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