rms=0.404 (0.001%), neg=0, invalid=96777
- 0612: dt=3.888000, rms=0.404 (-0.001%), neg=0, invalid=96777
- setting smoothness coefficient to 0.118
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.405, neg=0, invalid=96777
- iter 0, gcam->neg = 11
- after 200 iterations, nbhd size=4, neg = 1
- starting rms=0.007, neg=1, removing folds in lattice....
- iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.007 (0.000%)
- ---------- unfolding failed - restoring original position --------------------
- 0613: dt=8.000000, rms=0.405 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.405, neg=0, invalid=96777
- iter 0, gcam->neg = 15
- after 200 iterations, nbhd size=3, neg = 1
- starting rms=0.008, neg=1, removing folds in lattice....
- iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.008 (0.000%)
- ---------- unfolding failed - restoring original position --------------------
- 0614: dt=11.200000, rms=0.405 (0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 0.400
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.407, neg=0, invalid=96777
- iter 0, gcam->neg = 52
- after 200 iterations, nbhd size=2, neg = 1
- starting rms=0.004, neg=1, removing folds in lattice....
- iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.004 (0.000%)
- ---------- unfolding failed - restoring original position --------------------
- 0615: dt=3.088608, rms=0.407 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.407, neg=0, invalid=96777
- iter 0, gcam->neg = 58
- after 200 iterations, nbhd size=1, neg = 1
- starting rms=0.004, neg=1, removing folds in lattice....
- iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.004 (0.000%)
- ---------- unfolding failed - restoring original position --------------------
- 0616: dt=3.676471, rms=0.407 (0.000%), neg=0, invalid=96777
- setting smoothness coefficient to 1.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.411, neg=0, invalid=96777
- 0617: dt=0.000000, rms=0.411 (0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.411, neg=0, invalid=96777
- 0618: dt=0.001500, rms=0.411 (0.000%), neg=0, invalid=96777
- 0619: dt=0.000438, rms=0.411 (0.000%), neg=0, invalid=96777
- 0620: dt=0.000438, rms=0.411 (-0.000%), neg=0, invalid=96777
- resetting metric properties...
- setting smoothness coefficient to 2.000
- blurring input image with Gaussian with sigma=2.000...
- 0000: dt=0.000, rms=0.404, neg=0, invalid=96777
- iter 0, gcam->neg = 315
- after 28 iterations, nbhd size=2, neg = 0
- 0621: dt=0.463190, rms=0.396 (2.115%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0622: dt=0.005000, rms=0.396 (0.004%), neg=0, invalid=96777
- 0623: dt=0.005000, rms=0.396 (0.003%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 0 iterations, nbhd size=0, neg = 0
- 0624: dt=0.005000, rms=0.396 (0.006%), neg=0, invalid=96777
- 0625: dt=0.005000, rms=0.396 (0.009%), neg=0, invalid=96777
- 0626: dt=0.005000, rms=0.396 (0.011%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0627: dt=0.005000, rms=0.395 (0.013%), neg=0, invalid=96777
- 0628: dt=0.005000, rms=0.395 (0.015%), neg=0, invalid=96777
- 0629: dt=0.005000, rms=0.395 (0.016%), neg=0, invalid=96777
- 0630: dt=0.005000, rms=0.395 (0.017%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0631: dt=0.005000, rms=0.395 (0.018%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0632: dt=0.005000, rms=0.395 (0.019%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 18 iterations, nbhd size=2, neg = 0
- 0633: dt=0.005000, rms=0.395 (0.014%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 12 iterations, nbhd size=2, neg = 0
- 0634: dt=0.005000, rms=0.395 (0.019%), neg=0, invalid=96777
- 0635: dt=0.005000, rms=0.395 (0.020%), neg=0, invalid=96777
- 0636: dt=0.005000, rms=0.395 (0.020%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 22 iterations, nbhd size=3, neg = 0
- 0637: dt=0.005000, rms=0.395 (-0.000%), neg=0, invalid=96777
- blurring input image with Gaussian with sigma=0.500...
- 0000: dt=0.000, rms=0.395, neg=0, invalid=96777
- iter 0, gcam->neg = 23
- after 27 iterations, nbhd size=3, neg = 0
- 0638: dt=0.064000, rms=0.394 (0.097%), neg=0, invalid=96777
- iter 0, gcam->neg = 10
- after 6 iterations, nbhd size=1, neg = 0
- 0639: dt=0.028000, rms=0.394 (0.046%), neg=0, invalid=96777
- iter 0, gcam->neg = 10
- after 7 iterations, nbhd size=1, neg = 0
- 0640: dt=0.028000, rms=0.394 (0.049%), neg=0, invalid=96777
- iter 0, gcam->neg = 18
- after 10 iterations, nbhd size=1, neg = 0
- 0641: dt=0.028000, rms=0.394 (0.085%), neg=0, invalid=96777
- iter 0, gcam->neg = 32
- after 21 iterations, nbhd size=2, neg = 0
- 0642: dt=0.028000, rms=0.393 (0.110%), neg=0, invalid=96777
- iter 0, gcam->neg = 48
- after 17 iterations, nbhd size=2, neg = 0
- 0643: dt=0.028000, rms=0.393 (0.127%), neg=0, invalid=96777
- iter 0, gcam->neg = 54
- after 17 iterations, nbhd size=2, neg = 0
- 0644: dt=0.028000, rms=0.392 (0.131%), neg=0, invalid=96777
- iter 0, gcam->neg = 71
- after 29 iterations, nbhd size=3, neg = 0
- 0645: dt=0.028000, rms=0.392 (0.102%), neg=0, invalid=96777
- iter 0, gcam->neg = 71
- after 9 iterations, nbhd size=1, neg = 0
- 0646: dt=0.028000, rms=0.391 (0.124%), neg=0, invalid=96777
- iter 0, gcam->neg = 89
- after 20 iterations, nbhd size=2, neg = 0
- 0647: dt=0.028000, rms=0.391 (0.097%), neg=0, invalid=96777
- 0648: dt=0.007000, rms=0.391 (0.002%), neg=0, invalid=96777
- iter 0, gcam->neg = 1
- after 0 iterations, nbhd size=0, neg = 0
- 0649: dt=0.007000, rms=0.391 (0.002%), neg=0, invalid=96777
- iter 0, gcam->neg = 2
- after 1 iterations, nbhd size=0, neg = 0
- 0650: dt=0.007000, rms=0.391 (0.004%), neg=0, invalid=96777
- 0651: dt=0.007000, rms=0.391 (0.005%), neg=0, invalid=96777
- 0652: dt=0.007000, rms=0.391 (0.005%), neg=0, invalid=96777
- iter 0, gcam->neg = 3
- after 21 iterations, nbhd size=3, neg = 0
- 0653: dt=0.007000, rms=0.391 (-0.003%), neg=0, invalid=96777
- writing output transformation to transforms/talairach.m3z...
- GCAMwrite
- registration took 2 hours, 32 minutes and 35 seconds.
- #--------------------------------------
- #@# CA Reg Inv Sat Jan 14 11:57:34 UTC 2017
- /data/out/sub-02/mri
- mri_ca_register -invert-and-save transforms/talairach.m3z
- Loading, Inverting, Saving, Exiting ...
- Reading transforms/talairach.m3z
- Inverting GCAM
- Saving inverse
- #--------------------------------------
- #@# Remove Neck Sat Jan 14 11:58:33 UTC 2017
- mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz
- erasing everything more than 25 mm from possible brain
- reading atlas '/opt/freesurfer/average/RB_all_2008-03-26.gca'...
- reading input volume 'nu.mgz'...
- reading transform 'transforms/talairach.m3z'...
- removing structures at least 25 mm from brain...
- 11625469 nonbrain voxels erased
- writing output to nu_noneck.mgz...
- nonbrain removal took 1 minutes and 4 seconds.
- #--------------------------------------
- #@# SkullLTA Sat Jan 14 11:59:36 UTC 2017
- mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta
- aligning to atlas containing skull, setting unknown_nbr_spacing = 5
- using previously computed transform transforms/talairach.lta
- reading 1 input volumes...
- logging results to talairach_with_skull_2.log
- reading '/opt/freesurfer/average/RB_all_withskull_2008-03-26.gca'...
- average std = 23.1 using min determinant for regularization = 53.4
- 0 singular and 5702 ill-conditioned covariance matrices regularized
- reading 'nu_noneck.mgz'...
- freeing gibbs priors...done.
- bounding unknown intensity as < 20.2 or > 943.7
- total sample mean = 92.0 (1443 zeros)
- ************************************************
- spacing=8, using 3481 sample points, tol=1.00e-05...
- ************************************************
- register_mri: find_optimal_transform
- find_optimal_transform: nsamples 3481, passno 0, spacing 8
- resetting wm mean[0]: 117 --> 126
- resetting gm mean[0]: 74 --> 74
- input volume #1 is the most T1-like
- using real data threshold=8.0
- skull bounding box = (49, 33, 34) --> (209, 207, 230)
- using (102, 91, 132) as brain centroid...
- mean wm in atlas = 126, using box (82,70,108) --> (121, 112,156) to find MRI wm
- before smoothing, mri peak at 106
- after smoothing, mri peak at 106, scaling input intensities by 1.189
- scaling channel 0 by 1.18868
- ****************************************
- Nine parameter search. iteration 0 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-4.1 (thresh=-4.1)
- 1.175 -0.042 0.015 -23.302;
- 0.039 1.303 0.010 -34.946;
- -0.023 -0.011 1.159 -36.684;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 1 nscales = 0 ...
- ****************************************
- Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.175 -0.042 0.015 -23.302;
- 0.039 1.303 0.010 -34.946;
- -0.023 -0.011 1.159 -36.684;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.2500
- ****************************************
- Nine parameter search. iteration 2 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.197 -0.043 0.016 -26.097;
- 0.037 1.254 0.010 -29.094;
- -0.022 -0.010 1.095 -28.757;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 3 nscales = 1 ...
- ****************************************
- Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.197 -0.043 0.016 -26.097;
- 0.037 1.254 0.010 -29.094;
- -0.022 -0.010 1.095 -28.757;
- 0.000 0.000 0.000 1.000;
- reducing scale to 0.0625
- ****************************************
- Nine parameter search. iteration 4 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.198 -0.064 0.016 -23.326;
- 0.057 1.258 0.010 -31.157;
- -0.022 -0.010 1.095 -28.288;
- 0.000 0.000 0.000 1.000;
- ****************************************
- Nine parameter search. iteration 5 nscales = 2 ...
- ****************************************
- Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
- 1.198 -0.064 0.016 -23.326;
- 0.057 1.260 0.010 -31.514;
- -0.022 -0.010 1.097 -28.603;
- 0.000 0.000 0.000 1.000;
- min search scale 0.025000 reached
- ***********************************************
- Computing MAP estimate using 3481 samples...
- ***********************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-05
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.19810 -0.06363 0.01552 -23.32577;
- 0.05712 1.26048 0.00991 -31.51387;
- -0.02224 -0.01011 1.09735 -28.60259;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 3481
- Quasinewton: input matrix
- 1.19810 -0.06363 0.01552 -23.32577;
- 0.05712 1.26048 0.00991 -31.51387;
- -0.02224 -0.01011 1.09735 -28.60259;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010
- Resulting transform:
- 1.198 -0.064 0.016 -23.326;
- 0.057 1.260 0.010 -31.514;
- -0.022 -0.010 1.097 -28.603;
- 0.000 0.000 0.000 1.000;
- pass 1, spacing 8: log(p) = -3.9 (old=-4.1)
- transform before final EM align:
- 1.198 -0.064 0.016 -23.326;
- 0.057 1.260 0.010 -31.514;
- -0.022 -0.010 1.097 -28.603;
- 0.000 0.000 0.000 1.000;
- **************************************************
- EM alignment process ...
- Computing final MAP estimate using 382743 samples.
- **************************************************
- dt = 5.00e-06, momentum=0.80, tol=1.00e-07
- l_intensity = 1.0000
- Aligning input volume to GCA...
- Transform matrix
- 1.19810 -0.06363 0.01552 -23.32577;
- 0.05712 1.26048 0.00991 -31.51387;
- -0.02224 -0.01011 1.09735 -28.60259;
- 0.00000 0.00000 0.00000 1.00000;
- nsamples 382743
- Quasinewton: input matrix
- 1.19810 -0.06363 0.01552 -23.32577;
- 0.05712 1.26048 0.00991 -31.51387;
- -0.02224 -0.01011 1.09735 -28.60259;
- 0.00000 0.00000 0.00000 1.00000;
- IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 4.3 tol 0.000000
- final transform:
- 1.198 -0.064 0.016 -23.326;
- 0.057 1.260 0.010 -31.514;
- -0.022 -0.010 1.097 -28.603;
- 0.000 0.000 0.000 1.000;
- writing output transformation to transforms/talairach_with_skull_2.lta...
- registration took 20 minutes and 43 seconds.
- #--------------------------------------
- #@# SubCort Seg Sat Jan 14 12:20:20 UTC 2017
- mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz
- sysname Linux
- hostname 3dcbcfbafa99
- machine x86_64
- setenv SUBJECTS_DIR /data/out
- cd /data/out/sub-02/mri
- mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz
- renormalizing sequences with structure alignment, equivalent to:
- -renormalize
- -renormalize_mean 0.500
- -regularize 0.500
- reading 1 input volumes...
- reading classifier array from /opt/freesurfer/average/RB_all_2008-03-26.gca...
- reading input volume from norm.mgz...
- average std[0] = 6.9
- reading transform from transforms/talairach.m3z...
- Atlas used for the 3D morph was /opt/freesurfer/average/RB_all_2008-03-26.gca
- average std = 6.9 using min determinant for regularization = 4.7
- 0 singular and 0 ill-conditioned covariance matrices regularized
- labeling volume...
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.15151 (27)
- mri peak = 0.23415 ( 6)
- Left_Lateral_Ventricle (4): linear fit = 0.17 x + 0.0 (1494 voxels, overlap=0.005)
- Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1494 voxels, peak = 5), gca=10.8
- gca peak = 0.14982 (20)
- mri peak = 0.13535 ( 8)
- Right_Lateral_Ventricle (43): linear fit = 0.32 x + 0.0 (599 voxels, overlap=0.007)
- Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (599 voxels, peak = 6), gca=8.0
- gca peak = 0.28003 (97)
- mri peak = 0.16563 (93)
- Right_Pallidum (52): linear fit = 0.92 x + 0.0 (228 voxels, overlap=0.508)
- Right_Pallidum (52): linear fit = 0.92 x + 0.0 (228 voxels, peak = 89), gca=88.8
- gca peak = 0.18160 (96)
- mri peak = 0.13035 (93)
- Left_Pallidum (13): linear fit = 0.93 x + 0.0 (227 voxels, overlap=0.483)
- Left_Pallidum (13): linear fit = 0.93 x + 0.0 (227 voxels, peak = 89), gca=88.8
- gca peak = 0.27536 (62)
- mri peak = 0.07127 (45)
- Right_Hippocampus (53): linear fit = 0.75 x + 0.0 (644 voxels, overlap=0.029)
- Right_Hippocampus (53): linear fit = 0.75 x + 0.0 (644 voxels, peak = 47), gca=46.8
- gca peak = 0.32745 (63)
- mri peak = 0.08764 (44)
- Left_Hippocampus (17): linear fit = 0.69 x + 0.0 (824 voxels, overlap=0.028)
- Left_Hippocampus (17): linear fit = 0.69 x + 0.0 (824 voxels, peak = 43), gca=43.2
- gca peak = 0.08597 (105)
- mri peak = 0.07584 (108)
- Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (35533 voxels, overlap=0.653)
- Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (35533 voxels, peak = 110), gca=109.7
- gca peak = 0.09209 (106)
- mri peak = 0.08437 (108)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (35172 voxels, overlap=0.661)
- Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (35172 voxels, peak = 110), gca=109.7
- gca peak = 0.07826 (63)
- mri peak = 0.04011 (50)
- Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (12442 voxels, overlap=0.378)
- Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (12442 voxels, peak = 50), gca=50.1
- gca peak = 0.08598 (64)
- mri peak = 0.03955 (50)
- Right_Cerebral_Cortex (42): linear fit = 0.75 x + 0.0 (13588 voxels, overlap=0.206)
- Right_Cerebral_Cortex (42): linear fit = 0.75 x + 0.0 (13588 voxels, peak = 48), gca=48.3
- gca peak = 0.24164 (71)
- mri peak = 0.09607 (59)
- Right_Caudate (50): linear fit = 0.83 x + 0.0 (461 voxels, overlap=0.029)
- Right_Caudate (50): linear fit = 0.83 x + 0.0 (461 voxels, peak = 59), gca=59.3
- gca peak = 0.18227 (75)
- mri peak = 0.07931 (60)
- Left_Caudate (11): linear fit = 0.79 x + 0.0 (589 voxels, overlap=0.033)
- Left_Caudate (11): linear fit = 0.79 x + 0.0 (589 voxels, peak = 59), gca=58.9
- gca peak = 0.10629 (62)
- mri peak = 0.04849 (57)
- Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (19567 voxels, overlap=0.972)
- Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (19567 voxels, peak = 60), gca=59.8
- gca peak = 0.11668 (59)
- mri peak = 0.04888 (56)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (20267 voxels, overlap=0.987)
- Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (20267 voxels, peak = 57), gca=56.9
- gca peak = 0.17849 (88)
- mri peak = 0.09789 (94)
- Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4174 voxels, overlap=0.815)
- Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4174 voxels, peak = 94), gca=93.7
- gca peak = 0.16819 (86)
- mri peak = 0.10342 (93)
- Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (4525 voxels, overlap=0.279)
- Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (4525 voxels, peak = 93), gca=93.3
- gca peak = 0.41688 (64)
- mri peak = 0.20007 (51)
- Left_Amygdala (18): linear fit = 0.79 x + 0.0 (170 voxels, overlap=0.236)
- Left_Amygdala (18): linear fit = 0.79 x + 0.0 (170 voxels, peak = 50), gca=50.2
- gca peak = 0.42394 (62)
- mri peak = 0.13473 (52)
- Right_Amygdala (54): linear fit = 0.82 x + 0.0 (170 voxels, overlap=0.188)
- Right_Amygdala (54): linear fit = 0.82 x + 0.0 (170 voxels, peak = 51), gca=51.1
- gca peak = 0.10041 (96)
- mri peak = 0.08177 (88)
- Left_Thalamus_Proper (10): linear fit = 0.93 x + 0.0 (3063 voxels, overlap=0.532)
- Left_Thalamus_Proper (10): linear fit = 0.93 x + 0.0 (3063 voxels, peak = 89), gca=88.8
- gca peak = 0.13978 (88)
- mri peak = 0.08632 (83)
- Right_Thalamus_Proper (49): linear fit = 0.96 x + 0.0 (2987 voxels, overlap=0.932)
- Right_Thalamus_Proper (49): linear fit = 0.96 x + 0.0 (2987 voxels, peak = 85), gca=84.9
- gca peak = 0.08514 (81)
- mri peak = 0.06878 (61)
- Left_Putamen (12): linear fit = 0.81 x + 0.0 (1840 voxels, overlap=0.312)
- Left_Putamen (12): linear fit = 0.81 x + 0.0 (1840 voxels, peak = 65), gca=65.2
- gca peak = 0.09624 (82)
- mri peak = 0.07921 (62)
- Right_Putamen (51): linear fit = 0.81 x + 0.0 (1380 voxels, overlap=0.189)
- Right_Putamen (51): linear fit = 0.81 x + 0.0 (1380 voxels, peak = 66), gca=66.0
- gca peak = 0.07543 (88)
- mri peak = 0.07785 (80)
- Brain_Stem (16): linear fit = 0.99 x + 0.0 (9722 voxels, overlap=0.765)
- Brain_Stem (16): linear fit = 0.99 x + 0.0 (9722 voxels, peak = 87), gca=86.7
- gca peak = 0.12757 (95)
- mri peak = 0.06974 (100)
- Right_VentralDC (60): linear fit = 1.04 x + 0.0 (877 voxels, overlap=0.744)
- Right_VentralDC (60): linear fit = 1.04 x + 0.0 (877 voxels, peak = 99), gca=99.3
- gca peak = 0.17004 (92)
- mri peak = 0.07602 (90)
- Left_VentralDC (28): linear fit = 0.96 x + 0.0 (840 voxels, overlap=0.841)
- Left_VentralDC (28): linear fit = 0.96 x + 0.0 (840 voxels, peak = 89), gca=88.8
- gca peak = 0.21361 (36)
- mri peak = 0.36364 (11)
- gca peak = 0.26069 (23)
- mri peak = 0.16742 ( 8)
- Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (147 voxels, overlap=0.024)
- Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (147 voxels, peak = 6), gca=6.1
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.31795 (35)
- gca peak Third_Ventricle = 0.21361 (36)
- gca peak Fourth_Ventricle = 0.26069 (23)
- gca peak CSF = 0.14367 (38)
- gca peak Left_Accumbens_area = 0.57033 (70)
- gca peak Left_undetermined = 1.00000 (35)
- gca peak Left_vessel = 0.65201 (62)
- gca peak Left_choroid_plexus = 0.09084 (48)
- gca peak Right_Inf_Lat_Vent = 0.31129 (32)
- gca peak Right_Accumbens_area = 0.30219 (72)
- gca peak Right_vessel = 0.83418 (60)
- gca peak Right_choroid_plexus = 0.10189 (48)
- gca peak Fifth_Ventricle = 0.72939 (42)
- gca peak WM_hypointensities = 0.14821 (82)
- gca peak non_WM_hypointensities = 0.10354 (53)
- gca peak Optic_Chiasm = 0.34849 (76)
- not using caudate to estimate GM means
- estimating mean gm scale to be 0.77 x + 0.0
- estimating mean wm scale to be 1.04 x + 0.0
- estimating mean csf scale to be 0.40 x + 0.0
- saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
- renormalizing by structure alignment....
- renormalizing input #0
- gca peak = 0.31600 (11)
- mri peak = 0.23415 ( 6)
- Left_Lateral_Ventricle (4): linear fit = 0.46 x + 0.0 (1494 voxels, overlap=0.779)
- Left_Lateral_Ventricle (4): linear fit = 0.46 x + 0.0 (1494 voxels, peak = 5), gca=5.0
- gca peak = 0.29325 ( 9)
- mri peak = 0.13535 ( 8)
- Right_Lateral_Ventricle (43): linear fit = 0.85 x + 0.0 (599 voxels, overlap=0.649)
- Right_Lateral_Ventricle (43): linear fit = 0.85 x + 0.0 (599 voxels, peak = 8), gca=7.6
- gca peak = 0.32313 (89)
- mri peak = 0.16563 (93)
- Right_Pallidum (52): linear fit = 1.01 x + 0.0 (228 voxels, overlap=0.986)
- Right_Pallidum (52): linear fit = 1.01 x + 0.0 (228 voxels, peak = 90), gca=90.3
- gca peak = 0.18464 (89)
- mri peak = 0.13035 (93)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (227 voxels, overlap=1.007)
- Left_Pallidum (13): linear fit = 1.00 x + 0.0 (227 voxels, peak = 89), gca=88.6
- gca peak = 0.33510 (47)
- mri peak = 0.07127 (45)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (644 voxels, overlap=1.001)
- Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (644 voxels, peak = 47), gca=47.0
- gca peak = 0.31911 (43)
- mri peak = 0.08764 (44)
- Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (824 voxels, overlap=0.825)
- Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (824 voxels, peak = 42), gca=41.9
- gca peak = 0.08169 (110)
- mri peak = 0.07584 (108)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (35533 voxels, overlap=0.806)
- Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (35533 voxels, peak = 110), gca=110.0
- gca peak = 0.08542 (110)
- mri peak = 0.08437 (108)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35172 voxels, overlap=0.758)
- Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35172 voxels, peak = 110), gca=110.0
- gca peak = 0.09736 (50)
- mri peak = 0.04011 (50)
- Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (12442 voxels, overlap=0.999)
- Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (12442 voxels, peak = 48), gca=48.2
- gca peak = 0.11769 (48)
- mri peak = 0.03955 (50)
- Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (13588 voxels, overlap=0.995)
- Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (13588 voxels, peak = 50), gca=49.7
- gca peak = 0.25920 (59)
- mri peak = 0.09607 (59)
- Right_Caudate (50): linear fit = 0.99 x + 0.0 (461 voxels, overlap=1.006)
- Right_Caudate (50): linear fit = 0.99 x + 0.0 (461 voxels, peak = 58), gca=58.1
- gca peak = 0.18377 (59)
- mri peak = 0.07931 (60)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (589 voxels, overlap=1.006)
- Left_Caudate (11): linear fit = 1.00 x + 0.0 (589 voxels, peak = 59), gca=59.0
- gca peak = 0.10996 (60)
- mri peak = 0.04849 (57)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (19567 voxels, overlap=0.999)
- Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (19567 voxels, peak = 62), gca=61.5
- gca peak = 0.12282 (58)
- mri peak = 0.04888 (56)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (20267 voxels, overlap=1.000)
- Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (20267 voxels, peak = 57), gca=57.1
- gca peak = 0.17927 (93)
- mri peak = 0.09789 (94)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4174 voxels, overlap=0.991)
- Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4174 voxels, peak = 93), gca=92.5
- gca peak = 0.15749 (94)
- mri peak = 0.10342 (93)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4525 voxels, overlap=0.968)
- Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4525 voxels, peak = 94), gca=93.5
- gca peak = 0.46619 (50)
- mri peak = 0.20007 (51)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (170 voxels, overlap=0.939)
- Left_Amygdala (18): linear fit = 1.00 x + 0.0 (170 voxels, peak = 50), gca=50.0
- gca peak = 0.43982 (52)
- mri peak = 0.13473 (52)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (170 voxels, overlap=0.996)
- Right_Amygdala (54): linear fit = 1.00 x + 0.0 (170 voxels, peak = 52), gca=52.0
- gca peak = 0.11259 (89)
- mri peak = 0.08177 (88)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3063 voxels, overlap=0.741)
- Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3063 voxels, peak = 89), gca=88.6
- gca peak = 0.13475 (85)
- mri peak = 0.08632 (83)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2987 voxels, overlap=0.924)
- Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2987 voxels, peak = 85), gca=84.6
- gca peak = 0.10378 (65)
- mri peak = 0.06878 (61)
- Left_Putamen (12): linear fit = 1.02 x + 0.0 (1840 voxels, overlap=0.991)
- Left_Putamen (12): linear fit = 1.02 x + 0.0 (1840 voxels, peak = 67), gca=66.6
- gca peak = 0.11924 (61)
- mri peak = 0.07921 (62)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1380 voxels, overlap=0.999)
- Right_Putamen (51): linear fit = 1.00 x + 0.0 (1380 voxels, peak = 61), gca=61.0
- gca peak = 0.07696 (87)
- mri peak = 0.07785 (80)
- Brain_Stem (16): linear fit = 1.01 x + 0.0 (9722 voxels, overlap=0.724)
- Brain_Stem (16): linear fit = 1.01 x + 0.0 (9722 voxels, peak = 88), gca=88.3
- gca peak = 0.13023 (99)
- mri peak = 0.06974 (100)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (877 voxels, overlap=0.867)
- Right_VentralDC (60): linear fit = 1.00 x + 0.0 (877 voxels, peak = 99), gca=99.5
- gca peak = 0.16127 (89)
- mri peak = 0.07602 (90)
- Left_VentralDC (28): linear fit = 1.02 x + 0.0 (840 voxels, overlap=0.823)
- Left_VentralDC (28): linear fit = 1.02 x + 0.0 (840 voxels, peak = 91), gca=91.2
- gca peak = 0.35640 (14)
- mri peak = 0.36364 (11)
- gca peak = 0.33827 ( 9)
- mri peak = 0.16742 ( 8)
- Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (147 voxels, overlap=0.840)
- Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (147 voxels, peak = 6), gca=6.1
- gca peak Unknown = 0.94427 ( 0)
- gca peak Left_Inf_Lat_Vent = 0.34481 (24)
- gca peak Third_Ventricle = 0.35640 (14)
- gca peak CSF = 0.30128 (18)
- gca peak Left_Accumbens_area = 0.57077 (55)
- gca peak Left_undetermined = 1.00000 (35)
- gca peak Left_vessel = 0.25685 (61)
- gca peak Left_choroid_plexus = 0.10056 (53)
- gca peak Right_Inf_Lat_Vent = 0.36000 (24)
- gca peak Right_Accumbens_area = 0.37280 (60)
- gca peak Right_vessel = 0.31471 (59)
- gca peak Right_choroid_plexus = 0.11056 (46)
- gca peak Fifth_Ventricle = 0.45329 (19)
- gca peak WM_hypointensities = 0.17169 (85)
- gca peak non_WM_hypointensities = 0.11195 (55)
- gca peak Optic_Chiasm = 0.34840 (76)
- not using caudate to estimate GM means
- estimating mean gm scale to be 1.00 x + 0.0
- estimating mean wm scale to be 1.00 x + 0.0
- estimating mean csf scale to be 0.66 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
- 13336 gm and wm labels changed (%10 to gray, %90 to white out of all changed labels)
- 189 hippocampal voxels changed.
- 0 amygdala voxels changed.
- pass 1: 79251 changed. image ll: -2.159, PF=1.000
- pass 2: 15409 changed. image ll: -2.158, PF=1.000
- pass 3: 6256 changed.
- pass 4: 2978 changed.
- writing labeled volume to aseg.auto_noCCseg.mgz...
- auto-labeling took 17 minutes and 3 seconds.
- mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /data/out/sub-02/mri/transforms/cc_up.lta sub-02
- will read input aseg from aseg.auto_noCCseg.mgz
- writing aseg with cc labels to aseg.auto.mgz
- will write lta as /data/out/sub-02/mri/transforms/cc_up.lta
- reading aseg from /data/out/sub-02/mri/aseg.auto_noCCseg.mgz
- reading norm from /data/out/sub-02/mri/norm.mgz
- 32870 voxels in left wm, 22300 in right wm, xrange [125, 134]
- searching rotation angles z=[-5 9], y=[-6 8]
-
searching scale 1 Z rot -5.0
searching scale 1 Z rot -4.7
searching scale 1 Z rot -4.5
searching scale 1 Z rot -4.2
searching scale 1 Z rot -4.0
searching scale 1 Z rot -3.7
searching scale 1 Z rot -3.5
searching scale 1 Z rot -3.2
searching scale 1 Z rot -3.0
searching scale 1 Z rot -2.7
searching scale 1 Z rot -2.5
searching scale 1 Z rot -2.2
searching scale 1 Z rot -2.0
searching scale 1 Z rot -1.7
searching scale 1 Z rot -1.5
searching scale 1 Z rot -1.2
searching scale 1 Z rot -1.0
searching scale 1 Z rot -0.7
searching scale 1 Z rot -0.5
searching scale 1 Z rot -0.2
searching scale 1 Z rot 0.0
searching scale 1 Z rot 0.3
searching scale 1 Z rot 0.5
searching scale 1 Z rot 0.8
searching scale 1 Z rot 1.0
searching scale 1 Z rot 1.3
searching scale 1 Z rot 1.5
searching scale 1 Z rot 1.8
searching scale 1 Z rot 2.0
searching scale 1 Z rot 2.3
searching scale 1 Z rot 2.5
searching scale 1 Z rot 2.8
searching scale 1 Z rot 3.0
searching scale 1 Z rot 3.3
searching scale 1 Z rot 3.5
searching scale 1 Z rot 3.8
searching scale 1 Z rot 4.0
searching scale 1 Z rot 4.3
searching scale 1 Z rot 4.5
searching scale 1 Z rot 4.8
searching scale 1 Z rot 5.0
searching scale 1 Z rot 5.3
searching scale 1 Z rot 5.5
searching scale 1 Z rot 5.8
searching scale 1 Z rot 6.0
searching scale 1 Z rot 6.3
searching scale 1 Z rot 6.5
searching scale 1 Z rot 6.8
searching scale 1 Z rot 7.0
searching scale 1 Z rot 7.3
searching scale 1 Z rot 7.5
searching scale 1 Z rot 7.8
searching scale 1 Z rot 8.0
searching scale 1 Z rot 8.3
searching scale 1 Z rot 8.5
searching scale 1 Z rot 8.8 global minimum found at slice 128.4, rotations (1.23, 2.03)
- final transformation (x=128.4, yr=1.226, zr=2.032):
- 0.999 -0.035 0.021 0.609;
- 0.035 0.999 0.001 30.421;
- -0.021 0.000 1.000 18.774;
- 0.000 0.000 0.000 1.000;
- updating x range to be [125, 130] in xformed coordinates
- best xformed slice 128
- cc center is found at 128 156 180
- eigenvectors:
- -0.001 0.003 1.000;
- 0.151 -0.988 0.003;
- 0.988 0.151 0.000;
- error in mid anterior detected - correcting...
- writing aseg with callosum to /data/out/sub-02/mri/aseg.auto.mgz...
- corpus callosum matter segmentation took 0.6 minutes
- #--------------------------------------
- #@# Merge ASeg Sat Jan 14 12:37:57 UTC 2017
- cp aseg.auto.mgz aseg.mgz
- #--------------------------------------------
- #@# Intensity Normalization2 Sat Jan 14 12:37:57 UTC 2017
- /data/out/sub-02/mri
- mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
- using segmentation for initial intensity normalization
- using MR volume brainmask.mgz to mask input volume...
- reading from norm.mgz...
- Reading aseg aseg.mgz
- normalizing image...
- processing with aseg
- removing outliers in the aseg WM...
- 4091 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 111
- white matter peak found at 109
- gm peak at 55 (55), valley at 23 (23)
- csf peak at 10, setting threshold to 40
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- ---------------------------------
- 3d normalization pass 2 of 2
- white matter peak found at 111
- white matter peak found at 110
- gm peak at 56 (56), valley at 23 (23)
- csf peak at 10, setting threshold to 40
- building Voronoi diagram...
- performing soap bubble smoothing, sigma = 8...
- Done iterating ---------------------------------
- writing output to brain.mgz
- 3D bias adjustment took 2 minutes and 48 seconds.
- #--------------------------------------------
- #@# Mask BFS Sat Jan 14 12:40:46 UTC 2017
- /data/out/sub-02/mri
- mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
- threshold mask volume at 5
- DoAbs = 0
- Found 1397645 voxels in mask (pct= 8.33)
- Writing masked volume to brain.finalsurfs.mgz...done.
- #--------------------------------------------
- #@# WM Segmentation Sat Jan 14 12:40:48 UTC 2017
- mri_segment brain.mgz wm.seg.mgz
- doing initial intensity segmentation...
- using local statistics to label ambiguous voxels...
- computing class statistics for intensity windows...
- WM (105.0): 105.9 +- 4.5 [80.0 --> 125.0]
- GM (70.0) : 68.3 +- 9.8 [30.0 --> 96.0]
- setting bottom of white matter range to 78.1
- setting top of gray matter range to 87.9
- 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...
- 2073 sparsely connected voxels removed...
- thickening thin strands....
- 20 segments, 3637 filled
- 805 bright non-wm voxels segmented.
- 1496 diagonally connected voxels added...
- white matter segmentation took 1.1 minutes
- writing output to wm.seg.mgz...
- mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz
- preserving editing changes in input volume...
- auto filling took 0.48 minutes
- reading wm segmentation from wm.seg.mgz...
- 321 voxels added to wm to prevent paths from MTL structures to cortex
- 1625 additional wm voxels added
- 0 additional wm voxels added
- SEG EDIT: 49374 voxels turned on, 29815 voxels turned off.
- propagating editing to output volume from wm.seg.mgz
- 115,126,128 old 97 new 97
- 115,126,128 old 97 new 97
- writing edited volume to wm.asegedit.mgz....
- mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
- Iteration Number : 1
- pass 1 (xy+): 10 found - 10 modified | TOTAL: 10
- pass 2 (xy+): 0 found - 10 modified | TOTAL: 10
- pass 1 (xy-): 11 found - 11 modified | TOTAL: 21
- pass 2 (xy-): 0 found - 11 modified | TOTAL: 21
- pass 1 (yz+): 13 found - 13 modified | TOTAL: 34
- pass 2 (yz+): 0 found - 13 modified | TOTAL: 34
- pass 1 (yz-): 24 found - 24 modified | TOTAL: 58
- pass 2 (yz-): 0 found - 24 modified | TOTAL: 58
- pass 1 (xz+): 23 found - 23 modified | TOTAL: 81
- pass 2 (xz+): 0 found - 23 modified | TOTAL: 81
- pass 1 (xz-): 21 found - 21 modified | TOTAL: 102
- pass 2 (xz-): 0 found - 21 modified | TOTAL: 102
- Iteration Number : 1
- pass 1 (+++): 12 found - 12 modified | TOTAL: 12
- pass 2 (+++): 0 found - 12 modified | TOTAL: 12
- pass 1 (+++): 6 found - 6 modified | TOTAL: 18
- pass 2 (+++): 0 found - 6 modified | TOTAL: 18
- pass 1 (+++): 2 found - 2 modified | TOTAL: 20
- pass 2 (+++): 0 found - 2 modified | TOTAL: 20
- pass 1 (+++): 9 found - 9 modified | TOTAL: 29
- pass 2 (+++): 0 found - 9 modified | TOTAL: 29
- Iteration Number : 1
- pass 1 (++): 49 found - 49 modified | TOTAL: 49
- pass 2 (++): 0 found - 49 modified | TOTAL: 49
- pass 1 (+-): 46 found - 46 modified | TOTAL: 95
- pass 2 (+-): 0 found - 46 modified | TOTAL: 95
- pass 1 (--): 40 found - 40 modified | TOTAL: 135
- pass 2 (--): 0 found - 40 modified | TOTAL: 135
- pass 1 (-+): 59 found - 59 modified | TOTAL: 194
- pass 2 (-+): 0 found - 59 modified | TOTAL: 194
- Iteration Number : 2
- pass 1 (xy+): 4 found - 4 modified | TOTAL: 4
- pass 2 (xy+): 0 found - 4 modified | TOTAL: 4
- pass 1 (xy-): 2 found - 2 modified | TOTAL: 6
- pass 2 (xy-): 0 found - 2 modified | TOTAL: 6
- pass 1 (yz+): 3 found - 3 modified | TOTAL: 9
- pass 2 (yz+): 0 found - 3 modified | TOTAL: 9
- pass 1 (yz-): 2 found - 2 modified | TOTAL: 11
- pass 2 (yz-): 0 found - 2 modified | TOTAL: 11
- pass 1 (xz+): 5 found - 5 modified | TOTAL: 16
- pass 2 (xz+): 0 found - 5 modified | TOTAL: 16
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 16
- 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 (+-): 1 found - 1 modified | TOTAL: 1
- pass 2 (+-): 0 found - 1 modified | TOTAL: 1
- pass 1 (--): 1 found - 1 modified | TOTAL: 2
- pass 2 (--): 0 found - 1 modified | TOTAL: 2
- pass 1 (-+): 3 found - 3 modified | TOTAL: 5
- pass 2 (-+): 0 found - 3 modified | TOTAL: 5
- Iteration Number : 3
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 1 found - 1 modified | TOTAL: 1
- pass 2 (xy-): 0 found - 1 modified | TOTAL: 1
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 1
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 1
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 1
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 1
- Iteration Number : 3
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 3
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- 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 = 347 (out of 497322: 0.069774)
- binarizing input wm segmentation...
- Ambiguous edge configurations...
- mri_pretess done
- #--------------------------------------------
- #@# Fill Sat Jan 14 12:42:25 UTC 2017
- /data/out/sub-02/mri
- mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
- logging cutting plane coordinates to ../scripts/ponscc.cut.log...
- INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
- using segmentation aseg.auto_noCCseg.mgz...
- reading input volume...done.
- searching for cutting planes...voxel to talairach voxel transform
- 1.105 -0.040 0.014 -14.369;
- 0.036 1.212 0.009 -24.058;
- -0.022 -0.010 1.078 -26.727;
- 0.000 0.000 0.000 1.000;
- voxel to talairach voxel transform
- 1.105 -0.040 0.014 -14.369;
- 0.036 1.212 0.009 -24.058;
- -0.022 -0.010 1.078 -26.727;
- 0.000 0.000 0.000 1.000;
- reading segmented volume aseg.auto_noCCseg.mgz...
- Looking for area (min, max) = (350, 1400)
- area[0] = 1402 (min = 350, max = 1400), aspect = 0.49 (min = 0.10, max = 0.75)
- need search nearby
- using seed (125, 105, 94), TAL = (3.0, -34.0, 23.0)
- talairach voxel to voxel transform
- 0.904 0.030 -0.012 13.366;
- -0.027 0.824 -0.007 19.261;
- 0.018 0.008 0.927 25.235;
- 0.000 0.000 0.000 1.000;
- segmentation indicates cc at (125, 105, 94) --> (3.0, -34.0, 23.0)
- done.
- writing output to filled.mgz...
- filling took 0.6 minutes
- talairach cc position changed to (3.00, -34.00, 23.00)
- Erasing brainstem...done.
- seed_search_size = 9, min_neighbors = 5
- search rh wm seed point around talairach space:(21.00, -34.00, 23.00) SRC: (112.01, 102.28, 115.17)
- search lh wm seed point around talairach space (-15.00, -34.00, 23.00), SRC: (144.55, 101.31, 115.82)
- compute mri_fill using aseg
- Erasing Brain Stem and Cerebellum ...
- Define left and right masks using aseg:
- Building Voronoi diagram ...
- Using the Voronoi diagram to separate WM into two hemispheres ...
- Find the largest connected component for each hemisphere ...
- #--------------------------------------------
- #@# Tessellate lh Sat Jan 14 12:43:03 UTC 2017
- /data/out/sub-02/scripts
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- Iteration Number : 1
- pass 1 (xy+): 2 found - 2 modified | TOTAL: 2
- pass 2 (xy+): 0 found - 2 modified | TOTAL: 2
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 2
- pass 1 (yz+): 1 found - 1 modified | TOTAL: 3
- pass 2 (yz+): 0 found - 1 modified | TOTAL: 3
- pass 1 (yz-): 2 found - 2 modified | TOTAL: 5
- pass 2 (yz-): 0 found - 2 modified | TOTAL: 5
- pass 1 (xz+): 1 found - 1 modified | TOTAL: 6
- pass 2 (xz+): 0 found - 1 modified | TOTAL: 6
- pass 1 (xz-): 1 found - 1 modified | TOTAL: 7
- pass 2 (xz-): 0 found - 1 modified | TOTAL: 7
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 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
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 8 (out of 240376: 0.003328)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
- $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- slice 60: 1196 vertices, 1273 faces
- slice 70: 5653 vertices, 5845 faces
- slice 80: 12371 vertices, 12635 faces
- slice 90: 20982 vertices, 21290 faces
- slice 100: 30108 vertices, 30384 faces
- slice 110: 39384 vertices, 39687 faces
- slice 120: 50070 vertices, 50406 faces
- slice 130: 61067 vertices, 61459 faces
- slice 140: 71831 vertices, 72211 faces
- slice 150: 81969 vertices, 82326 faces
- slice 160: 90447 vertices, 90740 faces
- slice 170: 96961 vertices, 97221 faces
- slice 180: 103585 vertices, 103828 faces
- slice 190: 108886 vertices, 109107 faces
- slice 200: 114083 vertices, 114266 faces
- slice 210: 116335 vertices, 116387 faces
- slice 220: 116360 vertices, 116398 faces
- slice 230: 116360 vertices, 116398 faces
- slice 240: 116360 vertices, 116398 faces
- slice 250: 116360 vertices, 116398 faces
- using the conformed surface RAS to save vertex points...
- writing ../surf/lh.orig.nofix
- using vox2ras matrix:
- -1.000 0.000 0.000 128.000;
- 0.000 0.000 1.000 -128.000;
- 0.000 -1.000 0.000 128.000;
- 0.000 0.000 0.000 1.000;
- rm -f ../mri/filled-pretess255.mgz
- mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
- counting number of connected components...
- 116360 voxel in cpt #1: X=-38 [v=116360,e=349194,f=232796] located at (-27.656231, -0.385957, 23.281239)
- For the whole surface: X=-38 [v=116360,e=349194,f=232796]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 lh Sat Jan 14 12:43:08 UTC 2017
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- /data/out/sub-02/scripts
- setting seed for random number generator to 1234
- smoothing surface tessellation for 10 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation1 lh Sat Jan 14 12:43:10 UTC 2017
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- /data/out/sub-02/scripts
- avg radius = 44.7 mm, total surface area = 62766 mm^2
- writing inflated surface to ../surf/lh.inflated.nofix
- inflation took 0.3 minutes
- Not saving sulc
-
step 000: RMS=0.099 (target=0.015)
step 005: RMS=0.073 (target=0.015)
step 010: RMS=0.055 (target=0.015)
step 015: RMS=0.047 (target=0.015)
step 020: RMS=0.042 (target=0.015)
step 025: RMS=0.036 (target=0.015)
step 030: RMS=0.033 (target=0.015)
step 035: RMS=0.032 (target=0.015)
step 040: RMS=0.030 (target=0.015)
step 045: RMS=0.028 (target=0.015)
step 050: RMS=0.028 (target=0.015)
step 055: RMS=0.027 (target=0.015)
step 060: RMS=0.027 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere lh Sat Jan 14 12:43:30 UTC 2017
- /data/out/sub-02/scripts
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 1.07 +- 0.58 (0.00-->6.77) (max @ vno 84532 --> 85433)
- face area 0.03 +- 0.03 (-0.12-->0.69)
- scaling brain by 0.335...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.603, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.343, avgs=0
- 010/300: dt: 0.9000, rms radial error=175.783, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.049, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.212, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.319, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.399, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.462, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.518, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.571, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.625, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.682, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.743, avgs=0
- 065/300: dt: 0.9000, rms radial error=165.809, avgs=0
- 070/300: dt: 0.9000, rms radial error=164.879, avgs=0
- 075/300: dt: 0.9000, rms radial error=163.954, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.034, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.119, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.209, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.304, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.404, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.509, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.618, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.733, avgs=0
- 120/300: dt: 0.9000, rms radial error=155.852, avgs=0
- 125/300: dt: 0.9000, rms radial error=154.976, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.105, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.239, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.377, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.521, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.668, avgs=0
- 155/300: dt: 0.9000, rms radial error=149.821, avgs=0
- 160/300: dt: 0.9000, rms radial error=148.978, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.140, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.307, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.478, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.654, avgs=0
- 185/300: dt: 0.9000, rms radial error=144.835, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.020, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.209, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.403, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.601, avgs=0
- 210/300: dt: 0.9000, rms radial error=140.804, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.011, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.223, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.439, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.659, avgs=0
- 235/300: dt: 0.9000, rms radial error=136.884, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.113, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.347, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.584, avgs=0
- 255/300: dt: 0.9000, rms radial error=133.826, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.072, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.323, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.577, avgs=0
- 275/300: dt: 0.9000, rms radial error=130.836, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.099, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.366, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.637, avgs=0
- 295/300: dt: 0.9000, rms radial error=127.912, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.191, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 13183.95
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00017
- epoch 2 (K=40.0), pass 1, starting sse = 2050.59
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00017
- epoch 3 (K=160.0), pass 1, starting sse = 188.51
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.14/13 = 0.01062
- epoch 4 (K=640.0), pass 1, starting sse = 10.82
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.17/16 = 0.01081
- final writing spherical brain to ../surf/lh.qsphere.nofix
- spherical transformation took 0.05 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology lh Sat Jan 14 12:46:21 UTC 2017
- cp ../surf/lh.orig.nofix ../surf/lh.orig
- cp ../surf/lh.inflated.nofix ../surf/lh.inflated
- /data/out/sub-02/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub-02 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 1.48 2011/03/02 00:04:32 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- before topology correction, eno=-38 (nv=116360, nf=232796, ne=349194, g=20)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 9 iterations
- marking ambiguous vertices...
- 3789 ambiguous faces found in tessellation
- segmenting defects...
- 26 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- 26 defects to be corrected
- 0 vertices coincident
- reading input surface /data/out/sub-02/surf/lh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.4402 (-4.7201)
- -vertex loglikelihood: -6.6368 (-3.3184)
- -normal dot loglikelihood: -3.6205 (-3.6205)
- -quad curv loglikelihood: -6.4071 (-3.2035)
- Total Loglikelihood : -26.1046
- CORRECTING DEFECT 0 (vertices=403, convex hull=140)
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- normal vector of length zero at vertex 14969 with 4 faces
- After retessellation of defect 0, euler #=-23 (114201,342000,227776) : difference with theory (-23) = 0
- CORRECTING DEFECT 1 (vertices=50, convex hull=97)
- After retessellation of defect 1, euler #=-22 (114225,342115,227868) : difference with theory (-22) = 0
- CORRECTING DEFECT 2 (vertices=273, convex hull=186)
- After retessellation of defect 2, euler #=-21 (114239,342241,227981) : difference with theory (-21) = 0
- CORRECTING DEFECT 3 (vertices=7, convex hull=23)
- After retessellation of defect 3, euler #=-20 (114241,342253,227992) : difference with theory (-20) = 0
- CORRECTING DEFECT 4 (vertices=5, convex hull=24)
- After retessellation of defect 4, euler #=-19 (114243,342266,228004) : difference with theory (-19) = 0
- CORRECTING DEFECT 5 (vertices=11, convex hull=30)
- After retessellation of defect 5, euler #=-18 (114245,342280,228017) : difference with theory (-18) = 0
- CORRECTING DEFECT 6 (vertices=9, convex hull=21)
- After retessellation of defect 6, euler #=-17 (114247,342293,228029) : difference with theory (-17) = 0
- CORRECTING DEFECT 7 (vertices=33, convex hull=54)
- After retessellation of defect 7, euler #=-16 (114258,342346,228072) : difference with theory (-16) = 0
- CORRECTING DEFECT 8 (vertices=5, convex hull=13)
- After retessellation of defect 8, euler #=-15 (114259,342352,228078) : difference with theory (-15) = 0
- CORRECTING DEFECT 9 (vertices=13, convex hull=17)
- After retessellation of defect 9, euler #=-14 (114262,342364,228088) : difference with theory (-14) = 0
- CORRECTING DEFECT 10 (vertices=21, convex hull=23)
- After retessellation of defect 10, euler #=-13 (114263,342373,228097) : difference with theory (-13) = 0
- CORRECTING DEFECT 11 (vertices=82, convex hull=64)
- After retessellation of defect 11, euler #=-12 (114284,342464,228168) : difference with theory (-12) = 0
- CORRECTING DEFECT 12 (vertices=70, convex hull=102)
- After retessellation of defect 12, euler #=-11 (114305,342571,228255) : difference with theory (-11) = 0
- CORRECTING DEFECT 13 (vertices=425, convex hull=66)
- After retessellation of defect 13, euler #=-10 (114335,342686,228341) : difference with theory (-10) = 0
- CORRECTING DEFECT 14 (vertices=78, convex hull=25)
- After retessellation of defect 14, euler #=-9 (114342,342714,228363) : difference with theory (-9) = 0
- CORRECTING DEFECT 15 (vertices=15, convex hull=23)
- After retessellation of defect 15, euler #=-8 (114348,342740,228384) : difference with theory (-8) = 0
- CORRECTING DEFECT 16 (vertices=75, convex hull=59)
- After retessellation of defect 16, euler #=-7 (114359,342797,228431) : difference with theory (-7) = 0
- CORRECTING DEFECT 17 (vertices=270, convex hull=147)
- After retessellation of defect 17, euler #=-6 (114437,343107,228664) : difference with theory (-6) = 0
- CORRECTING DEFECT 18 (vertices=12, convex hull=21)
- After retessellation of defect 18, euler #=-5 (114439,343120,228676) : difference with theory (-5) = 0
- CORRECTING DEFECT 19 (vertices=62, convex hull=32)
- After retessellation of defect 19, euler #=-4 (114444,343148,228700) : difference with theory (-4) = 0
- CORRECTING DEFECT 20 (vertices=87, convex hull=86)
- After retessellation of defect 20, euler #=-3 (114499,343354,228852) : difference with theory (-3) = 0
- CORRECTING DEFECT 21 (vertices=65, convex hull=97)
- After retessellation of defect 21, euler #=-2 (114532,343494,228960) : difference with theory (-2) = 0
- CORRECTING DEFECT 22 (vertices=46, convex hull=84)
- After retessellation of defect 22, euler #=-1 (114563,343623,229059) : difference with theory (-1) = 0
- CORRECTING DEFECT 23 (vertices=19, convex hull=26)
- After retessellation of defect 23, euler #=0 (114566,343643,229077) : difference with theory (0) = 0
- CORRECTING DEFECT 24 (vertices=33, convex hull=56)
- After retessellation of defect 24, euler #=1 (114575,343691,229117) : difference with theory (1) = 0
- CORRECTING DEFECT 25 (vertices=37, convex hull=62)
- After retessellation of defect 25, euler #=2 (114591,343767,229178) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.89 +- 0.22 (0.06-->9.55) (max @ vno 40479 --> 42359)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.89 +- 0.22 (0.06-->9.55) (max @ vno 40479 --> 42359)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 112 mutations (37.0%), 191 crossovers (63.0%), 132 vertices were eliminated
- building final representation...
- 1769 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=114591, nf=229178, ne=343767, g=0)
- writing corrected surface to /data/out/sub-02/surf/lh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 12.6 minutes
- 0 defective edges
- removing intersecting faces
- 000: 167 intersecting
- 001: 2 intersecting
- mris_euler_number ../surf/lh.orig
- euler # = v-e+f = 2g-2: 114591 - 343767 + 229178 = 2 --> 0 holes
- F =2V-4: 229178 = 229182-4 (0)
- 2E=3F: 687534 = 687534 (0)
- total defect index = 0
- /data/out/sub-02/scripts
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 11 intersecting
- writing corrected surface to ../surf/lh.orig
- rm ../surf/lh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Sat Jan 14 12:59:01 UTC 2017
- /data/out/sub-02/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-02 lh
- only generating white matter surface
- 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 1.147 2014/01/29 20:42:02 fischl Exp $
- $Id: mrisurf.c,v 1.753 2014/01/17 15:25:29 fischl Exp $
- reading volume /data/out/sub-02/mri/filled.mgz...
- reading volume /data/out/sub-02/mri/brain.finalsurfs.mgz...
- reading volume /data/out/sub-02/mri/wm.mgz...
- 8190 bright wm thresholded.
- 895 bright non-wm voxels segmented.
- reading original surface position from /data/out/sub-02/surf/lh.orig...
- computing class statistics...
- border white: 221986 voxels (1.32%)
- border gray 239648 voxels (1.43%)
- WM (91.0): 92.0 +- 8.8 [70.0 --> 110.0]
- GM (77.0) : 73.9 +- 13.6 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 43.4 (was 70)
- setting MAX_BORDER_WHITE to 109.8 (was 105)
- setting MIN_BORDER_WHITE to 57.0 (was 85)
- setting MAX_CSF to 29.8 (was 40)
- setting MAX_GRAY to 92.2 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 50.2 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 16.3 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /data/out/sub-02/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.83 +- 0.22 (0.03-->4.69) (max @ vno 42396 --> 43708)
- face area 0.28 +- 0.12 (0.00-->5.77)
- mean absolute distance = 0.78 +- 0.92
- 3653 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=101+-6.1, GM=57+-10.4
- mean inside = 90.8, mean outside = 69.1
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=71.6, 84 (84) missing vertices, mean dist 0.5 [0.6 (%28.2)->0.9 (%71.8))]
- %64 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=3dcbc, 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 0.94 +- 0.27 (0.13-->5.24) (max @ vno 42396 --> 114236)
- face area 0.28 +- 0.14 (0.00-->6.50)
- mean absolute distance = 0.34 +- 0.62
- 3146 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=6234664.5, rms=14.164
- 001: dt: 0.5000, sse=5799036.5, rms=10.657 (24.760%)
- 002: dt: 0.5000, sse=5624206.0, rms=8.269 (22.408%)
- 003: dt: 0.5000, sse=5701711.0, rms=6.570 (20.548%)
- 004: dt: 0.5000, sse=5821447.5, rms=5.496 (16.343%)
- 005: dt: 0.5000, sse=6029941.5, rms=4.880 (11.206%)
- 006: dt: 0.5000, sse=6149151.5, rms=4.564 (6.475%)
- 007: dt: 0.5000, sse=6245105.0, rms=4.387 (3.882%)
- 008: dt: 0.5000, sse=6274058.5, rms=4.295 (2.101%)
- 009: dt: 0.5000, sse=6317709.0, rms=4.224 (1.663%)
- rms = 4.18, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=6296935.0, rms=4.183 (0.966%)
- 011: dt: 0.2500, sse=3867759.0, rms=2.812 (32.769%)
- 012: dt: 0.2500, sse=3409703.0, rms=2.398 (14.731%)
- 013: dt: 0.2500, sse=3210080.8, rms=2.268 (5.437%)
- 014: dt: 0.2500, sse=3133982.8, rms=2.182 (3.761%)
- rms = 2.13, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=3087130.2, rms=2.133 (2.257%)
- 016: dt: 0.1250, sse=2979705.5, rms=2.021 (5.243%)
- rms = 2.01, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=2951638.8, rms=2.007 (0.688%)
- positioning took 1.0 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- mean border=74.5, 75 (35) missing vertices, mean dist -0.2 [0.4 (%67.7)->0.2 (%32.3))]
- %71 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=3dcbc, 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 0.92 +- 0.26 (0.12-->5.33) (max @ vno 42396 --> 114236)
- face area 0.37 +- 0.18 (0.00-->9.03)
- mean absolute distance = 0.27 +- 0.43
- 3703 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3577226.5, rms=5.237
- 018: dt: 0.5000, sse=3960222.8, rms=3.781 (27.804%)
- rms = 4.02, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=3571384.5, rms=2.914 (22.914%)
- 020: dt: 0.2500, sse=3378659.0, rms=2.299 (21.120%)
- 021: dt: 0.2500, sse=3286406.5, rms=1.987 (13.568%)
- 022: dt: 0.2500, sse=3239123.0, rms=1.862 (6.317%)
- 023: dt: 0.2500, sse=3207787.2, rms=1.777 (4.556%)
- rms = 1.73, time step reduction 2 of 3 to 0.125...
- 024: dt: 0.2500, sse=3190898.5, rms=1.733 (2.443%)
- 025: dt: 0.1250, sse=3134503.8, rms=1.657 (4.389%)
- rms = 1.65, time step reduction 3 of 3 to 0.062...
- 026: dt: 0.1250, sse=3114409.2, rms=1.646 (0.690%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- mean border=77.0, 84 (29) missing vertices, mean dist -0.1 [0.3 (%66.6)->0.2 (%33.4))]
- %79 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=3dcbc, 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 0.91 +- 0.26 (0.11-->5.40) (max @ vno 42396 --> 114236)
- face area 0.35 +- 0.17 (0.00-->9.07)
- mean absolute distance = 0.23 +- 0.35
- 3008 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3335369.2, rms=3.768
- 027: dt: 0.5000, sse=3788653.2, rms=3.252 (13.700%)
- rms = 3.65, time step reduction 1 of 3 to 0.250...
- 028: dt: 0.2500, sse=3448166.5, rms=2.271 (30.160%)
- 029: dt: 0.2500, sse=3299074.2, rms=1.765 (22.288%)
- 030: dt: 0.2500, sse=3281309.8, rms=1.569 (11.083%)
- rms = 1.54, time step reduction 2 of 3 to 0.125...
- 031: dt: 0.2500, sse=3264882.0, rms=1.542 (1.735%)
- 032: dt: 0.1250, sse=3207634.2, rms=1.456 (5.608%)
- rms = 1.45, time step reduction 3 of 3 to 0.062...
- 033: dt: 0.1250, sse=3185686.0, rms=1.451 (0.338%)
- positioning took 0.4 minutes
- inhibiting deformation at non-cortical midline structures...
- mean border=78.1, 101 (27) missing vertices, mean dist -0.1 [0.3 (%55.7)->0.2 (%44.3))]
- %82 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=3dcbc, 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 /data/out/sub-02/surf/lh.white...
- writing smoothed curvature to lh.curv
- 000: dt: 0.0000, sse=3222305.5, rms=2.094
- rms = 2.34, time step reduction 1 of 3 to 0.250...
- 034: dt: 0.2500, sse=3305310.5, rms=1.530 (26.931%)
- 035: dt: 0.2500, sse=3469531.0, rms=1.185 (22.559%)
- rms = 1.16, time step reduction 2 of 3 to 0.125...
- 036: dt: 0.2500, sse=3499516.2, rms=1.161 (2.018%)
- rms = 1.15, time step reduction 3 of 3 to 0.062...
- 037: dt: 0.1250, sse=3525277.2, rms=1.147 (1.174%)
- positioning took 0.3 minutes
- generating cortex label...
- 33 non-cortical segments detected
- only using segment with 5852 vertices
- erasing segment 1 (vno[0] = 46705)
- erasing segment 2 (vno[0] = 47804)
- erasing segment 3 (vno[0] = 47894)
- erasing segment 4 (vno[0] = 48950)
- erasing segment 5 (vno[0] = 49892)
- erasing segment 6 (vno[0] = 49898)
- erasing segment 7 (vno[0] = 50904)
- erasing segment 8 (vno[0] = 53147)
- erasing segment 9 (vno[0] = 56381)
- erasing segment 10 (vno[0] = 58507)
- erasing segment 11 (vno[0] = 67598)
- erasing segment 12 (vno[0] = 69598)
- erasing segment 13 (vno[0] = 69717)
- erasing segment 14 (vno[0] = 71648)
- erasing segment 15 (vno[0] = 72992)
- erasing segment 16 (vno[0] = 73183)
- erasing segment 17 (vno[0] = 73903)
- erasing segment 18 (vno[0] = 74013)
- erasing segment 19 (vno[0] = 74190)
- erasing segment 20 (vno[0] = 75879)
- erasing segment 21 (vno[0] = 77983)
- erasing segment 22 (vno[0] = 78048)
- erasing segment 23 (vno[0] = 78995)
- erasing segment 24 (vno[0] = 79770)
- erasing segment 25 (vno[0] = 79794)
- erasing segment 26 (vno[0] = 81437)
- erasing segment 27 (vno[0] = 83162)
- erasing segment 28 (vno[0] = 87243)
- erasing segment 29 (vno[0] = 87246)
- erasing segment 30 (vno[0] = 87260)
- erasing segment 31 (vno[0] = 88650)
- erasing segment 32 (vno[0] = 89335)
- writing cortex label to /data/out/sub-02/label/lh.cortex.label...
- writing curvature file /data/out/sub-02/surf/lh.curv
- writing smoothed area to lh.area
- writing curvature file /data/out/sub-02/surf/lh.area
- vertex spacing 0.91 +- 0.26 (0.05-->5.42) (max @ vno 42396 --> 114236)
- face area 0.35 +- 0.17 (0.00-->9.16)
- refinement took 3.5 minutes
- #--------------------------------------------
- #@# Smooth2 lh Sat Jan 14 13:02:29 UTC 2017
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm
- /data/out/sub-02/scripts
- smoothing for 3 iterations
- setting seed for random number generator to 1234
- smoothing surface tessellation for 3 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation2 lh Sat Jan 14 13:02:32 UTC 2017
- /data/out/sub-02/scripts
- mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated
- avg radius = 44.8 mm, total surface area = 72022 mm^2
- writing inflated surface to ../surf/lh.inflated
- writing sulcal depths to ../surf/lh.sulc
-
step 000: RMS=0.113 (target=0.015)
step 005: RMS=0.079 (target=0.015)
step 010: RMS=0.057 (target=0.015)
step 015: RMS=0.046 (target=0.015)
step 020: RMS=0.039 (target=0.015)
step 025: RMS=0.032 (target=0.015)
step 030: RMS=0.027 (target=0.015)
step 035: RMS=0.023 (target=0.015)
step 040: RMS=0.020 (target=0.015)
step 045: RMS=0.018 (target=0.015)
step 050: RMS=0.017 (target=0.015)
step 055: RMS=0.015 (target=0.015)
- inflation complete.
- inflation took 0.3 minutes
- mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated
- normalizing curvature values.
- averaging curvature patterns 5 times.
- sampling 10 neighbors out to a distance of 10 mm
- 158 vertices thresholded to be in k1 ~ [-0.18 0.64], k2 ~ [-0.10 0.06]
- total integrated curvature = 0.631*4pi (7.924) --> 0 handles
- ICI = 1.4, FI = 7.4, variation=133.367
- 82 vertices thresholded to be in [-0.02 0.01]
- writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 123 vertices thresholded to be in [-0.12 0.27]
- done.
- writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.022
- done.
- #-----------------------------------------
- #@# Curvature Stats lh Sat Jan 14 13:03:48 UTC 2017
- /data/out/sub-02/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-02 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 [ sub-02/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 [ 232 ]
- Gb_filter = 0
- WARN: S lookup min: -0.312319
- WARN: S explicit min: 0.000000 vertex = 37
- #--------------------------------------------
- #@# Sphere lh Sat Jan 14 13:03:51 UTC 2017
- /data/out/sub-02/scripts
- mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- scaling brain by 0.312...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=3dcbc, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
- using quadratic fit line minimization
- complete_dist_mat 0
- rms 0
- smooth_averages 0
- remove_neg 0
- ico_order 0
- which_surface 0
- target_radius 0.000000
- nfields 0
- scale 1.000000
- desired_rms_height -1.000000
- momentum 0.900000
- nbhd_size 7
- max_nbrs 8
- niterations 25
- nsurfaces 0
- SURFACES 3
- flags 0 (0)
- use curv 0
- no sulc 0
- no rigid align 0
- mris->nsize 2
- mris->hemisphere 0
- randomSeed 1234
- --------------------
- mrisRemoveNegativeArea()
- pass 1: epoch 1 of 3 starting distance error %19.33
- pass 1: epoch 2 of 3 starting distance error %19.29
- unfolding complete - removing small folds...
- starting distance error %19.26
- removing remaining folds...
- final distance error %19.28
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/lh.sphere
- spherical transformation took 0.44 hours
- #--------------------------------------------
- #@# Surf Reg lh Sat Jan 14 13:30:11 UTC 2017
- /data/out/sub-02/scripts
- mris_register -curv ../surf/lh.sphere /opt/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg
- using smoothwm curvature for final alignment
- $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading surface from ../surf/lh.sphere...
- reading template parameterization from /opt/freesurfer/average/lh.average.curvature.filled.buckner40.tif...
- MRISregister() -------
- max_passes = 4
- min_degrees = 0.500000
- max_degrees = 64.000000
- nangles = 8
- tol=5.0e-01, sigma=0.0, host=3dcbc, 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=3dcbc, 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 = 0.600
- curvature mean = 0.041, std = 0.936
- curvature mean = 0.010, std = 0.879
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (0.00, 0.00, 16.00) sse = 266341.4, tmin=0.6163
- d=32.00 min @ (0.00, -8.00, 0.00) sse = 176606.5, tmin=1.2165
- d=16.00 min @ (0.00, 0.00, -4.00) sse = 160630.7, tmin=1.8217
- d=8.00 min @ (2.00, 0.00, 0.00) sse = 159829.5, tmin=2.4238
- d=4.00 min @ (-1.00, 0.00, 0.00) sse = 158169.2, tmin=3.0364
- d=2.00 min @ (0.00, 0.00, 0.50) sse = 157873.7, tmin=3.6286
- d=1.00 min @ (0.25, 0.25, 0.00) sse = 157749.4, tmin=4.2228
- d=0.50 min @ (-0.12, 0.00, -0.12) sse = 157742.6, tmin=4.8372
- tol=1.0e+00, sigma=0.5, host=3dcbc, 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 4.84 min
- curvature mean = 0.013, std = 0.969
- curvature mean = 0.005, std = 0.952
- curvature mean = 0.013, std = 0.982
- curvature mean = 0.002, std = 0.980
- curvature mean = 0.010, std = 0.986
- curvature mean = 0.000, std = 0.992
- 2 Reading smoothwm
- curvature mean = -0.023, std = 0.255
- curvature mean = 0.004, std = 0.067
- curvature mean = 0.042, std = 0.417
- curvature mean = 0.003, std = 0.080
- curvature mean = 0.023, std = 0.623
- curvature mean = 0.003, std = 0.087
- curvature mean = 0.013, std = 0.757
- curvature mean = 0.003, std = 0.090
- curvature mean = 0.004, std = 0.855
- MRISregister() return, current seed 0
- writing registered surface to ../surf/lh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white lh Sat Jan 14 13:44:00 UTC 2017
- mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white
- reading surface from ../surf/lh.white...
- writing curvature file ../surf/lh.jacobian_white
- #--------------------------------------------
- #@# AvgCurv lh Sat Jan 14 13:44:02 UTC 2017
- /data/out/sub-02/scripts
- mrisp_paint -a 5 /opt/freesurfer/average/lh.average.curvature.filled.buckner40.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 /opt/freesurfer/average/lh.average.curvature.filled.buckner40.tif...
- writing curvature file to ../surf/lh.avg_curv...
- #-----------------------------------------
- #@# Cortical Parc lh Sat Jan 14 13:44:03 UTC 2017
- /data/out/sub-02/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub-02 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot
- setting seed for random number generator to 1234
- using ../mri/aseg.mgz aseg volume to correct midline
- $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading atlas from /opt/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs...
- reading color table from GCSA file....
- average std = 1.0 using min determinant for regularization = 0.011
- 0 singular and 384 ill-conditioned covariance matrices regularized
- input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
- labeling surface...
- 900 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2603 changed, 114591 examined...
- 001: 568 changed, 11193 examined...
- 002: 148 changed, 3221 examined...
- 003: 41 changed, 910 examined...
- 004: 11 changed, 240 examined...
- 005: 2 changed, 73 examined...
- 006: 0 changed, 14 examined...
- 186 labels changed using aseg
- 000: 82 total segments, 41 labels (132 vertices) changed
- 001: 41 total segments, 2 labels (8 vertices) changed
- 002: 39 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 46 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1320 vertices marked for relabeling...
- 1320 labels changed in reclassification.
- writing output to ../label/lh.aparc.annot...
- classification took 0 minutes and 30 seconds.
- #--------------------------------------------
- #@# Make Pial Surf lh Sat Jan 14 13:44:33 UTC 2017
- /data/out/sub-02/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub-02 lh
- -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written...
- INFO: assuming MGZ format for volumes.
- using brain.finalsurfs as T1 volume...
- $Id: mris_make_surfaces.c,v 1.147 2014/01/29 20:42:02 fischl Exp $
- $Id: mrisurf.c,v 1.753 2014/01/17 15:25:29 fischl Exp $
- reading volume /data/out/sub-02/mri/filled.mgz...
- reading volume /data/out/sub-02/mri/brain.finalsurfs.mgz...
- reading volume /data/out/sub-02/mri/wm.mgz...
- 8190 bright wm thresholded.
- 895 bright non-wm voxels segmented.
- reading original surface position from /data/out/sub-02/surf/lh.orig...
- computing class statistics...
- border white: 221986 voxels (1.32%)
- border gray 239648 voxels (1.43%)
- WM (91.0): 92.0 +- 8.8 [70.0 --> 110.0]
- GM (77.0) : 73.9 +- 13.6 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 43.4 (was 70)
- setting MAX_BORDER_WHITE to 109.8 (was 105)
- setting MIN_BORDER_WHITE to 57.0 (was 85)
- setting MAX_CSF to 29.8 (was 40)
- setting MAX_GRAY to 92.2 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 50.2 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 16.3 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=101+-6.1, GM=57+-10.4
- mean inside = 90.8, mean outside = 69.1
- smoothing surface for 5 iterations...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /data/out/sub-02/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.83 +- 0.22 (0.03-->4.69) (max @ vno 42396 --> 43708)
- face area 0.28 +- 0.12 (0.00-->5.77)
- mean absolute distance = 0.78 +- 0.92
- 3663 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 73 points - only 0.00% unknown
- deleting segment 1 with 5 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 2 with 4 points - only 0.00% unknown
- deleting segment 3 with 7 points - only 0.00% unknown
- deleting segment 6 with 5 points - only 0.00% unknown
- deleting segment 7 with 12 points - only 0.00% unknown
- deleting segment 8 with 5 points - only 0.00% unknown
- deleting segment 9 with 43 points - only 0.00% unknown
- deleting segment 10 with 25 points - only 0.00% unknown
- deleting segment 11 with 30 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 12 with 4 points - only 0.00% unknown
- deleting segment 13 with 5 points - only 0.00% unknown
- mean border=71.6, 87 (84) missing vertices, mean dist 0.5 [0.6 (%28.2)->0.9 (%71.8))]
- %65 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=3dcbc, 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 0.94 +- 0.27 (0.13-->5.24) (max @ vno 42396 --> 114236)
- face area 0.28 +- 0.14 (0.00-->6.50)
- mean absolute distance = 0.34 +- 0.62
- 3165 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=6248949.0, rms=14.168
- 001: dt: 0.5000, sse=5805557.5, rms=10.659 (24.767%)
- 002: dt: 0.5000, sse=5626898.0, rms=8.270 (22.409%)
- 003: dt: 0.5000, sse=5700337.0, rms=6.572 (20.540%)
- 004: dt: 0.5000, sse=5821069.0, rms=5.497 (16.359%)
- 005: dt: 0.5000, sse=6025046.0, rms=4.879 (11.231%)
- 006: dt: 0.5000, sse=6146885.5, rms=4.563 (6.487%)
- 007: dt: 0.5000, sse=6236705.0, rms=4.386 (3.880%)
- 008: dt: 0.5000, sse=6269631.0, rms=4.294 (2.091%)
- 009: dt: 0.5000, sse=6313325.0, rms=4.223 (1.652%)
- rms = 4.18, time step reduction 1 of 3 to 0.250...
- 010: dt: 0.5000, sse=6294188.0, rms=4.183 (0.955%)
- 011: dt: 0.2500, sse=3858870.2, rms=2.811 (32.794%)
- 012: dt: 0.2500, sse=3401388.8, rms=2.396 (14.752%)
- 013: dt: 0.2500, sse=3201806.0, rms=2.265 (5.461%)
- 014: dt: 0.2500, sse=3124685.5, rms=2.180 (3.755%)
- rms = 2.13, time step reduction 2 of 3 to 0.125...
- 015: dt: 0.2500, sse=3080279.5, rms=2.131 (2.282%)
- 016: dt: 0.1250, sse=2971393.8, rms=2.019 (5.229%)
- rms = 2.01, time step reduction 3 of 3 to 0.062...
- 017: dt: 0.1250, sse=2943352.2, rms=2.005 (0.702%)
- positioning took 0.9 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 99 points - only 0.00% unknown
- deleting segment 1 with 17 points - only 0.00% unknown
- deleting segment 2 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- deleting segment 4 with 3 points - only 0.00% unknown
- deleting segment 5 with 6 points - only 0.00% unknown
- deleting segment 6 with 19 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 8 with 4 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 9 with 4 points - only 0.00% unknown
- deleting segment 11 with 12 points - only 0.00% unknown
- deleting segment 12 with 17 points - only 0.00% unknown
- deleting segment 13 with 9 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 14 with 4 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 15 with 3 points - only 0.00% unknown
- mean border=74.5, 80 (35) missing vertices, mean dist -0.2 [0.4 (%67.7)->0.2 (%32.3))]
- %71 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=3dcbc, 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 0.92 +- 0.26 (0.12-->5.33) (max @ vno 42396 --> 114236)
- face area 0.37 +- 0.18 (0.00-->9.03)
- mean absolute distance = 0.27 +- 0.43
- 3756 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3572321.2, rms=5.243
- 018: dt: 0.5000, sse=3949939.5, rms=3.786 (27.790%)
- rms = 4.02, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.2500, sse=3561653.5, rms=2.920 (22.881%)
- 020: dt: 0.2500, sse=3375034.8, rms=2.303 (21.137%)
- 021: dt: 0.2500, sse=3283596.2, rms=1.990 (13.588%)
- 022: dt: 0.2500, sse=3236670.2, rms=1.863 (6.381%)
- 023: dt: 0.2500, sse=3205537.0, rms=1.778 (4.526%)
- rms = 1.74, time step reduction 2 of 3 to 0.125...
- 024: dt: 0.2500, sse=3189643.5, rms=1.735 (2.437%)
- 025: dt: 0.1250, sse=3133923.2, rms=1.659 (4.375%)
- rms = 1.65, time step reduction 3 of 3 to 0.062...
- 026: dt: 0.1250, sse=3114100.5, rms=1.648 (0.690%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 97 points - only 0.00% unknown
- deleting segment 1 with 15 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- deleting segment 5 with 10 points - only 0.00% unknown
- deleting segment 6 with 20 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 7 with 4 points - only 0.00% unknown
- deleting segment 8 with 22 points - only 0.00% unknown
- deleting segment 9 with 6 points - only 0.00% unknown
- deleting segment 10 with 27 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 11 with 3 points - only 0.00% unknown
- deleting segment 12 with 7 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 13 with 4 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 14 with 3 points - only 0.00% unknown
- mean border=77.0, 86 (29) missing vertices, mean dist -0.1 [0.3 (%66.6)->0.2 (%33.4))]
- %79 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=3dcbc, 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 0.91 +- 0.25 (0.09-->5.40) (max @ vno 42396 --> 114236)
- face area 0.35 +- 0.17 (0.00-->9.07)
- mean absolute distance = 0.23 +- 0.36
- 3060 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3336158.5, rms=3.772
- 027: dt: 0.5000, sse=3787626.5, rms=3.251 (13.815%)
- rms = 3.65, time step reduction 1 of 3 to 0.250...
- 028: dt: 0.2500, sse=3448953.2, rms=2.271 (30.127%)
- 029: dt: 0.2500, sse=3303361.8, rms=1.767 (22.218%)
- 030: dt: 0.2500, sse=3285429.2, rms=1.571 (11.078%)
- rms = 1.54, time step reduction 2 of 3 to 0.125...
- 031: dt: 0.2500, sse=3267796.5, rms=1.543 (1.777%)
- 032: dt: 0.1250, sse=3210686.2, rms=1.456 (5.652%)
- rms = 1.45, time step reduction 3 of 3 to 0.062...
- 033: dt: 0.1250, sse=3188539.8, rms=1.451 (0.326%)
- positioning took 0.4 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 107 points - only 0.00% unknown
- deleting segment 1 with 12 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 2 with 3 points - only 0.00% unknown
- deleting segment 3 with 10 points - only 0.00% unknown
- deleting segment 4 with 24 points - only 0.00% unknown
- deleting segment 5 with 5 points - only 0.00% unknown
- deleting segment 6 with 21 points - only 0.00% unknown
- deleting segment 7 with 19 points - only 0.00% unknown
- deleting segment 8 with 27 points - only 0.00% unknown
- deleting segment 9 with 8 points - only 0.00% unknown
- deleting segment 10 with 6 points - only 0.00% unknown
- removing 3 vertex label from ripped group
- deleting segment 11 with 3 points - only 0.00% unknown
- mean border=78.1, 104 (27) missing vertices, mean dist -0.1 [0.3 (%55.8)->0.2 (%44.2))]
- %82 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=3dcbc, 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
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3225652.5, rms=2.095
- rms = 2.34, time step reduction 1 of 3 to 0.250...
- 034: dt: 0.2500, sse=3310784.5, rms=1.533 (26.845%)
- 035: dt: 0.2500, sse=3475621.5, rms=1.190 (22.335%)
- rms = 1.16, time step reduction 2 of 3 to 0.125...
- 036: dt: 0.2500, sse=3507151.0, rms=1.164 (2.234%)
- rms = 1.15, time step reduction 3 of 3 to 0.062...
- 037: dt: 0.1250, sse=3537235.0, rms=1.153 (0.957%)
- positioning took 0.2 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 2 with 5 points - only 0.00% unknown
- deleting segment 3 with 45 points - only 0.00% unknown
- smoothing surface for 5 iterations...
- mean border=46.4, 46 (46) missing vertices, mean dist 1.7 [1.0 (%0.0)->2.1 (%100.0))]
- %17 local maxima, %57 large gradients and %22 min vals, 1694 gradients ignored
- tol=1.0e-04, sigma=2.0, host=3dcbc, 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=24528248.0, rms=32.021
- 001: dt: 0.5000, sse=18080068.0, rms=27.035 (15.573%)
- 002: dt: 0.5000, sse=13431107.0, rms=22.795 (15.683%)
- 003: dt: 0.5000, sse=10448701.0, rms=19.384 (14.962%)
- 004: dt: 0.5000, sse=8715870.0, rms=16.589 (14.421%)
- 005: dt: 0.5000, sse=7526626.0, rms=14.279 (13.922%)
- 006: dt: 0.5000, sse=6672086.0, rms=12.381 (13.297%)
- 007: dt: 0.5000, sse=6092782.0, rms=10.759 (13.101%)
- 008: dt: 0.5000, sse=5732400.0, rms=9.308 (13.479%)
- 009: dt: 0.5000, sse=5510859.5, rms=8.033 (13.700%)
- 010: dt: 0.5000, sse=5420744.5, rms=6.942 (13.584%)
- 011: dt: 0.5000, sse=5382659.0, rms=6.041 (12.979%)
- 012: dt: 0.5000, sse=5420846.0, rms=5.353 (11.395%)
- 013: dt: 0.5000, sse=5492772.0, rms=4.909 (8.282%)
- 014: dt: 0.5000, sse=5564669.0, rms=4.596 (6.391%)
- 015: dt: 0.5000, sse=5605146.5, rms=4.410 (4.033%)
- 016: dt: 0.5000, sse=5651899.5, rms=4.266 (3.260%)
- 017: dt: 0.5000, sse=5685690.5, rms=4.194 (1.696%)
- 018: dt: 0.5000, sse=5725386.0, rms=4.112 (1.958%)
- rms = 4.08, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.5000, sse=5718409.0, rms=4.084 (0.672%)
- 020: dt: 0.2500, sse=3991155.2, rms=3.302 (19.152%)
- 021: dt: 0.2500, sse=3803980.2, rms=3.104 (5.990%)
- rms = 3.07, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=3708810.8, rms=3.065 (1.265%)
- 023: dt: 0.1250, sse=3537196.0, rms=2.928 (4.480%)
- rms = 2.91, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=3511780.5, rms=2.908 (0.662%)
- positioning took 1.3 minutes
- mean border=44.2, 638 (15) missing vertices, mean dist 0.2 [0.2 (%50.4)->0.7 (%49.6))]
- %33 local maxima, %45 large gradients and %17 min vals, 665 gradients ignored
- tol=1.0e-04, sigma=1.0, host=3dcbc, 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=4134124.2, rms=5.211
- 025: dt: 0.5000, sse=4300892.0, rms=4.332 (16.870%)
- 026: dt: 0.5000, sse=5404309.0, rms=4.187 (3.356%)
- 027: dt: 0.5000, sse=5331640.0, rms=4.107 (1.899%)
- rms = 4.08, time step reduction 1 of 3 to 0.250...
- 028: dt: 0.5000, sse=5927432.5, rms=4.084 (0.570%)
- 029: dt: 0.2500, sse=4279497.0, rms=3.152 (22.826%)
- 030: dt: 0.2500, sse=4239117.0, rms=2.908 (7.726%)
- rms = 2.87, time step reduction 2 of 3 to 0.125...
- 031: dt: 0.2500, sse=4121315.5, rms=2.868 (1.381%)
- 032: dt: 0.1250, sse=3963498.2, rms=2.703 (5.766%)
- rms = 2.68, time step reduction 3 of 3 to 0.062...
- 033: dt: 0.1250, sse=3949436.8, rms=2.677 (0.960%)
- positioning took 0.5 minutes
- mean border=42.6, 759 (7) missing vertices, mean dist 0.1 [0.2 (%48.1)->0.5 (%51.9))]
- %44 local maxima, %33 large gradients and %17 min vals, 687 gradients ignored
- tol=1.0e-04, sigma=0.5, host=3dcbc, 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=4112220.2, rms=3.656
- 034: dt: 0.5000, sse=4377695.0, rms=3.555 (2.747%)
- rms = 3.79, time step reduction 1 of 3 to 0.250...
- 035: dt: 0.2500, sse=4118622.5, rms=2.950 (17.018%)
- 036: dt: 0.2500, sse=4197449.5, rms=2.697 (8.595%)
- 037: dt: 0.2500, sse=4170852.2, rms=2.638 (2.162%)
- rms = 2.61, time step reduction 2 of 3 to 0.125...
- 038: dt: 0.2500, sse=4201753.5, rms=2.606 (1.218%)
- 039: dt: 0.1250, sse=4080120.5, rms=2.481 (4.795%)
- rms = 2.46, time step reduction 3 of 3 to 0.062...
- 040: dt: 0.1250, sse=4074926.5, rms=2.459 (0.876%)
- positioning took 0.4 minutes
- mean border=41.4, 1527 (6) missing vertices, mean dist 0.1 [0.2 (%48.7)->0.4 (%51.3))]
- %52 local maxima, %25 large gradients and %17 min vals, 666 gradients ignored
- tol=1.0e-04, sigma=0.2, host=3dcbc, 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 /data/out/sub-02/surf/lh.pial...
- writing smoothed curvature to lh.curv.pial
- 000: dt: 0.0000, sse=4138129.0, rms=2.983
- rms = 3.18, time step reduction 1 of 3 to 0.250...
- 041: dt: 0.2500, sse=4042992.0, rms=2.669 (10.514%)
- 042: dt: 0.2500, sse=4090238.2, rms=2.460 (7.819%)
- 043: dt: 0.2500, sse=4148573.8, rms=2.398 (2.524%)
- rms = 2.37, time step reduction 2 of 3 to 0.125...
- 044: dt: 0.2500, sse=4222307.0, rms=2.370 (1.171%)
- 045: dt: 0.1250, sse=4123835.8, rms=2.284 (3.649%)
- rms = 2.26, time step reduction 3 of 3 to 0.062...
- 046: dt: 0.1250, sse=4125890.5, rms=2.263 (0.915%)
- positioning took 0.4 minutes
- writing curvature file /data/out/sub-02/surf/lh.curv.pial
- writing smoothed area to lh.area.pial
- writing curvature file /data/out/sub-02/surf/lh.area.pial
- vertex spacing 1.04 +- 0.43 (0.09-->8.74) (max @ vno 76004 --> 74998)
- face area 0.43 +- 0.32 (0.00-->8.95)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 114591 vertices processed
- 25000 of 114591 vertices processed
- 50000 of 114591 vertices processed
- 75000 of 114591 vertices processed
- 100000 of 114591 vertices processed
- 0 of 114591 vertices processed
- 25000 of 114591 vertices processed
- 50000 of 114591 vertices processed
- 75000 of 114591 vertices processed
- 100000 of 114591 vertices processed
- thickness calculation complete, 276:1062 truncations.
- 30308 vertices at 0 distance
- 79434 vertices at 1 distance
- 69248 vertices at 2 distance
- 27007 vertices at 3 distance
- 8045 vertices at 4 distance
- 2451 vertices at 5 distance
- 908 vertices at 6 distance
- 285 vertices at 7 distance
- 112 vertices at 8 distance
- 60 vertices at 9 distance
- 36 vertices at 10 distance
- 26 vertices at 11 distance
- 17 vertices at 12 distance
- 16 vertices at 13 distance
- 18 vertices at 14 distance
- 11 vertices at 15 distance
- 3 vertices at 16 distance
- 5 vertices at 17 distance
- 8 vertices at 18 distance
- 9 vertices at 19 distance
- 7 vertices at 20 distance
- writing curvature file /data/out/sub-02/surf/lh.thickness
- positioning took 6.5 minutes
- #--------------------------------------------
- #@# Surf Volume lh Sat Jan 14 13:51:02 UTC 2017
- /data/out/sub-02/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_calc -o lh.volume lh.area.mid mul lh.thickness
- Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ]
- #-----------------------------------------
- #@# WM/GM Contrast lh Sat Jan 14 13:51:03 UTC 2017
- /data/out/sub-02/scripts
- pctsurfcon --s sub-02 --lh-only
- Log file is /data/out/sub-02/scripts/pctsurfcon.log
- Sat Jan 14 13:51:03 UTC 2017
- setenv SUBJECTS_DIR /data/out
- cd /data/out/sub-02/scripts
- /opt/freesurfer/bin/pctsurfcon
- $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
- Linux 3dcbcfbafa99 3.13.0-105-generic #152-Ubuntu SMP Fri Dec 2 15:37:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
- FREESURFER_HOME /opt/freesurfer
- mri_vol2surf --mov /data/out/sub-02/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /data/out/sub-02/surf/tmp.pctsurfcon.2005/lh.wm.mgh --regheader sub-02 --cortex
- srcvol = /data/out/sub-02/mri/rawavg.mgz
- srcreg unspecified
- srcregold = 0
- srcwarp unspecified
- surf = white
- hemi = lh
- ProjDist = -1
- reshape = 0
- interp = trilinear
- float2int = round
- GetProjMax = 0
- INFO: float2int code = 0
- Done loading volume
- Computing registration from header.
- Using /data/out/sub-02/mri/orig.mgz as target reference.
- Loading label /data/out/sub-02/label/lh.cortex.label
- Reading surface /data/out/sub-02/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 = 60058
- Masking with /data/out/sub-02/label/lh.cortex.label
- Writing to /data/out/sub-02/surf/tmp.pctsurfcon.2005/lh.wm.mgh
- Dim: 114591 1 1
- mri_vol2surf --mov /data/out/sub-02/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /data/out/sub-02/surf/tmp.pctsurfcon.2005/lh.gm.mgh --projfrac 0.3 --regheader sub-02 --cortex
- srcvol = /data/out/sub-02/mri/rawavg.mgz
- srcreg unspecified
- srcregold = 0
- srcwarp unspecified
- surf = white
- hemi = lh
- ProjFrac = 0.3
- thickness = thickness
- reshape = 0
- interp = trilinear
- float2int = round
- GetProjMax = 0
- INFO: float2int code = 0
- Done loading volume
- Computing registration from header.
- Using /data/out/sub-02/mri/orig.mgz as target reference.
- Loading label /data/out/sub-02/label/lh.cortex.label
- Reading surface /data/out/sub-02/surf/lh.white
- Done reading source surface
- Reading thickness /data/out/sub-02/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 = 69171
- Masking with /data/out/sub-02/label/lh.cortex.label
- Writing to /data/out/sub-02/surf/tmp.pctsurfcon.2005/lh.gm.mgh
- Dim: 114591 1 1
- mri_concat /data/out/sub-02/surf/tmp.pctsurfcon.2005/lh.wm.mgh /data/out/sub-02/surf/tmp.pctsurfcon.2005/lh.gm.mgh --paired-diff-norm --mul 100 --o /data/out/sub-02/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 /data/out/sub-02/surf/lh.w-g.pct.mgh
- mri_segstats --in /data/out/sub-02/surf/lh.w-g.pct.mgh --annot sub-02 lh aparc --sum /data/out/sub-02/stats/lh.w-g.pct.stats --snr
- $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
- cwd
- cmdline mri_segstats --in /data/out/sub-02/surf/lh.w-g.pct.mgh --annot sub-02 lh aparc --sum /data/out/sub-02/stats/lh.w-g.pct.stats --snr
- sysname Linux
- hostname 3dcbcfbafa99
- machine x86_64
- user root
- UseRobust 0
- Constructing seg from annotation
- Reading annotation
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Seg base 1000
- Loading /data/out/sub-02/surf/lh.w-g.pct.mgh
- Vertex Area is 0.685185 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 1000 unknown 0 0.000
- 1 1001 bankssts 1250 901.336
- 2 1002 caudalanteriorcingulate 631 410.432
- 3 1003 caudalmiddlefrontal 2974 1966.574
- 4 1004 corpuscallosum 0 0.000
- 5 1005 cuneus 1908 1329.156
- 6 1006 entorhinal 440 334.407
- 7 1007 fusiform 3791 2714.241
- 8 1008 inferiorparietal 6252 4317.362
- 9 1009 inferiortemporal 4614 3127.866
- 10 1010 isthmuscingulate 1592 1033.947
- 11 1011 lateraloccipital 6059 4108.501
- 12 1012 lateralorbitofrontal 3070 2225.667
- 13 1013 lingual 3684 2674.214
- 14 1014 medialorbitofrontal 2183 1591.643
- 15 1015 middletemporal 3939 2773.431
- 16 1016 parahippocampal 959 637.355
- 17 1017 paracentral 1612 1071.506
- 18 1018 parsopercularis 2318 1673.723
- 19 1019 parsorbitalis 756 541.075
- 20 1020 parstriangularis 1251 873.713
- 21 1021 pericalcarine 1415 1017.431
- 22 1022 postcentral 5864 3808.218
- 23 1023 posteriorcingulate 1349 913.892
- 24 1024 precentral 7151 4586.672
- 25 1025 precuneus 5162 3528.045
- 26 1026 rostralanteriorcingulate 922 636.001
- 27 1027 rostralmiddlefrontal 6490 4630.757
- 28 1028 superiorfrontal 9564 6606.737
- 29 1029 superiorparietal 6695 4515.375
- 30 1030 superiortemporal 4972 3364.080
- 31 1031 supramarginal 4440 3085.478
- 32 1032 frontalpole 333 229.509
- 33 1033 temporalpole 548 461.118
- 34 1034 transversetemporal 590 367.740
- 35 1035 insula 2886 1867.740
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats lh Sat Jan 14 13:51:07 UTC 2017
- /data/out/sub-02/scripts
- mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-02 lh white
- computing statistics for each annotation in ../label/lh.aparc.annot.
- reading volume /data/out/sub-02/mri/wm.mgz...
- reading input surface /data/out/sub-02/surf/lh.white...
- reading input pial surface /data/out/sub-02/surf/lh.pial...
- reading input white surface /data/out/sub-02/surf/lh.white...
- INFO: assuming MGZ format for volumes.
- INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/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
- 1250 901 1856 1.990 0.609 0.110 0.025 9 1.2 bankssts
- 631 410 1024 2.064 0.715 0.157 0.048 12 1.1 caudalanteriorcingulate
- 2974 1967 4700 2.135 0.611 0.123 0.033 27 3.9 caudalmiddlefrontal
- 1908 1329 2460 1.690 0.428 0.169 0.067 36 5.6 cuneus
- 440 334 1646 3.110 1.069 0.172 0.062 7 1.1 entorhinal
- 3791 2714 8245 2.545 0.667 0.145 0.052 49 7.5 fusiform
- 6252 4317 11436 2.387 0.676 0.136 0.039 76 10.1 inferiorparietal
- 4614 3128 10888 2.726 0.776 0.135 0.054 65 12.1 inferiortemporal
- 1592 1034 2394 2.229 1.047 0.150 0.111 46 4.1 isthmuscingulate
- 6059 4109 9946 2.248 0.641 0.152 0.051 92 11.6 lateraloccipital
- 3070 2226 6274 2.381 0.909 0.166 0.061 53 7.6 lateralorbitofrontal
- 3684 2674 5680 1.976 0.666 0.158 0.062 58 9.5 lingual
- 2183 1592 3980 2.045 0.820 0.179 0.074 61 6.6 medialorbitofrontal
- 3939 2773 9090 2.642 0.826 0.137 0.041 54 6.2 middletemporal
- 959 637 2158 2.619 0.939 0.109 0.039 8 1.4 parahippocampal
- 1612 1072 2669 2.186 0.596 0.125 0.041 15 2.9 paracentral
- 2318 1674 3915 2.050 0.557 0.128 0.033 25 3.2 parsopercularis
- 756 541 1795 2.432 0.728 0.160 0.059 12 1.9 parsorbitalis
- 1251 874 2167 2.057 0.609 0.125 0.032 13 1.5 parstriangularis
- 1415 1017 1372 1.402 0.371 0.152 0.050 22 3.0 pericalcarine
- 5864 3808 8181 1.902 0.694 0.112 0.036 58 9.3 postcentral
- 1349 914 2327 2.328 0.645 0.160 0.055 24 2.8 posteriorcingulate
- 7151 4587 12018 2.308 0.670 0.113 0.059 106 20.8 precentral
- 5162 3528 8444 2.126 0.657 0.150 0.046 78 9.7 precuneus
- 922 636 1365 1.873 0.616 0.153 0.055 20 1.9 rostralanteriorcingulate
- 6490 4631 10882 1.940 0.658 0.159 0.058 116 15.2 rostralmiddlefrontal
- 9564 6607 18870 2.408 0.610 0.137 0.042 116 16.1 superiorfrontal
- 6695 4515 9991 1.975 0.577 0.129 0.039 76 10.8 superiorparietal
- 4972 3364 10569 2.524 0.782 0.125 0.038 55 7.6 superiortemporal
- 4440 3085 8301 2.381 0.654 0.136 0.042 55 7.3 supramarginal
- 333 230 826 2.645 0.537 0.200 0.077 9 1.0 frontalpole
- 548 461 2287 3.345 0.923 0.304 0.360 282 9.2 temporalpole
- 590 368 795 2.180 0.507 0.141 0.043 7 1.0 transversetemporal
- 2886 1868 6039 2.898 1.108 0.116 0.057 37 5.7 insula
- #-----------------------------------------
- #@# Cortical Parc 2 lh Sat Jan 14 13:51:15 UTC 2017
- /data/out/sub-02/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub-02 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot
- setting seed for random number generator to 1234
- using ../mri/aseg.mgz aseg volume to correct midline
- $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading atlas from /opt/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs...
- reading color table from GCSA file....
- average std = 3.9 0.2 using min determinant for regularization = 0.000
- 0 singular and 1066 ill-conditioned covariance matrices regularized
- input 1: CURVATURE FILE, flags 0, avgs 0, name sulc
- input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
- labeling surface...
- 141 labels changed using aseg
- relabeling using gibbs priors...
- 000: 7634 changed, 114591 examined...
- 001: 1771 changed, 29544 examined...
- 002: 528 changed, 9222 examined...
- 003: 210 changed, 3099 examined...
- 004: 105 changed, 1179 examined...
- 005: 40 changed, 583 examined...
- 006: 22 changed, 199 examined...
- 007: 11 changed, 131 examined...
- 008: 7 changed, 68 examined...
- 009: 1 changed, 36 examined...
- 010: 0 changed, 9 examined...
- 50 labels changed using aseg
- 000: 233 total segments, 148 labels (1500 vertices) changed
- 001: 98 total segments, 15 labels (38 vertices) changed
- 002: 84 total segments, 1 labels (1 vertices) changed
- 003: 83 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 102 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 922 vertices marked for relabeling...
- 922 labels changed in reclassification.
- writing output to ../label/lh.aparc.a2009s.annot...
- classification took 0 minutes and 38 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 lh Sat Jan 14 13:51:53 UTC 2017
- /data/out/sub-02/scripts
- mris_anatomical_stats -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 sub-02 lh white
- computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
- reading volume /data/out/sub-02/mri/wm.mgz...
- reading input surface /data/out/sub-02/surf/lh.white...
- reading input pial surface /data/out/sub-02/surf/lh.pial...
- reading input white surface /data/out/sub-02/surf/lh.white...
- INFO: assuming MGZ format for volumes.
- INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
- reading colortable from annotation file...
- colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.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
- 1082 795 1914 1.881 0.806 0.164 0.059 21 2.2 G_and_S_frontomargin
- 1424 997 2618 2.431 0.619 0.147 0.041 20 2.2 G_and_S_occipital_inf
- 1243 765 2129 2.282 0.645 0.142 0.190 59 13.1 G_and_S_paracentral
- 1216 808 2389 2.525 0.579 0.140 0.039 15 1.9 G_and_S_subcentral
- 526 367 1137 2.347 0.609 0.165 0.060 10 1.3 G_and_S_transv_frontopol
- 1914 1332 2965 1.940 0.614 0.152 0.056 41 4.0 G_and_S_cingul-Ant
- 846 586 1392 2.153 0.511 0.142 0.048 13 1.6 G_and_S_cingul-Mid-Ant
- 968 667 1614 2.300 0.494 0.136 0.041 10 1.6 G_and_S_cingul-Mid-Post
- 454 322 1068 2.849 0.512 0.183 0.084 10 1.2 G_cingul-Post-dorsal
- 606 365 586 1.524 1.099 0.163 0.212 30 2.0 G_cingul-Post-ventral
- 1764 1281 2506 1.696 0.494 0.180 0.072 36 5.7 G_cuneus
- 1284 956 2794 2.315 0.479 0.161 0.051 23 2.6 G_front_inf-Opercular
- 231 161 599 2.744 0.504 0.162 0.050 4 0.5 G_front_inf-Orbital
- 712 508 1599 2.290 0.591 0.163 0.051 12 1.6 G_front_inf-Triangul
- 3650 2602 7766 2.319 0.593 0.175 0.070 81 10.5 G_front_middle
- 7073 4845 15354 2.542 0.610 0.145 0.046 94 13.4 G_front_sup
- 372 253 1059 3.270 0.854 0.154 0.068 9 1.2 G_Ins_lg_and_S_cent_ins
- 568 375 1942 3.696 0.918 0.144 0.111 14 1.8 G_insular_short
- 1851 1233 4526 2.856 0.556 0.159 0.053 32 3.7 G_occipital_middle
- 1416 974 2215 1.946 0.535 0.137 0.053 23 3.1 G_occipital_sup
- 1441 1030 3855 2.802 0.574 0.147 0.054 21 3.0 G_oc-temp_lat-fusifor
- 2411 1818 4007 1.901 0.626 0.177 0.074 45 7.4 G_oc-temp_med-Lingual
- 1167 807 3588 3.024 1.034 0.143 0.066 16 3.2 G_oc-temp_med-Parahip
- 2031 1510 5435 2.726 0.738 0.185 0.070 46 5.8 G_orbital
- 2239 1609 5122 2.634 0.752 0.162 0.056 37 5.3 G_pariet_inf-Angular
- 2197 1538 4702 2.511 0.643 0.145 0.044 31 3.8 G_pariet_inf-Supramar
- 2286 1550 4386 2.213 0.595 0.151 0.051 38 4.8 G_parietal_sup
- 2326 1416 3626 2.067 0.585 0.117 0.049 31 5.2 G_postcentral
- 2849 1724 5936 2.637 0.569 0.114 0.041 29 5.2 G_precentral
- 2779 1962 5392 2.292 0.657 0.172 0.058 57 6.8 G_precuneus
- 904 712 2292 2.571 0.637 0.244 0.140 41 5.2 G_rectus
- 121 78 285 2.857 1.249 0.087 0.027 1 0.1 G_subcallosal
- 448 285 701 2.182 0.524 0.147 0.049 6 0.9 G_temp_sup-G_T_transv
- 1800 1259 5581 2.977 0.718 0.161 0.062 33 4.2 G_temp_sup-Lateral
- 376 249 835 2.897 0.697 0.142 0.259 246 5.7 G_temp_sup-Plan_polar
- 861 590 1870 2.697 0.640 0.132 0.043 11 1.6 G_temp_sup-Plan_tempo
- 2587 1757 7536 3.041 0.714 0.153 0.073 50 9.4 G_temporal_inf
- 2482 1764 6828 2.816 0.781 0.149 0.045 39 4.5 G_temporal_middle
- 311 216 418 1.754 0.519 0.079 0.012 1 0.1 Lat_Fis-ant-Horizont
- 247 180 314 1.811 0.424 0.104 0.019 1 0.1 Lat_Fis-ant-Vertical
- 1042 677 1224 2.211 0.620 0.105 0.023 6 1.0 Lat_Fis-post
- 1914 1293 2610 1.910 0.583 0.166 0.065 35 4.4 Pole_occipital
- 1374 1138 4831 2.945 0.877 0.224 0.138 54 7.0 Pole_temporal
- 1921 1316 2049 1.706 0.680 0.130 0.045 26 3.6 S_calcarine
- 3021 2043 3039 1.603 0.616 0.097 0.022 15 2.9 S_central
- 1027 700 1359 1.899 0.590 0.134 0.034 11 1.5 S_cingul-Marginalis
- 378 254 567 2.173 0.705 0.117 0.028 2 0.4 S_circular_insula_ant
- 1328 846 1759 2.150 0.839 0.074 0.014 4 0.8 S_circular_insula_inf
- 1559 1067 1841 1.836 0.619 0.106 0.024 8 1.5 S_circular_insula_sup
- 948 648 1440 2.199 0.771 0.110 0.031 7 1.1 S_collat_transv_ant
- 326 213 471 2.231 0.639 0.135 0.038 3 0.5 S_collat_transv_post
- 2113 1424 2241 1.546 0.459 0.108 0.025 14 2.1 S_front_inf
- 954 695 1446 1.803 0.640 0.150 0.044 13 1.7 S_front_middle
- 2359 1604 3235 2.032 0.448 0.109 0.024 14 2.4 S_front_sup
- 368 243 563 2.263 0.663 0.128 0.034 5 0.6 S_interm_prim-Jensen
- 2785 1876 3424 1.827 0.500 0.111 0.025 21 2.8 S_intrapariet_and_P_trans
- 719 486 912 2.029 0.459 0.120 0.029 5 0.9 S_oc_middle_and_Lunatus
- 1265 866 1604 2.101 0.444 0.116 0.031 8 1.6 S_oc_sup_and_transversal
- 670 451 951 2.297 0.508 0.140 0.039 7 1.0 S_occipital_ant
- 964 657 1307 2.274 0.499 0.121 0.029 7 1.2 S_oc-temp_lat
- 1580 1094 2486 2.368 0.562 0.122 0.029 12 1.9 S_oc-temp_med_and_Lingual
- 238 160 268 1.705 0.384 0.106 0.020 1 0.2 S_orbital_lateral
- 762 508 1320 2.461 1.350 0.102 0.036 6 0.9 S_orbital_med-olfact
- 1183 835 1785 2.034 0.869 0.155 0.057 16 2.9 S_orbital-H_Shaped
- 1480 961 1678 1.768 0.451 0.122 0.032 12 2.0 S_parieto_occipital
- 908 542 849 1.965 0.850 0.139 0.043 17 1.6 S_pericallosal
- 2189 1502 2556 1.809 0.530 0.102 0.026 13 1.9 S_postcentral
- 1423 960 1939 2.136 0.580 0.088 0.017 6 1.0 S_precentral-inf-part
- 1281 841 1673 2.096 0.476 0.113 0.034 10 1.5 S_precentral-sup-part
- 585 410 665 1.480 0.494 0.157 0.039 11 1.0 S_suborbital
- 1137 772 1786 2.146 0.709 0.123 0.029 10 1.5 S_subparietal
- 1272 828 1713 2.343 0.715 0.110 0.026 8 1.5 S_temporal_inf
- 5297 3612 7714 2.156 0.628 0.119 0.030 53 6.2 S_temporal_sup
- 231 160 398 2.436 0.576 0.114 0.022 1 0.2 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 lh Sat Jan 14 13:52:01 UTC 2017
- /data/out/sub-02/scripts
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub-02 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot
- setting seed for random number generator to 1234
- using ../mri/aseg.mgz aseg volume to correct midline
- $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading atlas from /opt/freesurfer/average/lh.DKTatlas40.gcs...
- reading color table from GCSA file....
- average std = 0.9 using min determinant for regularization = 0.007
- 0 singular and 293 ill-conditioned covariance matrices regularized
- input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
- labeling surface...
- 1025 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2400 changed, 114591 examined...
- 001: 614 changed, 10322 examined...
- 002: 155 changed, 3381 examined...
- 003: 73 changed, 898 examined...
- 004: 35 changed, 429 examined...
- 005: 13 changed, 212 examined...
- 006: 4 changed, 78 examined...
- 007: 3 changed, 28 examined...
- 008: 4 changed, 23 examined...
- 009: 1 changed, 24 examined...
- 010: 1 changed, 7 examined...
- 011: 0 changed, 8 examined...
- 212 labels changed using aseg
- 000: 66 total segments, 33 labels (180 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 27 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 805 vertices marked for relabeling...
- 805 labels changed in reclassification.
- writing output to ../label/lh.aparc.DKTatlas40.annot...
- classification took 0 minutes and 29 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 lh Sat Jan 14 13:52:30 UTC 2017
- /data/out/sub-02/scripts
- mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab sub-02 lh white
- computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
- reading volume /data/out/sub-02/mri/wm.mgz...
- reading input surface /data/out/sub-02/surf/lh.white...
- reading input pial surface /data/out/sub-02/surf/lh.pial...
- reading input white surface /data/out/sub-02/surf/lh.white...
- INFO: assuming MGZ format for volumes.
- INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
- reading colortable from annotation file...
- colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt)
- Saving annotation colortable ../label/aparc.annot.DKTatlas40.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
- 1067 713 1707 2.091 0.657 0.153 0.053 21 2.1 caudalanteriorcingulate
- 3080 2035 4853 2.140 0.605 0.124 0.033 28 4.1 caudalmiddlefrontal
- 2491 1750 3283 1.709 0.433 0.159 0.061 41 6.5 cuneus
- 398 305 1498 3.040 1.092 0.176 0.063 7 1.1 entorhinal
- 3497 2469 7385 2.558 0.650 0.138 0.046 40 6.2 fusiform
- 5982 4138 11198 2.402 0.687 0.141 0.042 78 10.2 inferiorparietal
- 4537 3145 11142 2.741 0.805 0.142 0.060 70 12.9 inferiortemporal
- 1601 1039 2429 2.243 1.040 0.155 0.117 48 4.3 isthmuscingulate
- 6368 4309 10350 2.228 0.637 0.151 0.050 95 12.1 lateraloccipital
- 3467 2492 7405 2.546 1.009 0.167 0.068 65 9.1 lateralorbitofrontal
- 3664 2662 5639 1.973 0.669 0.157 0.061 57 9.2 lingual
- 1924 1407 3631 2.080 0.838 0.192 0.084 61 6.7 medialorbitofrontal
- 5197 3653 11182 2.542 0.792 0.132 0.037 64 7.6 middletemporal
- 959 635 2175 2.626 0.949 0.108 0.039 8 1.4 parahippocampal
- 1856 1233 3157 2.245 0.597 0.126 0.040 17 3.3 paracentral
- 2101 1521 3511 2.029 0.566 0.125 0.030 22 2.6 parsopercularis
- 833 586 1680 2.238 0.696 0.138 0.035 10 1.3 parsorbitalis
- 1537 1070 2484 2.006 0.581 0.135 0.039 18 2.3 parstriangularis
- 1411 1014 1369 1.406 0.375 0.153 0.051 22 3.2 pericalcarine
- 6305 4116 8832 1.915 0.687 0.112 0.036 62 9.7 postcentral
- 1438 967 2389 2.303 0.641 0.154 0.048 23 2.7 posteriorcingulate
- 7067 4526 11842 2.301 0.679 0.112 0.059 104 20.6 precentral
- 5235 3580 8663 2.133 0.659 0.150 0.045 80 9.9 precuneus
- 1217 838 1792 1.889 0.607 0.148 0.053 24 2.3 rostralanteriorcingulate
- 4547 3223 8034 2.010 0.680 0.157 0.057 76 10.8 rostralmiddlefrontal
- 10719 7482 20833 2.326 0.650 0.141 0.044 141 19.0 superiorfrontal
- 5307 3571 7892 1.971 0.590 0.130 0.039 62 8.8 superiorparietal
- 6615 4584 14558 2.545 0.829 0.140 0.067 349 19.1 superiortemporal
- 4311 2966 7843 2.368 0.653 0.132 0.040 50 6.8 supramarginal
- 552 344 748 2.193 0.499 0.142 0.043 7 0.9 transversetemporal
- 2381 1552 5087 2.801 1.042 0.113 0.049 28 3.8 insula
- #--------------------------------------------
- #@# Tessellate rh Sat Jan 14 13:52:38 UTC 2017
- /data/out/sub-02/scripts
- mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
- Iteration Number : 1
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 1 found - 1 modified | TOTAL: 1
- pass 2 (yz-): 0 found - 1 modified | TOTAL: 1
- pass 1 (xz+): 2 found - 2 modified | TOTAL: 3
- pass 2 (xz+): 0 found - 2 modified | TOTAL: 3
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 3
- Iteration Number : 1
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 1
- pass 1 (++): 1 found - 1 modified | TOTAL: 1
- pass 2 (++): 0 found - 1 modified | TOTAL: 1
- pass 1 (+-): 0 found - 0 modified | TOTAL: 1
- pass 1 (--): 0 found - 0 modified | TOTAL: 1
- pass 1 (-+): 0 found - 0 modified | TOTAL: 1
- Iteration Number : 2
- pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
- pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+++): 0 found - 0 modified | TOTAL: 0
- Iteration Number : 2
- pass 1 (++): 0 found - 0 modified | TOTAL: 0
- pass 1 (+-): 0 found - 0 modified | TOTAL: 0
- pass 1 (--): 0 found - 0 modified | TOTAL: 0
- pass 1 (-+): 0 found - 0 modified | TOTAL: 0
- Total Number of Modified Voxels = 4 (out of 240512: 0.001663)
- Ambiguous edge configurations...
- mri_pretess done
- mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix
- $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- slice 50: 40 vertices, 51 faces
- slice 60: 3278 vertices, 3442 faces
- slice 70: 8964 vertices, 9183 faces
- slice 80: 16096 vertices, 16355 faces
- slice 90: 25138 vertices, 25433 faces
- slice 100: 34095 vertices, 34360 faces
- slice 110: 43447 vertices, 43770 faces
- slice 120: 54148 vertices, 54527 faces
- slice 130: 64774 vertices, 65137 faces
- slice 140: 74918 vertices, 75249 faces
- slice 150: 84641 vertices, 84990 faces
- slice 160: 92380 vertices, 92665 faces
- slice 170: 98927 vertices, 99188 faces
- slice 180: 105063 vertices, 105321 faces
- slice 190: 110487 vertices, 110694 faces
- slice 200: 114806 vertices, 114979 faces
- slice 210: 116278 vertices, 116316 faces
- slice 220: 116278 vertices, 116316 faces
- slice 230: 116278 vertices, 116316 faces
- slice 240: 116278 vertices, 116316 faces
- slice 250: 116278 vertices, 116316 faces
- using the conformed surface RAS to save vertex points...
- writing ../surf/rh.orig.nofix
- using vox2ras matrix:
- -1.000 0.000 0.000 128.000;
- 0.000 0.000 1.000 -128.000;
- 0.000 -1.000 0.000 128.000;
- 0.000 0.000 0.000 1.000;
- rm -f ../mri/filled-pretess127.mgz
- mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix
- counting number of connected components...
- 116278 voxel in cpt #1: X=-38 [v=116278,e=348948,f=232632] located at (26.633421, -4.127918, 21.586155)
- For the whole surface: X=-38 [v=116278,e=348948,f=232632]
- One single component has been found
- nothing to do
- done
- #--------------------------------------------
- #@# Smooth1 rh Sat Jan 14 13:52:42 UTC 2017
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- /data/out/sub-02/scripts
- setting seed for random number generator to 1234
- smoothing surface tessellation for 10 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation1 rh Sat Jan 14 13:52:45 UTC 2017
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- /data/out/sub-02/scripts
- avg radius = 45.0 mm, total surface area = 62598 mm^2
- writing inflated surface to ../surf/rh.inflated.nofix
- inflation took 0.3 minutes
- Not saving sulc
-
step 000: RMS=0.097 (target=0.015)
step 005: RMS=0.073 (target=0.015)
step 010: RMS=0.053 (target=0.015)
step 015: RMS=0.045 (target=0.015)
step 020: RMS=0.039 (target=0.015)
step 025: RMS=0.034 (target=0.015)
step 030: RMS=0.031 (target=0.015)
step 035: RMS=0.029 (target=0.015)
step 040: RMS=0.027 (target=0.015)
step 045: RMS=0.025 (target=0.015)
step 050: RMS=0.025 (target=0.015)
step 055: RMS=0.024 (target=0.015)
step 060: RMS=0.024 (target=0.015)
- inflation complete.
- Not saving sulc
- #--------------------------------------------
- #@# QSphere rh Sat Jan 14 13:53:04 UTC 2017
- /data/out/sub-02/scripts
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- doing quick spherical unfolding.
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- vertex spacing 1.07 +- 0.59 (0.00-->7.10) (max @ vno 41271 --> 42178)
- face area 0.03 +- 0.03 (-0.23-->0.60)
- scaling brain by 0.330...
- inflating to sphere (rms error < 2.00)
- 000: dt: 0.0000, rms radial error=176.867, avgs=0
- 005/300: dt: 0.9000, rms radial error=176.607, avgs=0
- 010/300: dt: 0.9000, rms radial error=176.048, avgs=0
- 015/300: dt: 0.9000, rms radial error=175.313, avgs=0
- 020/300: dt: 0.9000, rms radial error=174.477, avgs=0
- 025/300: dt: 0.9000, rms radial error=173.582, avgs=0
- 030/300: dt: 0.9000, rms radial error=172.660, avgs=0
- 035/300: dt: 0.9000, rms radial error=171.721, avgs=0
- 040/300: dt: 0.9000, rms radial error=170.775, avgs=0
- 045/300: dt: 0.9000, rms radial error=169.826, avgs=0
- 050/300: dt: 0.9000, rms radial error=168.879, avgs=0
- 055/300: dt: 0.9000, rms radial error=167.935, avgs=0
- 060/300: dt: 0.9000, rms radial error=166.995, avgs=0
- 065/300: dt: 0.9000, rms radial error=166.059, avgs=0
- 070/300: dt: 0.9000, rms radial error=165.128, avgs=0
- 075/300: dt: 0.9000, rms radial error=164.202, avgs=0
- 080/300: dt: 0.9000, rms radial error=163.281, avgs=0
- 085/300: dt: 0.9000, rms radial error=162.365, avgs=0
- 090/300: dt: 0.9000, rms radial error=161.454, avgs=0
- 095/300: dt: 0.9000, rms radial error=160.548, avgs=0
- 100/300: dt: 0.9000, rms radial error=159.647, avgs=0
- 105/300: dt: 0.9000, rms radial error=158.751, avgs=0
- 110/300: dt: 0.9000, rms radial error=157.859, avgs=0
- 115/300: dt: 0.9000, rms radial error=156.973, avgs=0
- 120/300: dt: 0.9000, rms radial error=156.091, avgs=0
- 125/300: dt: 0.9000, rms radial error=155.215, avgs=0
- 130/300: dt: 0.9000, rms radial error=154.342, avgs=0
- 135/300: dt: 0.9000, rms radial error=153.475, avgs=0
- 140/300: dt: 0.9000, rms radial error=152.612, avgs=0
- 145/300: dt: 0.9000, rms radial error=151.754, avgs=0
- 150/300: dt: 0.9000, rms radial error=150.901, avgs=0
- 155/300: dt: 0.9000, rms radial error=150.052, avgs=0
- 160/300: dt: 0.9000, rms radial error=149.208, avgs=0
- 165/300: dt: 0.9000, rms radial error=148.368, avgs=0
- 170/300: dt: 0.9000, rms radial error=147.534, avgs=0
- 175/300: dt: 0.9000, rms radial error=146.703, avgs=0
- 180/300: dt: 0.9000, rms radial error=145.877, avgs=0
- 185/300: dt: 0.9000, rms radial error=145.056, avgs=0
- 190/300: dt: 0.9000, rms radial error=144.240, avgs=0
- 195/300: dt: 0.9000, rms radial error=143.427, avgs=0
- 200/300: dt: 0.9000, rms radial error=142.620, avgs=0
- 205/300: dt: 0.9000, rms radial error=141.816, avgs=0
- 210/300: dt: 0.9000, rms radial error=141.017, avgs=0
- 215/300: dt: 0.9000, rms radial error=140.223, avgs=0
- 220/300: dt: 0.9000, rms radial error=139.433, avgs=0
- 225/300: dt: 0.9000, rms radial error=138.647, avgs=0
- 230/300: dt: 0.9000, rms radial error=137.866, avgs=0
- 235/300: dt: 0.9000, rms radial error=137.089, avgs=0
- 240/300: dt: 0.9000, rms radial error=136.316, avgs=0
- 245/300: dt: 0.9000, rms radial error=135.548, avgs=0
- 250/300: dt: 0.9000, rms radial error=134.784, avgs=0
- 255/300: dt: 0.9000, rms radial error=134.024, avgs=0
- 260/300: dt: 0.9000, rms radial error=133.268, avgs=0
- 265/300: dt: 0.9000, rms radial error=132.517, avgs=0
- 270/300: dt: 0.9000, rms radial error=131.770, avgs=0
- 275/300: dt: 0.9000, rms radial error=131.027, avgs=0
- 280/300: dt: 0.9000, rms radial error=130.288, avgs=0
- 285/300: dt: 0.9000, rms radial error=129.553, avgs=0
- 290/300: dt: 0.9000, rms radial error=128.823, avgs=0
- 295/300: dt: 0.9000, rms radial error=128.096, avgs=0
- 300/300: dt: 0.9000, rms radial error=127.374, avgs=0
- spherical inflation complete.
- epoch 1 (K=10.0), pass 1, starting sse = 13255.52
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00015
- epoch 2 (K=40.0), pass 1, starting sse = 2097.96
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.00/10 = 0.00028
- epoch 3 (K=160.0), pass 1, starting sse = 203.36
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.05/10 = 0.00477
- epoch 4 (K=640.0), pass 1, starting sse = 15.20
- taking momentum steps...
- taking momentum steps...
- taking momentum steps...
- pass 1 complete, delta sse/iter = 0.09/12 = 0.00755
- final writing spherical brain to ../surf/rh.qsphere.nofix
- spherical transformation took 0.04 hours
- distance error %100000.00
- #--------------------------------------------
- #@# Fix Topology rh Sat Jan 14 13:55:27 UTC 2017
- cp ../surf/rh.orig.nofix ../surf/rh.orig
- cp ../surf/rh.inflated.nofix ../surf/rh.inflated
- /data/out/sub-02/scripts
- mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub-02 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 1.48 2011/03/02 00:04:32 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- before topology correction, eno=-38 (nv=116278, nf=232632, ne=348948, g=20)
- using quasi-homeomorphic spherical map to tessellate cortical surface...
- Correction of the Topology
- Finding true center and radius of Spherical Surface...done
- Surface centered at (0,0,0) with radius 100.0 in 10 iterations
- marking ambiguous vertices...
- 4693 ambiguous faces found in tessellation
- segmenting defects...
- 23 defects found, arbitrating ambiguous regions...
- analyzing neighboring defects...
- 23 defects to be corrected
- 0 vertices coincident
- reading input surface /data/out/sub-02/surf/rh.qsphere.nofix...
- reading brain volume from brain...
- reading wm segmentation from wm...
- Computing Initial Surface Statistics
- -face loglikelihood: -9.5027 (-4.7513)
- -vertex loglikelihood: -6.5810 (-3.2905)
- -normal dot loglikelihood: -3.6108 (-3.6108)
- -quad curv loglikelihood: -6.3909 (-3.1955)
- Total Loglikelihood : -26.0854
- CORRECTING DEFECT 0 (vertices=59, convex hull=83)
- After retessellation of defect 0, euler #=-19 (113584,339968,226365) : difference with theory (-20) = -1
- CORRECTING DEFECT 1 (vertices=532, convex hull=201)
- After retessellation of defect 1, euler #=-18 (113633,340212,226561) : difference with theory (-19) = -1
- CORRECTING DEFECT 2 (vertices=7, convex hull=27)
- Warning - incorrect dp selected!!!!(-73.261507 >= -73.261515 )
- After retessellation of defect 2, euler #=-17 (113635,340230,226578) : difference with theory (-18) = -1
- CORRECTING DEFECT 3 (vertices=94, convex hull=115)
- After retessellation of defect 3, euler #=-16 (113692,340453,226745) : difference with theory (-17) = -1
- CORRECTING DEFECT 4 (vertices=488, convex hull=188)
- After retessellation of defect 4, euler #=-15 (113755,340731,226961) : difference with theory (-16) = -1
- CORRECTING DEFECT 5 (vertices=11, convex hull=19)
- After retessellation of defect 5, euler #=-14 (113759,340747,226974) : difference with theory (-15) = -1
- CORRECTING DEFECT 6 (vertices=42, convex hull=32)
- After retessellation of defect 6, euler #=-13 (113767,340780,227000) : difference with theory (-14) = -1
- CORRECTING DEFECT 7 (vertices=32, convex hull=60)
- After retessellation of defect 7, euler #=-12 (113782,340848,227054) : difference with theory (-13) = -1
- CORRECTING DEFECT 8 (vertices=22, convex hull=79)
- After retessellation of defect 8, euler #=-11 (113794,340911,227106) : difference with theory (-12) = -1
- CORRECTING DEFECT 9 (vertices=67, convex hull=65)
- After retessellation of defect 9, euler #=-10 (113819,341010,227181) : difference with theory (-11) = -1
- CORRECTING DEFECT 10 (vertices=114, convex hull=118)
- After retessellation of defect 10, euler #=-9 (113857,341175,227309) : difference with theory (-10) = -1
- CORRECTING DEFECT 11 (vertices=369, convex hull=52)
- After retessellation of defect 11, euler #=-8 (113867,341227,227352) : difference with theory (-9) = -1
- CORRECTING DEFECT 12 (vertices=495, convex hull=268)
- After retessellation of defect 12, euler #=-7 (113949,341601,227645) : difference with theory (-8) = -1
- CORRECTING DEFECT 13 (vertices=114, convex hull=116)
- After retessellation of defect 13, euler #=-7 (113980,341754,227767) : difference with theory (-7) = 0
- CORRECTING DEFECT 14 (vertices=70, convex hull=111)
- After retessellation of defect 14, euler #=-6 (113998,341853,227849) : difference with theory (-6) = 0
- CORRECTING DEFECT 15 (vertices=7, convex hull=29)
- After retessellation of defect 15, euler #=-5 (113999,341867,227863) : difference with theory (-5) = 0
- CORRECTING DEFECT 16 (vertices=39, convex hull=36)
- After retessellation of defect 16, euler #=-4 (114018,341935,227913) : difference with theory (-4) = 0
- CORRECTING DEFECT 17 (vertices=16, convex hull=27)
- After retessellation of defect 17, euler #=-3 (114020,341949,227926) : difference with theory (-3) = 0
- CORRECTING DEFECT 18 (vertices=5, convex hull=24)
- After retessellation of defect 18, euler #=-2 (114020,341953,227931) : difference with theory (-2) = 0
- CORRECTING DEFECT 19 (vertices=37, convex hull=70)
- After retessellation of defect 19, euler #=-1 (114035,342029,227993) : difference with theory (-1) = 0
- CORRECTING DEFECT 20 (vertices=50, convex hull=91)
- After retessellation of defect 20, euler #=0 (114070,342171,228101) : difference with theory (0) = 0
- CORRECTING DEFECT 21 (vertices=25, convex hull=66)
- After retessellation of defect 21, euler #=1 (114080,342226,228147) : difference with theory (1) = 0
- CORRECTING DEFECT 22 (vertices=8, convex hull=23)
- After retessellation of defect 22, euler #=2 (114082,342240,228160) : difference with theory (2) = 0
- computing original vertex metric properties...
- storing new metric properties...
- computing tessellation statistics...
- vertex spacing 0.89 +- 0.23 (0.06-->13.02) (max @ vno 43315 --> 46409)
- face area 0.00 +- 0.00 (0.00-->0.00)
- performing soap bubble on retessellated vertices for 0 iterations...
- vertex spacing 0.89 +- 0.23 (0.06-->13.02) (max @ vno 43315 --> 46409)
- face area 0.00 +- 0.00 (0.00-->0.00)
- tessellation finished, orienting corrected surface...
- 77 mutations (32.8%), 158 crossovers (67.2%), 239 vertices were eliminated
- building final representation...
- 2196 vertices and 0 faces have been removed from triangulation
- after topology correction, eno=2 (nv=114082, nf=228160, ne=342240, g=0)
- writing corrected surface to /data/out/sub-02/surf/rh.orig...
- 0.000 % of the vertices (0 vertices) exhibit an orientation change
- topology fixing took 13.8 minutes
- 0 defective edges
- removing intersecting faces
- 000: 131 intersecting
- 001: 7 intersecting
- mris_euler_number ../surf/rh.orig
- euler # = v-e+f = 2g-2: 114082 - 342240 + 228160 = 2 --> 0 holes
- F =2V-4: 228160 = 228164-4 (0)
- 2E=3F: 684480 = 684480 (0)
- total defect index = 0
- /data/out/sub-02/scripts
- mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
- intersection removal took 0.00 hours
- removing intersecting faces
- 000: 14 intersecting
- 001: 2 intersecting
- writing corrected surface to ../surf/rh.orig
- rm ../surf/rh.inflated
- #--------------------------------------------
- #@# Make White Surf rh Sat Jan 14 14:09:18 UTC 2017
- /data/out/sub-02/scripts
- mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-02 rh
- only generating white matter surface
- 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 1.147 2014/01/29 20:42:02 fischl Exp $
- $Id: mrisurf.c,v 1.753 2014/01/17 15:25:29 fischl Exp $
- reading volume /data/out/sub-02/mri/filled.mgz...
- reading volume /data/out/sub-02/mri/brain.finalsurfs.mgz...
- reading volume /data/out/sub-02/mri/wm.mgz...
- 8549 bright wm thresholded.
- 895 bright non-wm voxels segmented.
- reading original surface position from /data/out/sub-02/surf/rh.orig...
- computing class statistics...
- border white: 221986 voxels (1.32%)
- border gray 239648 voxels (1.43%)
- WM (91.0): 91.9 +- 8.8 [70.0 --> 110.0]
- GM (77.0) : 74.1 +- 13.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 45.7 (was 70)
- setting MAX_BORDER_WHITE to 109.8 (was 105)
- setting MIN_BORDER_WHITE to 59.0 (was 85)
- setting MAX_CSF to 32.4 (was 40)
- setting MAX_GRAY to 92.2 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.3 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 19.1 (was 40)
- repositioning cortical surface to gray/white boundary
- reading volume /data/out/sub-02/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.83 +- 0.22 (0.02-->5.94) (max @ vno 43381 --> 113735)
- face area 0.28 +- 0.13 (0.00-->6.78)
- mean absolute distance = 0.76 +- 0.91
- 3261 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=101+-6.1, GM=59+-9.6
- mean inside = 90.8, mean outside = 69.4
- smoothing surface for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=72.9, 42 (42) missing vertices, mean dist 0.4 [0.6 (%30.0)->0.8 (%70.0))]
- %61 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=3dcbc, 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 0.93 +- 0.27 (0.14-->7.96) (max @ vno 43381 --> 113735)
- face area 0.28 +- 0.14 (0.00-->5.34)
- mean absolute distance = 0.34 +- 0.64
- 2916 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5862769.0, rms=13.464
- 001: dt: 0.5000, sse=5570311.5, rms=9.923 (26.297%)
- 002: dt: 0.5000, sse=5565130.5, rms=7.613 (23.280%)
- 003: dt: 0.5000, sse=5703136.0, rms=6.037 (20.700%)
- 004: dt: 0.5000, sse=5838578.0, rms=5.037 (16.569%)
- 005: dt: 0.5000, sse=6050955.5, rms=4.482 (11.009%)
- 006: dt: 0.5000, sse=6151160.5, rms=4.204 (6.208%)
- 007: dt: 0.5000, sse=6235503.5, rms=4.063 (3.360%)
- 008: dt: 0.5000, sse=6262997.0, rms=3.988 (1.856%)
- rms = 3.94, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=6265487.0, rms=3.942 (1.148%)
- 010: dt: 0.2500, sse=3790235.8, rms=2.577 (34.612%)
- 011: dt: 0.2500, sse=3339000.2, rms=2.137 (17.100%)
- 012: dt: 0.2500, sse=3152776.0, rms=2.014 (5.740%)
- 013: dt: 0.2500, sse=3076754.8, rms=1.939 (3.715%)
- rms = 1.90, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=3034426.2, rms=1.904 (1.835%)
- 015: dt: 0.1250, sse=2936889.8, rms=1.788 (6.055%)
- rms = 1.78, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=2911982.8, rms=1.776 (0.676%)
- positioning took 0.8 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 4 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=75.9, 30 (13) missing vertices, mean dist -0.2 [0.4 (%68.4)->0.2 (%31.6))]
- %68 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=3dcbc, 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 0.92 +- 0.26 (0.11-->8.62) (max @ vno 43381 --> 113735)
- face area 0.36 +- 0.18 (0.00-->7.01)
- mean absolute distance = 0.27 +- 0.46
- 3201 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3510799.5, rms=5.032
- 017: dt: 0.5000, sse=3889325.0, rms=3.519 (30.071%)
- rms = 3.78, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=3508970.2, rms=2.680 (23.856%)
- 019: dt: 0.2500, sse=3329103.8, rms=2.083 (22.258%)
- 020: dt: 0.2500, sse=3246290.0, rms=1.793 (13.904%)
- 021: dt: 0.2500, sse=3199403.2, rms=1.684 (6.101%)
- 022: dt: 0.2500, sse=3170642.2, rms=1.618 (3.899%)
- rms = 1.58, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=3154962.5, rms=1.582 (2.259%)
- 024: dt: 0.1250, sse=3103646.2, rms=1.507 (4.701%)
- rms = 1.50, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=3082448.2, rms=1.497 (0.697%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- removing 3 vertex label from ripped group
- mean border=78.3, 38 (7) missing vertices, mean dist -0.1 [0.3 (%67.0)->0.2 (%33.0))]
- %77 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=3dcbc, 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 0.91 +- 0.25 (0.09-->8.88) (max @ vno 43381 --> 113735)
- face area 0.35 +- 0.17 (0.00-->6.92)
- mean absolute distance = 0.24 +- 0.38
- 2820 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3295562.0, rms=3.616
- 026: dt: 0.5000, sse=3731903.8, rms=3.006 (16.868%)
- rms = 3.46, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.2500, sse=3404371.0, rms=2.035 (32.292%)
- 028: dt: 0.2500, sse=3280240.5, rms=1.564 (23.159%)
- 029: dt: 0.2500, sse=3250658.8, rms=1.405 (10.136%)
- rms = 1.39, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.2500, sse=3233018.2, rms=1.394 (0.805%)
- 031: dt: 0.1250, sse=3178156.5, rms=1.315 (5.656%)
- rms = 1.32, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=3160271.8, rms=1.316 (-0.019%)
- positioning took 0.4 minutes
- inhibiting deformation at non-cortical midline structures...
- removing 2 vertex label from ripped group
- removing 2 vertex label from ripped group
- mean border=79.4, 41 (6) missing vertices, mean dist -0.1 [0.3 (%56.3)->0.2 (%43.7))]
- %81 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=3dcbc, 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 /data/out/sub-02/surf/rh.white...
- writing smoothed curvature to rh.curv
- 000: dt: 0.0000, sse=3218702.2, rms=2.036
- rms = 2.26, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=3274785.5, rms=1.434 (29.576%)
- 034: dt: 0.2500, sse=3414192.2, rms=1.041 (27.388%)
- rms = 1.02, time step reduction 2 of 3 to 0.125...
- 035: dt: 0.2500, sse=3433757.8, rms=1.024 (1.624%)
- rms = 1.01, time step reduction 3 of 3 to 0.062...
- 036: dt: 0.1250, sse=3456552.2, rms=1.008 (1.557%)
- positioning took 0.2 minutes
- generating cortex label...
- 26 non-cortical segments detected
- only using segment with 5970 vertices
- erasing segment 0 (vno[0] = 25009)
- erasing segment 1 (vno[0] = 31660)
- erasing segment 2 (vno[0] = 33946)
- erasing segment 3 (vno[0] = 35741)
- erasing segment 5 (vno[0] = 49275)
- erasing segment 6 (vno[0] = 50307)
- erasing segment 7 (vno[0] = 51370)
- erasing segment 8 (vno[0] = 54697)
- erasing segment 9 (vno[0] = 57813)
- erasing segment 10 (vno[0] = 62929)
- erasing segment 11 (vno[0] = 69635)
- erasing segment 12 (vno[0] = 72329)
- erasing segment 13 (vno[0] = 73536)
- erasing segment 14 (vno[0] = 73541)
- erasing segment 15 (vno[0] = 75235)
- erasing segment 16 (vno[0] = 76003)
- erasing segment 17 (vno[0] = 76161)
- erasing segment 18 (vno[0] = 77134)
- erasing segment 19 (vno[0] = 79213)
- erasing segment 20 (vno[0] = 80097)
- erasing segment 21 (vno[0] = 80144)
- erasing segment 22 (vno[0] = 80148)
- erasing segment 23 (vno[0] = 80209)
- erasing segment 24 (vno[0] = 100844)
- erasing segment 25 (vno[0] = 113762)
- writing cortex label to /data/out/sub-02/label/rh.cortex.label...
- writing curvature file /data/out/sub-02/surf/rh.curv
- writing smoothed area to rh.area
- writing curvature file /data/out/sub-02/surf/rh.area
- vertex spacing 0.90 +- 0.26 (0.02-->8.97) (max @ vno 43381 --> 113735)
- face area 0.34 +- 0.17 (0.00-->6.84)
- refinement took 3.0 minutes
- #--------------------------------------------
- #@# Smooth2 rh Sat Jan 14 14:12:18 UTC 2017
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm
- /data/out/sub-02/scripts
- smoothing for 3 iterations
- setting seed for random number generator to 1234
- smoothing surface tessellation for 3 iterations...
- smoothing complete - recomputing first and second fundamental forms...
- #--------------------------------------------
- #@# Inflation2 rh Sat Jan 14 14:12:20 UTC 2017
- /data/out/sub-02/scripts
- mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated
- avg radius = 45.2 mm, total surface area = 71202 mm^2
- writing inflated surface to ../surf/rh.inflated
- writing sulcal depths to ../surf/rh.sulc
-
step 000: RMS=0.112 (target=0.015)
step 005: RMS=0.078 (target=0.015)
step 010: RMS=0.055 (target=0.015)
step 015: RMS=0.046 (target=0.015)
step 020: RMS=0.038 (target=0.015)
step 025: RMS=0.032 (target=0.015)
step 030: RMS=0.027 (target=0.015)
step 035: RMS=0.023 (target=0.015)
step 040: RMS=0.019 (target=0.015)
step 045: RMS=0.017 (target=0.015)
step 050: RMS=0.016 (target=0.015)
step 055: RMS=0.015 (target=0.015)
- inflation complete.
- inflation took 0.3 minutes
- mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated
- normalizing curvature values.
- averaging curvature patterns 5 times.
- sampling 10 neighbors out to a distance of 10 mm
- 155 vertices thresholded to be in k1 ~ [-0.28 1.91], k2 ~ [-0.16 0.07]
- total integrated curvature = 0.549*4pi (6.897) --> 0 handles
- ICI = 1.5, FI = 8.0, variation=143.136
- 101 vertices thresholded to be in [-0.07 0.02]
- writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level
- curvature mean = 0.000, std = 0.001
- 114 vertices thresholded to be in [-0.16 0.53]
- done.
- writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.018, std = 0.023
- done.
- #-----------------------------------------
- #@# Curvature Stats rh Sat Jan 14 14:13:26 UTC 2017
- /data/out/sub-02/surf
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub-02 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 [ sub-02/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 [ 213 ]
- Gb_filter = 0
- WARN: S lookup min: -0.278178
- WARN: S explicit min: 0.000000 vertex = 231
- #--------------------------------------------
- #@# Sphere rh Sat Jan 14 14:13:29 UTC 2017
- /data/out/sub-02/scripts
- mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere
- setting seed for random number genererator to 1234
- $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading original vertex positions...
- unfolding cortex into spherical form...
- surface projected - minimizing metric distortion...
- scaling brain by 0.310...
- MRISunfold() max_passes = 1 -------
- tol=5.0e-01, sigma=0.0, host=3dcbc, 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 %39.62
- pass 1: epoch 2 of 3 starting distance error %19.65
- unfolding complete - removing small folds...
- starting distance error %19.59
- removing remaining folds...
- final distance error %19.59
- MRISunfold() return, current seed 1234
- writing spherical brain to ../surf/rh.sphere
- spherical transformation took 0.25 hours
- #--------------------------------------------
- #@# Surf Reg rh Sat Jan 14 14:28:17 UTC 2017
- /data/out/sub-02/scripts
- mris_register -curv ../surf/rh.sphere /opt/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg
- using smoothwm curvature for final alignment
- $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading surface from ../surf/rh.sphere...
- reading template parameterization from /opt/freesurfer/average/rh.average.curvature.filled.buckner40.tif...
- MRISregister() -------
- max_passes = 4
- min_degrees = 0.500000
- max_degrees = 64.000000
- nangles = 8
- tol=5.0e-01, sigma=0.0, host=3dcbc, 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=3dcbc, 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 = 0.592
- curvature mean = 0.025, std = 0.932
- curvature mean = 0.016, std = 0.869
- Starting MRISrigidBodyAlignGlobal()
- d=64.00 min @ (16.00, 0.00, 16.00) sse = 302501.1, tmin=0.5102
- d=32.00 min @ (-8.00, -8.00, 0.00) sse = 226558.5, tmin=1.0303
- d=16.00 min @ (0.00, 4.00, 0.00) sse = 203424.0, tmin=1.5708
- d=8.00 min @ (-2.00, -2.00, 0.00) sse = 194744.9, tmin=2.1001
- d=4.00 min @ (0.00, 1.00, -1.00) sse = 192457.6, tmin=2.6250
- d=2.00 min @ (0.00, 0.00, 0.50) sse = 192395.4, tmin=3.1702
- d=1.00 min @ (-0.25, -0.25, -0.25) sse = 192213.5, tmin=3.7118
- d=0.50 min @ (0.12, 0.12, 0.00) sse = 192164.8, tmin=4.2627
- tol=1.0e+00, sigma=0.5, host=3dcbc, 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 4.26 min
- curvature mean = 0.002, std = 0.965
- curvature mean = 0.008, std = 0.948
- curvature mean = -0.003, std = 0.974
- curvature mean = 0.004, std = 0.978
- curvature mean = -0.003, std = 0.975
- curvature mean = 0.001, std = 0.991
- 2 Reading smoothwm
- curvature mean = -0.022, std = 0.267
- curvature mean = 0.005, std = 0.071
- curvature mean = 0.052, std = 0.392
- curvature mean = 0.005, std = 0.084
- curvature mean = 0.019, std = 0.597
- curvature mean = 0.005, std = 0.091
- curvature mean = 0.010, std = 0.726
- curvature mean = 0.005, std = 0.094
- curvature mean = 0.003, std = 0.816
- MRISregister() return, current seed 0
- writing registered surface to ../surf/rh.sphere.reg...
- expanding nbhd size to 1
- #--------------------------------------------
- #@# Jacobian white rh Sat Jan 14 14:41:19 UTC 2017
- mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white
- reading surface from ../surf/rh.white...
- writing curvature file ../surf/rh.jacobian_white
- #--------------------------------------------
- #@# AvgCurv rh Sat Jan 14 14:41:21 UTC 2017
- /data/out/sub-02/scripts
- mrisp_paint -a 5 /opt/freesurfer/average/rh.average.curvature.filled.buckner40.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 /opt/freesurfer/average/rh.average.curvature.filled.buckner40.tif...
- writing curvature file to ../surf/rh.avg_curv...
- #-----------------------------------------
- #@# Cortical Parc rh Sat Jan 14 14:41:22 UTC 2017
- /data/out/sub-02/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub-02 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot
- setting seed for random number generator to 1234
- using ../mri/aseg.mgz aseg volume to correct midline
- $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading atlas from /opt/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs...
- reading color table from GCSA file....
- average std = 0.7 using min determinant for regularization = 0.006
- 0 singular and 311 ill-conditioned covariance matrices regularized
- input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
- labeling surface...
- 1069 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2541 changed, 114082 examined...
- 001: 620 changed, 10914 examined...
- 002: 134 changed, 3284 examined...
- 003: 46 changed, 804 examined...
- 004: 16 changed, 273 examined...
- 005: 9 changed, 94 examined...
- 006: 2 changed, 51 examined...
- 007: 1 changed, 14 examined...
- 008: 0 changed, 8 examined...
- 147 labels changed using aseg
- 000: 95 total segments, 58 labels (285 vertices) changed
- 001: 38 total segments, 1 labels (14 vertices) changed
- 002: 37 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 56 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 1027 vertices marked for relabeling...
- 1027 labels changed in reclassification.
- writing output to ../label/rh.aparc.annot...
- classification took 0 minutes and 29 seconds.
- #--------------------------------------------
- #@# Make Pial Surf rh Sat Jan 14 14:41:51 UTC 2017
- /data/out/sub-02/scripts
- mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub-02 rh
- -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written...
- INFO: assuming MGZ format for volumes.
- using brain.finalsurfs as T1 volume...
- $Id: mris_make_surfaces.c,v 1.147 2014/01/29 20:42:02 fischl Exp $
- $Id: mrisurf.c,v 1.753 2014/01/17 15:25:29 fischl Exp $
- reading volume /data/out/sub-02/mri/filled.mgz...
- reading volume /data/out/sub-02/mri/brain.finalsurfs.mgz...
- reading volume /data/out/sub-02/mri/wm.mgz...
- 8549 bright wm thresholded.
- 895 bright non-wm voxels segmented.
- reading original surface position from /data/out/sub-02/surf/rh.orig...
- computing class statistics...
- border white: 221986 voxels (1.32%)
- border gray 239648 voxels (1.43%)
- WM (91.0): 91.9 +- 8.8 [70.0 --> 110.0]
- GM (77.0) : 74.1 +- 13.3 [30.0 --> 110.0]
- setting MIN_GRAY_AT_WHITE_BORDER to 45.7 (was 70)
- setting MAX_BORDER_WHITE to 109.8 (was 105)
- setting MIN_BORDER_WHITE to 59.0 (was 85)
- setting MAX_CSF to 32.4 (was 40)
- setting MAX_GRAY to 92.2 (was 95)
- setting MAX_GRAY_AT_CSF_BORDER to 52.3 (was 75)
- setting MIN_GRAY_AT_CSF_BORDER to 19.1 (was 40)
- smoothing contralateral hemisphere...
- using class modes intead of means, discounting robust sigmas....
- intensity peaks found at WM=101+-6.1, GM=59+-9.6
- mean inside = 90.8, mean outside = 69.4
- smoothing surface for 5 iterations...
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- repositioning cortical surface to gray/white boundary
- reading volume /data/out/sub-02/mri/aseg.mgz...
- smoothing T1 volume with sigma = 2.000
- vertex spacing 0.83 +- 0.22 (0.02-->5.94) (max @ vno 43381 --> 113735)
- face area 0.28 +- 0.13 (0.00-->6.78)
- mean absolute distance = 0.76 +- 0.92
- 3337 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 68 points - only 0.00% unknown
- deleting segment 1 with 23 points - only 0.00% unknown
- deleting segment 2 with 14 points - only 0.00% unknown
- deleting segment 3 with 6 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 6 with 5 points - only 0.00% unknown
- deleting segment 7 with 12 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 8 with 2 points - only 0.00% unknown
- deleting segment 9 with 232 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 10 with 2 points - only 0.00% unknown
- deleting segment 12 with 12 points - only 0.00% unknown
- deleting segment 13 with 14 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 14 with 2 points - only 0.00% unknown
- deleting segment 15 with 13 points - only 0.00% unknown
- deleting segment 16 with 6 points - only 0.00% unknown
- deleting segment 17 with 70 points - only 0.00% unknown
- deleting segment 18 with 5 points - only 0.00% unknown
- deleting segment 19 with 9 points - only 0.00% unknown
- deleting segment 20 with 12 points - only 0.00% unknown
- deleting segment 21 with 7 points - only 0.00% unknown
- mean border=72.9, 42 (42) missing vertices, mean dist 0.4 [0.6 (%30.0)->0.8 (%70.0))]
- %61 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=2.0, host=3dcbc, 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 0.93 +- 0.27 (0.13-->7.96) (max @ vno 43381 --> 113735)
- face area 0.28 +- 0.14 (0.00-->5.34)
- mean absolute distance = 0.34 +- 0.65
- 2971 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=5877932.0, rms=13.447
- 001: dt: 0.5000, sse=5584049.5, rms=9.908 (26.318%)
- 002: dt: 0.5000, sse=5582100.0, rms=7.602 (23.271%)
- 003: dt: 0.5000, sse=5721131.0, rms=6.029 (20.692%)
- 004: dt: 0.5000, sse=5861517.0, rms=5.033 (16.522%)
- 005: dt: 0.5000, sse=6076501.0, rms=4.480 (10.999%)
- 006: dt: 0.5000, sse=6177430.0, rms=4.203 (6.173%)
- 007: dt: 0.5000, sse=6262777.0, rms=4.062 (3.364%)
- 008: dt: 0.5000, sse=6297835.0, rms=3.988 (1.815%)
- rms = 3.94, time step reduction 1 of 3 to 0.250...
- 009: dt: 0.5000, sse=6294249.0, rms=3.942 (1.141%)
- 010: dt: 0.2500, sse=3806516.5, rms=2.584 (34.469%)
- 011: dt: 0.2500, sse=3353964.2, rms=2.147 (16.881%)
- 012: dt: 0.2500, sse=3167317.0, rms=2.029 (5.517%)
- 013: dt: 0.2500, sse=3091362.8, rms=1.958 (3.519%)
- rms = 1.92, time step reduction 2 of 3 to 0.125...
- 014: dt: 0.2500, sse=3049890.0, rms=1.925 (1.686%)
- 015: dt: 0.1250, sse=2952711.8, rms=1.810 (5.970%)
- rms = 1.80, time step reduction 3 of 3 to 0.062...
- 016: dt: 0.1250, sse=2928304.0, rms=1.797 (0.714%)
- positioning took 0.8 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 7 points - only 0.00% unknown
- deleting segment 1 with 83 points - only 0.00% unknown
- deleting segment 2 with 27 points - only 0.00% unknown
- deleting segment 3 with 18 points - only 0.00% unknown
- deleting segment 4 with 8 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- removing 4 vertex label from ripped group
- deleting segment 6 with 4 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 201 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- deleting segment 10 with 11 points - only 0.00% unknown
- deleting segment 12 with 48 points - only 33.33% unknown
- deleting segment 13 with 8 points - only 12.50% unknown
- deleting segment 14 with 12 points - only 0.00% unknown
- deleting segment 15 with 8 points - only 0.00% unknown
- deleting segment 17 with 12 points - only 0.00% unknown
- deleting segment 18 with 9 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 19 with 2 points - only 0.00% unknown
- deleting segment 20 with 9 points - only 0.00% unknown
- removing 4 vertex label from ripped group
- deleting segment 21 with 4 points - only 0.00% unknown
- mean border=75.8, 38 (15) missing vertices, mean dist -0.2 [0.4 (%68.4)->0.2 (%31.6))]
- %68 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=1.0, host=3dcbc, 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 0.92 +- 0.25 (0.11-->8.62) (max @ vno 43381 --> 113735)
- face area 0.36 +- 0.17 (0.00-->7.01)
- mean absolute distance = 0.27 +- 0.46
- 3231 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3531225.2, rms=5.032
- 017: dt: 0.5000, sse=3913545.2, rms=3.523 (29.978%)
- rms = 3.78, time step reduction 1 of 3 to 0.250...
- 018: dt: 0.2500, sse=3532369.5, rms=2.688 (23.714%)
- 019: dt: 0.2500, sse=3353997.5, rms=2.097 (21.967%)
- 020: dt: 0.2500, sse=3269288.8, rms=1.806 (13.895%)
- 021: dt: 0.2500, sse=3223193.0, rms=1.695 (6.165%)
- 022: dt: 0.2500, sse=3193997.0, rms=1.627 (3.962%)
- rms = 1.59, time step reduction 2 of 3 to 0.125...
- 023: dt: 0.2500, sse=3179783.2, rms=1.590 (2.270%)
- 024: dt: 0.1250, sse=3128265.2, rms=1.515 (4.713%)
- rms = 1.50, time step reduction 3 of 3 to 0.062...
- 025: dt: 0.1250, sse=3106038.2, rms=1.504 (0.752%)
- positioning took 0.5 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 7 points - only 0.00% unknown
- deleting segment 1 with 81 points - only 0.00% unknown
- deleting segment 2 with 27 points - only 0.00% unknown
- deleting segment 3 with 18 points - only 0.00% unknown
- deleting segment 4 with 6 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 7 with 5 points - only 0.00% unknown
- deleting segment 8 with 7 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- deleting segment 10 with 222 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 11 with 2 points - only 0.00% unknown
- deleting segment 12 with 9 points - only 0.00% unknown
- deleting segment 13 with 48 points - only 33.33% unknown
- deleting segment 14 with 8 points - only 12.50% unknown
- deleting segment 15 with 12 points - only 0.00% unknown
- deleting segment 16 with 10 points - only 0.00% unknown
- deleting segment 17 with 18 points - only 0.00% unknown
- deleting segment 18 with 9 points - only 0.00% unknown
- deleting segment 19 with 14 points - only 0.00% unknown
- deleting segment 20 with 6 points - only 0.00% unknown
- mean border=78.3, 54 (7) missing vertices, mean dist -0.1 [0.3 (%66.9)->0.2 (%33.1))]
- %77 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.5, host=3dcbc, 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 0.91 +- 0.25 (0.10-->8.88) (max @ vno 43381 --> 113735)
- face area 0.35 +- 0.17 (0.00-->6.92)
- mean absolute distance = 0.24 +- 0.38
- 2846 vertices more than 2 sigmas from mean.
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3319716.2, rms=3.613
- 026: dt: 0.5000, sse=3754918.8, rms=3.006 (16.811%)
- rms = 3.46, time step reduction 1 of 3 to 0.250...
- 027: dt: 0.2500, sse=3425367.2, rms=2.038 (32.209%)
- 028: dt: 0.2500, sse=3303110.2, rms=1.566 (23.166%)
- 029: dt: 0.2500, sse=3272005.8, rms=1.408 (10.069%)
- rms = 1.40, time step reduction 2 of 3 to 0.125...
- 030: dt: 0.2500, sse=3253756.0, rms=1.397 (0.808%)
- 031: dt: 0.1250, sse=3198808.8, rms=1.318 (5.629%)
- rms = 1.32, time step reduction 3 of 3 to 0.062...
- 032: dt: 0.1250, sse=3178909.5, rms=1.317 (0.056%)
- positioning took 0.4 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 10 points - only 0.00% unknown
- deleting segment 1 with 81 points - only 0.00% unknown
- deleting segment 2 with 27 points - only 0.00% unknown
- deleting segment 3 with 21 points - only 0.00% unknown
- deleting segment 4 with 8 points - only 0.00% unknown
- deleting segment 5 with 5 points - only 0.00% unknown
- deleting segment 6 with 7 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 216 points - only 0.00% unknown
- removing 2 vertex label from ripped group
- deleting segment 9 with 2 points - only 0.00% unknown
- deleting segment 10 with 12 points - only 0.00% unknown
- deleting segment 11 with 48 points - only 33.33% unknown
- deleting segment 12 with 8 points - only 12.50% unknown
- deleting segment 13 with 18 points - only 0.00% unknown
- deleting segment 14 with 10 points - only 0.00% unknown
- deleting segment 15 with 21 points - only 0.00% unknown
- deleting segment 16 with 13 points - only 0.00% unknown
- deleting segment 17 with 14 points - only 0.00% unknown
- deleting segment 18 with 6 points - only 0.00% unknown
- mean border=79.4, 65 (6) missing vertices, mean dist -0.1 [0.3 (%56.3)->0.2 (%43.7))]
- %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
- tol=1.0e-04, sigma=0.2, host=3dcbc, 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
- repositioning cortical surface to gray/csf boundary.
- smoothing T1 volume with sigma = 2.000
- averaging target values for 5 iterations...
- 000: dt: 0.0000, sse=3219045.0, rms=2.031
- rms = 2.22, time step reduction 1 of 3 to 0.250...
- 033: dt: 0.2500, sse=3287218.8, rms=1.428 (29.677%)
- 034: dt: 0.2500, sse=3436878.2, rms=1.034 (27.587%)
- rms = 1.02, time step reduction 2 of 3 to 0.125...
- 035: dt: 0.2500, sse=3455538.8, rms=1.023 (1.072%)
- rms = 1.01, time step reduction 3 of 3 to 0.062...
- 036: dt: 0.1250, sse=3477497.2, rms=1.009 (1.343%)
- positioning took 0.2 minutes
- inhibiting deformation at non-cortical midline structures...
- deleting segment 0 with 16 points - only 0.00% unknown
- deleting segment 3 with 8 points - only 12.50% unknown
- removing 3 vertex label from ripped group
- deleting segment 4 with 3 points - only 0.00% unknown
- smoothing surface for 5 iterations...
- mean border=48.4, 32 (32) missing vertices, mean dist 1.7 [2.8 (%0.0)->2.1 (%100.0))]
- %19 local maxima, %58 large gradients and %19 min vals, 1556 gradients ignored
- tol=1.0e-04, sigma=2.0, host=3dcbc, 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=23504074.0, rms=31.299
- 001: dt: 0.5000, sse=17319794.0, rms=26.401 (15.651%)
- 002: dt: 0.5000, sse=12811391.0, rms=22.191 (15.946%)
- 003: dt: 0.5000, sse=9943925.0, rms=18.763 (15.446%)
- 004: dt: 0.5000, sse=8304721.0, rms=15.943 (15.029%)
- 005: dt: 0.5000, sse=7182176.0, rms=13.598 (14.708%)
- 006: dt: 0.5000, sse=6401434.5, rms=11.695 (13.996%)
- 007: dt: 0.5000, sse=5918791.5, rms=10.114 (13.523%)
- 008: dt: 0.5000, sse=5639673.5, rms=8.766 (13.327%)
- 009: dt: 0.5000, sse=5481005.5, rms=7.625 (13.018%)
- 010: dt: 0.5000, sse=5408327.5, rms=6.649 (12.797%)
- 011: dt: 0.5000, sse=5389850.0, rms=5.843 (12.120%)
- 012: dt: 0.5000, sse=5435097.0, rms=5.218 (10.697%)
- 013: dt: 0.5000, sse=5508441.0, rms=4.770 (8.579%)
- 014: dt: 0.5000, sse=5586907.0, rms=4.457 (6.561%)
- 015: dt: 0.5000, sse=5633055.0, rms=4.261 (4.396%)
- 016: dt: 0.5000, sse=5697846.0, rms=4.125 (3.202%)
- 017: dt: 0.5000, sse=5689973.0, rms=4.044 (1.975%)
- 018: dt: 0.5000, sse=5741489.5, rms=3.990 (1.335%)
- rms = 3.95, time step reduction 1 of 3 to 0.250...
- 019: dt: 0.5000, sse=5736440.5, rms=3.948 (1.051%)
- 020: dt: 0.2500, sse=3956924.2, rms=3.141 (20.438%)
- 021: dt: 0.2500, sse=3756215.5, rms=2.932 (6.636%)
- rms = 2.91, time step reduction 2 of 3 to 0.125...
- 022: dt: 0.2500, sse=3654508.8, rms=2.905 (0.918%)
- 023: dt: 0.1250, sse=3501170.5, rms=2.762 (4.922%)
- rms = 2.75, time step reduction 3 of 3 to 0.062...
- 024: dt: 0.1250, sse=3479485.2, rms=2.748 (0.537%)
- positioning took 1.2 minutes
- mean border=45.9, 517 (8) missing vertices, mean dist 0.2 [0.2 (%49.5)->0.7 (%50.5))]
- %36 local maxima, %44 large gradients and %15 min vals, 539 gradients ignored
- tol=1.0e-04, sigma=1.0, host=3dcbc, 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=4139738.8, rms=5.313
- 025: dt: 0.5000, sse=4287975.5, rms=4.349 (18.134%)
- 026: dt: 0.5000, sse=5348138.5, rms=4.180 (3.894%)
- 027: dt: 0.5000, sse=5361595.0, rms=4.045 (3.237%)
- rms = 4.06, time step reduction 1 of 3 to 0.250...
- 028: dt: 0.2500, sse=4424044.0, rms=3.284 (18.816%)
- 029: dt: 0.2500, sse=4204766.5, rms=2.969 (9.565%)
- 030: dt: 0.2500, sse=4097702.2, rms=2.874 (3.230%)
- rms = 2.83, time step reduction 2 of 3 to 0.125...
- 031: dt: 0.2500, sse=4098569.8, rms=2.832 (1.446%)
- 032: dt: 0.1250, sse=3955687.0, rms=2.690 (5.031%)
- rms = 2.66, time step reduction 3 of 3 to 0.062...
- 033: dt: 0.1250, sse=3940948.8, rms=2.663 (0.978%)
- positioning took 0.5 minutes
- mean border=44.2, 598 (6) missing vertices, mean dist 0.2 [0.2 (%46.8)->0.5 (%53.2))]
- %48 local maxima, %32 large gradients and %15 min vals, 672 gradients ignored
- tol=1.0e-04, sigma=0.5, host=3dcbc, 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=4128795.2, rms=3.805
- 034: dt: 0.5000, sse=4376580.0, rms=3.549 (6.712%)
- rms = 3.79, time step reduction 1 of 3 to 0.250...
- 035: dt: 0.2500, sse=4110299.2, rms=2.920 (17.734%)
- 036: dt: 0.2500, sse=4195482.5, rms=2.634 (9.792%)
- 037: dt: 0.2500, sse=4160833.5, rms=2.580 (2.047%)
- rms = 2.55, time step reduction 2 of 3 to 0.125...
- 038: dt: 0.2500, sse=4186050.2, rms=2.554 (1.003%)
- 039: dt: 0.1250, sse=4065941.2, rms=2.420 (5.233%)
- rms = 2.40, time step reduction 3 of 3 to 0.062...
- 040: dt: 0.1250, sse=4059228.8, rms=2.400 (0.849%)
- positioning took 0.4 minutes
- mean border=43.0, 1256 (6) missing vertices, mean dist 0.1 [0.2 (%48.1)->0.4 (%51.9))]
- %56 local maxima, %24 large gradients and %15 min vals, 631 gradients ignored
- tol=1.0e-04, sigma=0.2, host=3dcbc, 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 /data/out/sub-02/surf/rh.pial...
- writing smoothed curvature to rh.curv.pial
- 000: dt: 0.0000, sse=4119651.0, rms=2.915
- rms = 3.19, time step reduction 1 of 3 to 0.250...
- 041: dt: 0.2500, sse=4029261.8, rms=2.590 (11.148%)
- 042: dt: 0.2500, sse=4089537.2, rms=2.396 (7.480%)
- 043: dt: 0.2500, sse=4148241.8, rms=2.339 (2.396%)
- rms = 2.31, time step reduction 2 of 3 to 0.125...
- 044: dt: 0.2500, sse=4215910.0, rms=2.311 (1.196%)
- 045: dt: 0.1250, sse=4124139.0, rms=2.225 (3.721%)
- rms = 2.21, time step reduction 3 of 3 to 0.062...
- 046: dt: 0.1250, sse=4131916.8, rms=2.208 (0.761%)
- positioning took 0.3 minutes
- writing curvature file /data/out/sub-02/surf/rh.curv.pial
- writing smoothed area to rh.area.pial
- writing curvature file /data/out/sub-02/surf/rh.area.pial
- vertex spacing 1.03 +- 0.43 (0.07-->10.02) (max @ vno 44218 --> 113711)
- face area 0.43 +- 0.31 (0.00-->9.28)
- measuring cortical thickness...
- writing cortical thickness estimate to 'thickness' file.
- 0 of 114082 vertices processed
- 25000 of 114082 vertices processed
- 50000 of 114082 vertices processed
- 75000 of 114082 vertices processed
- 100000 of 114082 vertices processed
- 0 of 114082 vertices processed
- 25000 of 114082 vertices processed
- 50000 of 114082 vertices processed
- 75000 of 114082 vertices processed
- 100000 of 114082 vertices processed
- thickness calculation complete, 271:614 truncations.
- 31422 vertices at 0 distance
- 81355 vertices at 1 distance
- 69122 vertices at 2 distance
- 25978 vertices at 3 distance
- 7067 vertices at 4 distance
- 1808 vertices at 5 distance
- 538 vertices at 6 distance
- 206 vertices at 7 distance
- 85 vertices at 8 distance
- 43 vertices at 9 distance
- 23 vertices at 10 distance
- 24 vertices at 11 distance
- 13 vertices at 12 distance
- 10 vertices at 13 distance
- 8 vertices at 14 distance
- 8 vertices at 15 distance
- 8 vertices at 16 distance
- 6 vertices at 17 distance
- 7 vertices at 18 distance
- 8 vertices at 19 distance
- 9 vertices at 20 distance
- writing curvature file /data/out/sub-02/surf/rh.thickness
- positioning took 6.1 minutes
- #--------------------------------------------
- #@# Surf Volume rh Sat Jan 14 14:47:58 UTC 2017
- /data/out/sub-02/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_calc -o rh.volume rh.area.mid mul rh.thickness
- Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ]
- #-----------------------------------------
- #@# WM/GM Contrast rh Sat Jan 14 14:47:59 UTC 2017
- /data/out/sub-02/scripts
- pctsurfcon --s sub-02 --rh-only
- Log file is /data/out/sub-02/scripts/pctsurfcon.log
- Sat Jan 14 14:47:59 UTC 2017
- setenv SUBJECTS_DIR /data/out
- cd /data/out/sub-02/scripts
- /opt/freesurfer/bin/pctsurfcon
- $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
- Linux 3dcbcfbafa99 3.13.0-105-generic #152-Ubuntu SMP Fri Dec 2 15:37:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
- FREESURFER_HOME /opt/freesurfer
- mri_vol2surf --mov /data/out/sub-02/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /data/out/sub-02/surf/tmp.pctsurfcon.2545/rh.wm.mgh --regheader sub-02 --cortex
- srcvol = /data/out/sub-02/mri/rawavg.mgz
- srcreg unspecified
- srcregold = 0
- srcwarp unspecified
- surf = white
- hemi = rh
- ProjDist = -1
- reshape = 0
- interp = trilinear
- float2int = round
- GetProjMax = 0
- INFO: float2int code = 0
- Done loading volume
- Computing registration from header.
- Using /data/out/sub-02/mri/orig.mgz as target reference.
- Loading label /data/out/sub-02/label/rh.cortex.label
- Reading surface /data/out/sub-02/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 = 59241
- Masking with /data/out/sub-02/label/rh.cortex.label
- Writing to /data/out/sub-02/surf/tmp.pctsurfcon.2545/rh.wm.mgh
- Dim: 114082 1 1
- mri_vol2surf --mov /data/out/sub-02/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /data/out/sub-02/surf/tmp.pctsurfcon.2545/rh.gm.mgh --projfrac 0.3 --regheader sub-02 --cortex
- srcvol = /data/out/sub-02/mri/rawavg.mgz
- srcreg unspecified
- srcregold = 0
- srcwarp unspecified
- surf = white
- hemi = rh
- ProjFrac = 0.3
- thickness = thickness
- reshape = 0
- interp = trilinear
- float2int = round
- GetProjMax = 0
- INFO: float2int code = 0
- Done loading volume
- Computing registration from header.
- Using /data/out/sub-02/mri/orig.mgz as target reference.
- Loading label /data/out/sub-02/label/rh.cortex.label
- Reading surface /data/out/sub-02/surf/rh.white
- Done reading source surface
- Reading thickness /data/out/sub-02/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 = 68425
- Masking with /data/out/sub-02/label/rh.cortex.label
- Writing to /data/out/sub-02/surf/tmp.pctsurfcon.2545/rh.gm.mgh
- Dim: 114082 1 1
- mri_concat /data/out/sub-02/surf/tmp.pctsurfcon.2545/rh.wm.mgh /data/out/sub-02/surf/tmp.pctsurfcon.2545/rh.gm.mgh --paired-diff-norm --mul 100 --o /data/out/sub-02/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 /data/out/sub-02/surf/rh.w-g.pct.mgh
- mri_segstats --in /data/out/sub-02/surf/rh.w-g.pct.mgh --annot sub-02 rh aparc --sum /data/out/sub-02/stats/rh.w-g.pct.stats --snr
- $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
- cwd
- cmdline mri_segstats --in /data/out/sub-02/surf/rh.w-g.pct.mgh --annot sub-02 rh aparc --sum /data/out/sub-02/stats/rh.w-g.pct.stats --snr
- sysname Linux
- hostname 3dcbcfbafa99
- machine x86_64
- user root
- UseRobust 0
- Constructing seg from annotation
- Reading annotation
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Seg base 2000
- Loading /data/out/sub-02/surf/rh.w-g.pct.mgh
- Vertex Area is 0.679038 mm^3
- Generating list of segmentation ids
- Found 36 segmentations
- Computing statistics for each segmentation
- 0 2000 unknown 0 0.000
- 1 2001 bankssts 1070 744.081
- 2 2002 caudalanteriorcingulate 994 714.533
- 3 2003 caudalmiddlefrontal 2847 1987.838
- 4 2004 corpuscallosum 0 0.000
- 5 2005 cuneus 2054 1389.597
- 6 2006 entorhinal 367 261.418
- 7 2007 fusiform 4220 2925.217
- 8 2008 inferiorparietal 7671 5132.108
- 9 2009 inferiortemporal 3936 2725.115
- 10 2010 isthmuscingulate 1283 856.534
- 11 2011 lateraloccipital 6308 4129.805
- 12 2012 lateralorbitofrontal 3106 2227.054
- 13 2013 lingual 3748 2493.256
- 14 2014 medialorbitofrontal 2023 1389.261
- 15 2015 middletemporal 4460 3114.754
- 16 2016 parahippocampal 1066 680.971
- 17 2017 paracentral 2138 1394.664
- 18 2018 parsopercularis 2037 1385.190
- 19 2019 parsorbitalis 875 639.484
- 20 2020 parstriangularis 1567 1110.711
- 21 2021 pericalcarine 1700 1165.218
- 22 2022 postcentral 4608 2967.026
- 23 2023 posteriorcingulate 1434 1000.565
- 24 2024 precentral 6764 4359.088
- 25 2025 precuneus 5320 3623.952
- 26 2026 rostralanteriorcingulate 854 558.004
- 27 2027 rostralmiddlefrontal 7048 5008.757
- 28 2028 superiorfrontal 8448 5867.314
- 29 2029 superiorparietal 6501 4347.060
- 30 2030 superiortemporal 4387 2951.488
- 31 2031 supramarginal 4276 2869.393
- 32 2032 frontalpole 379 265.674
- 33 2033 temporalpole 513 365.752
- 34 2034 transversetemporal 444 277.472
- 35 2035 insula 2529 1788.766
- Reporting on 34 segmentations
- mri_segstats done
- Cleaning up
- #-----------------------------------------
- #@# Parcellation Stats rh Sat Jan 14 14:48:03 UTC 2017
- /data/out/sub-02/scripts
- mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-02 rh white
- computing statistics for each annotation in ../label/rh.aparc.annot.
- reading volume /data/out/sub-02/mri/wm.mgz...
- reading input surface /data/out/sub-02/surf/rh.white...
- reading input pial surface /data/out/sub-02/surf/rh.pial...
- reading input white surface /data/out/sub-02/surf/rh.white...
- INFO: assuming MGZ format for volumes.
- INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/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
- 1070 744 1779 2.319 0.474 0.113 0.025 8 1.0 bankssts
- 994 715 1740 1.927 0.848 0.164 0.049 18 2.0 caudalanteriorcingulate
- 2847 1988 5055 2.218 0.596 0.130 0.036 29 4.2 caudalmiddlefrontal
- 2054 1390 2966 1.885 0.557 0.155 0.050 31 4.4 cuneus
- 367 261 1108 2.720 1.188 0.148 0.053 5 0.8 entorhinal
- 4220 2925 8929 2.546 0.746 0.151 0.073 423 9.4 fusiform
- 7671 5132 15088 2.550 0.671 0.138 0.043 96 13.0 inferiorparietal
- 3936 2725 9279 2.681 0.900 0.144 0.048 55 7.6 inferiortemporal
- 1283 857 2045 2.268 0.793 0.146 0.055 21 2.5 isthmuscingulate
- 6308 4130 9986 2.204 0.658 0.147 0.044 81 11.4 lateraloccipital
- 3106 2227 6059 2.231 0.817 0.153 0.062 52 8.2 lateralorbitofrontal
- 3748 2493 4833 1.776 0.581 0.143 0.055 61 8.4 lingual
- 2023 1389 3367 1.955 0.730 0.152 0.056 42 4.6 medialorbitofrontal
- 4460 3115 10739 2.620 0.886 0.138 0.050 70 7.5 middletemporal
- 1066 681 1967 2.504 0.759 0.106 0.032 9 1.2 parahippocampal
- 2138 1395 3466 2.240 0.597 0.111 0.058 36 5.5 paracentral
- 2037 1385 3256 2.040 0.561 0.129 0.039 25 3.2 parsopercularis
- 875 639 2021 2.331 0.731 0.164 0.066 17 2.3 parsorbitalis
- 1567 1111 2775 2.025 0.777 0.128 0.037 19 2.4 parstriangularis
- 1700 1165 1752 1.573 0.415 0.146 0.050 30 3.5 pericalcarine
- 4608 2967 6131 1.791 0.660 0.118 0.039 52 7.3 postcentral
- 1434 1001 2347 2.113 0.592 0.157 0.047 24 2.8 posteriorcingulate
- 6764 4359 10900 2.235 0.686 0.116 0.035 62 9.7 precentral
- 5320 3624 8611 2.182 0.629 0.135 0.041 64 8.6 precuneus
- 854 558 1210 1.866 0.638 0.172 0.067 22 2.3 rostralanteriorcingulate
- 7048 5009 11935 1.971 0.645 0.161 0.061 132 16.1 rostralmiddlefrontal
- 8448 5867 16192 2.355 0.569 0.147 0.097 173 47.0 superiorfrontal
- 6501 4347 10110 2.078 0.595 0.128 0.039 69 9.7 superiorparietal
- 4387 2951 8176 2.370 0.681 0.118 0.043 50 5.8 superiortemporal
- 4276 2869 7476 2.289 0.655 0.127 0.034 46 6.0 supramarginal
- 379 266 1000 2.560 0.728 0.226 0.142 16 1.6 frontalpole
- 513 366 1590 2.722 0.881 0.182 0.105 11 2.2 temporalpole
- 444 277 681 2.401 0.505 0.116 0.029 4 0.5 transversetemporal
- 2529 1789 5327 2.816 0.981 0.137 0.099 47 14.7 insula
- #-----------------------------------------
- #@# Cortical Parc 2 rh Sat Jan 14 14:48:10 UTC 2017
- /data/out/sub-02/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub-02 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot
- setting seed for random number generator to 1234
- using ../mri/aseg.mgz aseg volume to correct midline
- $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading atlas from /opt/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs...
- reading color table from GCSA file....
- average std = 1.9 0.2 using min determinant for regularization = 0.000
- 0 singular and 851 ill-conditioned covariance matrices regularized
- input 1: CURVATURE FILE, flags 0, avgs 0, name sulc
- input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
- labeling surface...
- 18 labels changed using aseg
- relabeling using gibbs priors...
- 000: 8327 changed, 114082 examined...
- 001: 1844 changed, 31492 examined...
- 002: 542 changed, 9412 examined...
- 003: 244 changed, 3042 examined...
- 004: 126 changed, 1330 examined...
- 005: 69 changed, 673 examined...
- 006: 31 changed, 381 examined...
- 007: 14 changed, 190 examined...
- 008: 9 changed, 92 examined...
- 009: 1 changed, 54 examined...
- 010: 0 changed, 7 examined...
- 18 labels changed using aseg
- 000: 228 total segments, 143 labels (1813 vertices) changed
- 001: 96 total segments, 11 labels (54 vertices) changed
- 002: 85 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 105 changed)
- rationalizing unknown annotations with cortex label
- relabeling Medial_wall label...
- 715 vertices marked for relabeling...
- 715 labels changed in reclassification.
- writing output to ../label/rh.aparc.a2009s.annot...
- classification took 0 minutes and 36 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 2 rh Sat Jan 14 14:48:47 UTC 2017
- /data/out/sub-02/scripts
- mris_anatomical_stats -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 sub-02 rh white
- computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
- reading volume /data/out/sub-02/mri/wm.mgz...
- reading input surface /data/out/sub-02/surf/rh.white...
- reading input pial surface /data/out/sub-02/surf/rh.pial...
- reading input white surface /data/out/sub-02/surf/rh.white...
- INFO: assuming MGZ format for volumes.
- INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
- reading colortable from annotation file...
- colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.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
- 931 640 1573 1.996 0.685 0.175 0.081 23 2.5 G_and_S_frontomargin
- 1342 891 2437 2.584 0.651 0.140 0.036 16 1.9 G_and_S_occipital_inf
- 1409 820 2111 2.184 0.677 0.128 0.089 43 6.0 G_and_S_paracentral
- 925 633 1767 2.440 0.575 0.141 0.037 10 1.4 G_and_S_subcentral
- 896 622 1954 2.402 0.571 0.179 0.073 25 2.7 G_and_S_transv_frontopol
- 2154 1476 3073 1.923 0.568 0.135 0.046 33 4.0 G_and_S_cingul-Ant
- 1034 775 2108 2.313 0.559 0.163 0.052 18 2.2 G_and_S_cingul-Mid-Ant
- 1034 729 1643 2.027 0.478 0.134 0.041 11 1.8 G_and_S_cingul-Mid-Post
- 502 354 1165 2.724 0.502 0.181 0.064 11 1.2 G_cingul-Post-dorsal
- 279 173 576 2.708 0.767 0.161 0.091 6 0.8 G_cingul-Post-ventral
- 1877 1264 2641 1.838 0.530 0.170 0.064 41 5.2 G_cuneus
- 1220 869 2524 2.297 0.526 0.163 0.059 24 2.9 G_front_inf-Opercular
- 306 217 667 2.240 0.713 0.154 0.063 5 0.9 G_front_inf-Orbital
- 852 615 1873 2.264 0.765 0.159 0.051 16 1.8 G_front_inf-Triangul
- 3290 2385 7267 2.385 0.613 0.173 0.069 64 8.9 G_front_middle
- 5859 4091 13238 2.548 0.563 0.163 0.130 159 44.3 G_front_sup
- 331 280 1000 3.407 0.939 0.146 0.064 6 0.7 G_Ins_lg_and_S_cent_ins
- 489 353 1620 3.052 0.888 0.197 0.322 25 11.3 G_insular_short
- 1861 1257 4356 2.721 0.666 0.152 0.050 29 3.6 G_occipital_middle
- 1857 1257 3167 2.160 0.592 0.150 0.051 25 3.4 G_occipital_sup
- 1509 1018 3894 2.889 0.604 0.163 0.124 388 4.5 G_oc-temp_lat-fusifor
- 2204 1479 3236 1.813 0.632 0.162 0.070 46 6.2 G_oc-temp_med-Lingual
- 1439 948 3361 2.728 1.013 0.146 0.068 23 3.7 G_oc-temp_med-Parahip
- 2132 1608 5852 2.605 0.695 0.190 0.092 60 7.4 G_orbital
- 3112 2077 7813 2.848 0.668 0.165 0.057 56 7.0 G_pariet_inf-Angular
- 1910 1279 4173 2.539 0.656 0.141 0.043 27 3.3 G_pariet_inf-Supramar
- 1748 1144 3513 2.342 0.624 0.134 0.038 22 2.7 G_parietal_sup
- 1651 1009 2537 1.955 0.622 0.124 0.051 21 3.2 G_postcentral
- 2548 1534 5394 2.652 0.600 0.117 0.040 29 4.2 G_precentral
- 2861 1981 5541 2.252 0.510 0.157 0.051 47 6.0 G_precuneus
- 522 389 1272 2.389 0.579 0.207 0.087 16 2.1 G_rectus
- 141 82 255 2.896 0.433 0.140 0.107 5 0.3 G_subcallosal
- 348 209 570 2.346 0.492 0.108 0.027 3 0.4 G_temp_sup-G_T_transv
- 1606 1083 3982 2.645 0.659 0.144 0.072 28 2.9 G_temp_sup-Lateral
- 432 311 946 2.522 0.887 0.128 0.056 4 0.9 G_temp_sup-Plan_polar
- 697 491 1313 2.317 0.554 0.091 0.021 3 0.5 G_temp_sup-Plan_tempo
- 1922 1378 6135 3.202 0.693 0.168 0.067 38 5.0 G_temporal_inf
- 2675 1871 7980 3.045 0.742 0.153 0.066 54 5.7 G_temporal_middle
- 359 243 400 1.820 0.473 0.096 0.021 2 0.2 Lat_Fis-ant-Horizont
- 135 89 228 2.334 0.637 0.087 0.025 1 0.1 Lat_Fis-ant-Vertical
- 1289 848 1623 2.206 0.590 0.110 0.026 8 1.4 Lat_Fis-post
- 3023 1926 4015 1.895 0.525 0.154 0.053 48 6.7 Pole_occipital
- 1635 1213 4446 2.431 0.948 0.177 0.076 39 4.8 Pole_temporal
- 2031 1381 2234 1.800 0.658 0.124 0.034 19 2.8 S_calcarine
- 2805 1907 2823 1.593 0.527 0.113 0.028 19 3.4 S_central
- 1210 791 1547 1.980 0.503 0.096 0.022 7 1.1 S_cingul-Marginalis
- 406 289 568 2.108 0.580 0.127 0.051 4 0.9 S_circular_insula_ant
- 914 599 1376 2.527 1.013 0.073 0.014 2 0.4 S_circular_insula_inf
- 1203 799 1377 1.956 0.507 0.112 0.029 7 1.4 S_circular_insula_sup
- 846 581 1480 2.535 0.925 0.118 0.027 6 1.0 S_collat_transv_ant
- 310 203 402 1.979 0.608 0.136 0.033 3 0.4 S_collat_transv_post
- 1759 1185 1937 1.613 0.487 0.112 0.025 14 1.7 S_front_inf
- 1723 1201 2359 1.754 0.521 0.153 0.054 29 3.5 S_front_middle
- 2585 1781 3751 2.041 0.508 0.120 0.030 22 3.3 S_front_sup
- 739 500 963 2.145 0.559 0.113 0.027 5 0.8 S_interm_prim-Jensen
- 2788 1857 3508 2.031 0.516 0.120 0.033 24 3.7 S_intrapariet_and_P_trans
- 1036 689 1344 2.079 0.809 0.145 0.040 11 1.7 S_oc_middle_and_Lunatus
- 1142 794 1394 1.925 0.488 0.117 0.027 8 1.3 S_oc_sup_and_transversal
- 439 285 710 2.319 0.458 0.108 0.032 4 0.5 S_occipital_ant
- 966 665 1452 2.388 0.494 0.129 0.033 9 1.3 S_oc-temp_lat
- 1897 1286 2392 1.981 0.617 0.101 0.019 11 1.6 S_oc-temp_med_and_Lingual
- 380 253 363 1.356 0.345 0.110 0.024 2 0.4 S_orbital_lateral
- 602 429 797 1.617 0.946 0.105 0.026 4 0.6 S_orbital_med-olfact
- 1214 842 1787 1.917 0.619 0.124 0.037 9 1.9 S_orbital-H_Shaped
- 1760 1190 2308 2.124 0.699 0.117 0.032 14 2.1 S_parieto_occipital
- 1569 988 1283 1.592 0.691 0.131 0.031 22 2.0 S_pericallosal
- 1552 1022 1644 1.682 0.554 0.093 0.019 7 1.2 S_postcentral
- 1369 928 1814 2.019 0.469 0.102 0.022 8 1.2 S_precentral-inf-part
- 1243 854 1508 1.873 0.584 0.111 0.026 9 1.3 S_precentral-sup-part
- 316 210 400 1.629 0.758 0.154 0.044 6 0.6 S_suborbital
- 965 669 1309 1.836 0.508 0.128 0.035 9 1.3 S_subparietal
- 1085 730 1405 1.929 0.588 0.122 0.025 9 1.2 S_temporal_inf
- 5485 3707 7984 2.181 0.528 0.109 0.026 39 5.7 S_temporal_sup
- 290 190 433 2.426 0.634 0.133 0.036 3 0.4 S_temporal_transverse
- #-----------------------------------------
- #@# Cortical Parc 3 rh Sat Jan 14 14:48:55 UTC 2017
- /data/out/sub-02/scripts
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub-02 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot
- setting seed for random number generator to 1234
- using ../mri/aseg.mgz aseg volume to correct midline
- $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
- $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
- reading atlas from /opt/freesurfer/average/rh.DKTatlas40.gcs...
- reading color table from GCSA file....
- average std = 0.9 using min determinant for regularization = 0.008
- 0 singular and 237 ill-conditioned covariance matrices regularized
- input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
- labeling surface...
- 981 labels changed using aseg
- relabeling using gibbs priors...
- 000: 2424 changed, 114082 examined...
- 001: 573 changed, 10447 examined...
- 002: 124 changed, 3164 examined...
- 003: 46 changed, 721 examined...
- 004: 17 changed, 287 examined...
- 005: 12 changed, 102 examined...
- 006: 5 changed, 62 examined...
- 007: 7 changed, 27 examined...
- 008: 5 changed, 37 examined...
- 009: 3 changed, 34 examined...
- 010: 2 changed, 20 examined...
- 011: 2 changed, 13 examined...
- 012: 2 changed, 14 examined...
- 013: 2 changed, 14 examined...
- 014: 3 changed, 11 examined...
- 015: 3 changed, 15 examined...
- 016: 2 changed, 13 examined...
- 017: 2 changed, 14 examined...
- 018: 2 changed, 12 examined...
- 019: 1 changed, 14 examined...
- 020: 0 changed, 7 examined...
- 176 labels changed using aseg
- 000: 56 total segments, 23 labels (56 vertices) changed
- 001: 33 total segments, 0 labels (0 vertices) changed
- 10 filter iterations complete (10 requested, 50 changed)
- rationalizing unknown annotations with cortex label
- relabeling unknown label...
- relabeling corpuscallosum label...
- 666 vertices marked for relabeling...
- 666 labels changed in reclassification.
- writing output to ../label/rh.aparc.DKTatlas40.annot...
- classification took 0 minutes and 29 seconds.
- #-----------------------------------------
- #@# Parcellation Stats 3 rh Sat Jan 14 14:49:24 UTC 2017
- /data/out/sub-02/scripts
- mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab sub-02 rh white
- computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
- reading volume /data/out/sub-02/mri/wm.mgz...
- reading input surface /data/out/sub-02/surf/rh.white...
- reading input pial surface /data/out/sub-02/surf/rh.pial...
- reading input white surface /data/out/sub-02/surf/rh.white...
- INFO: assuming MGZ format for volumes.
- INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
- reading colortable from annotation file...
- colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt)
- Saving annotation colortable ../label/aparc.annot.DKTatlas40.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
- 1013 729 1786 1.937 0.849 0.164 0.049 19 2.0 caudalanteriorcingulate
- 2965 2054 5145 2.200 0.602 0.130 0.036 30 4.3 caudalmiddlefrontal
- 2375 1623 3349 1.859 0.558 0.150 0.047 33 4.7 cuneus
- 406 288 1135 2.625 1.176 0.156 0.053 6 0.9 entorhinal
- 3658 2509 7625 2.590 0.722 0.148 0.075 412 7.8 fusiform
- 7272 4871 14357 2.559 0.674 0.140 0.044 92 12.4 inferiorparietal
- 4417 3094 10520 2.651 0.903 0.148 0.050 64 8.9 inferiortemporal
- 1318 877 2068 2.246 0.791 0.145 0.054 22 2.5 isthmuscingulate
- 6698 4387 10635 2.206 0.661 0.148 0.044 88 12.2 lateraloccipital
- 3333 2417 7004 2.310 0.817 0.164 0.074 69 9.2 lateralorbitofrontal
- 3765 2506 4865 1.781 0.586 0.143 0.055 62 8.4 lingual
- 1465 1037 2800 2.083 0.805 0.167 0.065 35 3.8 medialorbitofrontal
- 5265 3674 12091 2.576 0.846 0.133 0.046 75 8.4 middletemporal
- 1031 658 1906 2.480 0.751 0.101 0.031 8 1.1 parahippocampal
- 2200 1444 3636 2.251 0.599 0.112 0.045 23 4.0 paracentral
- 2192 1506 3554 2.045 0.568 0.131 0.040 28 3.5 parsopercularis
- 1081 768 2194 2.208 0.685 0.138 0.048 14 2.3 parsorbitalis
- 1627 1130 2636 1.915 0.775 0.131 0.036 20 2.5 parstriangularis
- 1689 1156 1737 1.573 0.414 0.146 0.050 29 3.5 pericalcarine
- 4912 3174 6645 1.813 0.669 0.118 0.038 54 7.5 postcentral
- 1467 1025 2380 2.111 0.583 0.156 0.047 24 2.8 posteriorcingulate
- 6491 4162 10457 2.236 0.692 0.116 0.039 73 11.2 precentral
- 5428 3700 8905 2.187 0.619 0.137 0.042 68 9.1 precuneus
- 1020 659 1385 1.861 0.621 0.164 0.060 23 2.5 rostralanteriorcingulate
- 4489 3219 7692 1.982 0.653 0.161 0.063 81 10.4 rostralmiddlefrontal
- 11200 7770 20726 2.261 0.616 0.149 0.088 230 53.2 superiorfrontal
- 5555 3702 8736 2.084 0.597 0.125 0.038 56 8.2 superiorparietal
- 5821 3950 11428 2.433 0.729 0.127 0.050 74 9.7 superiortemporal
- 4058 2704 6947 2.294 0.642 0.124 0.034 41 5.5 supramarginal
- 431 268 663 2.398 0.504 0.116 0.029 4 0.5 transversetemporal
- 2333 1655 4886 2.729 0.934 0.135 0.098 42 14.2 insula
- #--------------------------------------------
- #@# Cortical ribbon mask Sat Jan 14 14:49:31 UTC 2017
- /data/out/sub-02/mri
- mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub-02
- SUBJECTS_DIR is /data/out
- 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 = 16
- writing volume /data/out/sub-02/mri/ribbon.mgz
- writing ribbon files
- #--------------------------------------------
- #@# ASeg Stats Sat Jan 14 14:54:33 UTC 2017
- /data/out/sub-02
- 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 /opt/freesurfer/ASegStatsLUT.txt --subject sub-02
- $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 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 /opt/freesurfer/ASegStatsLUT.txt --subject sub-02
- sysname Linux
- hostname 3dcbcfbafa99
- machine x86_64
- user root
- UseRobust 0
- atlas_icv (eTIV) = 1373373 mm^3 (det: 1.418483 )
- Computing euler number
- orig.nofix lheno = -38, rheno = -38
- orig.nofix lhholes = 20, rhholes = 20
- Loading mri/aseg.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 192641.315 192658.000 diff= -16.7 pctdiff=-0.009
- rhCtxGM: 188353.253 188239.000 diff= 114.3 pctdiff= 0.061
- lhCtxWM: 220453.081 220705.000 diff= -251.9 pctdiff=-0.114
- rhCtxWM: 219008.860 218915.000 diff= 93.9 pctdiff= 0.043
- SubCortGMVol 51292.000
- SupraTentVol 889322.508 (888499.000) diff=823.508 pctdiff=0.093
- SupraTentVolNotVent 872805.508 (871982.000) diff=823.508 pctdiff=0.094
- BrainSegVol 1005371.000 (1002880.000) diff=2491.000 pctdiff=0.248
- BrainSegVolNotVent 985614.000 (985262.508) diff=351.492 pctdiff=0.036
- BrainSegVolNotVent 985614.000
- CerebellumVol 113341.000
- VentChorVol 16517.000
- 3rd4th5thCSF 3240.000
- CSFVol 777.000, OptChiasmVol 263.000
- MaskVol 1428003.000
- 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
- 3 4 Left-Lateral-Ventricle 7616 7616.040
- 4 5 Left-Inf-Lat-Vent 245 245.079
- 5 7 Left-Cerebellum-White-Matter 11590 11590.050
- 6 8 Left-Cerebellum-Cortex 44812 44812.375
- 7 10 Left-Thalamus-Proper 6590 6589.548
- 8 11 Left-Caudate 3138 3138.069
- 9 12 Left-Putamen 5833 5832.516
- 10 13 Left-Pallidum 1548 1547.668
- 11 14 3rd-Ventricle 790 789.560
- 12 15 4th-Ventricle 1900 1900.477
- 13 16 Brain-Stem 19425 19424.900
- 14 17 Left-Hippocampus 3457 3456.723
- 15 18 Left-Amygdala 1106 1106.415
- 16 24 CSF 792 791.705
- 17 26 Left-Accumbens-area 538 538.281
- 18 28 Left-VentralDC 2997 2996.927
- 19 30 Left-vessel 87 87.368
- 20 31 Left-choroid-plexus 1257 1256.759
- 23 43 Right-Lateral-Ventricle 5541 5541.193
- 24 44 Right-Inf-Lat-Vent 391 390.787
- 25 46 Right-Cerebellum-White-Matter 12496 12495.676
- 26 47 Right-Cerebellum-Cortex 47318 47318.152
- 27 49 Right-Thalamus-Proper 6324 6324.468
- 28 50 Right-Caudate 3228 3228.324
- 29 51 Right-Putamen 4926 4925.653
- 30 52 Right-Pallidum 1501 1500.911
- 31 53 Right-Hippocampus 3436 3436.031
- 32 54 Right-Amygdala 1087 1087.252
- 33 58 Right-Accumbens-area 539 538.705
- 34 60 Right-VentralDC 3348 3347.931
- 35 62 Right-vessel 67 67.209
- 36 63 Right-choroid-plexus 1619 1618.629
- 37 72 5th-Ventricle 0 0.000
- 38 77 WM-hypointensities 2527 2527.497
- 39 78 Left-WM-hypointensities 0 0.000
- 40 79 Right-WM-hypointensities 0 0.000
- 41 80 non-WM-hypointensities 21 20.935
- 42 81 Left-non-WM-hypointensities 0 0.000
- 43 82 Right-non-WM-hypointensities 0 0.000
- 44 85 Optic-Chiasm 272 272.193
- 45 251 CC_Posterior 971 971.336
- 46 252 CC_Mid_Posterior 394 394.298
- 47 253 CC_Central 398 398.377
- 48 254 CC_Mid_Anterior 406 406.480
- 49 255 CC_Anterior 731 730.573
- Reporting on 45 segmentations
- mri_segstats done
- #-----------------------------------------
- #@# AParc-to-ASeg Sat Jan 14 14:56:30 UTC 2017
- /data/out/sub-02
- mri_aparc2aseg --s sub-02 --volmask
- SUBJECTS_DIR /data/out
- subject sub-02
- outvol /data/out/sub-02/mri/aparc+aseg.mgz
- useribbon 0
- baseoffset 0
- RipUnknown 0
- Reading lh white surface
- /data/out/sub-02/surf/lh.white
- Reading lh pial surface
- /data/out/sub-02/surf/lh.pial
- Loading lh annotations from /data/out/sub-02/label/lh.aparc.annot
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Reading rh white surface
- /data/out/sub-02/surf/rh.white
- Reading rh pial surface
- /data/out/sub-02/surf/rh.pial
- Loading rh annotations from /data/out/sub-02/label/rh.aparc.annot
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Have color table for lh white annotation
- Have color table for rh white annotation
- Loading ribbon segmentation from /data/out/sub-02/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 /data/out/sub-02/mri/aseg.mgz
- ASeg Vox2RAS: -----------
- -1.000 0.000 0.000 128.000;
- 0.000 0.000 1.000 -128.000;
- 0.000 -1.000 0.000 128.000;
- 0.000 0.000 0.000 1.000;
- -------------------------
- 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 = 379019
- Used brute-force search on 0 voxels
- Writing output aseg to /data/out/sub-02/mri/aparc+aseg.mgz
- /data/out/sub-02
- mri_aparc2aseg --s sub-02 --volmask --a2009s
- SUBJECTS_DIR /data/out
- subject sub-02
- outvol /data/out/sub-02/mri/aparc.a2009s+aseg.mgz
- useribbon 0
- baseoffset 10100
- RipUnknown 0
- Reading lh white surface
- /data/out/sub-02/surf/lh.white
- Reading lh pial surface
- /data/out/sub-02/surf/lh.pial
- Loading lh annotations from /data/out/sub-02/label/lh.aparc.a2009s.annot
- reading colortable from annotation file...
- colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)
- Reading rh white surface
- /data/out/sub-02/surf/rh.white
- Reading rh pial surface
- /data/out/sub-02/surf/rh.pial
- Loading rh annotations from /data/out/sub-02/label/rh.aparc.a2009s.annot
- reading colortable from annotation file...
- colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)
- Have color table for lh white annotation
- Have color table for rh white annotation
- Loading ribbon segmentation from /data/out/sub-02/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 /data/out/sub-02/mri/aseg.mgz
- ASeg Vox2RAS: -----------
- -1.000 0.000 0.000 128.000;
- 0.000 0.000 1.000 -128.000;
- 0.000 -1.000 0.000 128.000;
- 0.000 0.000 0.000 1.000;
- -------------------------
- 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 = 379019
- Used brute-force search on 0 voxels
- Writing output aseg to /data/out/sub-02/mri/aparc.a2009s+aseg.mgz
- #-----------------------------------------
- #@# WMParc Sat Jan 14 14:57:52 UTC 2017
- /data/out/sub-02
- mri_aparc2aseg --s sub-02 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz
- SUBJECTS_DIR /data/out
- subject sub-02
- outvol mri/wmparc.mgz
- useribbon 0
- baseoffset 0
- labeling wm
- labeling hypo-intensities as wm
- dmaxctx 5.000000
- RipUnknown 1
- CtxSeg /data/out/sub-02/mri/aparc+aseg.mgz
- Reading lh white surface
- /data/out/sub-02/surf/lh.white
- Reading lh pial surface
- /data/out/sub-02/surf/lh.pial
- Loading lh annotations from /data/out/sub-02/label/lh.aparc.annot
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Reading rh white surface
- /data/out/sub-02/surf/rh.white
- Reading rh pial surface
- /data/out/sub-02/surf/rh.pial
- Loading rh annotations from /data/out/sub-02/label/rh.aparc.annot
- reading colortable from annotation file...
- colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
- Have color table for lh white annotation
- Have color table for rh white annotation
- Loading ribbon segmentation from /data/out/sub-02/mri/ribbon.mgz
- Loading filled from /data/out/sub-02/mri/filled.mgz
- Ripping vertices labeled as unkown
- Ripped 6927 vertices from left hemi
- Ripped 7107 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 /data/out/sub-02/mri/aseg.mgz
- Loading Ctx Seg File /data/out/sub-02/mri/aparc+aseg.mgz
- ASeg Vox2RAS: -----------
- -1.000 0.000 0.000 128.000;
- 0.000 0.000 1.000 -128.000;
- 0.000 -1.000 0.000 128.000;
- 0.000 0.000 0.000 1.000;
- -------------------------
- 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 = 817502
- Used brute-force search on 326 voxels
- Fixing Parahip LH WM
- Found 9 clusters
- 0 k 1586.000000
- 1 k 1.000000
- 2 k 3.000000
- 3 k 1.000000
- 4 k 1.000000
- 5 k 1.000000
- 6 k 6.000000
- 7 k 2.000000
- 8 k 1.000000
- Fixing Parahip RH WM
- Found 15 clusters
- 0 k 1.000000
- 1 k 3.000000
- 2 k 1.000000
- 3 k 1867.000000
- 4 k 2.000000
- 5 k 1.000000
- 6 k 1.000000
- 7 k 2.000000
- 8 k 1.000000
- 9 k 1.000000
- 10 k 1.000000
- 11 k 3.000000
- 12 k 3.000000
- 13 k 1.000000
- 14 k 39.000000
- Writing output aseg to mri/wmparc.mgz
- /data/out/sub-02
- 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 sub-02 --surf-wm-vol --ctab /opt/freesurfer/WMParcStatsLUT.txt --etiv
- $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 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 sub-02 --surf-wm-vol --ctab /opt/freesurfer/WMParcStatsLUT.txt --etiv
- sysname Linux
- hostname 3dcbcfbafa99
- machine x86_64
- user root
- UseRobust 0
- atlas_icv (eTIV) = 1373373 mm^3 (det: 1.418483 )
- Loading mri/wmparc.mgz
- Getting Brain Volume Statistics
- lhCtxGM: 192641.315 192658.000 diff= -16.7 pctdiff=-0.009
- rhCtxGM: 188353.253 188239.000 diff= 114.3 pctdiff= 0.061
- lhCtxWM: 220453.081 220705.000 diff= -251.9 pctdiff=-0.114
- rhCtxWM: 219008.860 218915.000 diff= 93.9 pctdiff= 0.043
- SubCortGMVol 51292.000
- SupraTentVol 889322.508 (888499.000) diff=823.508 pctdiff=0.093
- SupraTentVolNotVent 872805.508 (871982.000) diff=823.508 pctdiff=0.094
- BrainSegVol 1005371.000 (1002880.000) diff=2491.000 pctdiff=0.248
- BrainSegVolNotVent 985614.000 (985262.508) diff=351.492 pctdiff=0.036
- BrainSegVolNotVent 985614.000
- CerebellumVol 113341.000
- VentChorVol 16517.000
- 3rd4th5thCSF 3240.000
- CSFVol 777.000, OptChiasmVol 263.000
- MaskVol 1428003.000
- 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
- 0 3000 wm-lh-unknown 0 0.000
- 1 3001 wm-lh-bankssts 2733 2732.770
- 2 3002 wm-lh-caudalanteriorcingulate 2024 2024.344
- 3 3003 wm-lh-caudalmiddlefrontal 6460 6460.477
- 4 3004 wm-lh-corpuscallosum 0 0.000
- 5 3005 wm-lh-cuneus 2474 2474.325
- 6 3006 wm-lh-entorhinal 708 708.430
- 7 3007 wm-lh-fusiform 6236 6235.684
- 8 3008 wm-lh-inferiorparietal 11011 11011.376
- 9 3009 wm-lh-inferiortemporal 6104 6104.214
- 10 3010 wm-lh-isthmuscingulate 4058 4057.677
- 11 3011 wm-lh-lateraloccipital 8960 8959.717
- 12 3012 wm-lh-lateralorbitofrontal 6188 6188.493
- 13 3013 wm-lh-lingual 5362 5362.019
- 14 3014 wm-lh-medialorbitofrontal 2770 2770.321
- 15 3015 wm-lh-middletemporal 5412 5411.934
- 16 3016 wm-lh-parahippocampal 1674 1673.960
- 17 3017 wm-lh-paracentral 3073 3073.227
- 18 3018 wm-lh-parsopercularis 3926 3926.433
- 19 3019 wm-lh-parsorbitalis 833 832.727
- 20 3020 wm-lh-parstriangularis 2101 2100.933
- 21 3021 wm-lh-pericalcarine 3313 3313.310
- 22 3022 wm-lh-postcentral 7623 7622.912
- 23 3023 wm-lh-posteriorcingulate 3658 3658.461
- 24 3024 wm-lh-precentral 13037 13036.872
- 25 3025 wm-lh-precuneus 8700 8700.146
- 26 3026 wm-lh-rostralanteriorcingulate 2619 2619.252
- 27 3027 wm-lh-rostralmiddlefrontal 11101 11101.173
- 28 3028 wm-lh-superiorfrontal 17799 17799.164
- 29 3029 wm-lh-superiorparietal 11805 11805.061
- 30 3030 wm-lh-superiortemporal 6989 6988.738
- 31 3031 wm-lh-supramarginal 7053 7053.475
- 32 3032 wm-lh-frontalpole 253 253.424
- 33 3033 wm-lh-temporalpole 841 840.945
- 34 3034 wm-lh-transversetemporal 960 959.987
- 35 3035 wm-lh-insula 6608 6608.330
- 36 3100 wm-lh-Unknown 0 0.000
- 37 3101 wm-lh-Corpus_callosum 0 0.000
- 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 0.000
- 39 3103 wm-lh-G_cingulate-Isthmus 0 0.000
- 40 3104 wm-lh-G_cingulate-Main_part 0 0.000
- 41 3105 wm-lh-G_cuneus 0 0.000
- 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 0.000
- 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 0.000
- 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 0.000
- 45 3109 wm-lh-G_frontal_middle 0 0.000
- 46 3110 wm-lh-G_frontal_superior 0 0.000
- 47 3111 wm-lh-G_frontomarginal 0 0.000
- 48 3112 wm-lh-G_insular_long 0 0.000
- 49 3113 wm-lh-G_insular_short 0 0.000
- 50 3114 wm-lh-G_and_S_occipital_inferior 0 0.000
- 51 3115 wm-lh-G_occipital_middle 0 0.000
- 52 3116 wm-lh-G_occipital_superior 0 0.000
- 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 0.000
- 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 0.000
- 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 0.000
- 56 3120 wm-lh-G_orbital 0 0.000
- 57 3121 wm-lh-G_paracentral 0 0.000
- 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 0.000
- 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 0.000
- 60 3124 wm-lh-G_parietal_superior 0 0.000
- 61 3125 wm-lh-G_postcentral 0 0.000
- 62 3126 wm-lh-G_precentral 0 0.000
- 63 3127 wm-lh-G_precuneus 0 0.000
- 64 3128 wm-lh-G_rectus 0 0.000
- 65 3129 wm-lh-G_subcallosal 0 0.000
- 66 3130 wm-lh-G_subcentral 0 0.000
- 67 3131 wm-lh-G_temporal_inferior 0 0.000
- 68 3132 wm-lh-G_temporal_middle 0 0.000
- 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000
- 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 0.000
- 71 3135 wm-lh-G_temp_sup-Planum_polare 0 0.000
- 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 0.000
- 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 0.000
- 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000
- 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000
- 76 3140 wm-lh-Lat_Fissure-post_sgt 0 0.000
- 77 3141 wm-lh-Medial_wall 0 0.000
- 78 3142 wm-lh-Pole_occipital 0 0.000
- 79 3143 wm-lh-Pole_temporal 0 0.000
- 80 3144 wm-lh-S_calcarine 0 0.000
- 81 3145 wm-lh-S_central 0 0.000
- 82 3146 wm-lh-S_central_insula 0 0.000
- 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 0.000
- 84 3148 wm-lh-S_cingulate-Marginalis_part 0 0.000
- 85 3149 wm-lh-S_circular_insula_anterior 0 0.000
- 86 3150 wm-lh-S_circular_insula_inferior 0 0.000
- 87 3151 wm-lh-S_circular_insula_superior 0 0.000
- 88 3152 wm-lh-S_collateral_transverse_ant 0 0.000
- 89 3153 wm-lh-S_collateral_transverse_post 0 0.000
- 90 3154 wm-lh-S_frontal_inferior 0 0.000
- 91 3155 wm-lh-S_frontal_middle 0 0.000
- 92 3156 wm-lh-S_frontal_superior 0 0.000
- 93 3157 wm-lh-S_frontomarginal 0 0.000
- 94 3158 wm-lh-S_intermedius_primus-Jensen 0 0.000
- 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 0.000
- 96 3160 wm-lh-S_occipital_anterior 0 0.000
- 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 0.000
- 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 0.000
- 99 3163 wm-lh-S_occipito-temporal_lateral 0 0.000
- 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 0.000
- 101 3165 wm-lh-S_orbital-H_shapped 0 0.000
- 102 3166 wm-lh-S_orbital_lateral 0 0.000
- 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 0.000
- 104 3168 wm-lh-S_paracentral 0 0.000
- 105 3169 wm-lh-S_parieto_occipital 0 0.000
- 106 3170 wm-lh-S_pericallosal 0 0.000
- 107 3171 wm-lh-S_postcentral 0 0.000
- 108 3172 wm-lh-S_precentral-Inferior-part 0 0.000
- 109 3173 wm-lh-S_precentral-Superior-part 0 0.000
- 110 3174 wm-lh-S_subcentral_ant 0 0.000
- 111 3175 wm-lh-S_subcentral_post 0 0.000
- 112 3176 wm-lh-S_suborbital 0 0.000
- 113 3177 wm-lh-S_subparietal 0 0.000
- 114 3178 wm-lh-S_supracingulate 0 0.000
- 115 3179 wm-lh-S_temporal_inferior 0 0.000
- 116 3180 wm-lh-S_temporal_superior 0 0.000
- 117 3181 wm-lh-S_temporal_transverse 0 0.000
- 118 4000 wm-rh-unknown 0 0.000
- 119 4001 wm-rh-bankssts 2576 2575.695
- 120 4002 wm-rh-caudalanteriorcingulate 2967 2966.731
- 121 4003 wm-rh-caudalmiddlefrontal 5722 5721.840
- 122 4004 wm-rh-corpuscallosum 0 0.000
- 123 4005 wm-rh-cuneus 2554 2554.307
- 124 4006 wm-rh-entorhinal 556 555.937
- 125 4007 wm-rh-fusiform 6459 6459.154
- 126 4008 wm-rh-inferiorparietal 11881 11880.652
- 127 4009 wm-rh-inferiortemporal 5859 5859.203
- 128 4010 wm-rh-isthmuscingulate 3380 3379.849
- 129 4011 wm-rh-lateraloccipital 9302 9301.646
- 130 4012 wm-rh-lateralorbitofrontal 6263 6262.751
- 131 4013 wm-rh-lingual 5390 5390.483
- 132 4014 wm-rh-medialorbitofrontal 2957 2957.315
- 133 4015 wm-rh-middletemporal 5477 5476.634
- 134 4016 wm-rh-parahippocampal 1923 1923.179
- 135 4017 wm-rh-paracentral 4469 4468.850
- 136 4018 wm-rh-parsopercularis 3550 3549.918
- 137 4019 wm-rh-parsorbitalis 928 927.541
- 138 4020 wm-rh-parstriangularis 2418 2418.011
- 139 4021 wm-rh-pericalcarine 2963 2963.309
- 140 4022 wm-rh-postcentral 6048 6047.921
- 141 4023 wm-rh-posteriorcingulate 3782 3782.359
- 142 4024 wm-rh-precentral 13127 13126.647
- 143 4025 wm-rh-precuneus 8939 8938.644
- 144 4026 wm-rh-rostralanteriorcingulate 1597 1596.706
- 145 4027 wm-rh-rostralmiddlefrontal 11665 11665.422
- 146 4028 wm-rh-superiorfrontal 16078 16078.182
- 147 4029 wm-rh-superiorparietal 11718 11718.198
- 148 4030 wm-rh-superiortemporal 6077 6077.490
- 149 4031 wm-rh-supramarginal 7097 7096.615
- 150 4032 wm-rh-frontalpole 307 307.187
- 151 4033 wm-rh-temporalpole 542 541.848
- 152 4034 wm-rh-transversetemporal 667 666.628
- 153 4035 wm-rh-insula 6984 6983.980
- 154 4100 wm-rh-Unknown 0 0.000
- 155 4101 wm-rh-Corpus_callosum 0 0.000
- 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 0.000
- 157 4103 wm-rh-G_cingulate-Isthmus 0 0.000
- 158 4104 wm-rh-G_cingulate-Main_part 0 0.000
- 159 4105 wm-rh-G_cuneus 0 0.000
- 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 0.000
- 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 0.000
- 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 0.000
- 163 4109 wm-rh-G_frontal_middle 0 0.000
- 164 4110 wm-rh-G_frontal_superior 0 0.000
- 165 4111 wm-rh-G_frontomarginal 0 0.000
- 166 4112 wm-rh-G_insular_long 0 0.000
- 167 4113 wm-rh-G_insular_short 0 0.000
- 168 4114 wm-rh-G_and_S_occipital_inferior 0 0.000
- 169 4115 wm-rh-G_occipital_middle 0 0.000
- 170 4116 wm-rh-G_occipital_superior 0 0.000
- 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 0.000
- 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 0.000
- 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 0.000
- 174 4120 wm-rh-G_orbital 0 0.000
- 175 4121 wm-rh-G_paracentral 0 0.000
- 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 0.000
- 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 0.000
- 178 4124 wm-rh-G_parietal_superior 0 0.000
- 179 4125 wm-rh-G_postcentral 0 0.000
- 180 4126 wm-rh-G_precentral 0 0.000
- 181 4127 wm-rh-G_precuneus 0 0.000
- 182 4128 wm-rh-G_rectus 0 0.000
- 183 4129 wm-rh-G_subcallosal 0 0.000
- 184 4130 wm-rh-G_subcentral 0 0.000
- 185 4131 wm-rh-G_temporal_inferior 0 0.000
- 186 4132 wm-rh-G_temporal_middle 0 0.000
- 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000
- 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 0.000
- 189 4135 wm-rh-G_temp_sup-Planum_polare 0 0.000
- 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 0.000
- 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 0.000
- 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000
- 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000
- 194 4140 wm-rh-Lat_Fissure-post_sgt 0 0.000
- 195 4141 wm-rh-Medial_wall 0 0.000
- 196 4142 wm-rh-Pole_occipital 0 0.000
- 197 4143 wm-rh-Pole_temporal 0 0.000
- 198 4144 wm-rh-S_calcarine 0 0.000
- 199 4145 wm-rh-S_central 0 0.000
- 200 4146 wm-rh-S_central_insula 0 0.000
- 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 0.000
- 202 4148 wm-rh-S_cingulate-Marginalis_part 0 0.000
- 203 4149 wm-rh-S_circular_insula_anterior 0 0.000
- 204 4150 wm-rh-S_circular_insula_inferior 0 0.000
- 205 4151 wm-rh-S_circular_insula_superior 0 0.000
- 206 4152 wm-rh-S_collateral_transverse_ant 0 0.000
- 207 4153 wm-rh-S_collateral_transverse_post 0 0.000
- 208 4154 wm-rh-S_frontal_inferior 0 0.000
- 209 4155 wm-rh-S_frontal_middle 0 0.000
- 210 4156 wm-rh-S_frontal_superior 0 0.000
- 211 4157 wm-rh-S_frontomarginal 0 0.000
- 212 4158 wm-rh-S_intermedius_primus-Jensen 0 0.000
- 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 0.000
- 214 4160 wm-rh-S_occipital_anterior 0 0.000
- 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 0.000
- 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 0.000
- 217 4163 wm-rh-S_occipito-temporal_lateral 0 0.000
- 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 0.000
- 219 4165 wm-rh-S_orbital-H_shapped 0 0.000
- 220 4166 wm-rh-S_orbital_lateral 0 0.000
- 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 0.000
- 222 4168 wm-rh-S_paracentral 0 0.000
- 223 4169 wm-rh-S_parieto_occipital 0 0.000
- 224 4170 wm-rh-S_pericallosal 0 0.000
- 225 4171 wm-rh-S_postcentral 0 0.000
- 226 4172 wm-rh-S_precentral-Inferior-part 0 0.000
- 227 4173 wm-rh-S_precentral-Superior-part 0 0.000
- 228 4174 wm-rh-S_subcentral_ant 0 0.000
- 229 4175 wm-rh-S_subcentral_post 0 0.000
- 230 4176 wm-rh-S_suborbital 0 0.000
- 231 4177 wm-rh-S_subparietal 0 0.000
- 232 4178 wm-rh-S_supracingulate 0 0.000
- 233 4179 wm-rh-S_temporal_inferior 0 0.000
- 234 4180 wm-rh-S_temporal_superior 0 0.000
- 235 4181 wm-rh-S_temporal_transverse 0 0.000
- 236 5001 Left-UnsegmentedWhiteMatter 32836 32836.305
- 237 5002 Right-UnsegmentedWhiteMatter 33453 33452.680
- 238 13100 wm_lh_Unknown 0 0.000
- 239 13101 wm_lh_G_and_S_frontomargin 0 0.000
- 240 13102 wm_lh_G_and_S_occipital_inf 0 0.000
- 241 13103 wm_lh_G_and_S_paracentral 0 0.000
- 242 13104 wm_lh_G_and_S_subcentral 0 0.000
- 243 13105 wm_lh_G_and_S_transv_frontopol 0 0.000
- 244 13106 wm_lh_G_and_S_cingul-Ant 0 0.000
- 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 0.000
- 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 0.000
- 247 13109 wm_lh_G_cingul-Post-dorsal 0 0.000
- 248 13110 wm_lh_G_cingul-Post-ventral 0 0.000
- 249 13111 wm_lh_G_cuneus 0 0.000
- 250 13112 wm_lh_G_front_inf-Opercular 0 0.000
- 251 13113 wm_lh_G_front_inf-Orbital 0 0.000
- 252 13114 wm_lh_G_front_inf-Triangul 0 0.000
- 253 13115 wm_lh_G_front_middle 0 0.000
- 254 13116 wm_lh_G_front_sup 0 0.000
- 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 0.000
- 256 13118 wm_lh_G_insular_short 0 0.000
- 257 13119 wm_lh_G_occipital_middle 0 0.000
- 258 13120 wm_lh_G_occipital_sup 0 0.000
- 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 0.000
- 260 13122 wm_lh_G_oc-temp_med-Lingual 0 0.000
- 261 13123 wm_lh_G_oc-temp_med-Parahip 0 0.000
- 262 13124 wm_lh_G_orbital 0 0.000
- 263 13125 wm_lh_G_pariet_inf-Angular 0 0.000
- 264 13126 wm_lh_G_pariet_inf-Supramar 0 0.000
- 265 13127 wm_lh_G_parietal_sup 0 0.000
- 266 13128 wm_lh_G_postcentral 0 0.000
- 267 13129 wm_lh_G_precentral 0 0.000
- 268 13130 wm_lh_G_precuneus 0 0.000
- 269 13131 wm_lh_G_rectus 0 0.000
- 270 13132 wm_lh_G_subcallosal 0 0.000
- 271 13133 wm_lh_G_temp_sup-G_T_transv 0 0.000
- 272 13134 wm_lh_G_temp_sup-Lateral 0 0.000
- 273 13135 wm_lh_G_temp_sup-Plan_polar 0 0.000
- 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 0.000
- 275 13137 wm_lh_G_temporal_inf 0 0.000
- 276 13138 wm_lh_G_temporal_middle 0 0.000
- 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 0.000
- 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 0.000
- 279 13141 wm_lh_Lat_Fis-post 0 0.000
- 280 13142 wm_lh_Medial_wall 0 0.000
- 281 13143 wm_lh_Pole_occipital 0 0.000
- 282 13144 wm_lh_Pole_temporal 0 0.000
- 283 13145 wm_lh_S_calcarine 0 0.000
- 284 13146 wm_lh_S_central 0 0.000
- 285 13147 wm_lh_S_cingul-Marginalis 0 0.000
- 286 13148 wm_lh_S_circular_insula_ant 0 0.000
- 287 13149 wm_lh_S_circular_insula_inf 0 0.000
- 288 13150 wm_lh_S_circular_insula_sup 0 0.000
- 289 13151 wm_lh_S_collat_transv_ant 0 0.000
- 290 13152 wm_lh_S_collat_transv_post 0 0.000
- 291 13153 wm_lh_S_front_inf 0 0.000
- 292 13154 wm_lh_S_front_middle 0 0.000
- 293 13155 wm_lh_S_front_sup 0 0.000
- 294 13156 wm_lh_S_interm_prim-Jensen 0 0.000
- 295 13157 wm_lh_S_intrapariet_and_P_trans 0 0.000
- 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 0.000
- 297 13159 wm_lh_S_oc_sup_and_transversal 0 0.000
- 298 13160 wm_lh_S_occipital_ant 0 0.000
- 299 13161 wm_lh_S_oc-temp_lat 0 0.000
- 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 0.000
- 301 13163 wm_lh_S_orbital_lateral 0 0.000
- 302 13164 wm_lh_S_orbital_med-olfact 0 0.000
- 303 13165 wm_lh_S_orbital-H_Shaped 0 0.000
- 304 13166 wm_lh_S_parieto_occipital 0 0.000
- 305 13167 wm_lh_S_pericallosal 0 0.000
- 306 13168 wm_lh_S_postcentral 0 0.000
- 307 13169 wm_lh_S_precentral-inf-part 0 0.000
- 308 13170 wm_lh_S_precentral-sup-part 0 0.000
- 309 13171 wm_lh_S_suborbital 0 0.000
- 310 13172 wm_lh_S_subparietal 0 0.000
- 311 13173 wm_lh_S_temporal_inf 0 0.000
- 312 13174 wm_lh_S_temporal_sup 0 0.000
- 313 13175 wm_lh_S_temporal_transverse 0 0.000
- 314 14100 wm_rh_Unknown 0 0.000
- 315 14101 wm_rh_G_and_S_frontomargin 0 0.000
- 316 14102 wm_rh_G_and_S_occipital_inf 0 0.000
- 317 14103 wm_rh_G_and_S_paracentral 0 0.000
- 318 14104 wm_rh_G_and_S_subcentral 0 0.000
- 319 14105 wm_rh_G_and_S_transv_frontopol 0 0.000
- 320 14106 wm_rh_G_and_S_cingul-Ant 0 0.000
- 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 0.000
- 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 0.000
- 323 14109 wm_rh_G_cingul-Post-dorsal 0 0.000
- 324 14110 wm_rh_G_cingul-Post-ventral 0 0.000
- 325 14111 wm_rh_G_cuneus 0 0.000
- 326 14112 wm_rh_G_front_inf-Opercular 0 0.000
- 327 14113 wm_rh_G_front_inf-Orbital 0 0.000
- 328 14114 wm_rh_G_front_inf-Triangul 0 0.000
- 329 14115 wm_rh_G_front_middle 0 0.000
- 330 14116 wm_rh_G_front_sup 0 0.000
- 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 0.000
- 332 14118 wm_rh_G_insular_short 0 0.000
- 333 14119 wm_rh_G_occipital_middle 0 0.000
- 334 14120 wm_rh_G_occipital_sup 0 0.000
- 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 0.000
- 336 14122 wm_rh_G_oc-temp_med-Lingual 0 0.000
- 337 14123 wm_rh_G_oc-temp_med-Parahip 0 0.000
- 338 14124 wm_rh_G_orbital 0 0.000
- 339 14125 wm_rh_G_pariet_inf-Angular 0 0.000
- 340 14126 wm_rh_G_pariet_inf-Supramar 0 0.000
- 341 14127 wm_rh_G_parietal_sup 0 0.000
- 342 14128 wm_rh_G_postcentral 0 0.000
- 343 14129 wm_rh_G_precentral 0 0.000
- 344 14130 wm_rh_G_precuneus 0 0.000
- 345 14131 wm_rh_G_rectus 0 0.000
- 346 14132 wm_rh_G_subcallosal 0 0.000
- 347 14133 wm_rh_G_temp_sup-G_T_transv 0 0.000
- 348 14134 wm_rh_G_temp_sup-Lateral 0 0.000
- 349 14135 wm_rh_G_temp_sup-Plan_polar 0 0.000
- 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 0.000
- 351 14137 wm_rh_G_temporal_inf 0 0.000
- 352 14138 wm_rh_G_temporal_middle 0 0.000
- 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 0.000
- 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 0.000
- 355 14141 wm_rh_Lat_Fis-post 0 0.000
- 356 14142 wm_rh_Medial_wall 0 0.000
- 357 14143 wm_rh_Pole_occipital 0 0.000
- 358 14144 wm_rh_Pole_temporal 0 0.000
- 359 14145 wm_rh_S_calcarine 0 0.000
- 360 14146 wm_rh_S_central 0 0.000
- 361 14147 wm_rh_S_cingul-Marginalis 0 0.000
- 362 14148 wm_rh_S_circular_insula_ant 0 0.000
- 363 14149 wm_rh_S_circular_insula_inf 0 0.000
- 364 14150 wm_rh_S_circular_insula_sup 0 0.000
- 365 14151 wm_rh_S_collat_transv_ant 0 0.000
- 366 14152 wm_rh_S_collat_transv_post 0 0.000
- 367 14153 wm_rh_S_front_inf 0 0.000
- 368 14154 wm_rh_S_front_middle 0 0.000
- 369 14155 wm_rh_S_front_sup 0 0.000
- 370 14156 wm_rh_S_interm_prim-Jensen 0 0.000
- 371 14157 wm_rh_S_intrapariet_and_P_trans 0 0.000
- 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 0.000
- 373 14159 wm_rh_S_oc_sup_and_transversal 0 0.000
- 374 14160 wm_rh_S_occipital_ant 0 0.000
- 375 14161 wm_rh_S_oc-temp_lat 0 0.000
- 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 0.000
- 377 14163 wm_rh_S_orbital_lateral 0 0.000
- 378 14164 wm_rh_S_orbital_med-olfact 0 0.000
- 379 14165 wm_rh_S_orbital-H_Shaped 0 0.000
- 380 14166 wm_rh_S_parieto_occipital 0 0.000
- 381 14167 wm_rh_S_pericallosal 0 0.000
- 382 14168 wm_rh_S_postcentral 0 0.000
- 383 14169 wm_rh_S_precentral-inf-part 0 0.000
- 384 14170 wm_rh_S_precentral-sup-part 0 0.000
- 385 14171 wm_rh_S_suborbital 0 0.000
- 386 14172 wm_rh_S_subparietal 0 0.000
- 387 14173 wm_rh_S_temporal_inf 0 0.000
- 388 14174 wm_rh_S_temporal_sup 0 0.000
- 389 14175 wm_rh_S_temporal_transverse 0 0.000
- Reporting on 70 segmentations
- mri_segstats done
- /data/out/sub-02/label
- #--------------------------------------------
- #@# BA Labels lh Sat Jan 14 15:04:52 UTC 2017
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA1.label --trgsubject sub-02 --trglabel ./lh.BA1.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.BA1.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.BA1.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 4129 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 183
- Checking for and removing duplicates
- Writing label file ./lh.BA1.label 4312
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA2.label --trgsubject sub-02 --trglabel ./lh.BA2.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.BA2.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.BA2.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 7909 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 198
- Checking for and removing duplicates
- Writing label file ./lh.BA2.label 8107
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA3a.label --trgsubject sub-02 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.BA3a.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.BA3a.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 4077 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 141
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.label 4218
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA3b.label --trgsubject sub-02 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.BA3b.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.BA3b.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 5983 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 224
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.label 6207
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA4a.label --trgsubject sub-02 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.BA4a.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.BA4a.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 5784 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 342
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.label 6126
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA4p.label --trgsubject sub-02 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.BA4p.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.BA4p.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 4070 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 172
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.label 4242
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA6.label --trgsubject sub-02 --trglabel ./lh.BA6.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.BA6.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.BA6.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 13589 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 1074
- Checking for and removing duplicates
- Writing label file ./lh.BA6.label 14663
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA44.label --trgsubject sub-02 --trglabel ./lh.BA44.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.BA44.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.BA44.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 4181 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 274
- Checking for and removing duplicates
- Writing label file ./lh.BA44.label 4455
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA45.label --trgsubject sub-02 --trglabel ./lh.BA45.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.BA45.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.BA45.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 3422 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 291
- Checking for and removing duplicates
- Writing label file ./lh.BA45.label 3713
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.V1.label --trgsubject sub-02 --trglabel ./lh.V1.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.V1.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.V1.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 4641 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 912
- Checking for and removing duplicates
- Writing label file ./lh.V1.label 5553
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.V2.label --trgsubject sub-02 --trglabel ./lh.V2.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.V2.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.V2.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 8114 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 1786
- Checking for and removing duplicates
- Writing label file ./lh.V2.label 9900
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.MT.label --trgsubject sub-02 --trglabel ./lh.MT.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.MT.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.MT.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 2018 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 222
- Checking for and removing duplicates
- Writing label file ./lh.MT.label 2240
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.perirhinal.label --trgsubject sub-02 --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.perirhinal.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.perirhinal.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 1199 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 23
- Checking for and removing duplicates
- Writing label file ./lh.perirhinal.label 1222
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA1.thresh.label --trgsubject sub-02 --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.BA1.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.BA1.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 1014 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 68
- Checking for and removing duplicates
- Writing label file ./lh.BA1.thresh.label 1082
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA2.thresh.label --trgsubject sub-02 --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.BA2.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.BA2.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 2092 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 43
- Checking for and removing duplicates
- Writing label file ./lh.BA2.thresh.label 2135
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub-02 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.BA3a.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.BA3a.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 1504 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 38
- Checking for and removing duplicates
- Writing label file ./lh.BA3a.thresh.label 1542
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub-02 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.BA3b.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.BA3b.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 1996 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 110
- Checking for and removing duplicates
- Writing label file ./lh.BA3b.thresh.label 2106
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub-02 --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.BA4a.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.BA4a.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 2319 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 172
- Checking for and removing duplicates
- Writing label file ./lh.BA4a.thresh.label 2491
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub-02 --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.BA4p.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.BA4p.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 1549 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 55
- Checking for and removing duplicates
- Writing label file ./lh.BA4p.thresh.label 1604
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA6.thresh.label --trgsubject sub-02 --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.BA6.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.BA6.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 7035 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 503
- Checking for and removing duplicates
- Writing label file ./lh.BA6.thresh.label 7538
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA44.thresh.label --trgsubject sub-02 --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.BA44.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.BA44.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 1912 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 122
- Checking for and removing duplicates
- Writing label file ./lh.BA44.thresh.label 2034
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA45.thresh.label --trgsubject sub-02 --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.BA45.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.BA45.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 1151 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 94
- Checking for and removing duplicates
- Writing label file ./lh.BA45.thresh.label 1245
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.V1.thresh.label --trgsubject sub-02 --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.V1.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.V1.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 3405 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 614
- Checking for and removing duplicates
- Writing label file ./lh.V1.thresh.label 4019
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.V2.thresh.label --trgsubject sub-02 --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.V2.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.V2.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 3334 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 851
- Checking for and removing duplicates
- Writing label file ./lh.V2.thresh.label 4185
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.MT.thresh.label --trgsubject sub-02 --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface
- srclabel = /data/out/fsaverage/label/lh.MT.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./lh.MT.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 513 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/lh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/lh.white
- Reading target registration
- /data/out/sub-02/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 114591
- Number of reverse mapping hits = 90
- Checking for and removing duplicates
- Writing label file ./lh.MT.thresh.label 603
- mri_label2label: Done
- mris_label2annot --s sub-02 --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose
- Reading ctab /opt/freesurfer/average/colortable_BA.txt
- Number of ctab entries 14
- $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
- cwd /data/out/sub-02/label
- cmdline mris_label2annot --s sub-02 --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose
- sysname Linux
- hostname 3dcbcfbafa99
- machine x86_64
- user root
- subject sub-02
- hemi lh
- SUBJECTS_DIR /data/out
- ColorTable /opt/freesurfer/average/colortable_BA.txt
- AnnotName BA
- nlables 13
- LabelThresh 0 0.000000
- Loading /data/out/sub-02/surf/lh.orig
- 1 1530880 BA1
- 2 16749699 BA2
- 3 16711680 BA3a
- 4 3368703 BA3b
- 5 1376196 BA4a
- 6 13382655 BA4p
- 7 10036737 BA6
- 8 2490521 BA44
- 9 39283 BA45
- 10 3993 V1
- 11 8508928 V2
- 12 10027163 MT
- 13 16422433 perirhinal
- Mapping unhit to unknown
- Found 78830 unhit vertices
- Writing annot to /data/out/sub-02/label/lh.BA.annot
- mris_label2annot --s sub-02 --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose
- Reading ctab /opt/freesurfer/average/colortable_BA.txt
- Number of ctab entries 14
- $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
- cwd /data/out/sub-02/label
- cmdline mris_label2annot --s sub-02 --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose
- sysname Linux
- hostname 3dcbcfbafa99
- machine x86_64
- user root
- subject sub-02
- hemi lh
- SUBJECTS_DIR /data/out
- ColorTable /opt/freesurfer/average/colortable_BA.txt
- AnnotName BA.thresh
- nlables 12
- LabelThresh 0 0.000000
- Loading /data/out/sub-02/surf/lh.orig
- 1 1530880 BA1
- 2 16749699 BA2
- 3 16711680 BA3a
- 4 3368703 BA3b
- 5 1376196 BA4a
- 6 13382655 BA4p
- 7 10036737 BA6
- 8 2490521 BA44
- 9 39283 BA45
- 10 3993 V1
- 11 8508928 V2
- 12 10027163 MT
- Mapping unhit to unknown
- Found 93242 unhit vertices
- Writing annot to /data/out/sub-02/label/lh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub-02 lh white
- computing statistics for each annotation in ./lh.BA.annot.
- reading volume /data/out/sub-02/mri/wm.mgz...
- reading input surface /data/out/sub-02/surf/lh.white...
- reading input pial surface /data/out/sub-02/surf/lh.pial...
- reading input white surface /data/out/sub-02/surf/lh.white...
- INFO: assuming MGZ format for volumes.
- reading colortable from annotation file...
- colortable with 14 entries read (originally /opt/freesurfer/average/colortable_BA.txt)
- Saving annotation colortable ./BA.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
- 1080 583 1740 2.218 0.506 0.135 0.058 21 3.1 BA1
- 3057 2074 4315 1.984 0.588 0.103 0.024 21 3.2 BA2
- 1028 657 767 1.430 0.373 0.121 0.032 9 1.4 BA3a
- 2219 1504 2568 1.546 0.590 0.115 0.041 22 3.8 BA3b
- 1540 885 2848 2.586 0.605 0.122 0.164 62 14.2 BA4a
- 1163 815 1821 2.240 0.574 0.098 0.025 6 1.2 BA4p
- 9046 6041 17836 2.472 0.588 0.125 0.039 89 14.1 BA6
- 2253 1639 3929 2.149 0.602 0.113 0.028 21 2.6 BA44
- 2290 1591 3613 1.913 0.608 0.132 0.037 26 3.3 BA45
- 2877 2071 3312 1.488 0.452 0.164 0.076 55 8.7 V1
- 6892 4840 10014 1.942 0.552 0.159 0.056 112 15.7 V2
- 1616 1114 3402 2.620 0.597 0.139 0.042 19 2.5 MT
- 700 531 2376 3.094 1.043 0.156 0.061 9 1.7 perirhinal
- mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub-02 lh white
- computing statistics for each annotation in ./lh.BA.thresh.annot.
- reading volume /data/out/sub-02/mri/wm.mgz...
- reading input surface /data/out/sub-02/surf/lh.white...
- reading input pial surface /data/out/sub-02/surf/lh.pial...
- reading input white surface /data/out/sub-02/surf/lh.white...
- INFO: assuming MGZ format for volumes.
- reading colortable from annotation file...
- colortable with 14 entries read (originally /opt/freesurfer/average/colortable_BA.txt)
- Saving annotation colortable ./BA.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
- 693 348 1159 2.343 0.469 0.150 0.080 17 2.8 BA1
- 1283 882 2079 2.071 0.586 0.083 0.017 5 0.8 BA2
- 841 529 591 1.444 0.374 0.127 0.033 7 1.1 BA3a
- 1446 999 1372 1.285 0.356 0.092 0.025 9 1.6 BA3b
- 1520 885 2796 2.604 0.582 0.112 0.153 57 13.1 BA4a
- 987 688 1460 2.182 0.567 0.101 0.039 7 1.8 BA4p
- 5154 3401 10372 2.520 0.598 0.128 0.041 53 8.8 BA6
- 1418 1053 2649 2.229 0.555 0.121 0.030 15 1.8 BA44
- 910 638 1839 2.222 0.596 0.150 0.045 13 1.7 BA45
- 3101 2225 3660 1.526 0.498 0.166 0.076 61 9.2 V1
- 3512 2517 4880 1.842 0.526 0.174 0.066 70 9.6 V2
- 484 320 739 2.394 0.578 0.149 0.041 6 0.9 MT
- #--------------------------------------------
- #@# BA Labels rh Sat Jan 14 15:07:16 UTC 2017
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA1.label --trgsubject sub-02 --trglabel ./rh.BA1.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.BA1.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.BA1.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 3962 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 112
- Checking for and removing duplicates
- Writing label file ./rh.BA1.label 4074
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA2.label --trgsubject sub-02 --trglabel ./rh.BA2.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.BA2.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.BA2.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 6687 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 84
- Checking for and removing duplicates
- Writing label file ./rh.BA2.label 6771
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA3a.label --trgsubject sub-02 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.BA3a.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.BA3a.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 3980 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 139
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.label 4119
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA3b.label --trgsubject sub-02 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.BA3b.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.BA3b.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 4522 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 157
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.label 4679
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA4a.label --trgsubject sub-02 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.BA4a.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.BA4a.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 5747 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 275
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.label 6022
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA4p.label --trgsubject sub-02 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.BA4p.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.BA4p.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 4473 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 244
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.label 4717
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA6.label --trgsubject sub-02 --trglabel ./rh.BA6.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.BA6.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.BA6.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 12256 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 525
- Checking for and removing duplicates
- Writing label file ./rh.BA6.label 12781
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA44.label --trgsubject sub-02 --trglabel ./rh.BA44.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.BA44.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.BA44.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 6912 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 603
- Checking for and removing duplicates
- Writing label file ./rh.BA44.label 7515
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA45.label --trgsubject sub-02 --trglabel ./rh.BA45.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.BA45.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.BA45.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 5355 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 563
- Checking for and removing duplicates
- Writing label file ./rh.BA45.label 5918
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.V1.label --trgsubject sub-02 --trglabel ./rh.V1.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.V1.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.V1.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 4727 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 942
- Checking for and removing duplicates
- Writing label file ./rh.V1.label 5669
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.V2.label --trgsubject sub-02 --trglabel ./rh.V2.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.V2.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.V2.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 8016 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 2144
- Checking for and removing duplicates
- Writing label file ./rh.V2.label 10160
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.MT.label --trgsubject sub-02 --trglabel ./rh.MT.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.MT.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.MT.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 1932 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 279
- Checking for and removing duplicates
- Writing label file ./rh.MT.label 2211
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.perirhinal.label --trgsubject sub-02 --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.perirhinal.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.perirhinal.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 752 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 85
- Checking for and removing duplicates
- Writing label file ./rh.perirhinal.label 837
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA1.thresh.label --trgsubject sub-02 --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.BA1.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.BA1.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 876 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 30
- Checking for and removing duplicates
- Writing label file ./rh.BA1.thresh.label 906
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA2.thresh.label --trgsubject sub-02 --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.BA2.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.BA2.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 2688 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 16
- Checking for and removing duplicates
- Writing label file ./rh.BA2.thresh.label 2704
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub-02 --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.BA3a.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.BA3a.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 1698 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 36
- Checking for and removing duplicates
- Writing label file ./rh.BA3a.thresh.label 1734
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub-02 --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.BA3b.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.BA3b.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 2183 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 88
- Checking for and removing duplicates
- Writing label file ./rh.BA3b.thresh.label 2271
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub-02 --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.BA4a.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.BA4a.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 1388 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 68
- Checking for and removing duplicates
- Writing label file ./rh.BA4a.thresh.label 1456
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub-02 --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.BA4p.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.BA4p.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 1489 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 102
- Checking for and removing duplicates
- Writing label file ./rh.BA4p.thresh.label 1591
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA6.thresh.label --trgsubject sub-02 --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.BA6.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.BA6.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 6959 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 290
- Checking for and removing duplicates
- Writing label file ./rh.BA6.thresh.label 7249
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA44.thresh.label --trgsubject sub-02 --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.BA44.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.BA44.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 1012 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 182
- Checking for and removing duplicates
- Writing label file ./rh.BA44.thresh.label 1194
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA45.thresh.label --trgsubject sub-02 --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.BA45.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.BA45.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 1178 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 93
- Checking for and removing duplicates
- Writing label file ./rh.BA45.thresh.label 1271
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.V1.thresh.label --trgsubject sub-02 --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.V1.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.V1.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 3232 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 557
- Checking for and removing duplicates
- Writing label file ./rh.V1.thresh.label 3789
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.V2.thresh.label --trgsubject sub-02 --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.V2.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.V2.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 3437 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 1052
- Checking for and removing duplicates
- Writing label file ./rh.V2.thresh.label 4489
- mri_label2label: Done
- mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.MT.thresh.label --trgsubject sub-02 --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface
- srclabel = /data/out/fsaverage/label/rh.MT.thresh.label
- srcsubject = fsaverage
- trgsubject = sub-02
- trglabel = ./rh.MT.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 /data/out
- FREESURFER_HOME /opt/freesurfer
- Loading source label.
- Found 268 points in source label.
- Starting surface-based mapping
- Reading source registration
- /data/out/fsaverage/surf/rh.sphere.reg
- Rescaling ... original radius = 100
- Reading target surface
- /data/out/sub-02/surf/rh.white
- Reading target registration
- /data/out/sub-02/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 114082
- Number of reverse mapping hits = 69
- Checking for and removing duplicates
- Writing label file ./rh.MT.thresh.label 337
- mri_label2label: Done
- mris_label2annot --s sub-02 --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose
- Reading ctab /opt/freesurfer/average/colortable_BA.txt
- Number of ctab entries 14
- $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
- cwd /data/out/sub-02/label
- cmdline mris_label2annot --s sub-02 --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose
- sysname Linux
- hostname 3dcbcfbafa99
- machine x86_64
- user root
- subject sub-02
- hemi rh
- SUBJECTS_DIR /data/out
- ColorTable /opt/freesurfer/average/colortable_BA.txt
- AnnotName BA
- nlables 13
- LabelThresh 0 0.000000
- Loading /data/out/sub-02/surf/rh.orig
- 1 1530880 BA1
- 2 16749699 BA2
- 3 16711680 BA3a
- 4 3368703 BA3b
- 5 1376196 BA4a
- 6 13382655 BA4p
- 7 10036737 BA6
- 8 2490521 BA44
- 9 39283 BA45
- 10 3993 V1
- 11 8508928 V2
- 12 10027163 MT
- 13 16422433 perirhinal
- Mapping unhit to unknown
- Found 79125 unhit vertices
- Writing annot to /data/out/sub-02/label/rh.BA.annot
- mris_label2annot --s sub-02 --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose
- Reading ctab /opt/freesurfer/average/colortable_BA.txt
- Number of ctab entries 14
- $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
- cwd /data/out/sub-02/label
- cmdline mris_label2annot --s sub-02 --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose
- sysname Linux
- hostname 3dcbcfbafa99
- machine x86_64
- user root
- subject sub-02
- hemi rh
- SUBJECTS_DIR /data/out
- ColorTable /opt/freesurfer/average/colortable_BA.txt
- AnnotName BA.thresh
- nlables 12
- LabelThresh 0 0.000000
- Loading /data/out/sub-02/surf/rh.orig
- 1 1530880 BA1
- 2 16749699 BA2
- 3 16711680 BA3a
- 4 3368703 BA3b
- 5 1376196 BA4a
- 6 13382655 BA4p
- 7 10036737 BA6
- 8 2490521 BA44
- 9 39283 BA45
- 10 3993 V1
- 11 8508928 V2
- 12 10027163 MT
- Mapping unhit to unknown
- Found 94758 unhit vertices
- Writing annot to /data/out/sub-02/label/rh.BA.thresh.annot
- mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub-02 rh white
- computing statistics for each annotation in ./rh.BA.annot.
- reading volume /data/out/sub-02/mri/wm.mgz...
- reading input surface /data/out/sub-02/surf/rh.white...
- reading input pial surface /data/out/sub-02/surf/rh.pial...
- reading input white surface /data/out/sub-02/surf/rh.white...
- INFO: assuming MGZ format for volumes.
- reading colortable from annotation file...
- colortable with 14 entries read (originally /opt/freesurfer/average/colortable_BA.txt)
- Saving annotation colortable ./BA.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
- 676 366 1192 2.281 0.556 0.144 0.070 13 1.6 BA1
- 1982 1321 2689 1.841 0.673 0.100 0.024 13 2.0 BA2
- 1063 680 832 1.425 0.444 0.131 0.040 10 1.9 BA3a
- 1780 1163 1988 1.494 0.533 0.120 0.039 24 3.2 BA3b
- 1432 830 2648 2.657 0.573 0.112 0.049 19 3.2 BA4a
- 1282 820 1706 2.058 0.510 0.112 0.059 24 4.0 BA4p
- 6729 4624 13349 2.400 0.636 0.133 0.103 127 41.3 BA6
- 3580 2446 5435 2.022 0.573 0.123 0.034 38 5.0 BA44
- 3352 2343 5867 2.014 0.743 0.140 0.046 45 6.3 BA45
- 3068 2064 3441 1.574 0.452 0.151 0.060 55 7.7 V1
- 7563 4992 10661 1.975 0.581 0.153 0.051 118 15.8 V2
- 1825 1206 3296 2.631 0.657 0.133 0.037 21 2.6 MT
- 625 435 1610 2.581 1.089 0.154 0.083 12 2.8 perirhinal
- mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub-02 rh white
- computing statistics for each annotation in ./rh.BA.thresh.annot.
- reading volume /data/out/sub-02/mri/wm.mgz...
- reading input surface /data/out/sub-02/surf/rh.white...
- reading input pial surface /data/out/sub-02/surf/rh.pial...
- reading input white surface /data/out/sub-02/surf/rh.white...
- INFO: assuming MGZ format for volumes.
- reading colortable from annotation file...
- colortable with 14 entries read (originally /opt/freesurfer/average/colortable_BA.txt)
- Saving annotation colortable ./BA.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
- 455 241 764 2.235 0.538 0.143 0.079 9 1.2 BA1
- 1152 777 1568 1.798 0.636 0.089 0.023 6 0.9 BA2
- 917 581 644 1.388 0.376 0.127 0.032 7 1.3 BA3a
- 1426 966 1415 1.365 0.397 0.110 0.027 11 1.7 BA3b
- 919 516 1716 2.754 0.529 0.119 0.089 29 4.3 BA4a
- 1066 708 1467 2.084 0.486 0.108 0.033 7 1.5 BA4p
- 4376 2957 8497 2.387 0.650 0.132 0.127 82 35.0 BA6
- 959 690 1858 2.185 0.535 0.155 0.053 18 2.1 BA44
- 878 649 2089 2.405 0.763 0.157 0.054 15 1.9 BA45
- 2933 1971 3205 1.562 0.435 0.147 0.058 50 7.1 V1
- 3938 2587 5225 1.855 0.536 0.159 0.057 72 9.4 V2
- 305 204 557 2.393 0.400 0.128 0.031 3 0.5 MT
- /data/out/sub-02/label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label lh Sat Jan 14 15:09:37 UTC 2017
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub-02 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
- painting output onto subject sub-02.
- processing subject lh.EC_average...
- reading output surface /data/out/sub-02/surf/lh.sphere.reg...
- eroding label 1 times before writing
- thresholding label stat at 0.400 before writing
- only 1 subject - copying statistics...
- writing label with 761 points to lh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub-02 lh white
- limiting computations to label ./lh.entorhinal_exvivo.label.
- reading volume /data/out/sub-02/mri/wm.mgz...
- reading input surface /data/out/sub-02/surf/lh.white...
- reading input pial surface /data/out/sub-02/surf/lh.pial...
- reading input white surface /data/out/sub-02/surf/lh.white...
- INFO: assuming MGZ format for volumes.
- 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
- 267 179 994 3.274 0.789 0.120 0.029 2 0.4 ./lh.entorhinal_exvivo.label
- #--------------------------------------------
- #@# Ex-vivo Entorhinal Cortex Label rh Sat Jan 14 15:09:47 UTC 2017
- mris_spherical_average -erode 1 -orig white -t 0.4 -o sub-02 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label
- painting output onto subject sub-02.
- processing subject rh.EC_average...
- reading output surface /data/out/sub-02/surf/rh.sphere.reg...
- eroding label 1 times before writing
- thresholding label stat at 0.400 before writing
- only 1 subject - copying statistics...
- writing label with 763 points to rh.entorhinal_exvivo.label...
- mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub-02 rh white
- limiting computations to label ./rh.entorhinal_exvivo.label.
- reading volume /data/out/sub-02/mri/wm.mgz...
- reading input surface /data/out/sub-02/surf/rh.white...
- reading input pial surface /data/out/sub-02/surf/rh.pial...
- reading input white surface /data/out/sub-02/surf/rh.white...
- INFO: assuming MGZ format for volumes.
- 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
- 243 156 758 2.998 0.936 0.144 0.127 5 1.9 ./rh.entorhinal_exvivo.label
- #------------------------------------------
- Started at Sat Jan 14 08:35:50 UTC 2017
- Ended at Sat Jan 14 15:09:56 UTC 2017
- #@#%# recon-all-run-time-hours 6.568
- recon-all -s sub-02 finished without error at Sat Jan 14 15:09:56 UTC 2017
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