Mon Jan 15 18:04:07 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205 /usr/local/freesurfer-6.0.0//bin/recon-all -s icbm-205 -all subjid icbm-205 setenv SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Actual FREESURFER_HOME /usr/local/freesurfer-6.0.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux kaplan 3.13.0-137-generic #186-Ubuntu SMP Mon Dec 4 19:09:19 UTC 2017 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 1024 memorylocked 64 kbytes maxproc 128142 maxlocks unlimited maxsignal 128142 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 16424584 12028520 4396064 27312 208148 10418172 -/+ buffers/cache: 1402200 15022384 Swap: 7812092 14956 7797136 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:07-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:08-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:09-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:09-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:09-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:09-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:09-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:09-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:09-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:09-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/01/15-23:04:09-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: trisanna Machine: kaplan Platform: Linux PlatformVersion: 3.13.0-137-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer-6.0.0//average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer-6.0.0//average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# MotionCor Mon Jan 15 18:04:09 EST 2018 Found 1 runs /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/orig/001.mgz /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/rawavg.mgz /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205 mri_convert /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/rawavg.mgz /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/orig.mgz --conform mri_convert.bin /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/rawavg.mgz /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/orig.mgz... mri_add_xform_to_header -c /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/transforms/talairach.xfm /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/orig.mgz /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Jan 15 18:04:17 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri /usr/local/freesurfer-6.0.0//bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux kaplan 3.13.0-137-generic #186-Ubuntu SMP Mon Dec 4 19:09:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Mon Jan 15 18:04:17 EST 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.13296 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.13296/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.13296/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.13296/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Jan 15 18:04:19 EST 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.13296/nu0.mnc ./tmp.mri_nu_correct.mni.13296/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.13296/0/ -iterations 1000 -distance 50 [trisanna@kaplan:/data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/] [2018-01-15 18:04:19] running: /usr/local/freesurfer-6.0.0//mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.13296/0/ ./tmp.mri_nu_correct.mni.13296/nu0.mnc ./tmp.mri_nu_correct.mni.13296/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 32 CV of field change: 0.000986518 mri_convert ./tmp.mri_nu_correct.mni.13296/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.13296/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.13296/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Mon Jan 15 18:05:12 EST 2018 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Mon Jan 15 18:05:12 EST 2018 Ended at Mon Jan 15 18:05:57 EST 2018 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Jan 15 18:05:59 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5433, pval=0.2115 >= threshold=0.0050) awk -f /usr/local/freesurfer-6.0.0//bin/extract_talairach_avi_QA.awk /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/transforms/talairach_avi.log tal_QC_AZS /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/transforms/talairach_avi.log TalAviQA: 0.97691 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Mon Jan 15 18:05:59 EST 2018 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri /usr/local/freesurfer-6.0.0//bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux kaplan 3.13.0-137-generic #186-Ubuntu SMP Mon Dec 4 19:09:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Mon Jan 15 18:05:59 EST 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.13993 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.13993/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.13993/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.13993/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Jan 15 18:06:01 EST 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.13993/nu0.mnc ./tmp.mri_nu_correct.mni.13993/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.13993/0/ [trisanna@kaplan:/data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/] [2018-01-15 18:06:01] running: /usr/local/freesurfer-6.0.0//mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.13993/0/ ./tmp.mri_nu_correct.mni.13993/nu0.mnc ./tmp.mri_nu_correct.mni.13993/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 21 CV of field change: 0.000989423 -------------------------------------------------------- Iteration 2 Mon Jan 15 18:06:34 EST 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.13993/nu1.mnc ./tmp.mri_nu_correct.mni.13993/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.13993/1/ [trisanna@kaplan:/data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/] [2018-01-15 18:06:35] running: /usr/local/freesurfer-6.0.0//mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.13993/1/ ./tmp.mri_nu_correct.mni.13993/nu1.mnc ./tmp.mri_nu_correct.mni.13993/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 11 CV of field change: 0.000960273 mri_binarize --i ./tmp.mri_nu_correct.mni.13993/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.13993/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.13993/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.13993/ones.mgz sysname Linux hostname kaplan machine x86_64 user trisanna input ./tmp.mri_nu_correct.mni.13993/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.13993/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.13993/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.13993/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13993/input.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.13993/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.13993/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13993/input.mean.dat sysname Linux hostname kaplan machine x86_64 user trisanna UseRobust 0 Loading ./tmp.mri_nu_correct.mni.13993/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.13993/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.13993/ones.mgz --i ./tmp.mri_nu_correct.mni.13993/nu2.mnc --sum ./tmp.mri_nu_correct.mni.13993/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13993/output.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.13993/ones.mgz --i ./tmp.mri_nu_correct.mni.13993/nu2.mnc --sum ./tmp.mri_nu_correct.mni.13993/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13993/output.mean.dat sysname Linux hostname kaplan machine x86_64 user trisanna UseRobust 0 Loading ./tmp.mri_nu_correct.mni.13993/ones.mgz Loading ./tmp.mri_nu_correct.mni.13993/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.13993/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.13993/nu2.mnc ./tmp.mri_nu_correct.mni.13993/nu2.mnc mul .95061789652705117556 Saving result to './tmp.mri_nu_correct.mni.13993/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.13993/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.13993/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.13993/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 9 seconds. mapping (13, 170) to ( 3, 110) Mon Jan 15 18:07:36 EST 2018 mri_nu_correct.mni done mri_add_xform_to_header -c /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Mon Jan 15 18:07:38 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 0.96924 0.01413 0.00081 -0.22357; -0.04790 0.99002 0.04953 -1.62454; 0.00150 0.00832 0.95359 -0.50464; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 15 Starting OpenSpline(): npoints = 15 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 81 (81), valley at 29 (29) csf peak at 41, setting threshold to 67 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 82 (82), valley at 30 (30) csf peak at 42, setting threshold to 68 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 35 seconds. #-------------------------------------------- #@# Skull Stripping Mon Jan 15 18:10:14 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri mri_em_register -rusage /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /usr/local/freesurfer-6.0.0//average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer-6.0.0//average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (41, 50, 25) --> (213, 222, 232) using (98, 107, 129) as brain centroid... mean wm in atlas = 108, using box (77,86,103) --> (119, 128,154) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 108 +- 5.9 after smoothing, mri peak at 108, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.561 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.420510 @ (-9.091, -27.273, -9.091) max log p = -4.221228 @ (4.545, 4.545, -13.636) max log p = -4.115177 @ (2.273, 2.273, 6.818) max log p = -4.100500 @ (-1.136, 1.136, -3.409) max log p = -4.083338 @ (-0.568, -0.568, 1.705) max log p = -4.083338 @ (0.000, 0.000, 0.000) Found translation: (-4.0, -19.9, -17.6): log p = -4.083 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.083, old_max_log_p =-4.083 (thresh=-4.1) 1.00000 0.00000 0.00000 -3.97727; 0.00000 1.00000 0.00000 -19.88637; 0.00000 0.00000 1.00000 -17.61364; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.036, old_max_log_p =-4.083 (thresh=-4.1) 0.96214 0.02912 0.00214 -2.34201; -0.03693 1.05397 -0.06659 -11.37898; -0.00435 0.06644 0.97915 -24.89919; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.033, old_max_log_p =-4.036 (thresh=-4.0) 0.97809 0.06131 -0.03364 -4.86619; -0.06822 1.04982 -0.09757 -4.63850; 0.02544 0.09988 0.95769 -31.22150; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.009, old_max_log_p =-4.033 (thresh=-4.0) 0.97925 0.06100 -0.03383 -4.47213; -0.06795 1.04863 -0.09720 -3.60560; 0.02573 0.09938 0.95546 -30.40921; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.005, old_max_log_p =-4.009 (thresh=-4.0) 0.97810 0.06093 -0.03379 -4.32019; -0.06811 1.05109 -0.09743 -3.94727; 0.02570 0.09926 0.95435 -30.24358; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3243 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.97810 0.06093 -0.03379 -4.32019; -0.06811 1.05109 -0.09743 -3.94727; 0.02570 0.09926 0.95435 -30.24358; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 0.97810 0.06093 -0.03379 -4.32019; -0.06811 1.05109 -0.09743 -3.94727; 0.02570 0.09926 0.95435 -30.24358; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.97810 0.06093 -0.03379 -4.32019; -0.06811 1.05109 -0.09743 -3.94727; 0.02570 0.09926 0.95435 -30.24358; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.005 (old=-4.561) transform before final EM align: 0.97810 0.06093 -0.03379 -4.32019; -0.06811 1.05109 -0.09743 -3.94727; 0.02570 0.09926 0.95435 -30.24358; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364799 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.97810 0.06093 -0.03379 -4.32019; -0.06811 1.05109 -0.09743 -3.94727; 0.02570 0.09926 0.95435 -30.24358; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 0.97810 0.06093 -0.03379 -4.32019; -0.06811 1.05109 -0.09743 -3.94727; 0.02570 0.09926 0.95435 -30.24358; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = 4.4 tol 0.000000 final transform: 0.97810 0.06093 -0.03379 -4.32019; -0.06811 1.05109 -0.09743 -3.94727; 0.02570 0.09926 0.95435 -30.24358; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 850.890466 mri_em_register stimesec 0.755781 mri_em_register ru_maxrss 609836 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157313 mri_em_register ru_majflt 6 mri_em_register ru_nswap 0 mri_em_register ru_inblock 150296 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 26 mri_em_register ru_nivcsw 81418 registration took 14 minutes and 12 seconds. mri_watershed -rusage /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/touch/rusage.mri_watershed.dat -T1 -brain_atlas /usr/local/freesurfer-6.0.0//average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=128 y=134 z=131 r=74 first estimation of the main basin volume: 1699016 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=108, y=108, z=95, Imax=255 CSF=12, 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=428000540 voxels, voxel volume =1.000 = 428000540 mmm3 = 428000.544 cm3 done. PostAnalyze...Basin Prior 2 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=138, z=122, r=10053 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=5, CSF_MAX=25 , nb = 42796 RIGHT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=15 , nb = -1031589565 LEFT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=14 , nb = -1045254526 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=25 , nb = 1065245083 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=23 , nb = 1077537490 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=46 , nb = 1075478778 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 25, 37, 55, 82 after analyzing : 25, 49, 55, 57 RIGHT_CER before analyzing : 15, 29, 59, 82 after analyzing : 15, 49, 59, 57 LEFT_CER before analyzing : 14, 27, 60, 84 after analyzing : 14, 49, 60, 57 RIGHT_BRAIN before analyzing : 25, 35, 54, 81 after analyzing : 25, 47, 54, 55 LEFT_BRAIN before analyzing : 23, 33, 54, 82 after analyzing : 23, 47, 54, 55 OTHER before analyzing : 46, 77, 83, 91 after analyzing : 46, 81, 83, 83 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...71 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.009 curvature mean = 76.336, std = 7.290 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.63, sigma = 5.02 after rotation: sse = 3.63, sigma = 5.02 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.84, its var is 5.08 before Erosion-Dilatation 0.93% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...56 iterations mri_strip_skull: done peeling brain Brain Size = 2209159 voxels, voxel volume = 1.000 mm3 = 2209159 mmm3 = 2209.159 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 27.599967 mri_watershed stimesec 0.271971 mri_watershed ru_maxrss 837936 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 214783 mri_watershed ru_majflt 9 mri_watershed ru_nswap 0 mri_watershed ru_inblock 9952 mri_watershed ru_oublock 3320 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 52 mri_watershed ru_nivcsw 2350 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Mon Jan 15 18:24:55 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri mri_em_register -rusage /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer-6.0.0//average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer-6.0.0//average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=18.0 skull bounding box = (54, 62, 38) --> (200, 210, 220) using (103, 111, 129) as brain centroid... mean wm in atlas = 107, using box (85,93,107) --> (120, 129,151) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 107 +- 5.4 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.313 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.134126 @ (-9.091, -9.091, -9.091) max log p = -3.901116 @ (4.545, -4.545, -4.545) max log p = -3.847772 @ (2.273, -2.273, -2.273) max log p = -3.773204 @ (-1.136, -1.136, -3.409) max log p = -3.773204 @ (0.000, 0.000, 0.000) max log p = -3.761414 @ (-0.852, -0.284, 0.852) Found translation: (-4.3, -17.3, -18.5): log p = -3.761 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.692, old_max_log_p =-3.761 (thresh=-3.8) 1.00000 0.00000 0.00000 -4.26137; 0.00000 0.91375 0.00000 -5.54611; 0.00000 0.00000 0.92500 -9.17264; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.676, old_max_log_p =-3.692 (thresh=-3.7) 1.00000 0.00000 0.00000 -4.26137; 0.00000 0.98228 0.00000 -14.90883; 0.00000 0.00000 0.92500 -9.17264; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.676, old_max_log_p =-3.676 (thresh=-3.7) 1.00000 0.00000 0.00000 -4.26137; 0.00000 0.98228 0.00000 -14.90883; 0.00000 0.00000 0.92500 -9.17264; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.582, old_max_log_p =-3.676 (thresh=-3.7) 0.96044 0.06170 -0.00381 -5.16186; -0.06410 0.95640 -0.08993 8.16702; -0.00210 0.09679 0.93789 -23.71829; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.577, old_max_log_p =-3.582 (thresh=-3.6) 0.94055 0.05420 -0.06392 7.75261; -0.06289 0.93847 -0.08824 8.37558; 0.06072 0.10062 0.93563 -32.06835; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.577, old_max_log_p =-3.577 (thresh=-3.6) 0.94055 0.05420 -0.06392 7.75261; -0.06289 0.93847 -0.08824 8.37558; 0.06072 0.10062 0.93563 -32.06835; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.561, old_max_log_p =-3.577 (thresh=-3.6) 0.93937 0.06257 -0.05685 5.85289; -0.06921 0.94015 -0.06491 6.53076; 0.05460 0.07716 0.93689 -27.74172; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.553, old_max_log_p =-3.561 (thresh=-3.6) 0.93937 0.06257 -0.05685 5.85289; -0.06966 0.93949 -0.07256 7.15284; 0.05384 0.08457 0.93304 -28.19084; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.550, old_max_log_p =-3.553 (thresh=-3.5) 0.93937 0.06257 -0.05685 5.85289; -0.06966 0.93949 -0.07256 7.15284; 0.05378 0.08447 0.93194 -28.03424; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.93937 0.06257 -0.05685 5.85289; -0.06966 0.93949 -0.07256 7.15284; 0.05378 0.08447 0.93194 -28.03424; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.93937 0.06257 -0.05685 5.85289; -0.06966 0.93949 -0.07256 7.15284; 0.05378 0.08447 0.93194 -28.03424; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.93937 0.06257 -0.05685 5.85289; -0.06966 0.93949 -0.07256 7.15284; 0.05378 0.08447 0.93194 -28.03424; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.550 (old=-4.313) transform before final EM align: 0.93937 0.06257 -0.05685 5.85289; -0.06966 0.93949 -0.07256 7.15284; 0.05378 0.08447 0.93194 -28.03424; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.93937 0.06257 -0.05685 5.85289; -0.06966 0.93949 -0.07256 7.15284; 0.05378 0.08447 0.93194 -28.03424; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.93937 0.06257 -0.05685 5.85289; -0.06966 0.93949 -0.07256 7.15284; 0.05378 0.08447 0.93194 -28.03424; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 013: -log(p) = 4.0 tol 0.000000 final transform: 0.93937 0.06257 -0.05685 5.85289; -0.06966 0.93949 -0.07256 7.15284; 0.05378 0.08447 0.93194 -28.03424; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1273.730813 mri_em_register stimesec 1.323438 mri_em_register ru_maxrss 601008 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 159069 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 140160 mri_em_register ru_oublock 16 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 85 mri_em_register ru_nivcsw 149301 registration took 21 minutes and 16 seconds. #-------------------------------------- #@# CA Normalize Mon Jan 15 18:46:10 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer-6.0.0//average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer-6.0.0//average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=17.0 skull bounding box = (54, 62, 38) --> (201, 210, 220) using (103, 111, 129) as brain centroid... mean wm in atlas = 107, using box (85,93,107) --> (121, 129,151) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 107 +- 5.4 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 using 246344 sample points... INFO: compute sample coordinates transform 0.93937 0.06257 -0.05685 5.85289; -0.06966 0.93949 -0.07256 7.15284; 0.05378 0.08447 0.93194 -28.03424; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (120, 67, 36) --> (197, 198, 217) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 6459 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (57, 65, 40) --> (131, 194, 219) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 9 of 6471 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (123, 155, 57) --> (173, 202, 116) Left_Cerebellum_White_Matter: limiting intensities to 102.0 --> 132.0 1 of 173 (0.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (74, 155, 57) --> (123, 199, 119) Right_Cerebellum_White_Matter: limiting intensities to 108.0 --> 132.0 1 of 135 (0.7%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (106, 148, 92) --> (143, 222, 130) Brain_Stem: limiting intensities to 91.0 --> 132.0 0 of 362 (0.0%) samples deleted using 13600 total control points for intensity normalization... bias field = 0.957 +- 0.067 96 of 13589 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (120, 67, 36) --> (197, 198, 217) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 7093 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (57, 65, 40) --> (131, 194, 219) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 6 of 7020 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (123, 155, 57) --> (173, 202, 116) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 32 of 302 (10.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (74, 155, 57) --> (123, 199, 119) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 24 of 218 (11.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (106, 148, 92) --> (143, 222, 130) Brain_Stem: limiting intensities to 88.0 --> 132.0 144 of 581 (24.8%) samples deleted using 15214 total control points for intensity normalization... bias field = 1.044 +- 0.058 20 of 14886 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (120, 67, 36) --> (197, 198, 217) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 8 of 7211 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (57, 65, 40) --> (131, 194, 219) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 7070 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (123, 155, 57) --> (173, 202, 116) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 148 of 371 (39.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (74, 155, 57) --> (123, 199, 119) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 78 of 254 (30.7%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (106, 148, 92) --> (143, 222, 130) Brain_Stem: limiting intensities to 88.0 --> 132.0 409 of 669 (61.1%) samples deleted using 15575 total control points for intensity normalization... bias field = 1.037 +- 0.045 6 of 14795 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 35 seconds. #-------------------------------------- #@# CA Reg Mon Jan 15 18:47:45 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri mri_ca_register -rusage /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer-6.0.0//average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer-6.0.0//average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 0.84 (predicted orig area = 9.6) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.889, neg=0, invalid=762 0001: dt=337.038640, rms=0.760 (14.456%), neg=0, invalid=762 0002: dt=203.414013, rms=0.736 (3.157%), neg=0, invalid=762 0003: dt=443.904000, rms=0.721 (2.075%), neg=0, invalid=762 0004: dt=129.472000, rms=0.714 (0.935%), neg=0, invalid=762 0005: dt=887.808000, rms=0.706 (1.113%), neg=0, invalid=762 0006: dt=178.871795, rms=0.701 (0.784%), neg=0, invalid=762 0007: dt=129.472000, rms=0.700 (0.093%), neg=0, invalid=762 0008: dt=129.472000, rms=0.699 (0.109%), neg=0, invalid=762 0009: dt=129.472000, rms=0.698 (0.185%), neg=0, invalid=762 0010: dt=129.472000, rms=0.696 (0.265%), neg=0, invalid=762 0011: dt=129.472000, rms=0.694 (0.286%), neg=0, invalid=762 0012: dt=129.472000, rms=0.692 (0.281%), neg=0, invalid=762 0013: dt=129.472000, rms=0.690 (0.263%), neg=0, invalid=762 0014: dt=129.472000, rms=0.689 (0.250%), neg=0, invalid=762 0015: dt=129.472000, rms=0.687 (0.227%), neg=0, invalid=762 0016: dt=129.472000, rms=0.686 (0.206%), neg=0, invalid=762 0017: dt=129.472000, rms=0.684 (0.208%), neg=0, invalid=762 0018: dt=129.472000, rms=0.683 (0.211%), neg=0, invalid=762 0019: dt=129.472000, rms=0.681 (0.207%), neg=0, invalid=762 0020: dt=129.472000, rms=0.680 (0.190%), neg=0, invalid=762 0021: dt=129.472000, rms=0.679 (0.177%), neg=0, invalid=762 0022: dt=129.472000, rms=0.678 (0.178%), neg=0, invalid=762 0023: dt=129.472000, rms=0.677 (0.179%), neg=0, invalid=762 0024: dt=129.472000, rms=0.675 (0.169%), neg=0, invalid=762 0025: dt=129.472000, rms=0.674 (0.165%), neg=0, invalid=762 0026: dt=129.472000, rms=0.673 (0.137%), neg=0, invalid=762 0027: dt=129.472000, rms=0.673 (0.128%), neg=0, invalid=762 0028: dt=129.472000, rms=0.672 (0.115%), neg=0, invalid=762 0029: dt=129.472000, rms=0.671 (0.125%), neg=0, invalid=762 0030: dt=129.472000, rms=0.670 (0.131%), neg=0, invalid=762 0031: dt=129.472000, rms=0.669 (0.123%), neg=0, invalid=762 0032: dt=129.472000, rms=0.669 (0.094%), neg=0, invalid=762 0033: dt=295.936000, rms=0.668 (0.009%), neg=0, invalid=762 0034: dt=295.936000, rms=0.668 (0.072%), neg=0, invalid=762 0035: dt=295.936000, rms=0.668 (-0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.669, neg=0, invalid=762 0036: dt=129.472000, rms=0.667 (0.246%), neg=0, invalid=762 0037: dt=443.904000, rms=0.666 (0.083%), neg=0, invalid=762 0038: dt=443.904000, rms=0.665 (0.140%), neg=0, invalid=762 0039: dt=443.904000, rms=0.665 (-0.047%), neg=0, invalid=762 0040: dt=32.368000, rms=0.665 (0.006%), neg=0, invalid=762 0041: dt=32.368000, rms=0.665 (0.005%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.677, neg=0, invalid=762 0042: dt=100.731830, rms=0.673 (0.637%), neg=0, invalid=762 0043: dt=187.977143, rms=0.661 (1.709%), neg=0, invalid=762 0044: dt=36.288000, rms=0.658 (0.581%), neg=0, invalid=762 0045: dt=72.911392, rms=0.656 (0.163%), neg=0, invalid=762 0046: dt=72.911392, rms=0.653 (0.542%), neg=0, invalid=762 0047: dt=72.911392, rms=0.648 (0.691%), neg=0, invalid=762 0048: dt=72.911392, rms=0.644 (0.701%), neg=0, invalid=762 0049: dt=72.911392, rms=0.639 (0.766%), neg=0, invalid=762 0050: dt=72.911392, rms=0.633 (0.877%), neg=0, invalid=762 0051: dt=72.911392, rms=0.629 (0.729%), neg=0, invalid=762 0052: dt=72.911392, rms=0.626 (0.483%), neg=0, invalid=762 0053: dt=72.911392, rms=0.623 (0.404%), neg=0, invalid=762 0054: dt=72.911392, rms=0.622 (0.205%), neg=0, invalid=762 0055: dt=72.911392, rms=0.621 (0.101%), neg=0, invalid=762 0056: dt=72.911392, rms=0.621 (-0.020%), neg=0, invalid=762 0057: dt=0.000000, rms=0.621 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.622, neg=0, invalid=762 0058: dt=120.216216, rms=0.619 (0.428%), neg=0, invalid=762 0059: dt=31.104000, rms=0.619 (0.004%), neg=0, invalid=762 0060: dt=31.104000, rms=0.619 (0.024%), neg=0, invalid=762 0061: dt=31.104000, rms=0.619 (0.011%), neg=0, invalid=762 0062: dt=31.104000, rms=0.619 (0.013%), neg=0, invalid=762 0063: dt=31.104000, rms=0.619 (0.035%), neg=0, invalid=762 0064: dt=31.104000, rms=0.618 (0.048%), neg=0, invalid=762 0065: dt=31.104000, rms=0.618 (0.038%), neg=0, invalid=762 0066: dt=248.832000, rms=0.618 (0.067%), neg=0, invalid=762 0067: dt=103.680000, rms=0.617 (0.085%), neg=0, invalid=762 0068: dt=31.104000, rms=0.617 (0.011%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.648, neg=0, invalid=762 0069: dt=9.600000, rms=0.646 (0.194%), neg=0, invalid=762 0070: dt=8.000000, rms=0.646 (0.041%), neg=0, invalid=762 0071: dt=8.000000, rms=0.646 (0.033%), neg=0, invalid=762 0072: dt=8.000000, rms=0.646 (-0.016%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.646, neg=0, invalid=762 0073: dt=4.800000, rms=0.646 (0.088%), neg=0, invalid=762 0074: dt=2.800000, rms=0.646 (0.006%), neg=0, invalid=762 0075: dt=2.800000, rms=0.646 (0.001%), neg=0, invalid=762 0076: dt=2.800000, rms=0.646 (-0.005%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.713, neg=0, invalid=762 0077: dt=6.540146, rms=0.701 (1.632%), neg=0, invalid=762 0078: dt=5.904762, rms=0.700 (0.186%), neg=0, invalid=762 0079: dt=5.904762, rms=0.700 (0.019%), neg=0, invalid=762 0080: dt=5.904762, rms=0.700 (-0.192%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.700, neg=0, invalid=762 0081: dt=0.000000, rms=0.700 (0.065%), neg=0, invalid=762 0082: dt=0.000000, rms=0.700 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.765, neg=0, invalid=762 0083: dt=0.000000, rms=0.765 (0.054%), neg=0, invalid=762 0084: dt=0.000000, rms=0.765 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.765, neg=0, invalid=762 0085: dt=0.112000, rms=0.765 (0.058%), neg=0, invalid=762 0086: dt=0.048000, rms=0.765 (0.001%), neg=0, invalid=762 0087: dt=0.048000, rms=0.765 (0.000%), neg=0, invalid=762 0088: dt=0.048000, rms=0.765 (-0.003%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.656, neg=0, invalid=762 0089: dt=0.691099, rms=0.644 (1.957%), neg=0, invalid=762 0090: dt=0.064000, rms=0.643 (0.082%), neg=0, invalid=762 0091: dt=0.064000, rms=0.643 (-0.050%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.644, neg=0, invalid=762 0092: dt=0.024000, rms=0.643 (0.086%), neg=0, invalid=762 0093: dt=0.000000, rms=0.643 (-0.001%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.11731 (24) Left_Lateral_Ventricle (4): linear fit = 1.14 x + 0.0 (2854 voxels, overlap=0.712) Left_Lateral_Ventricle (4): linear fit = 1.14 x + 0.0 (2854 voxels, peak = 23), gca=22.9 gca peak = 0.15565 (16) mri peak = 0.15951 (22) Right_Lateral_Ventricle (43): linear fit = 1.28 x + 0.0 (3135 voxels, overlap=0.487) Right_Lateral_Ventricle (43): linear fit = 1.28 x + 0.0 (3135 voxels, peak = 21), gca=20.6 gca peak = 0.26829 (96) mri peak = 0.08577 (92) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (1617 voxels, overlap=0.978) Right_Pallidum (52): linear fit = 0.95 x + 0.0 (1617 voxels, peak = 92), gca=91.7 gca peak = 0.20183 (93) mri peak = 0.09596 (93) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (1367 voxels, overlap=0.998) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (1367 voxels, peak = 91), gca=90.7 gca peak = 0.21683 (55) mri peak = 0.08673 (72) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (1889 voxels, overlap=0.012) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (1889 voxels, peak = 70), gca=69.6 gca peak = 0.30730 (58) mri peak = 0.04598 (74) Left_Hippocampus (17): linear fit = 1.28 x + 0.0 (1945 voxels, overlap=0.028) Left_Hippocampus (17): linear fit = 1.28 x + 0.0 (1945 voxels, peak = 75), gca=74.5 gca peak = 0.11430 (101) mri peak = 0.09911 (103) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (120053 voxels, overlap=0.748) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (120053 voxels, peak = 104), gca=103.5 gca peak = 0.12076 (102) mri peak = 0.09336 (105) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (121095 voxels, overlap=0.719) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (121095 voxels, peak = 106), gca=105.6 gca peak = 0.14995 (59) mri peak = 0.03308 (80) Left_Cerebral_Cortex (3): linear fit = 1.41 x + 0.0 (63000 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.41 x + 0.0 (63000 voxels, peak = 83), gca=83.5 gca peak = 0.15082 (58) mri peak = 0.03411 (75) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (61235 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (61235 voxels, peak = 78), gca=78.0 gca peak = 0.14161 (67) mri peak = 0.17095 (76) Right_Caudate (50): linear fit = 1.13 x + 0.0 (1444 voxels, overlap=0.100) Right_Caudate (50): linear fit = 1.13 x + 0.0 (1444 voxels, peak = 76), gca=76.0 gca peak = 0.15243 (71) mri peak = 0.10506 (84) Left_Caudate (11): linear fit = 1.11 x + 0.0 (1837 voxels, overlap=0.368) Left_Caudate (11): linear fit = 1.11 x + 0.0 (1837 voxels, peak = 78), gca=78.5 gca peak = 0.13336 (57) mri peak = 0.03966 (71) Left_Cerebellum_Cortex (8): linear fit = 1.29 x + 0.0 (39104 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.29 x + 0.0 (39104 voxels, peak = 74), gca=73.8 gca peak = 0.13252 (56) mri peak = 0.03966 (68) Right_Cerebellum_Cortex (47): linear fit = 1.24 x + 0.0 (42333 voxels, overlap=0.093) Right_Cerebellum_Cortex (47): linear fit = 1.24 x + 0.0 (42333 voxels, peak = 69), gca=69.2 gca peak = 0.18181 (84) mri peak = 0.04196 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (16485 voxels, overlap=0.993) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (16485 voxels, peak = 89), gca=88.6 gca peak = 0.20573 (83) mri peak = 0.04696 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (14289 voxels, overlap=0.830) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (14289 voxels, peak = 88), gca=87.6 gca peak = 0.21969 (57) mri peak = 0.07566 (75) Left_Amygdala (18): linear fit = 1.33 x + 0.0 (804 voxels, overlap=0.057) Left_Amygdala (18): linear fit = 1.33 x + 0.0 (804 voxels, peak = 76), gca=75.5 gca peak = 0.39313 (56) mri peak = 0.11929 (74) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (963 voxels, overlap=0.032) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (963 voxels, peak = 73), gca=72.5 gca peak = 0.14181 (85) mri peak = 0.06809 (89) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (8074 voxels, overlap=0.909) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (8074 voxels, peak = 88), gca=88.0 gca peak = 0.11978 (83) mri peak = 0.07701 (90) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (7230 voxels, overlap=0.852) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (7230 voxels, peak = 88), gca=87.6 gca peak = 0.13399 (79) mri peak = 0.10464 (88) Left_Putamen (12): linear fit = 1.12 x + 0.0 (3994 voxels, overlap=0.157) Left_Putamen (12): linear fit = 1.12 x + 0.0 (3994 voxels, peak = 89), gca=88.9 gca peak = 0.14159 (79) mri peak = 0.11230 (87) Right_Putamen (51): linear fit = 1.11 x + 0.0 (4120 voxels, overlap=0.337) Right_Putamen (51): linear fit = 1.11 x + 0.0 (4120 voxels, peak = 87), gca=87.3 gca peak = 0.10025 (80) mri peak = 0.08783 (88) Brain_Stem (16): linear fit = 1.10 x + 0.0 (19225 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (19225 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.09735 (94) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (2503 voxels, overlap=0.553) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (2503 voxels, peak = 93), gca=93.3 gca peak = 0.12801 (89) mri peak = 0.10108 (94) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (2537 voxels, overlap=0.648) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (2537 voxels, peak = 93), gca=93.0 gca peak = 0.20494 (23) mri peak = 0.23009 (25) Third_Ventricle (14): linear fit = 1.02 x + 0.0 (62 voxels, overlap=0.851) Third_Ventricle (14): linear fit = 1.02 x + 0.0 (62 voxels, peak = 24), gca=23.6 gca peak = 0.15061 (21) mri peak = 0.10220 (28) Fourth_Ventricle (15): linear fit = 1.60 x + 0.0 (1075 voxels, overlap=0.196) Fourth_Ventricle (15): linear fit = 1.60 x + 0.0 (1075 voxels, peak = 33), gca=33.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Fourth_Ventricle = 0.15061 (21) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.32 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.15 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.655, neg=0, invalid=762 0094: dt=103.314588, rms=0.623 (4.818%), neg=0, invalid=762 0095: dt=129.472000, rms=0.620 (0.485%), neg=0, invalid=762 0096: dt=369.920000, rms=0.617 (0.516%), neg=0, invalid=762 0097: dt=517.888000, rms=0.613 (0.608%), neg=0, invalid=762 0098: dt=129.472000, rms=0.612 (0.165%), neg=0, invalid=762 0099: dt=295.936000, rms=0.612 (0.060%), neg=0, invalid=762 0100: dt=517.888000, rms=0.610 (0.207%), neg=0, invalid=762 0101: dt=92.480000, rms=0.610 (0.136%), neg=0, invalid=762 0102: dt=1183.744000, rms=0.609 (0.131%), neg=0, invalid=762 0103: dt=369.920000, rms=0.607 (0.350%), neg=0, invalid=762 0104: dt=73.984000, rms=0.606 (0.068%), neg=0, invalid=762 0105: dt=8.092000, rms=0.606 (-0.003%), neg=0, invalid=762 0106: dt=8.092000, rms=0.606 (0.000%), neg=0, invalid=762 0107: dt=8.092000, rms=0.606 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.606, neg=0, invalid=762 0108: dt=443.904000, rms=0.602 (0.665%), neg=0, invalid=762 0109: dt=55.488000, rms=0.602 (0.042%), neg=0, invalid=762 0110: dt=55.488000, rms=0.602 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.603, neg=0, invalid=762 0111: dt=65.652324, rms=0.599 (0.538%), neg=0, invalid=762 0112: dt=414.720000, rms=0.584 (2.621%), neg=0, invalid=762 0113: dt=113.258427, rms=0.579 (0.786%), neg=0, invalid=762 0114: dt=140.108108, rms=0.574 (0.884%), neg=0, invalid=762 0115: dt=36.288000, rms=0.572 (0.273%), neg=0, invalid=762 0116: dt=124.416000, rms=0.571 (0.184%), neg=0, invalid=762 0117: dt=145.152000, rms=0.568 (0.536%), neg=0, invalid=762 0118: dt=36.288000, rms=0.567 (0.176%), neg=0, invalid=762 0119: dt=145.152000, rms=0.566 (0.195%), neg=0, invalid=762 0120: dt=145.152000, rms=0.564 (0.387%), neg=0, invalid=762 0121: dt=36.288000, rms=0.563 (0.162%), neg=0, invalid=762 0122: dt=145.152000, rms=0.562 (0.165%), neg=0, invalid=762 0123: dt=145.152000, rms=0.560 (0.307%), neg=0, invalid=762 0124: dt=36.288000, rms=0.560 (0.137%), neg=0, invalid=762 0125: dt=145.152000, rms=0.559 (0.140%), neg=0, invalid=762 0126: dt=145.152000, rms=0.557 (0.255%), neg=0, invalid=762 0127: dt=36.288000, rms=0.557 (0.118%), neg=0, invalid=762 0128: dt=145.152000, rms=0.556 (0.121%), neg=0, invalid=762 0129: dt=145.152000, rms=0.555 (0.210%), neg=0, invalid=762 0130: dt=36.288000, rms=0.554 (0.106%), neg=0, invalid=762 0131: dt=145.152000, rms=0.554 (0.107%), neg=0, invalid=762 0132: dt=145.152000, rms=0.553 (0.176%), neg=0, invalid=762 0133: dt=36.288000, rms=0.552 (0.100%), neg=0, invalid=762 0134: dt=145.152000, rms=0.552 (0.092%), neg=0, invalid=762 0135: dt=145.152000, rms=0.551 (0.157%), neg=0, invalid=762 0136: dt=36.288000, rms=0.550 (0.096%), neg=0, invalid=762 0137: dt=145.152000, rms=0.550 (0.074%), neg=0, invalid=762 0138: dt=145.152000, rms=0.549 (0.144%), neg=0, invalid=762 0139: dt=36.288000, rms=0.549 (0.076%), neg=0, invalid=762 0140: dt=145.152000, rms=0.548 (0.067%), neg=0, invalid=762 0141: dt=145.152000, rms=0.548 (0.126%), neg=0, invalid=762 0142: dt=36.288000, rms=0.547 (0.068%), neg=0, invalid=762 0143: dt=145.152000, rms=0.547 (0.055%), neg=0, invalid=762 0144: dt=145.152000, rms=0.546 (0.126%), neg=0, invalid=762 0145: dt=36.288000, rms=0.546 (0.057%), neg=0, invalid=762 0146: dt=145.152000, rms=0.546 (0.049%), neg=0, invalid=762 0147: dt=145.152000, rms=0.545 (0.128%), neg=0, invalid=762 0148: dt=145.152000, rms=0.544 (0.165%), neg=0, invalid=762 0149: dt=145.152000, rms=0.543 (0.201%), neg=0, invalid=762 0150: dt=145.152000, rms=0.541 (0.328%), neg=0, invalid=762 0151: dt=145.152000, rms=0.540 (0.266%), neg=0, invalid=762 0152: dt=145.152000, rms=0.538 (0.240%), neg=0, invalid=762 0153: dt=145.152000, rms=0.537 (0.316%), neg=0, invalid=762 0154: dt=145.152000, rms=0.536 (0.224%), neg=0, invalid=762 0155: dt=145.152000, rms=0.534 (0.197%), neg=0, invalid=762 0156: dt=145.152000, rms=0.533 (0.258%), neg=0, invalid=762 0157: dt=145.152000, rms=0.532 (0.150%), neg=0, invalid=762 0158: dt=145.152000, rms=0.532 (0.127%), neg=0, invalid=762 0159: dt=145.152000, rms=0.531 (0.184%), neg=0, invalid=762 0160: dt=145.152000, rms=0.530 (0.155%), neg=0, invalid=762 0161: dt=145.152000, rms=0.529 (0.136%), neg=0, invalid=762 0162: dt=145.152000, rms=0.528 (0.136%), neg=0, invalid=762 0163: dt=145.152000, rms=0.528 (0.105%), neg=0, invalid=762 0164: dt=145.152000, rms=0.527 (0.104%), neg=0, invalid=762 0165: dt=145.152000, rms=0.527 (0.117%), neg=0, invalid=762 0166: dt=145.152000, rms=0.526 (0.087%), neg=0, invalid=762 0167: dt=145.152000, rms=0.526 (0.068%), neg=0, invalid=762 0168: dt=145.152000, rms=0.525 (0.082%), neg=0, invalid=762 0169: dt=145.152000, rms=0.525 (0.079%), neg=0, invalid=762 0170: dt=145.152000, rms=0.525 (0.082%), neg=0, invalid=762 0171: dt=145.152000, rms=0.524 (0.069%), neg=0, invalid=762 0172: dt=145.152000, rms=0.524 (0.052%), neg=0, invalid=762 0173: dt=145.152000, rms=0.524 (0.060%), neg=0, invalid=762 0174: dt=145.152000, rms=0.523 (0.064%), neg=0, invalid=762 0175: dt=145.152000, rms=0.523 (0.077%), neg=0, invalid=762 0176: dt=145.152000, rms=0.523 (0.045%), neg=0, invalid=762 0177: dt=145.152000, rms=0.522 (0.040%), neg=0, invalid=762 0178: dt=145.152000, rms=0.522 (0.071%), neg=0, invalid=762 0179: dt=145.152000, rms=0.522 (0.040%), neg=0, invalid=762 0180: dt=145.152000, rms=0.522 (0.050%), neg=0, invalid=762 0181: dt=145.152000, rms=0.521 (0.050%), neg=0, invalid=762 0182: dt=145.152000, rms=0.521 (0.027%), neg=0, invalid=762 0183: dt=145.152000, rms=0.521 (0.052%), neg=0, invalid=762 0184: dt=145.152000, rms=0.521 (0.061%), neg=0, invalid=762 0185: dt=145.152000, rms=0.520 (0.024%), neg=0, invalid=762 0186: dt=145.152000, rms=0.520 (0.033%), neg=0, invalid=762 0187: dt=145.152000, rms=0.520 (0.062%), neg=0, invalid=762 0188: dt=145.152000, rms=0.520 (0.031%), neg=0, invalid=762 0189: dt=145.152000, rms=0.520 (0.021%), neg=0, invalid=762 0190: dt=145.152000, rms=0.520 (0.039%), neg=0, invalid=762 0191: dt=145.152000, rms=0.519 (0.027%), neg=0, invalid=762 0192: dt=145.152000, rms=0.519 (0.017%), neg=0, invalid=762 0193: dt=145.152000, rms=0.519 (0.038%), neg=0, invalid=762 0194: dt=145.152000, rms=0.519 (0.028%), neg=0, invalid=762 0195: dt=145.152000, rms=0.519 (0.013%), neg=0, invalid=762 0196: dt=145.152000, rms=0.519 (0.023%), neg=0, invalid=762 0197: dt=145.152000, rms=0.519 (0.036%), neg=0, invalid=762 0198: dt=145.152000, rms=0.518 (0.015%), neg=0, invalid=762 0199: dt=145.152000, rms=0.518 (0.025%), neg=0, invalid=762 0200: dt=145.152000, rms=0.518 (0.022%), neg=0, invalid=762 0201: dt=145.152000, rms=0.518 (0.005%), neg=0, invalid=762 0202: dt=145.152000, rms=0.518 (-0.012%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.518, neg=0, invalid=762 0203: dt=145.152000, rms=0.516 (0.566%), neg=0, invalid=762 0204: dt=36.288000, rms=0.515 (0.028%), neg=0, invalid=762 0205: dt=36.288000, rms=0.515 (0.013%), neg=0, invalid=762 0206: dt=18.144000, rms=0.515 (0.008%), neg=0, invalid=762 0207: dt=0.283500, rms=0.515 (0.000%), neg=0, invalid=762 0208: dt=0.141750, rms=0.515 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.529, neg=0, invalid=762 0209: dt=25.600000, rms=0.528 (0.211%), neg=0, invalid=762 0210: dt=85.478705, rms=0.526 (0.390%), neg=0, invalid=762 0211: dt=44.800000, rms=0.523 (0.625%), neg=0, invalid=762 0212: dt=179.200000, rms=0.517 (1.051%), neg=0, invalid=762 0213: dt=44.800000, rms=0.515 (0.359%), neg=0, invalid=762 0214: dt=38.400000, rms=0.514 (0.185%), neg=0, invalid=762 0215: dt=44.800000, rms=0.513 (0.198%), neg=0, invalid=762 0216: dt=44.800000, rms=0.512 (0.184%), neg=0, invalid=762 0217: dt=44.800000, rms=0.512 (0.132%), neg=0, invalid=762 0218: dt=44.800000, rms=0.511 (0.163%), neg=0, invalid=762 0219: dt=44.800000, rms=0.510 (0.132%), neg=0, invalid=762 0220: dt=44.800000, rms=0.509 (0.137%), neg=0, invalid=762 0221: dt=38.400000, rms=0.509 (0.118%), neg=0, invalid=762 0222: dt=44.800000, rms=0.508 (0.114%), neg=0, invalid=762 0223: dt=38.400000, rms=0.508 (0.092%), neg=0, invalid=762 0224: dt=38.400000, rms=0.507 (0.093%), neg=0, invalid=762 0225: dt=44.800000, rms=0.507 (0.094%), neg=0, invalid=762 0226: dt=38.400000, rms=0.506 (0.084%), neg=0, invalid=762 0227: dt=38.400000, rms=0.506 (0.080%), neg=0, invalid=762 0228: dt=38.400000, rms=0.506 (0.059%), neg=0, invalid=762 0229: dt=38.400000, rms=0.505 (0.081%), neg=0, invalid=762 0230: dt=38.400000, rms=0.505 (0.057%), neg=0, invalid=762 0231: dt=38.400000, rms=0.505 (0.070%), neg=0, invalid=762 0232: dt=32.000000, rms=0.504 (0.046%), neg=0, invalid=762 0233: dt=32.000000, rms=0.504 (0.066%), neg=0, invalid=762 0234: dt=32.000000, rms=0.504 (0.080%), neg=0, invalid=762 0235: dt=32.000000, rms=0.503 (0.049%), neg=0, invalid=762 0236: dt=32.000000, rms=0.503 (0.092%), neg=0, invalid=762 0237: dt=32.000000, rms=0.502 (0.113%), neg=0, invalid=762 0238: dt=32.000000, rms=0.502 (0.127%), neg=0, invalid=762 0239: dt=32.000000, rms=0.501 (0.150%), neg=0, invalid=762 0240: dt=32.000000, rms=0.500 (0.167%), neg=0, invalid=762 0241: dt=32.000000, rms=0.499 (0.163%), neg=0, invalid=762 0242: dt=32.000000, rms=0.499 (0.152%), neg=0, invalid=762 0243: dt=32.000000, rms=0.498 (0.040%), neg=0, invalid=762 0244: dt=32.000000, rms=0.498 (0.029%), neg=0, invalid=762 0245: dt=32.000000, rms=0.498 (0.043%), neg=0, invalid=762 0246: dt=32.000000, rms=0.498 (0.061%), neg=0, invalid=762 0247: dt=32.000000, rms=0.497 (0.056%), neg=0, invalid=762 0248: dt=16.000000, rms=0.497 (0.009%), neg=0, invalid=762 0249: dt=16.000000, rms=0.497 (0.011%), neg=0, invalid=762 0250: dt=16.000000, rms=0.497 (0.015%), neg=0, invalid=762 0251: dt=16.000000, rms=0.497 (0.008%), neg=0, invalid=762 0252: dt=2.800000, rms=0.497 (0.000%), neg=0, invalid=762 0253: dt=2.800000, rms=0.497 (0.001%), neg=0, invalid=762 0254: dt=0.700000, rms=0.497 (0.001%), neg=0, invalid=762 0255: dt=0.175000, rms=0.497 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.498, neg=0, invalid=762 0256: dt=85.333333, rms=0.494 (0.639%), neg=0, invalid=762 0257: dt=11.200000, rms=0.494 (0.079%), neg=0, invalid=762 0258: dt=11.200000, rms=0.494 (0.024%), neg=0, invalid=762 0259: dt=11.200000, rms=0.494 (0.005%), neg=0, invalid=762 0260: dt=11.200000, rms=0.494 (-0.010%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.517, neg=0, invalid=762 0261: dt=0.000000, rms=0.517 (0.046%), neg=0, invalid=762 0262: dt=0.000000, rms=0.517 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.517, neg=0, invalid=762 0263: dt=1.008000, rms=0.517 (0.056%), neg=0, invalid=762 0264: dt=0.252000, rms=0.517 (0.001%), neg=0, invalid=762 0265: dt=0.252000, rms=0.517 (0.000%), neg=0, invalid=762 0266: dt=0.252000, rms=0.517 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.561, neg=0, invalid=762 0267: dt=2.412791, rms=0.553 (1.559%), neg=0, invalid=762 0268: dt=1.280000, rms=0.552 (0.136%), neg=0, invalid=762 0269: dt=0.448000, rms=0.552 (0.016%), neg=0, invalid=762 0270: dt=0.448000, rms=0.552 (0.004%), neg=0, invalid=762 0271: dt=0.448000, rms=0.552 (-0.022%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.552, neg=0, invalid=762 0272: dt=1.792000, rms=0.551 (0.230%), neg=0, invalid=762 0273: dt=1.536000, rms=0.551 (0.045%), neg=0, invalid=762 0274: dt=1.536000, rms=0.550 (0.006%), neg=0, invalid=762 0275: dt=1.536000, rms=0.550 (-0.115%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.523, neg=0, invalid=762 0276: dt=0.448000, rms=0.510 (2.432%), neg=0, invalid=762 0277: dt=0.448000, rms=0.506 (0.676%), neg=0, invalid=762 0278: dt=0.448000, rms=0.504 (0.392%), neg=0, invalid=762 0279: dt=0.448000, rms=0.503 (0.255%), neg=0, invalid=762 0280: dt=0.448000, rms=0.502 (0.187%), neg=0, invalid=762 0281: dt=0.448000, rms=0.502 (0.142%), neg=0, invalid=762 0282: dt=0.448000, rms=0.501 (0.114%), neg=0, invalid=762 0283: dt=0.448000, rms=0.501 (0.090%), neg=0, invalid=762 0284: dt=0.448000, rms=0.500 (0.076%), neg=0, invalid=762 0285: dt=0.448000, rms=0.500 (0.063%), neg=0, invalid=762 0286: dt=0.448000, rms=0.500 (0.055%), neg=0, invalid=762 0287: dt=0.448000, rms=0.499 (0.047%), neg=0, invalid=762 0288: dt=0.448000, rms=0.499 (0.040%), neg=0, invalid=762 0289: dt=0.448000, rms=0.499 (0.072%), neg=0, invalid=762 0290: dt=0.448000, rms=0.498 (0.088%), neg=0, invalid=762 0291: dt=0.448000, rms=0.498 (0.092%), neg=0, invalid=762 0292: dt=0.448000, rms=0.497 (0.086%), neg=0, invalid=762 0293: dt=0.448000, rms=0.497 (0.072%), neg=0, invalid=762 0294: dt=0.448000, rms=0.497 (0.051%), neg=0, invalid=762 0295: dt=0.448000, rms=0.497 (0.034%), neg=0, invalid=762 0296: dt=0.448000, rms=0.497 (-0.009%), neg=0, invalid=762 0297: dt=0.000000, rms=0.497 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.497, neg=0, invalid=762 0298: dt=0.448000, rms=0.494 (0.559%), neg=0, invalid=762 0299: dt=0.448000, rms=0.494 (0.050%), neg=0, invalid=762 0300: dt=0.448000, rms=0.494 (0.005%), neg=0, invalid=762 0301: dt=0.448000, rms=0.494 (-0.009%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.491, neg=0, invalid=762 0302: dt=0.000000, rms=0.491 (0.055%), neg=0, invalid=762 0303: dt=0.000000, rms=0.491 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.491, neg=0, invalid=762 0304: dt=295.936000, rms=0.490 (0.188%), neg=0, invalid=762 0305: dt=110.976000, rms=0.490 (0.061%), neg=0, invalid=762 0306: dt=110.976000, rms=0.490 (0.017%), neg=0, invalid=762 0307: dt=110.976000, rms=0.490 (0.018%), neg=0, invalid=762 0308: dt=110.976000, rms=0.490 (0.030%), neg=0, invalid=762 0309: dt=110.976000, rms=0.489 (0.033%), neg=0, invalid=762 0310: dt=110.976000, rms=0.489 (0.048%), neg=0, invalid=762 0311: dt=110.976000, rms=0.489 (0.034%), neg=0, invalid=762 0312: dt=110.976000, rms=0.489 (0.020%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.489, neg=0, invalid=762 0313: dt=9.072000, rms=0.489 (0.058%), neg=0, invalid=762 0314: dt=6.480000, rms=0.489 (0.002%), neg=0, invalid=762 0315: dt=6.480000, rms=0.489 (0.001%), neg=0, invalid=762 0316: dt=6.480000, rms=0.489 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.489, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0317: dt=331.776000, rms=0.485 (0.947%), neg=0, invalid=762 0318: dt=36.288000, rms=0.484 (0.146%), neg=0, invalid=762 0319: dt=36.288000, rms=0.484 (0.026%), neg=0, invalid=762 0320: dt=36.288000, rms=0.484 (0.026%), neg=0, invalid=762 0321: dt=36.288000, rms=0.483 (0.053%), neg=0, invalid=762 0322: dt=36.288000, rms=0.483 (0.130%), neg=0, invalid=762 0323: dt=36.288000, rms=0.482 (0.191%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0324: dt=36.288000, rms=0.481 (0.196%), neg=0, invalid=762 0325: dt=36.288000, rms=0.480 (0.172%), neg=0, invalid=762 0326: dt=36.288000, rms=0.479 (0.142%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0327: dt=36.288000, rms=0.479 (0.110%), neg=0, invalid=762 0328: dt=36.288000, rms=0.478 (0.092%), neg=0, invalid=762 0329: dt=145.152000, rms=0.478 (0.074%), neg=0, invalid=762 0330: dt=145.152000, rms=0.478 (-0.161%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.479, neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0331: dt=32.000000, rms=0.477 (0.432%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0332: dt=91.511312, rms=0.473 (0.775%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0333: dt=38.400000, rms=0.471 (0.509%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0334: dt=44.800000, rms=0.469 (0.403%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0335: dt=32.000000, rms=0.468 (0.232%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0336: dt=32.000000, rms=0.467 (0.150%), neg=0, invalid=762 0337: dt=32.000000, rms=0.466 (0.283%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0338: dt=32.000000, rms=0.464 (0.343%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 4 iterations, nbhd size=0, neg = 0 0339: dt=32.000000, rms=0.463 (0.292%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 0340: dt=32.000000, rms=0.462 (0.244%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0341: dt=32.000000, rms=0.461 (0.297%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 5 iterations, nbhd size=0, neg = 0 0342: dt=32.000000, rms=0.459 (0.266%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=0, neg = 0 0343: dt=32.000000, rms=0.458 (0.194%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 8 iterations, nbhd size=0, neg = 0 0344: dt=32.000000, rms=0.458 (0.109%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=0, neg = 0 0345: dt=32.000000, rms=0.457 (0.147%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0346: dt=32.000000, rms=0.457 (0.157%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 5 iterations, nbhd size=0, neg = 0 0347: dt=32.000000, rms=0.456 (0.091%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0348: dt=32.000000, rms=0.456 (0.039%), neg=0, invalid=762 0349: dt=32.000000, rms=0.456 (0.082%), neg=0, invalid=762 0350: dt=11.200000, rms=0.456 (0.005%), neg=0, invalid=762 0351: dt=11.200000, rms=0.455 (0.013%), neg=0, invalid=762 0352: dt=11.200000, rms=0.455 (0.006%), neg=0, invalid=762 0353: dt=11.200000, rms=0.455 (0.013%), neg=0, invalid=762 0354: dt=11.200000, rms=0.455 (0.023%), neg=0, invalid=762 0355: dt=11.200000, rms=0.455 (0.023%), neg=0, invalid=762 0356: dt=11.200000, rms=0.455 (0.019%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.455, neg=0, invalid=762 0357: dt=80.000000, rms=0.452 (0.837%), neg=0, invalid=762 0358: dt=24.353982, rms=0.451 (0.199%), neg=0, invalid=762 0359: dt=24.353982, rms=0.451 (0.016%), neg=0, invalid=762 0360: dt=24.353982, rms=0.450 (0.027%), neg=0, invalid=762 0361: dt=24.353982, rms=0.450 (0.054%), neg=0, invalid=762 0362: dt=24.353982, rms=0.450 (0.057%), neg=0, invalid=762 0363: dt=24.353982, rms=0.450 (0.049%), neg=0, invalid=762 0364: dt=24.353982, rms=0.450 (0.031%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0365: dt=25.600000, rms=0.449 (0.029%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.459, neg=0, invalid=762 0366: dt=0.000176, rms=0.459 (0.052%), neg=0, invalid=762 0367: dt=0.000000, rms=0.459 (0.000%), neg=0, invalid=762 0368: dt=0.150000, rms=0.459 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.459, neg=0, invalid=762 0369: dt=2.000000, rms=0.459 (0.064%), neg=0, invalid=762 0370: dt=0.252000, rms=0.459 (0.004%), neg=0, invalid=762 0371: dt=0.252000, rms=0.459 (0.001%), neg=0, invalid=762 0372: dt=0.252000, rms=0.459 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.476, neg=0, invalid=762 0373: dt=1.536000, rms=0.473 (0.559%), neg=0, invalid=762 0374: dt=0.448000, rms=0.473 (0.028%), neg=0, invalid=762 0375: dt=0.448000, rms=0.473 (0.000%), neg=0, invalid=762 0376: dt=0.448000, rms=0.473 (-0.060%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.473, neg=0, invalid=762 0377: dt=1.280000, rms=0.472 (0.161%), neg=0, invalid=762 0378: dt=0.448000, rms=0.472 (0.007%), neg=0, invalid=762 0379: dt=0.448000, rms=0.472 (-0.002%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.460, neg=0, invalid=762 iter 0, gcam->neg = 339 after 15 iterations, nbhd size=1, neg = 0 0380: dt=2.170013, rms=0.434 (5.536%), neg=0, invalid=762 0381: dt=0.112000, rms=0.434 (0.073%), neg=0, invalid=762 0382: dt=0.112000, rms=0.434 (-0.082%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.434, neg=0, invalid=762 0383: dt=0.048000, rms=0.434 (0.089%), neg=0, invalid=762 0384: dt=0.004000, rms=0.434 (0.000%), neg=0, invalid=762 0385: dt=0.004000, rms=0.434 (-0.001%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.420, neg=0, invalid=762 0386: dt=0.000000, rms=0.420 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.420, neg=0, invalid=762 0387: dt=73.984000, rms=0.420 (0.005%), neg=0, invalid=762 0388: dt=443.904000, rms=0.420 (0.028%), neg=0, invalid=762 0389: dt=92.480000, rms=0.420 (0.003%), neg=0, invalid=762 0390: dt=92.480000, rms=0.420 (0.001%), neg=0, invalid=762 0391: dt=92.480000, rms=0.420 (0.001%), neg=0, invalid=762 0392: dt=92.480000, rms=0.420 (0.001%), neg=0, invalid=762 0393: dt=92.480000, rms=0.420 (0.002%), neg=0, invalid=762 0394: dt=92.480000, rms=0.420 (0.003%), neg=0, invalid=762 0395: dt=92.480000, rms=0.420 (0.002%), neg=0, invalid=762 0396: dt=92.480000, rms=0.420 (0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.420, neg=0, invalid=762 0397: dt=0.000000, rms=0.420 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.420, neg=0, invalid=762 0398: dt=331.776000, rms=0.419 (0.188%), neg=0, invalid=762 0399: dt=103.680000, rms=0.419 (0.084%), neg=0, invalid=762 0400: dt=103.680000, rms=0.419 (0.035%), neg=0, invalid=762 0401: dt=103.680000, rms=0.418 (0.079%), neg=0, invalid=762 0402: dt=103.680000, rms=0.418 (0.062%), neg=0, invalid=762 0403: dt=103.680000, rms=0.418 (0.103%), neg=0, invalid=762 0404: dt=103.680000, rms=0.417 (0.051%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.418, neg=0, invalid=762 0405: dt=11.200000, rms=0.418 (0.048%), neg=0, invalid=762 0406: dt=9.600000, rms=0.418 (0.016%), neg=0, invalid=762 0407: dt=9.600000, rms=0.418 (0.012%), neg=0, invalid=762 0408: dt=9.600000, rms=0.418 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.418, neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0409: dt=89.185476, rms=0.414 (0.929%), neg=0, invalid=762 0410: dt=25.513514, rms=0.413 (0.240%), neg=0, invalid=762 0411: dt=25.513514, rms=0.413 (0.082%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0412: dt=25.513514, rms=0.412 (0.127%), neg=0, invalid=762 0413: dt=25.513514, rms=0.411 (0.180%), neg=0, invalid=762 0414: dt=25.513514, rms=0.410 (0.234%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0415: dt=25.513514, rms=0.409 (0.248%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 9 iterations, nbhd size=1, neg = 0 0416: dt=25.513514, rms=0.409 (0.197%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0417: dt=25.513514, rms=0.408 (0.180%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0418: dt=25.513514, rms=0.407 (0.148%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0419: dt=25.513514, rms=0.407 (0.118%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0420: dt=25.513514, rms=0.406 (0.098%), neg=0, invalid=762 0421: dt=76.800000, rms=0.406 (0.035%), neg=0, invalid=762 0422: dt=76.800000, rms=0.406 (-0.073%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.412, neg=0, invalid=762 0423: dt=0.000000, rms=0.412 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.412, neg=0, invalid=762 0424: dt=2.880000, rms=0.411 (0.018%), neg=0, invalid=762 0425: dt=1.008000, rms=0.411 (0.002%), neg=0, invalid=762 0426: dt=1.008000, rms=0.411 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.421, neg=0, invalid=762 0427: dt=0.000000, rms=0.421 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.421, neg=0, invalid=762 0428: dt=0.000000, rms=0.421 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.405, neg=0, invalid=762 iter 0, gcam->neg = 325 after 13 iterations, nbhd size=1, neg = 0 0429: dt=1.411043, rms=0.395 (2.334%), neg=0, invalid=762 0430: dt=0.000023, rms=0.395 (0.000%), neg=0, invalid=762 0431: dt=0.000023, rms=0.395 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.395, neg=0, invalid=762 0432: dt=0.064000, rms=0.395 (0.018%), neg=0, invalid=762 0433: dt=0.016000, rms=0.395 (0.001%), neg=0, invalid=762 0434: dt=0.016000, rms=0.395 (-0.000%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 53 minutes and 14 seconds. mri_ca_register utimesec 10379.322638 mri_ca_register stimesec 7.242620 mri_ca_register ru_maxrss 1361132 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 5080850 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 62920 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 46 mri_ca_register ru_nivcsw 981509 FSRUNTIME@ mri_ca_register 2.8873 hours 1 threads #-------------------------------------- #@# SubCort Seg Mon Jan 15 21:41:00 EST 2018 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer-6.0.0//average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname kaplan machine x86_64 setenv SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 cd /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer-6.0.0//average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes reading classifier array from /usr/local/freesurfer-6.0.0//average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 9.58 Atlas used for the 3D morph was /usr/local/freesurfer-6.0.0//average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.10997 (22) Left_Lateral_Ventricle (4): linear fit = 1.08 x + 0.0 (4868 voxels, overlap=0.917) Left_Lateral_Ventricle (4): linear fit = 1.08 x + 0.0 (4868 voxels, peak = 22), gca=21.5 gca peak = 0.17677 (13) mri peak = 0.14086 (20) Right_Lateral_Ventricle (43): linear fit = 1.47 x + 0.0 (5507 voxels, overlap=0.368) Right_Lateral_Ventricle (43): linear fit = 1.47 x + 0.0 (5507 voxels, peak = 19), gca=19.0 gca peak = 0.28129 (95) mri peak = 0.13346 (94) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (1025 voxels, overlap=1.007) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (1025 voxels, peak = 93), gca=92.6 gca peak = 0.16930 (96) mri peak = 0.13500 (94) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (1000 voxels, overlap=1.002) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (1000 voxels, peak = 95), gca=94.6 gca peak = 0.24553 (55) mri peak = 0.12614 (72) Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (1753 voxels, overlap=0.019) Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (1753 voxels, peak = 70), gca=70.1 gca peak = 0.30264 (59) mri peak = 0.12808 (72) Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (1621 voxels, overlap=0.016) Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (1621 voxels, peak = 73), gca=73.5 gca peak = 0.07580 (103) mri peak = 0.11104 (103) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (68856 voxels, overlap=0.641) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (68856 voxels, peak = 103), gca=103.0 gca peak = 0.07714 (104) mri peak = 0.10804 (105) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (60427 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (60427 voxels, peak = 106), gca=105.6 gca peak = 0.09712 (58) mri peak = 0.04044 (80) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (76231 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (76231 voxels, peak = 78), gca=78.0 gca peak = 0.11620 (58) mri peak = 0.04225 (75) Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (70881 voxels, overlap=0.003) Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (70881 voxels, peak = 75), gca=75.1 gca peak = 0.30970 (66) mri peak = 0.14491 (79) Right_Caudate (50): linear fit = 1.14 x + 0.0 (2192 voxels, overlap=0.016) Right_Caudate (50): linear fit = 1.14 x + 0.0 (2192 voxels, peak = 76), gca=75.6 gca peak = 0.15280 (69) mri peak = 0.16524 (82) Left_Caudate (11): linear fit = 1.07 x + 0.0 (2037 voxels, overlap=0.311) Left_Caudate (11): linear fit = 1.07 x + 0.0 (2037 voxels, peak = 73), gca=73.5 gca peak = 0.13902 (56) mri peak = 0.06455 (71) Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (44079 voxels, overlap=0.036) Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (44079 voxels, peak = 71), gca=70.8 gca peak = 0.14777 (55) mri peak = 0.06041 (68) Right_Cerebellum_Cortex (47): linear fit = 1.25 x + 0.0 (47219 voxels, overlap=0.085) Right_Cerebellum_Cortex (47): linear fit = 1.25 x + 0.0 (47219 voxels, peak = 68), gca=68.5 gca peak = 0.16765 (84) mri peak = 0.09796 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (8018 voxels, overlap=0.637) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (8018 voxels, peak = 91), gca=91.1 gca peak = 0.18739 (84) mri peak = 0.10341 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (9240 voxels, overlap=0.672) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (9240 voxels, peak = 89), gca=89.5 gca peak = 0.29869 (57) mri peak = 0.11677 (76) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (768 voxels, overlap=0.049) Left_Amygdala (18): linear fit = 1.29 x + 0.0 (768 voxels, peak = 74), gca=73.8 gca peak = 0.33601 (57) mri peak = 0.15538 (72) Right_Amygdala (54): linear fit = 1.27 x + 0.0 (894 voxels, overlap=0.042) Right_Amygdala (54): linear fit = 1.27 x + 0.0 (894 voxels, peak = 73), gca=72.7 gca peak = 0.11131 (90) mri peak = 0.07337 (90) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (6401 voxels, overlap=0.952) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (6401 voxels, peak = 91), gca=91.3 gca peak = 0.11793 (83) mri peak = 0.08761 (90) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (5902 voxels, overlap=0.863) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (5902 voxels, peak = 87), gca=86.7 gca peak = 0.08324 (81) mri peak = 0.12788 (88) Left_Putamen (12): linear fit = 1.11 x + 0.0 (2562 voxels, overlap=0.291) Left_Putamen (12): linear fit = 1.11 x + 0.0 (2562 voxels, peak = 90), gca=89.5 gca peak = 0.10360 (77) mri peak = 0.13524 (87) Right_Putamen (51): linear fit = 1.09 x + 0.0 (2698 voxels, overlap=0.374) Right_Putamen (51): linear fit = 1.09 x + 0.0 (2698 voxels, peak = 84), gca=83.5 gca peak = 0.08424 (78) mri peak = 0.07888 (88) Brain_Stem (16): linear fit = 1.11 x + 0.0 (15818 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.11 x + 0.0 (15818 voxels, peak = 86), gca=86.2 gca peak = 0.12631 (89) mri peak = 0.09517 (94) Right_VentralDC (60): linear fit = 1.07 x + 0.0 (2229 voxels, overlap=0.682) Right_VentralDC (60): linear fit = 1.07 x + 0.0 (2229 voxels, peak = 95), gca=94.8 gca peak = 0.14500 (87) mri peak = 0.12005 (94) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (2389 voxels, overlap=0.651) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (2389 voxels, peak = 93), gca=92.7 gca peak = 0.14975 (24) mri peak = 0.18841 (26) Third_Ventricle (14): linear fit = 0.98 x + 0.0 (143 voxels, overlap=0.876) Third_Ventricle (14): linear fit = 0.98 x + 0.0 (143 voxels, peak = 23), gca=23.4 gca peak = 0.19357 (14) mri peak = 0.19966 (26) Fourth_Ventricle (15): linear fit = 1.66 x + 0.0 (291 voxels, overlap=0.177) Fourth_Ventricle (15): linear fit = 1.66 x + 0.0 (291 voxels, peak = 23), gca=23.3 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Fourth_Ventricle = 0.19357 (14) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.29 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.17 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.14335 (22) mri peak = 0.10997 (22) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (4868 voxels, overlap=0.918) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (4868 voxels, peak = 23), gca=22.5 gca peak = 0.12269 (18) mri peak = 0.14086 (20) Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (5507 voxels, overlap=0.640) Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (5507 voxels, peak = 18), gca=18.0 gca peak = 0.25109 (91) mri peak = 0.13346 (94) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1025 voxels, overlap=1.002) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1025 voxels, peak = 91), gca=90.5 gca peak = 0.20278 (95) mri peak = 0.13500 (94) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (1000 voxels, overlap=1.000) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (1000 voxels, peak = 95), gca=94.5 gca peak = 0.24225 (71) mri peak = 0.12614 (72) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1753 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1753 voxels, peak = 71), gca=71.0 gca peak = 0.29890 (70) mri peak = 0.12808 (72) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1621 voxels, overlap=1.001) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1621 voxels, peak = 70), gca=70.0 gca peak = 0.07594 (103) mri peak = 0.11104 (103) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (68856 voxels, overlap=0.641) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (68856 voxels, peak = 103), gca=103.0 gca peak = 0.07832 (106) mri peak = 0.10804 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (60427 voxels, overlap=0.679) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (60427 voxels, peak = 105), gca=105.5 gca peak = 0.07289 (78) mri peak = 0.04044 (80) Left_Cerebral_Cortex (3): linear fit = 1.01 x + 0.0 (76231 voxels, overlap=0.953) Left_Cerebral_Cortex (3): linear fit = 1.01 x + 0.0 (76231 voxels, peak = 79), gca=79.2 gca peak = 0.09099 (75) mri peak = 0.04225 (75) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (70881 voxels, overlap=0.952) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (70881 voxels, peak = 75), gca=75.0 gca peak = 0.24442 (76) mri peak = 0.14491 (79) Right_Caudate (50): linear fit = 1.01 x + 0.0 (2192 voxels, overlap=1.003) Right_Caudate (50): linear fit = 1.01 x + 0.0 (2192 voxels, peak = 77), gca=77.1 gca peak = 0.12679 (73) mri peak = 0.16524 (82) Left_Caudate (11): linear fit = 1.01 x + 0.0 (2037 voxels, overlap=0.665) Left_Caudate (11): linear fit = 1.01 x + 0.0 (2037 voxels, peak = 74), gca=74.1 gca peak = 0.11373 (70) mri peak = 0.06455 (71) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (44079 voxels, overlap=0.972) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (44079 voxels, peak = 70), gca=70.0 gca peak = 0.12601 (68) mri peak = 0.06041 (68) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (47219 voxels, overlap=0.979) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (47219 voxels, peak = 68), gca=68.0 gca peak = 0.15503 (91) mri peak = 0.09796 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (8018 voxels, overlap=0.964) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (8018 voxels, peak = 91), gca=90.5 gca peak = 0.15227 (90) mri peak = 0.10341 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (9240 voxels, overlap=0.941) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (9240 voxels, peak = 90), gca=89.6 gca peak = 0.28754 (75) mri peak = 0.11677 (76) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (768 voxels, overlap=1.003) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (768 voxels, peak = 76), gca=76.1 gca peak = 0.24959 (73) mri peak = 0.15538 (72) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (894 voxels, overlap=0.999) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (894 voxels, peak = 73), gca=73.0 gca peak = 0.11078 (90) mri peak = 0.07337 (90) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (6401 voxels, overlap=0.973) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (6401 voxels, peak = 90), gca=89.6 gca peak = 0.09871 (90) mri peak = 0.08761 (90) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5902 voxels, overlap=0.967) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5902 voxels, peak = 90), gca=90.0 gca peak = 0.07544 (83) mri peak = 0.12788 (88) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2562 voxels, overlap=0.730) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2562 voxels, peak = 83), gca=83.0 gca peak = 0.08953 (85) mri peak = 0.13524 (87) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2698 voxels, overlap=0.768) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2698 voxels, peak = 86), gca=86.3 gca peak = 0.07310 (86) mri peak = 0.07888 (88) Brain_Stem (16): linear fit = 1.00 x + 0.0 (15818 voxels, overlap=0.807) Brain_Stem (16): linear fit = 1.00 x + 0.0 (15818 voxels, peak = 86), gca=85.6 gca peak = 0.11678 (95) mri peak = 0.09517 (94) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (2229 voxels, overlap=0.823) Right_VentralDC (60): linear fit = 0.99 x + 0.0 (2229 voxels, peak = 94), gca=93.6 gca peak = 0.15664 (91) mri peak = 0.12005 (94) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (2389 voxels, overlap=0.906) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (2389 voxels, peak = 91), gca=91.0 gca peak = 0.20072 (25) mri peak = 0.18841 (26) Third_Ventricle (14): linear fit = 0.99 x + 0.0 (143 voxels, overlap=0.846) Third_Ventricle (14): linear fit = 0.99 x + 0.0 (143 voxels, peak = 25), gca=24.6 gca peak = 0.17270 (17) mri peak = 0.19966 (26) Fourth_Ventricle (15): linear fit = 1.45 x + 0.0 (291 voxels, overlap=0.177) Fourth_Ventricle (15): linear fit = 1.45 x + 0.0 (291 voxels, peak = 25), gca=24.6 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16017 (40) gca peak Left_Thalamus = 0.36646 (104) gca peak CSF = 0.19803 (42) gca peak Left_Accumbens_area = 0.59962 (67) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.11914 (35) gca peak Right_Inf_Lat_Vent = 0.19636 (29) gca peak Right_Accumbens_area = 0.33129 (74) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14539 (37) gca peak Fifth_Ventricle = 0.65175 (37) gca peak WM_hypointensities = 0.08220 (77) gca peak non_WM_hypointensities = 0.10019 (77) gca peak Optic_Chiasm = 0.68998 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.11 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 73463 voxels changed in iteration 0 of unlikely voxel relabeling 434 voxels changed in iteration 1 of unlikely voxel relabeling 11 voxels changed in iteration 2 of unlikely voxel relabeling 4 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 111591 gm and wm labels changed (%29 to gray, %71 to white out of all changed labels) 590 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 85067 changed. image ll: -2.181, PF=0.500 pass 2: 23774 changed. image ll: -2.179, PF=0.500 pass 3: 8132 changed. pass 4: 3237 changed. 93010 voxels changed in iteration 0 of unlikely voxel relabeling 629 voxels changed in iteration 1 of unlikely voxel relabeling 12 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 8855 voxels changed in iteration 0 of unlikely voxel relabeling 232 voxels changed in iteration 1 of unlikely voxel relabeling 16 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6627 voxels changed in iteration 0 of unlikely voxel relabeling 115 voxels changed in iteration 1 of unlikely voxel relabeling 6 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6359 voxels changed in iteration 0 of unlikely voxel relabeling 56 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 5522.505229 mri_ca_label stimesec 1.555455 mri_ca_label ru_maxrss 2128384 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 1010002 mri_ca_label ru_majflt 23 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 4616 mri_ca_label ru_oublock 536 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 118 mri_ca_label ru_nivcsw 515110 auto-labeling took 92 minutes and 6 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/transforms/cc_up.lta icbm-205 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/transforms/cc_up.lta reading aseg from /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/aseg.auto_noCCseg.mgz reading norm from /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/norm.mgz 57143 voxels in left wm, 51885 in right wm, xrange [124, 134] searching rotation angles z=[-7 7], y=[-8 6] searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.2 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.2 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.2 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.2 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.6 searching scale 1 Z rot 6.8 global minimum found at slice 128.0, rotations (-0.57, 0.08) final transformation (x=128.0, yr=-0.572, zr=0.083): 0.99995 -0.00144 -0.00999 1.43386; 0.00144 1.00000 -0.00001 10.81745; 0.00999 0.00000 0.99995 0.72760; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 132] in xformed coordinates best xformed slice 128 cc center is found at 128 117 126 eigenvectors: -0.00010 -0.00029 1.00000; 0.15778 -0.98747 -0.00027; 0.98747 0.15778 0.00014; error in mid anterior detected - correcting... writing aseg with callosum to /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/aseg.auto.mgz... corpus callosum segmentation took 0.9 minutes #-------------------------------------- #@# Merge ASeg Mon Jan 15 23:14:02 EST 2018 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Mon Jan 15 23:14:02 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 638 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 83 (83), valley at 47 (47) csf peak at 10, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 84 (84), valley at 27 (27) csf peak at 42, setting threshold to 70 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 49 seconds. #-------------------------------------------- #@# Mask BFS Mon Jan 15 23:17:54 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 2160123 voxels in mask (pct= 12.88) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Jan 15 23:17:55 EST 2018 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (101.0): 101.1 +- 6.1 [79.0 --> 125.0] GM (77.0) : 76.0 +- 11.2 [30.0 --> 95.0] setting bottom of white matter range to 87.1 setting top of gray matter range to 98.3 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... 2775 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3304 filled 1061 bright non-wm voxels segmented. 2023 diagonally connected voxels added... white matter segmentation took 2.4 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.56 minutes reading wm segmentation from wm.seg.mgz... 199 voxels added to wm to prevent paths from MTL structures to cortex 4847 additional wm voxels added 0 additional wm voxels added SEG EDIT: 72350 voxels turned on, 57052 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 10 found - 10 modified | TOTAL: 10 pass 2 (xy+): 0 found - 10 modified | TOTAL: 10 pass 1 (xy-): 20 found - 20 modified | TOTAL: 30 pass 2 (xy-): 0 found - 20 modified | TOTAL: 30 pass 1 (yz+): 19 found - 19 modified | TOTAL: 49 pass 2 (yz+): 0 found - 19 modified | TOTAL: 49 pass 1 (yz-): 23 found - 23 modified | TOTAL: 72 pass 2 (yz-): 0 found - 23 modified | TOTAL: 72 pass 1 (xz+): 10 found - 10 modified | TOTAL: 82 pass 2 (xz+): 0 found - 10 modified | TOTAL: 82 pass 1 (xz-): 10 found - 10 modified | TOTAL: 92 pass 2 (xz-): 0 found - 10 modified | TOTAL: 92 Iteration Number : 1 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 11 found - 11 modified | TOTAL: 15 pass 2 (+++): 0 found - 11 modified | TOTAL: 15 pass 1 (+++): 13 found - 13 modified | TOTAL: 28 pass 2 (+++): 0 found - 13 modified | TOTAL: 28 pass 1 (+++): 14 found - 14 modified | TOTAL: 42 pass 2 (+++): 0 found - 14 modified | TOTAL: 42 Iteration Number : 1 pass 1 (++): 37 found - 37 modified | TOTAL: 37 pass 2 (++): 0 found - 37 modified | TOTAL: 37 pass 1 (+-): 26 found - 26 modified | TOTAL: 63 pass 2 (+-): 0 found - 26 modified | TOTAL: 63 pass 1 (--): 26 found - 26 modified | TOTAL: 89 pass 2 (--): 0 found - 26 modified | TOTAL: 89 pass 1 (-+): 32 found - 32 modified | TOTAL: 121 pass 2 (-+): 0 found - 32 modified | TOTAL: 121 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 3 found - 3 modified | TOTAL: 4 pass 2 (xy-): 0 found - 3 modified | TOTAL: 4 pass 1 (yz+): 4 found - 4 modified | TOTAL: 8 pass 2 (yz+): 0 found - 4 modified | TOTAL: 8 pass 1 (yz-): 1 found - 1 modified | TOTAL: 9 pass 2 (yz-): 0 found - 1 modified | TOTAL: 9 pass 1 (xz+): 1 found - 1 modified | TOTAL: 10 pass 2 (xz+): 0 found - 1 modified | TOTAL: 10 pass 1 (xz-): 3 found - 3 modified | TOTAL: 13 pass 2 (xz-): 0 found - 3 modified | TOTAL: 13 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 0 found - 0 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 modified | TOTAL: 3 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 1 found - 1 modified | TOTAL: 3 pass 2 (xz+): 0 found - 1 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 Iteration Number : 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 = 276 (out of 795993: 0.034674) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Mon Jan 15 23:20:59 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.93937 0.06257 -0.05685 5.85288; -0.06966 0.93949 -0.07256 7.15284; 0.05378 0.08447 0.93194 -28.03424; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 0.93937 0.06257 -0.05685 5.85288; -0.06966 0.93949 -0.07256 7.15284; 0.05378 0.08447 0.93194 -28.03424; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1435 (min = 350, max = 1400), aspect = 0.42 (min = 0.10, max = 0.75) need search nearby using seed (129, 112, 88), TAL = (-1.0, -40.0, 16.0) talairach voxel to voxel transform 1.05559 -0.07556 0.05851 -3.99754; 0.07305 1.05178 0.08634 -5.53023; -0.06754 -0.09097 1.06183 30.81347; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (129, 112, 88) --> (-1.0, -40.0, 16.0) done. writing output to filled.mgz... filling took 0.7 minutes talairach cc position changed to (-1.00, -40.00, 16.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(17.00, -40.00, 16.00) SRC: (109.86, 127.98, 106.57) search lh wm seed point around talairach space (-19.00, -40.00, 16.00), SRC: (147.86, 130.61, 104.14) 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 Mon Jan 15 23:21:42 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 1 found - 1 modified | TOTAL: 3 pass 2 (yz-): 0 found - 1 modified | TOTAL: 3 pass 1 (xz+): 2 found - 2 modified | TOTAL: 5 pass 2 (xz+): 0 found - 2 modified | TOTAL: 5 pass 1 (xz-): 0 found - 0 modified | TOTAL: 5 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 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 = 6 (out of 383301: 0.001565) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 183 vertices, 215 faces slice 50: 4181 vertices, 4360 faces slice 60: 12338 vertices, 12667 faces slice 70: 23027 vertices, 23405 faces slice 80: 34954 vertices, 35393 faces slice 90: 47728 vertices, 48156 faces slice 100: 59408 vertices, 59812 faces slice 110: 72735 vertices, 73213 faces slice 120: 86251 vertices, 86709 faces slice 130: 100181 vertices, 100723 faces slice 140: 114437 vertices, 114927 faces slice 150: 126923 vertices, 127369 faces slice 160: 138000 vertices, 138376 faces slice 170: 147568 vertices, 147914 faces slice 180: 156413 vertices, 156762 faces slice 190: 164054 vertices, 164358 faces slice 200: 171619 vertices, 171923 faces slice 210: 176036 vertices, 176227 faces slice 220: 176994 vertices, 177064 faces slice 230: 176994 vertices, 177064 faces slice 240: 176994 vertices, 177064 faces slice 250: 176994 vertices, 177064 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 176994 voxel in cpt #1: X=-70 [v=176994,e=531192,f=354128] located at (-29.741426, -6.428766, -0.867883) For the whole surface: X=-70 [v=176994,e=531192,f=354128] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Mon Jan 15 23:21:48 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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+): 3 found - 3 modified | TOTAL: 3 pass 2 (yz+): 0 found - 3 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 2 found - 2 modified | TOTAL: 6 pass 2 (xz+): 0 found - 2 modified | TOTAL: 6 pass 1 (xz-): 2 found - 2 modified | TOTAL: 8 pass 2 (xz-): 0 found - 2 modified | TOTAL: 8 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 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 modified | TOTAL: 3 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 = 11 (out of 389574: 0.002824) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 1943 vertices, 2097 faces slice 60: 8300 vertices, 8533 faces slice 70: 16964 vertices, 17333 faces slice 80: 28086 vertices, 28478 faces slice 90: 40977 vertices, 41423 faces slice 100: 53396 vertices, 53830 faces slice 110: 66574 vertices, 67006 faces slice 120: 80715 vertices, 81196 faces slice 130: 94286 vertices, 94744 faces slice 140: 107914 vertices, 108409 faces slice 150: 121439 vertices, 121868 faces slice 160: 134694 vertices, 135204 faces slice 170: 145669 vertices, 146026 faces slice 180: 155275 vertices, 155657 faces slice 190: 164240 vertices, 164585 faces slice 200: 171373 vertices, 171669 faces slice 210: 177462 vertices, 177646 faces slice 220: 179378 vertices, 179440 faces slice 230: 179378 vertices, 179440 faces slice 240: 179378 vertices, 179440 faces slice 250: 179378 vertices, 179440 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 179378 voxel in cpt #1: X=-62 [v=179378,e=538320,f=358880] located at (30.023598, -1.477115, -0.888448) For the whole surface: X=-62 [v=179378,e=538320,f=358880] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Mon Jan 15 23:21:55 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh Mon Jan 15 23:22:02 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Mon Jan 15 23:22:09 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 51.8 mm, total surface area = 95599 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.8 minutes step 000: RMS=0.149 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.085 (target=0.015) step 015: RMS=0.072 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.055 (target=0.015) step 030: RMS=0.049 (target=0.015) step 035: RMS=0.045 (target=0.015) step 040: RMS=0.043 (target=0.015) step 045: RMS=0.040 (target=0.015) step 050: RMS=0.039 (target=0.015) step 055: RMS=0.038 (target=0.015) step 060: RMS=0.037 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 45.261896 mris_inflate stimesec 0.047975 mris_inflate ru_maxrss 225856 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 29000 mris_inflate ru_majflt 14 mris_inflate ru_nswap 0 mris_inflate ru_inblock 2808 mris_inflate ru_oublock 12456 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 15 mris_inflate ru_nivcsw 3885 #-------------------------------------------- #@# Inflation1 rh Mon Jan 15 23:22:54 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 51.7 mm, total surface area = 96871 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.8 minutes step 000: RMS=0.148 (target=0.015) step 005: RMS=0.113 (target=0.015) step 010: RMS=0.085 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.057 (target=0.015) step 030: RMS=0.051 (target=0.015) step 035: RMS=0.047 (target=0.015) step 040: RMS=0.045 (target=0.015) step 045: RMS=0.042 (target=0.015) step 050: RMS=0.041 (target=0.015) step 055: RMS=0.041 (target=0.015) step 060: RMS=0.040 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 45.766205 mris_inflate stimesec 0.059960 mris_inflate ru_maxrss 228880 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 28752 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 12624 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 3862 #-------------------------------------------- #@# QSphere lh Mon Jan 15 23:23:40 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.86 +- 0.50 (0.00-->6.70) (max @ vno 60184 --> 61323) face area 0.02 +- 0.03 (-0.07-->0.66) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.280... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.330, avgs=0 005/300: dt: 0.9000, rms radial error=176.071, avgs=0 010/300: dt: 0.9000, rms radial error=175.514, avgs=0 015/300: dt: 0.9000, rms radial error=174.784, avgs=0 020/300: dt: 0.9000, rms radial error=173.954, avgs=0 025/300: dt: 0.9000, rms radial error=173.065, avgs=0 030/300: dt: 0.9000, rms radial error=172.143, avgs=0 035/300: dt: 0.9000, rms radial error=171.205, avgs=0 040/300: dt: 0.9000, rms radial error=170.259, avgs=0 045/300: dt: 0.9000, rms radial error=169.311, avgs=0 050/300: dt: 0.9000, rms radial error=168.364, avgs=0 055/300: dt: 0.9000, rms radial error=167.419, avgs=0 060/300: dt: 0.9000, rms radial error=166.479, avgs=0 065/300: dt: 0.9000, rms radial error=165.543, avgs=0 070/300: dt: 0.9000, rms radial error=164.613, avgs=0 075/300: dt: 0.9000, rms radial error=163.687, avgs=0 080/300: dt: 0.9000, rms radial error=162.766, avgs=0 085/300: dt: 0.9000, rms radial error=161.851, avgs=0 090/300: dt: 0.9000, rms radial error=160.941, avgs=0 095/300: dt: 0.9000, rms radial error=160.035, avgs=0 100/300: dt: 0.9000, rms radial error=159.135, avgs=0 105/300: dt: 0.9000, rms radial error=158.240, avgs=0 110/300: dt: 0.9000, rms radial error=157.349, avgs=0 115/300: dt: 0.9000, rms radial error=156.464, avgs=0 120/300: dt: 0.9000, rms radial error=155.583, avgs=0 125/300: dt: 0.9000, rms radial error=154.707, avgs=0 130/300: dt: 0.9000, rms radial error=153.836, avgs=0 135/300: dt: 0.9000, rms radial error=152.970, avgs=0 140/300: dt: 0.9000, rms radial error=152.108, avgs=0 145/300: dt: 0.9000, rms radial error=151.251, avgs=0 150/300: dt: 0.9000, rms radial error=150.399, avgs=0 155/300: dt: 0.9000, rms radial error=149.552, avgs=0 160/300: dt: 0.9000, rms radial error=148.709, avgs=0 165/300: dt: 0.9000, rms radial error=147.871, avgs=0 170/300: dt: 0.9000, rms radial error=147.038, avgs=0 175/300: dt: 0.9000, rms radial error=146.209, avgs=0 180/300: dt: 0.9000, rms radial error=145.385, avgs=0 185/300: dt: 0.9000, rms radial error=144.565, avgs=0 190/300: dt: 0.9000, rms radial error=143.750, avgs=0 195/300: dt: 0.9000, rms radial error=142.940, avgs=0 200/300: dt: 0.9000, rms radial error=142.133, avgs=0 205/300: dt: 0.9000, rms radial error=141.332, avgs=0 210/300: dt: 0.9000, rms radial error=140.535, avgs=0 215/300: dt: 0.9000, rms radial error=139.742, avgs=0 220/300: dt: 0.9000, rms radial error=138.954, avgs=0 225/300: dt: 0.9000, rms radial error=138.170, avgs=0 230/300: dt: 0.9000, rms radial error=137.391, avgs=0 235/300: dt: 0.9000, rms radial error=136.615, avgs=0 240/300: dt: 0.9000, rms radial error=135.845, avgs=0 245/300: dt: 0.9000, rms radial error=135.078, avgs=0 250/300: dt: 0.9000, rms radial error=134.316, avgs=0 255/300: dt: 0.9000, rms radial error=133.558, avgs=0 260/300: dt: 0.9000, rms radial error=132.804, avgs=0 265/300: dt: 0.9000, rms radial error=132.055, avgs=0 270/300: dt: 0.9000, rms radial error=131.309, avgs=0 275/300: dt: 0.9000, rms radial error=130.568, avgs=0 280/300: dt: 0.9000, rms radial error=129.831, avgs=0 285/300: dt: 0.9000, rms radial error=129.098, avgs=0 290/300: dt: 0.9000, rms radial error=128.369, avgs=0 295/300: dt: 0.9000, rms radial error=127.645, avgs=0 300/300: dt: 0.9000, rms radial error=126.924, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 21276.05 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 2 (K=40.0), pass 1, starting sse = 3733.56 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 408.39 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00729 epoch 4 (K=640.0), pass 1, starting sse = 26.27 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.25/20 = 0.01242 final distance error %26.50 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.09 hours mris_sphere utimesec 327.016799 mris_sphere stimesec 0.151898 mris_sphere ru_maxrss 226032 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 28536 mris_sphere ru_majflt 18 mris_sphere ru_nswap 0 mris_sphere ru_inblock 3456 mris_sphere ru_oublock 12456 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 25 mris_sphere ru_nivcsw 30351 FSRUNTIME@ mris_sphere 0.0909 hours 1 threads #-------------------------------------------- #@# QSphere rh Mon Jan 15 23:29:08 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.86 +- 0.49 (0.00-->6.26) (max @ vno 67400 --> 67421) face area 0.02 +- 0.03 (-0.06-->0.65) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.281... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.102, avgs=0 005/300: dt: 0.9000, rms radial error=175.842, avgs=0 010/300: dt: 0.9000, rms radial error=175.283, avgs=0 015/300: dt: 0.9000, rms radial error=174.551, avgs=0 020/300: dt: 0.9000, rms radial error=173.716, avgs=0 025/300: dt: 0.9000, rms radial error=172.824, avgs=0 030/300: dt: 0.9000, rms radial error=171.900, avgs=0 035/300: dt: 0.9000, rms radial error=170.961, avgs=0 040/300: dt: 0.9000, rms radial error=170.014, avgs=0 045/300: dt: 0.9000, rms radial error=169.067, avgs=0 050/300: dt: 0.9000, rms radial error=168.122, avgs=0 055/300: dt: 0.9000, rms radial error=167.180, avgs=0 060/300: dt: 0.9000, rms radial error=166.242, avgs=0 065/300: dt: 0.9000, rms radial error=165.309, avgs=0 070/300: dt: 0.9000, rms radial error=164.380, avgs=0 075/300: dt: 0.9000, rms radial error=163.457, avgs=0 080/300: dt: 0.9000, rms radial error=162.538, avgs=0 085/300: dt: 0.9000, rms radial error=161.624, avgs=0 090/300: dt: 0.9000, rms radial error=160.716, avgs=0 095/300: dt: 0.9000, rms radial error=159.812, avgs=0 100/300: dt: 0.9000, rms radial error=158.913, avgs=0 105/300: dt: 0.9000, rms radial error=158.020, avgs=0 110/300: dt: 0.9000, rms radial error=157.131, avgs=0 115/300: dt: 0.9000, rms radial error=156.247, avgs=0 120/300: dt: 0.9000, rms radial error=155.367, avgs=0 125/300: dt: 0.9000, rms radial error=154.493, avgs=0 130/300: dt: 0.9000, rms radial error=153.624, avgs=0 135/300: dt: 0.9000, rms radial error=152.759, avgs=0 140/300: dt: 0.9000, rms radial error=151.899, avgs=0 145/300: dt: 0.9000, rms radial error=151.043, avgs=0 150/300: dt: 0.9000, rms radial error=150.193, avgs=0 155/300: dt: 0.9000, rms radial error=149.347, avgs=0 160/300: dt: 0.9000, rms radial error=148.506, avgs=0 165/300: dt: 0.9000, rms radial error=147.669, avgs=0 170/300: dt: 0.9000, rms radial error=146.837, avgs=0 175/300: dt: 0.9000, rms radial error=146.009, avgs=0 180/300: dt: 0.9000, rms radial error=145.186, avgs=0 185/300: dt: 0.9000, rms radial error=144.368, avgs=0 190/300: dt: 0.9000, rms radial error=143.554, avgs=0 195/300: dt: 0.9000, rms radial error=142.745, avgs=0 200/300: dt: 0.9000, rms radial error=141.940, avgs=0 205/300: dt: 0.9000, rms radial error=141.140, avgs=0 210/300: dt: 0.9000, rms radial error=140.344, avgs=0 215/300: dt: 0.9000, rms radial error=139.552, avgs=0 220/300: dt: 0.9000, rms radial error=138.765, avgs=0 225/300: dt: 0.9000, rms radial error=137.982, avgs=0 230/300: dt: 0.9000, rms radial error=137.204, avgs=0 235/300: dt: 0.9000, rms radial error=136.430, avgs=0 240/300: dt: 0.9000, rms radial error=135.660, avgs=0 245/300: dt: 0.9000, rms radial error=134.895, avgs=0 250/300: dt: 0.9000, rms radial error=134.134, avgs=0 255/300: dt: 0.9000, rms radial error=133.377, avgs=0 260/300: dt: 0.9000, rms radial error=132.624, avgs=0 265/300: dt: 0.9000, rms radial error=131.876, avgs=0 270/300: dt: 0.9000, rms radial error=131.132, avgs=0 275/300: dt: 0.9000, rms radial error=130.392, avgs=0 280/300: dt: 0.9000, rms radial error=129.656, avgs=0 285/300: dt: 0.9000, rms radial error=128.924, avgs=0 290/300: dt: 0.9000, rms radial error=128.196, avgs=0 295/300: dt: 0.9000, rms radial error=127.472, avgs=0 300/300: dt: 0.9000, rms radial error=126.753, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 21528.52 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 2 (K=40.0), pass 1, starting sse = 3756.78 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00008 epoch 3 (K=160.0), pass 1, starting sse = 405.39 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/11 = 0.00781 epoch 4 (K=640.0), pass 1, starting sse = 25.92 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.20/19 = 0.01070 final distance error %25.54 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.09 hours mris_sphere utimesec 334.626151 mris_sphere stimesec 0.067949 mris_sphere ru_maxrss 229068 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 28798 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 12624 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 1 mris_sphere ru_nivcsw 32345 FSRUNTIME@ mris_sphere 0.0930 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Mon Jan 15 23:34:43 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Mon Jan 15 23:34:43 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Mon Jan 15 23:34:43 EST 2018 mris_fix_topology -rusage /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 icbm-205 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-70 (nv=176994, nf=354128, ne=531192, g=36) 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... 5722 ambiguous faces found in tessellation segmenting defects... 46 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 46 defects to be corrected 0 vertices coincident reading input surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.5408 (-4.2704) -vertex loglikelihood: -5.2815 (-2.6408) -normal dot loglikelihood: -3.5818 (-3.5818) -quad curv loglikelihood: -6.0559 (-3.0280) Total Loglikelihood : -23.4601 CORRECTING DEFECT 0 (vertices=34, convex hull=70, v0=6698) After retessellation of defect 0 (v0=6698), euler #=-42 (173567,519458,345849) : difference with theory (-43) = -1 CORRECTING DEFECT 1 (vertices=37, convex hull=82, v0=8771) After retessellation of defect 1 (v0=8771), euler #=-41 (173588,519554,345925) : difference with theory (-42) = -1 CORRECTING DEFECT 2 (vertices=27, convex hull=67, v0=12592) After retessellation of defect 2 (v0=12592), euler #=-40 (173597,519606,345969) : difference with theory (-41) = -1 CORRECTING DEFECT 3 (vertices=693, convex hull=226, v0=14976) After retessellation of defect 3 (v0=14976), euler #=-39 (173695,520005,346271) : difference with theory (-40) = -1 CORRECTING DEFECT 4 (vertices=82, convex hull=111, v0=25380) After retessellation of defect 4 (v0=25380), euler #=-38 (173727,520145,346380) : difference with theory (-39) = -1 CORRECTING DEFECT 5 (vertices=32, convex hull=55, v0=33954) After retessellation of defect 5 (v0=33954), euler #=-37 (173738,520200,346425) : difference with theory (-38) = -1 CORRECTING DEFECT 6 (vertices=40, convex hull=72, v0=35581) After retessellation of defect 6 (v0=35581), euler #=-36 (173761,520298,346501) : difference with theory (-37) = -1 CORRECTING DEFECT 7 (vertices=20, convex hull=24, v0=43434) After retessellation of defect 7 (v0=43434), euler #=-35 (173763,520311,346513) : difference with theory (-36) = -1 CORRECTING DEFECT 8 (vertices=19, convex hull=52, v0=57046) After retessellation of defect 8 (v0=57046), euler #=-34 (173772,520357,346551) : difference with theory (-35) = -1 CORRECTING DEFECT 9 (vertices=65, convex hull=82, v0=62695) After retessellation of defect 9 (v0=62695), euler #=-33 (173795,520459,346631) : difference with theory (-34) = -1 CORRECTING DEFECT 10 (vertices=50, convex hull=77, v0=71378) After retessellation of defect 10 (v0=71378), euler #=-32 (173827,520588,346729) : difference with theory (-33) = -1 CORRECTING DEFECT 11 (vertices=11, convex hull=34, v0=75276) After retessellation of defect 11 (v0=75276), euler #=-31 (173830,520607,346746) : difference with theory (-32) = -1 CORRECTING DEFECT 12 (vertices=145, convex hull=79, v0=88661) After retessellation of defect 12 (v0=88661), euler #=-30 (173840,520671,346801) : difference with theory (-31) = -1 CORRECTING DEFECT 13 (vertices=46, convex hull=76, v0=95441) After retessellation of defect 13 (v0=95441), euler #=-29 (173864,520773,346880) : difference with theory (-30) = -1 CORRECTING DEFECT 14 (vertices=16, convex hull=59, v0=96539) After retessellation of defect 14 (v0=96539), euler #=-28 (173874,520825,346923) : difference with theory (-29) = -1 CORRECTING DEFECT 15 (vertices=202, convex hull=64, v0=104318) After retessellation of defect 15 (v0=104318), euler #=-27 (173898,520920,346995) : difference with theory (-28) = -1 CORRECTING DEFECT 16 (vertices=35, convex hull=22, v0=104883) After retessellation of defect 16 (v0=104883), euler #=-26 (173904,520945,347015) : difference with theory (-27) = -1 CORRECTING DEFECT 17 (vertices=31, convex hull=26, v0=112548) After retessellation of defect 17 (v0=112548), euler #=-25 (173907,520963,347031) : difference with theory (-26) = -1 CORRECTING DEFECT 18 (vertices=193, convex hull=141, v0=112639) After retessellation of defect 18 (v0=112639), euler #=-24 (173967,521202,347211) : difference with theory (-25) = -1 CORRECTING DEFECT 19 (vertices=20, convex hull=18, v0=115152) After retessellation of defect 19 (v0=115152), euler #=-23 (173971,521220,347226) : difference with theory (-24) = -1 CORRECTING DEFECT 20 (vertices=34, convex hull=44, v0=117780) After retessellation of defect 20 (v0=117780), euler #=-22 (173980,521262,347260) : difference with theory (-23) = -1 CORRECTING DEFECT 21 (vertices=255, convex hull=74, v0=121758) After retessellation of defect 21 (v0=121758), euler #=-21 (173988,521321,347312) : difference with theory (-22) = -1 CORRECTING DEFECT 22 (vertices=13, convex hull=22, v0=123947) After retessellation of defect 22 (v0=123947), euler #=-20 (173990,521333,347323) : difference with theory (-21) = -1 CORRECTING DEFECT 23 (vertices=45, convex hull=23, v0=124302) After retessellation of defect 23 (v0=124302), euler #=-19 (173997,521360,347344) : difference with theory (-20) = -1 CORRECTING DEFECT 24 (vertices=57, convex hull=29, v0=126587) After retessellation of defect 24 (v0=126587), euler #=-18 (174004,521389,347367) : difference with theory (-19) = -1 CORRECTING DEFECT 25 (vertices=40, convex hull=28, v0=129324) After retessellation of defect 25 (v0=129324), euler #=-17 (174012,521420,347391) : difference with theory (-18) = -1 CORRECTING DEFECT 26 (vertices=27, convex hull=22, v0=131588) After retessellation of defect 26 (v0=131588), euler #=-16 (174016,521439,347407) : difference with theory (-17) = -1 CORRECTING DEFECT 27 (vertices=43, convex hull=82, v0=133794) After retessellation of defect 27 (v0=133794), euler #=-15 (174048,521566,347503) : difference with theory (-16) = -1 CORRECTING DEFECT 28 (vertices=50, convex hull=87, v0=134713) After retessellation of defect 28 (v0=134713), euler #=-14 (174057,521631,347560) : difference with theory (-15) = -1 CORRECTING DEFECT 29 (vertices=52, convex hull=89, v0=137956) After retessellation of defect 29 (v0=137956), euler #=-13 (174080,521735,347642) : difference with theory (-14) = -1 CORRECTING DEFECT 30 (vertices=37, convex hull=54, v0=138215) After retessellation of defect 30 (v0=138215), euler #=-12 (174088,521778,347678) : difference with theory (-13) = -1 CORRECTING DEFECT 31 (vertices=11, convex hull=13, v0=142138) After retessellation of defect 31 (v0=142138), euler #=-11 (174091,521790,347688) : difference with theory (-12) = -1 CORRECTING DEFECT 32 (vertices=39, convex hull=62, v0=142864) After retessellation of defect 32 (v0=142864), euler #=-10 (174104,521857,347743) : difference with theory (-11) = -1 CORRECTING DEFECT 33 (vertices=123, convex hull=75, v0=142878) After retessellation of defect 33 (v0=142878), euler #=-9 (174129,521967,347829) : difference with theory (-10) = -1 CORRECTING DEFECT 34 (vertices=118, convex hull=58, v0=142908) After retessellation of defect 34 (v0=142908), euler #=-8 (174148,522050,347894) : difference with theory (-9) = -1 CORRECTING DEFECT 35 (vertices=7, convex hull=25, v0=146308) After retessellation of defect 35 (v0=146308), euler #=-7 (174151,522066,347908) : difference with theory (-8) = -1 CORRECTING DEFECT 36 (vertices=137, convex hull=142, v0=154672) After retessellation of defect 36 (v0=154672), euler #=-6 (174201,522285,348078) : difference with theory (-7) = -1 CORRECTING DEFECT 37 (vertices=30, convex hull=61, v0=157715) After retessellation of defect 37 (v0=157715), euler #=-5 (174210,522339,348124) : difference with theory (-6) = -1 CORRECTING DEFECT 38 (vertices=109, convex hull=121, v0=158837) After retessellation of defect 38 (v0=158837), euler #=-5 (174267,522574,348302) : difference with theory (-5) = 0 CORRECTING DEFECT 39 (vertices=50, convex hull=78, v0=159485) After retessellation of defect 39 (v0=159485), euler #=-4 (174292,522681,348385) : difference with theory (-4) = 0 CORRECTING DEFECT 40 (vertices=191, convex hull=119, v0=160294) After retessellation of defect 40 (v0=160294), euler #=-3 (174348,522901,348550) : difference with theory (-3) = 0 CORRECTING DEFECT 41 (vertices=44, convex hull=73, v0=162221) After retessellation of defect 41 (v0=162221), euler #=-2 (174364,522977,348611) : difference with theory (-2) = 0 CORRECTING DEFECT 42 (vertices=15, convex hull=37, v0=171293) After retessellation of defect 42 (v0=171293), euler #=-1 (174367,523000,348632) : difference with theory (-1) = 0 CORRECTING DEFECT 43 (vertices=37, convex hull=69, v0=171354) After retessellation of defect 43 (v0=171354), euler #=0 (174378,523060,348682) : difference with theory (0) = 0 CORRECTING DEFECT 44 (vertices=40, convex hull=77, v0=172200) After retessellation of defect 44 (v0=172200), euler #=1 (174402,523167,348766) : difference with theory (1) = 0 CORRECTING DEFECT 45 (vertices=43, convex hull=73, v0=172549) After retessellation of defect 45 (v0=172549), euler #=2 (174418,523248,348832) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.22 (0.05-->8.34) (max @ vno 121126 --> 126010) 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 (0.05-->8.34) (max @ vno 121126 --> 126010) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 173 mutations (33.7%), 341 crossovers (66.3%), 171 vertices were eliminated building final representation... 2576 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=174418, nf=348832, ne=523248, g=0) writing corrected surface to /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 34.3 minutes 0 defective edges removing intersecting faces 000: 275 intersecting mris_fix_topology utimesec 2056.689996 mris_fix_topology stimesec 0.195852 mris_fix_topology ru_maxrss 538696 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 54503 mris_fix_topology ru_majflt 25 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 4448 mris_fix_topology ru_oublock 16424 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 39 mris_fix_topology ru_nivcsw 177913 FSRUNTIME@ mris_fix_topology lh 0.5718 hours 1 threads #@# Fix Topology rh Tue Jan 16 00:09:01 EST 2018 mris_fix_topology -rusage /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 icbm-205 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-62 (nv=179378, nf=358880, ne=538320, g=32) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 7 iterations marking ambiguous vertices... 6768 ambiguous faces found in tessellation segmenting defects... 39 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 20 into 19 -merging segment 32 into 31 37 defects to be corrected 0 vertices coincident reading input surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.6132 (-4.3066) -vertex loglikelihood: -5.2775 (-2.6388) -normal dot loglikelihood: -3.5798 (-3.5798) -quad curv loglikelihood: -5.9112 (-2.9556) Total Loglikelihood : -23.3817 CORRECTING DEFECT 0 (vertices=379, convex hull=218, v0=489) After retessellation of defect 0 (v0=489), euler #=-36 (175494,525303,349773) : difference with theory (-34) = 2 CORRECTING DEFECT 1 (vertices=725, convex hull=215, v0=13599) After retessellation of defect 1 (v0=13599), euler #=-35 (175538,525544,349971) : difference with theory (-33) = 2 CORRECTING DEFECT 2 (vertices=16, convex hull=57, v0=26901) After retessellation of defect 2 (v0=26901), euler #=-34 (175546,525587,350007) : difference with theory (-32) = 2 CORRECTING DEFECT 3 (vertices=21, convex hull=61, v0=33457) After retessellation of defect 3 (v0=33457), euler #=-33 (175556,525640,350051) : difference with theory (-31) = 2 CORRECTING DEFECT 4 (vertices=20, convex hull=69, v0=49494) After retessellation of defect 4 (v0=49494), euler #=-32 (175568,525700,350100) : difference with theory (-30) = 2 CORRECTING DEFECT 5 (vertices=5, convex hull=16, v0=55075) After retessellation of defect 5 (v0=55075), euler #=-31 (175568,525704,350105) : difference with theory (-29) = 2 CORRECTING DEFECT 6 (vertices=53, convex hull=71, v0=59473) After retessellation of defect 6 (v0=59473), euler #=-30 (175599,525826,350197) : difference with theory (-28) = 2 CORRECTING DEFECT 7 (vertices=41, convex hull=97, v0=65256) After retessellation of defect 7 (v0=65256), euler #=-29 (175620,525927,350278) : difference with theory (-27) = 2 CORRECTING DEFECT 8 (vertices=37, convex hull=33, v0=85241) After retessellation of defect 8 (v0=85241), euler #=-28 (175624,525950,350298) : difference with theory (-26) = 2 CORRECTING DEFECT 9 (vertices=33, convex hull=74, v0=89583) After retessellation of defect 9 (v0=89583), euler #=-27 (175647,526045,350371) : difference with theory (-25) = 2 CORRECTING DEFECT 10 (vertices=68, convex hull=33, v0=102036) After retessellation of defect 10 (v0=102036), euler #=-26 (175652,526073,350395) : difference with theory (-24) = 2 CORRECTING DEFECT 11 (vertices=64, convex hull=57, v0=103319) After retessellation of defect 11 (v0=103319), euler #=-25 (175667,526140,350448) : difference with theory (-23) = 2 CORRECTING DEFECT 12 (vertices=23, convex hull=34, v0=104618) After retessellation of defect 12 (v0=104618), euler #=-24 (175672,526167,350471) : difference with theory (-22) = 2 CORRECTING DEFECT 13 (vertices=36, convex hull=41, v0=104873) After retessellation of defect 13 (v0=104873), euler #=-23 (175673,526192,350496) : difference with theory (-21) = 2 CORRECTING DEFECT 14 (vertices=166, convex hull=68, v0=106493) After retessellation of defect 14 (v0=106493), euler #=-22 (175681,526246,350543) : difference with theory (-20) = 2 CORRECTING DEFECT 15 (vertices=103, convex hull=135, v0=111916) After retessellation of defect 15 (v0=111916), euler #=-21 (175716,526411,350674) : difference with theory (-19) = 2 CORRECTING DEFECT 16 (vertices=165, convex hull=158, v0=113173) After retessellation of defect 16 (v0=113173), euler #=-20 (175739,526548,350789) : difference with theory (-18) = 2 CORRECTING DEFECT 17 (vertices=14, convex hull=34, v0=113351) After retessellation of defect 17 (v0=113351), euler #=-19 (175741,526566,350806) : difference with theory (-17) = 2 CORRECTING DEFECT 18 (vertices=101, convex hull=79, v0=118793) After retessellation of defect 18 (v0=118793), euler #=-18 (175779,526714,350917) : difference with theory (-16) = 2 CORRECTING DEFECT 19 (vertices=254, convex hull=102, v0=118830) After retessellation of defect 19 (v0=118830), euler #=-16 (175795,526817,351006) : difference with theory (-15) = 1 CORRECTING DEFECT 20 (vertices=75, convex hull=52, v0=121212) After retessellation of defect 20 (v0=121212), euler #=-15 (175810,526882,351057) : difference with theory (-14) = 1 CORRECTING DEFECT 21 (vertices=166, convex hull=88, v0=122679) After retessellation of defect 21 (v0=122679), euler #=-14 (175833,526990,351143) : difference with theory (-13) = 1 CORRECTING DEFECT 22 (vertices=690, convex hull=296, v0=125194) After retessellation of defect 22 (v0=125194), euler #=-13 (176003,527653,351637) : difference with theory (-12) = 1 CORRECTING DEFECT 23 (vertices=19, convex hull=26, v0=127528) After retessellation of defect 23 (v0=127528), euler #=-12 (176006,527673,351655) : difference with theory (-11) = 1 CORRECTING DEFECT 24 (vertices=87, convex hull=64, v0=129013) After retessellation of defect 24 (v0=129013), euler #=-11 (176024,527755,351720) : difference with theory (-10) = 1 CORRECTING DEFECT 25 (vertices=9, convex hull=22, v0=131872) After retessellation of defect 25 (v0=131872), euler #=-10 (176027,527771,351734) : difference with theory (-9) = 1 CORRECTING DEFECT 26 (vertices=20, convex hull=31, v0=134244) After retessellation of defect 26 (v0=134244), euler #=-9 (176032,527797,351756) : difference with theory (-8) = 1 CORRECTING DEFECT 27 (vertices=30, convex hull=50, v0=136740) After retessellation of defect 27 (v0=136740), euler #=-8 (176043,527847,351796) : difference with theory (-7) = 1 CORRECTING DEFECT 28 (vertices=195, convex hull=198, v0=136908) After retessellation of defect 28 (v0=136908), euler #=-7 (176134,528211,352070) : difference with theory (-6) = 1 CORRECTING DEFECT 29 (vertices=28, convex hull=24, v0=140399) After retessellation of defect 29 (v0=140399), euler #=-6 (176140,528235,352089) : difference with theory (-5) = 1 CORRECTING DEFECT 30 (vertices=58, convex hull=133, v0=153192) After retessellation of defect 30 (v0=153192), euler #=-4 (176171,528401,352226) : difference with theory (-4) = 0 CORRECTING DEFECT 31 (vertices=19, convex hull=21, v0=156266) After retessellation of defect 31 (v0=156266), euler #=-3 (176172,528410,352235) : difference with theory (-3) = 0 CORRECTING DEFECT 32 (vertices=44, convex hull=22, v0=158130) After retessellation of defect 32 (v0=158130), euler #=-2 (176172,528417,352243) : difference with theory (-2) = 0 CORRECTING DEFECT 33 (vertices=120, convex hull=61, v0=159774) After retessellation of defect 33 (v0=159774), euler #=-1 (176192,528502,352309) : difference with theory (-1) = 0 CORRECTING DEFECT 34 (vertices=41, convex hull=75, v0=160197) After retessellation of defect 34 (v0=160197), euler #=0 (176216,528606,352390) : difference with theory (0) = 0 CORRECTING DEFECT 35 (vertices=17, convex hull=48, v0=174217) After retessellation of defect 35 (v0=174217), euler #=1 (176223,528644,352422) : difference with theory (1) = 0 CORRECTING DEFECT 36 (vertices=24, convex hull=51, v0=174651) After retessellation of defect 36 (v0=174651), euler #=2 (176232,528690,352460) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.22 (0.03-->11.64) (max @ vno 3195 --> 5712) 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 (0.03-->11.64) (max @ vno 3195 --> 5712) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 130 mutations (35.8%), 233 crossovers (64.2%), 217 vertices were eliminated building final representation... 3146 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=176232, nf=352460, ne=528690, g=0) writing corrected surface to /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 34.5 minutes 0 defective edges removing intersecting faces 000: 331 intersecting mris_fix_topology utimesec 2068.148082 mris_fix_topology stimesec 0.623608 mris_fix_topology ru_maxrss 544964 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 56025 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 16624 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 9 mris_fix_topology ru_nivcsw 195215 FSRUNTIME@ mris_fix_topology rh 0.5750 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 174418 - 523248 + 348832 = 2 --> 0 holes F =2V-4: 348832 = 348836-4 (0) 2E=3F: 1046496 = 1046496 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 176232 - 528690 + 352460 = 2 --> 0 holes F =2V-4: 352460 = 352464-4 (0) 2E=3F: 1057380 = 1057380 (0) total defect index = 0 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 21 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 35 intersecting 001: 3 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Tue Jan 16 00:43:44 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs icbm-205 lh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/filled.mgz... reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/brain.finalsurfs.mgz... reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/../mri/aseg.presurf.mgz... reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/wm.mgz... 15250 bright wm thresholded. 1356 bright non-wm voxels segmented. reading original surface position from /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.orig... computing class statistics... border white: 337784 voxels (2.01%) border gray 364708 voxels (2.17%) WM (99.0): 99.8 +- 5.5 [70.0 --> 110.0] GM (84.0) : 83.0 +- 8.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 72.1 (was 70) setting MAX_BORDER_WHITE to 107.5 (was 105) setting MIN_BORDER_WHITE to 81.0 (was 85) setting MAX_CSF to 63.1 (was 40) setting MAX_GRAY to 96.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 72.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 54.2 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.21 (0.03-->3.21) (max @ vno 28044 --> 32594) face area 0.28 +- 0.12 (0.00-->2.50) mean absolute distance = 0.81 +- 1.01 5309 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-4.3, GM=81+-7.0 mean inside = 96.7, mean outside = 86.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=88.9, 125 (125) missing vertices, mean dist 0.3 [0.7 (%33.7)->0.8 (%66.3))] %55 local maxima, %41 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=kapla, 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 0.92 +- 0.25 (0.06-->3.37) (max @ vno 160199 --> 174305) face area 0.28 +- 0.13 (0.00-->2.74) mean absolute distance = 0.51 +- 0.88 7314 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2040248.1, rms=6.257 001: dt: 0.5000, sse=1370936.9, rms=4.435 (29.125%) 002: dt: 0.5000, sse=1053213.0, rms=3.207 (27.689%) 003: dt: 0.5000, sse=902797.1, rms=2.406 (24.987%) 004: dt: 0.5000, sse=832409.7, rms=1.912 (20.506%) 005: dt: 0.5000, sse=801334.4, rms=1.637 (14.407%) 006: dt: 0.5000, sse=788675.0, rms=1.503 (8.185%) 007: dt: 0.5000, sse=783763.9, rms=1.441 (4.113%) rms = 1.42, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=781562.9, rms=1.416 (1.703%) 009: dt: 0.2500, sse=762090.1, rms=1.080 (23.750%) rms = 1.05, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=759740.8, rms=1.053 (2.543%) rms = 1.05, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=759524.7, rms=1.046 (0.629%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=90.8, 41 (15) missing vertices, mean dist -0.3 [0.6 (%65.9)->0.3 (%34.1))] %65 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=kapla, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.10-->3.87) (max @ vno 87519 --> 88822) face area 0.35 +- 0.16 (0.00-->2.88) mean absolute distance = 0.44 +- 0.60 7693 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1248790.2, rms=3.287 012: dt: 0.5000, sse=1029486.8, rms=2.099 (36.156%) 013: dt: 0.5000, sse=963208.1, rms=1.583 (24.595%) 014: dt: 0.5000, sse=937125.5, rms=1.321 (16.509%) 015: dt: 0.5000, sse=923420.9, rms=1.160 (12.238%) 016: dt: 0.5000, sse=919006.4, rms=1.094 (5.633%) rms = 1.05, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=917150.6, rms=1.053 (3.744%) 018: dt: 0.2500, sse=906598.8, rms=0.863 (18.058%) rms = 0.84, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=906095.6, rms=0.841 (2.550%) rms = 0.83, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=904851.8, rms=0.835 (0.772%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=92.8, 29 (7) missing vertices, mean dist -0.3 [0.5 (%70.4)->0.2 (%29.6))] %79 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=kapla, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.88 +- 0.24 (0.05-->3.97) (max @ vno 87519 --> 88822) face area 0.34 +- 0.16 (0.00-->2.85) mean absolute distance = 0.33 +- 0.44 5969 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1129600.9, rms=2.909 021: dt: 0.5000, sse=937620.6, rms=1.624 (44.177%) 022: dt: 0.5000, sse=893818.1, rms=1.124 (30.774%) 023: dt: 0.5000, sse=886451.0, rms=0.948 (15.649%) 024: dt: 0.5000, sse=877303.7, rms=0.894 (5.678%) rms = 0.93, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=873215.8, rms=0.806 (9.838%) rms = 0.78, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=873568.1, rms=0.775 (3.848%) rms = 0.77, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=873476.9, rms=0.773 (0.309%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=93.7, 44 (6) missing vertices, mean dist -0.1 [0.4 (%60.1)->0.3 (%39.9))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=kapla, 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-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=894862.6, rms=1.464 028: dt: 0.5000, sse=845553.9, rms=0.736 (49.738%) rms = 0.75, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=839396.1, rms=0.681 (7.479%) rms = 0.65, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=840789.3, rms=0.649 (4.665%) rms = 0.64, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=838768.0, rms=0.641 (1.147%) positioning took 0.6 minutes generating cortex label... 7 non-cortical segments detected only using segment with 9360 vertices erasing segment 1 (vno[0] = 89028) erasing segment 2 (vno[0] = 111136) erasing segment 3 (vno[0] = 119817) erasing segment 4 (vno[0] = 124745) erasing segment 5 (vno[0] = 125865) erasing segment 6 (vno[0] = 131252) writing cortex label to /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/lh.cortex.label... writing curvature file /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.curv writing smoothed area to lh.area writing curvature file /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.area vertex spacing 0.88 +- 0.25 (0.03-->4.02) (max @ vno 87519 --> 88822) face area 0.32 +- 0.15 (0.00-->2.67) refinement took 6.3 minutes #-------------------------------------------- #@# Make White Surf rh Tue Jan 16 00:50:03 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs icbm-205 rh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/filled.mgz... reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/brain.finalsurfs.mgz... reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/../mri/aseg.presurf.mgz... reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/wm.mgz... 15250 bright wm thresholded. 1356 bright non-wm voxels segmented. reading original surface position from /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.orig... computing class statistics... border white: 337784 voxels (2.01%) border gray 364708 voxels (2.17%) WM (99.0): 99.8 +- 5.5 [70.0 --> 110.0] GM (84.0) : 83.0 +- 8.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 72.1 (was 70) setting MAX_BORDER_WHITE to 107.5 (was 105) setting MIN_BORDER_WHITE to 81.0 (was 85) setting MAX_CSF to 63.1 (was 40) setting MAX_GRAY to 96.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 72.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 54.2 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.21 (0.04-->4.12) (max @ vno 5713 --> 175482) face area 0.28 +- 0.12 (0.00-->3.11) mean absolute distance = 0.79 +- 0.99 5310 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-4.3, GM=81+-7.0 mean inside = 96.7, mean outside = 86.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=89.1, 45 (45) missing vertices, mean dist 0.3 [0.7 (%34.3)->0.8 (%65.7))] %55 local maxima, %40 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=kapla, 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 0.92 +- 0.25 (0.09-->4.02) (max @ vno 108719 --> 106094) face area 0.28 +- 0.13 (0.00-->3.01) mean absolute distance = 0.51 +- 0.88 7592 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1980203.6, rms=6.051 001: dt: 0.5000, sse=1329940.9, rms=4.251 (29.750%) 002: dt: 0.5000, sse=1031892.9, rms=3.059 (28.050%) 003: dt: 0.5000, sse=894656.5, rms=2.302 (24.723%) 004: dt: 0.5000, sse=831806.4, rms=1.846 (19.815%) 005: dt: 0.5000, sse=804074.6, rms=1.594 (13.637%) 006: dt: 0.5000, sse=792686.4, rms=1.468 (7.934%) 007: dt: 0.5000, sse=788117.4, rms=1.409 (3.984%) rms = 1.38, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=785557.4, rms=1.384 (1.826%) 009: dt: 0.2500, sse=764202.4, rms=1.015 (26.655%) rms = 0.98, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=761229.6, rms=0.980 (3.473%) rms = 0.97, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=760802.4, rms=0.972 (0.766%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=90.9, 49 (4) missing vertices, mean dist -0.3 [0.7 (%63.9)->0.3 (%36.1))] %63 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=kapla, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.06-->4.22) (max @ vno 108719 --> 106094) face area 0.35 +- 0.16 (0.00-->3.57) mean absolute distance = 0.45 +- 0.62 7011 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1239824.6, rms=3.215 012: dt: 0.5000, sse=1030805.6, rms=2.054 (36.123%) 013: dt: 0.5000, sse=964958.6, rms=1.547 (24.684%) 014: dt: 0.5000, sse=941843.6, rms=1.306 (15.560%) 015: dt: 0.5000, sse=931274.1, rms=1.166 (10.719%) rms = 1.12, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=926260.7, rms=1.116 (4.272%) 017: dt: 0.2500, sse=916318.7, rms=0.934 (16.298%) rms = 0.90, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=915344.6, rms=0.904 (3.232%) rms = 0.89, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=913960.8, rms=0.894 (1.179%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group mean border=92.9, 48 (2) missing vertices, mean dist -0.3 [0.5 (%68.5)->0.3 (%31.5))] %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=kapla, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.88 +- 0.24 (0.06-->4.31) (max @ vno 108719 --> 106094) face area 0.34 +- 0.16 (0.00-->3.70) mean absolute distance = 0.35 +- 0.46 5541 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1132041.6, rms=2.862 020: dt: 0.5000, sse=947871.3, rms=1.630 (43.043%) 021: dt: 0.5000, sse=908927.0, rms=1.140 (30.042%) 022: dt: 0.5000, sse=892423.8, rms=0.974 (14.616%) 023: dt: 0.5000, sse=888272.8, rms=0.918 (5.754%) rms = 0.95, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=883400.4, rms=0.832 (9.350%) rms = 0.80, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=883080.2, rms=0.803 (3.430%) rms = 0.80, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=892707.8, rms=0.801 (0.323%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group mean border=93.7, 72 (2) missing vertices, mean dist -0.1 [0.4 (%59.7)->0.3 (%40.3))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=kapla, 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-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=917748.1, rms=1.507 027: dt: 0.5000, sse=858794.4, rms=0.765 (49.214%) rms = 0.77, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=851407.8, rms=0.710 (7.256%) rms = 0.68, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=851463.2, rms=0.675 (4.861%) rms = 0.67, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=849349.9, rms=0.667 (1.286%) positioning took 0.6 minutes generating cortex label... 10 non-cortical segments detected only using segment with 9250 vertices erasing segment 1 (vno[0] = 93556) erasing segment 2 (vno[0] = 109655) erasing segment 3 (vno[0] = 109668) erasing segment 4 (vno[0] = 115120) erasing segment 5 (vno[0] = 116802) erasing segment 6 (vno[0] = 117539) erasing segment 7 (vno[0] = 120272) erasing segment 8 (vno[0] = 125013) erasing segment 9 (vno[0] = 129068) writing cortex label to /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/rh.cortex.label... writing curvature file /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.curv writing smoothed area to rh.area writing curvature file /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.area vertex spacing 0.88 +- 0.25 (0.04-->4.36) (max @ vno 106094 --> 108719) face area 0.32 +- 0.15 (0.00-->3.74) refinement took 6.3 minutes #-------------------------------------------- #@# Smooth2 lh Tue Jan 16 00:56:22 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth2 rh Tue Jan 16 00:56:29 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Tue Jan 16 00:56:36 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_inflate -rusage /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 51.8 mm, total surface area = 103127 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.164 (target=0.015) step 005: RMS=0.116 (target=0.015) step 010: RMS=0.087 (target=0.015) step 015: RMS=0.072 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.022 (target=0.015) step 060: RMS=0.021 (target=0.015) inflation complete. inflation took 0.7 minutes mris_inflate utimesec 44.397012 mris_inflate stimesec 0.095924 mris_inflate ru_maxrss 222692 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 28226 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 13640 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 3750 #-------------------------------------------- #@# Inflation2 rh Tue Jan 16 00:57:21 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_inflate -rusage /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 51.5 mm, total surface area = 104085 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.165 (target=0.015) step 005: RMS=0.117 (target=0.015) step 010: RMS=0.089 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. inflation took 0.7 minutes mris_inflate utimesec 44.777959 mris_inflate stimesec 0.071951 mris_inflate ru_maxrss 224984 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 28288 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 13784 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 3787 #-------------------------------------------- #@# Curv .H and .K lh Tue Jan 16 00:58:06 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf mris_curvature -w lh.white.preaparc total integrated curvature = 1.960*4pi (24.627) --> -1 handles ICI = 196.3, FI = 1673.3, variation=27716.585 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 218 vertices thresholded to be in k1 ~ [-0.21 1.34], k2 ~ [-0.11 0.04] total integrated curvature = 0.448*4pi (5.628) --> 1 handles ICI = 1.6, FI = 12.9, variation=209.027 170 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 149 vertices thresholded to be in [-0.13 0.34] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.025 done. #-------------------------------------------- #@# Curv .H and .K rh Tue Jan 16 00:59:59 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf mris_curvature -w rh.white.preaparc total integrated curvature = 5.897*4pi (74.106) --> -5 handles ICI = 205.8, FI = 1689.8, variation=28231.099 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 235 vertices thresholded to be in k1 ~ [-0.30 0.52], k2 ~ [-0.13 0.07] total integrated curvature = 0.370*4pi (4.653) --> 1 handles ICI = 1.7, FI = 13.1, variation=216.162 172 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 172 vertices thresholded to be in [-0.15 0.23] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.025 done. #----------------------------------------- #@# Curvature Stats lh Tue Jan 16 01:01:55 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm icbm-205 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 [ icbm-205/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 [ 335 ] Gb_filter = 0 WARN: S lookup min: -0.339294 WARN: S explicit min: 0.000000 vertex = 587 #----------------------------------------- #@# Curvature Stats rh Tue Jan 16 01:02:00 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm icbm-205 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 [ icbm-205/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 [ 348 ] Gb_filter = 0 WARN: S lookup min: -0.205061 WARN: S explicit min: 0.000000 vertex = 33 #-------------------------------------------- #@# Sphere lh Tue Jan 16 01:02:05 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_sphere -rusage /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.267... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=kapla, 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 %19.04 pass 1: epoch 2 of 3 starting distance error %18.99 unfolding complete - removing small folds... starting distance error %18.94 removing remaining folds... final distance error %18.96 MRISunfold() return, current seed 1234 -01: dt=0.0000, 111 negative triangles 178: dt=0.9900, 111 negative triangles 179: dt=0.9900, 85 negative triangles 180: dt=0.9900, 76 negative triangles 181: dt=0.9900, 71 negative triangles 182: dt=0.9900, 62 negative triangles 183: dt=0.9900, 66 negative triangles 184: dt=0.9900, 61 negative triangles 185: dt=0.9900, 57 negative triangles 186: dt=0.9900, 59 negative triangles 187: dt=0.9900, 58 negative triangles 188: dt=0.9900, 51 negative triangles 189: dt=0.9900, 50 negative triangles 190: dt=0.9900, 54 negative triangles 191: dt=0.9900, 51 negative triangles 192: dt=0.9900, 40 negative triangles 193: dt=0.9900, 36 negative triangles 194: dt=0.9900, 36 negative triangles 195: dt=0.9900, 46 negative triangles 196: dt=0.9900, 36 negative triangles 197: dt=0.9900, 41 negative triangles 198: dt=0.9900, 41 negative triangles 199: dt=0.9900, 40 negative triangles 200: dt=0.9900, 42 negative triangles 201: dt=0.9900, 48 negative triangles 202: dt=0.9900, 45 negative triangles 203: dt=0.9405, 46 negative triangles 204: dt=0.9405, 39 negative triangles 205: dt=0.9405, 47 negative triangles 206: dt=0.9405, 47 negative triangles 207: dt=0.9405, 47 negative triangles 208: dt=0.9405, 42 negative triangles 209: dt=0.9405, 42 negative triangles 210: dt=0.9405, 43 negative triangles 211: dt=0.9405, 47 negative triangles 212: dt=0.9405, 41 negative triangles 213: dt=0.8935, 45 negative triangles 214: dt=0.8935, 43 negative triangles 215: dt=0.8935, 45 negative triangles 216: dt=0.8935, 44 negative triangles 217: dt=0.8935, 45 negative triangles 218: dt=0.8935, 42 negative triangles 219: dt=0.8935, 42 negative triangles 220: dt=0.8935, 41 negative triangles 221: dt=0.8935, 45 negative triangles 222: dt=0.8935, 47 negative triangles 223: dt=0.8488, 47 negative triangles 224: dt=0.8488, 43 negative triangles 225: dt=0.8488, 44 negative triangles 226: dt=0.8488, 45 negative triangles 227: dt=0.8488, 45 negative triangles 228: dt=0.8488, 47 negative triangles 229: dt=0.8488, 43 negative triangles 230: dt=0.8488, 47 negative triangles 231: dt=0.8488, 48 negative triangles 232: dt=0.8488, 46 negative triangles 233: dt=0.8064, 44 negative triangles 234: dt=0.8064, 48 negative triangles 235: dt=0.8064, 43 negative triangles 236: dt=0.8064, 50 negative triangles 237: dt=0.8064, 46 negative triangles 238: dt=0.8064, 52 negative triangles 239: dt=0.8064, 50 negative triangles 240: dt=0.8064, 47 negative triangles 241: dt=0.8064, 48 negative triangles 242: dt=0.8064, 45 negative triangles 243: dt=0.7660, 48 negative triangles expanding nbhd size to 1 244: dt=0.9900, 48 negative triangles 245: dt=0.9900, 45 negative triangles 246: dt=0.9900, 41 negative triangles 247: dt=0.9900, 39 negative triangles 248: dt=0.9900, 35 negative triangles 249: dt=0.9900, 34 negative triangles 250: dt=0.9900, 31 negative triangles 251: dt=0.9900, 32 negative triangles 252: dt=0.9900, 36 negative triangles 253: dt=0.9900, 35 negative triangles 254: dt=0.9900, 31 negative triangles 255: dt=0.9900, 32 negative triangles 256: dt=0.9900, 38 negative triangles 257: dt=0.9900, 34 negative triangles 258: dt=0.9900, 34 negative triangles 259: dt=0.9900, 36 negative triangles 260: dt=0.9405, 37 negative triangles 261: dt=0.9405, 35 negative triangles 262: dt=0.9405, 33 negative triangles 263: dt=0.9405, 33 negative triangles 264: dt=0.9405, 33 negative triangles 265: dt=0.9405, 32 negative triangles 266: dt=0.9405, 33 negative triangles 267: dt=0.9405, 33 negative triangles 268: dt=0.9405, 32 negative triangles 269: dt=0.9405, 31 negative triangles 270: dt=0.8935, 31 negative triangles 271: dt=0.8935, 30 negative triangles 272: dt=0.8935, 33 negative triangles 273: dt=0.8935, 32 negative triangles 274: dt=0.8935, 33 negative triangles 275: dt=0.8935, 34 negative triangles 276: dt=0.8935, 32 negative triangles 277: dt=0.8935, 32 negative triangles 278: dt=0.8935, 35 negative triangles 279: dt=0.8935, 36 negative triangles 280: dt=0.8935, 33 negative triangles 281: dt=0.8488, 31 negative triangles 282: dt=0.8488, 30 negative triangles 283: dt=0.8488, 31 negative triangles 284: dt=0.8488, 35 negative triangles 285: dt=0.8488, 33 negative triangles 286: dt=0.8488, 31 negative triangles 287: dt=0.8488, 29 negative triangles 288: dt=0.8488, 29 negative triangles 289: dt=0.8488, 30 negative triangles 290: dt=0.8488, 28 negative triangles 291: dt=0.8488, 26 negative triangles 292: dt=0.8488, 27 negative triangles 293: dt=0.8488, 27 negative triangles 294: dt=0.8488, 29 negative triangles 295: dt=0.8488, 27 negative triangles 296: dt=0.8488, 25 negative triangles 297: dt=0.8488, 26 negative triangles 298: dt=0.8488, 27 negative triangles 299: dt=0.8488, 25 negative triangles 300: dt=0.8488, 25 negative triangles 301: dt=0.8488, 24 negative triangles 302: dt=0.8488, 25 negative triangles 303: dt=0.8488, 26 negative triangles 304: dt=0.8488, 25 negative triangles 305: dt=0.8488, 26 negative triangles 306: dt=0.8488, 24 negative triangles 307: dt=0.8488, 26 negative triangles 308: dt=0.8488, 24 negative triangles 309: dt=0.8488, 25 negative triangles 310: dt=0.8488, 23 negative triangles 311: dt=0.8488, 22 negative triangles 312: dt=0.8488, 24 negative triangles 313: dt=0.8488, 23 negative triangles 314: dt=0.8488, 20 negative triangles 315: dt=0.8488, 21 negative triangles 316: dt=0.8488, 20 negative triangles 317: dt=0.8488, 23 negative triangles 318: dt=0.8488, 21 negative triangles 319: dt=0.8488, 20 negative triangles 320: dt=0.8488, 20 negative triangles 321: dt=0.8488, 19 negative triangles 322: dt=0.8488, 20 negative triangles 323: dt=0.8488, 20 negative triangles 324: dt=0.8488, 17 negative triangles 325: dt=0.8488, 18 negative triangles 326: dt=0.8488, 16 negative triangles 327: dt=0.8488, 18 negative triangles 328: dt=0.8488, 17 negative triangles 329: dt=0.8488, 15 negative triangles 330: dt=0.8488, 13 negative triangles 331: dt=0.8488, 14 negative triangles 332: dt=0.8488, 13 negative triangles 333: dt=0.8488, 12 negative triangles 334: dt=0.8488, 13 negative triangles 335: dt=0.8488, 12 negative triangles 336: dt=0.8488, 11 negative triangles 337: dt=0.8488, 10 negative triangles 338: dt=0.8488, 11 negative triangles 339: dt=0.8488, 11 negative triangles 340: dt=0.8488, 10 negative triangles 341: dt=0.8488, 11 negative triangles 342: dt=0.8488, 12 negative triangles 343: dt=0.8488, 10 negative triangles 344: dt=0.8488, 10 negative triangles 345: dt=0.8488, 9 negative triangles 346: dt=0.8488, 11 negative triangles 347: dt=0.8488, 9 negative triangles 348: dt=0.8488, 8 negative triangles 349: dt=0.8488, 9 negative triangles 350: dt=0.8488, 7 negative triangles 351: dt=0.8488, 7 negative triangles 352: dt=0.8488, 7 negative triangles 353: dt=0.8488, 6 negative triangles 354: dt=0.8488, 5 negative triangles 355: dt=0.8488, 4 negative triangles 356: dt=0.8488, 5 negative triangles 357: dt=0.8488, 3 negative triangles 358: dt=0.8488, 5 negative triangles 359: dt=0.8488, 1 negative triangles 360: dt=0.8488, 1 negative triangles 361: dt=0.8488, 2 negative triangles 362: dt=0.8488, 3 negative triangles 363: dt=0.8488, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 1.30 hours mris_sphere utimesec 4672.451508 mris_sphere stimesec 0.395773 mris_sphere ru_maxrss 306772 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 49237 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 12272 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 2 mris_sphere ru_nivcsw 407010 FSRUNTIME@ mris_sphere 1.2988 hours 1 threads #-------------------------------------------- #@# Sphere rh Tue Jan 16 02:20:01 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_sphere -rusage /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.269... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=kapla, 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 %18.71 pass 1: epoch 2 of 3 starting distance error %18.70 unfolding complete - removing small folds... starting distance error %18.60 removing remaining folds... final distance error %18.62 MRISunfold() return, current seed 1234 -01: dt=0.0000, 78 negative triangles 184: dt=0.9900, 78 negative triangles 185: dt=0.9900, 45 negative triangles 186: dt=0.9900, 32 negative triangles 187: dt=0.9900, 30 negative triangles 188: dt=0.9900, 23 negative triangles 189: dt=0.9900, 19 negative triangles 190: dt=0.9900, 17 negative triangles 191: dt=0.9900, 12 negative triangles 192: dt=0.9900, 15 negative triangles 193: dt=0.9900, 17 negative triangles 194: dt=0.9900, 21 negative triangles 195: dt=0.9900, 19 negative triangles 196: dt=0.9900, 22 negative triangles 197: dt=0.9900, 20 negative triangles 198: dt=0.9900, 21 negative triangles 199: dt=0.9900, 20 negative triangles 200: dt=0.9900, 22 negative triangles 201: dt=0.9405, 23 negative triangles 202: dt=0.9405, 23 negative triangles 203: dt=0.9405, 25 negative triangles 204: dt=0.9405, 21 negative triangles 205: dt=0.9405, 20 negative triangles 206: dt=0.9405, 24 negative triangles 207: dt=0.9405, 23 negative triangles 208: dt=0.9405, 21 negative triangles 209: dt=0.9405, 18 negative triangles 210: dt=0.9405, 17 negative triangles 211: dt=0.8935, 20 negative triangles 212: dt=0.8935, 18 negative triangles 213: dt=0.8935, 18 negative triangles 214: dt=0.8935, 20 negative triangles 215: dt=0.8935, 20 negative triangles 216: dt=0.8935, 19 negative triangles 217: dt=0.8935, 16 negative triangles 218: dt=0.8935, 16 negative triangles 219: dt=0.8935, 13 negative triangles 220: dt=0.8935, 13 negative triangles 221: dt=0.8935, 11 negative triangles 222: dt=0.8935, 14 negative triangles 223: dt=0.8935, 14 negative triangles 224: dt=0.8935, 8 negative triangles 225: dt=0.8935, 11 negative triangles 226: dt=0.8935, 9 negative triangles 227: dt=0.8935, 9 negative triangles 228: dt=0.8935, 5 negative triangles 229: dt=0.8935, 6 negative triangles 230: dt=0.8935, 4 negative triangles 231: dt=0.8935, 6 negative triangles 232: dt=0.8935, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 1.10 hours mris_sphere utimesec 3964.265243 mris_sphere stimesec 0.195856 mris_sphere ru_maxrss 309948 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 49527 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 12400 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 8 mris_sphere ru_nivcsw 373422 FSRUNTIME@ mris_sphere 1.1021 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Tue Jan 16 03:26:08 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_register -curv -rusage /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /usr/local/freesurfer-6.0.0//average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts cmdline mris_register -curv -rusage /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /usr/local/freesurfer-6.0.0//average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer-6.0.0//average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=kapla, 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=kapla, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = 0.000, std = 5.753 curvature mean = 0.032, std = 0.822 curvature mean = 0.024, std = 0.847 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 16.00) sse = 366202.1, tmin=1.4872 d=32.00 min @ (0.00, 8.00, 0.00) sse = 321623.7, tmin=3.0217 d=16.00 min @ (4.00, 0.00, -4.00) sse = 249866.6, tmin=4.5643 d=4.00 min @ (-1.00, -1.00, 0.00) sse = 244112.5, tmin=7.7312 d=2.00 min @ (0.00, -0.50, 0.50) sse = 243052.4, tmin=9.3547 d=1.00 min @ (0.25, 0.25, -0.25) sse = 243047.6, tmin=10.9120 d=0.50 min @ (-0.12, -0.12, 0.12) sse = 242935.1, tmin=12.4963 tol=1.0e+00, sigma=0.5, host=kapla, 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 12.50 min curvature mean = -0.018, std = 0.830 curvature mean = 0.009, std = 0.943 curvature mean = -0.027, std = 0.838 curvature mean = 0.003, std = 0.977 curvature mean = -0.030, std = 0.838 curvature mean = 0.000, std = 0.991 2 Reading smoothwm curvature mean = -0.030, std = 0.254 curvature mean = 0.032, std = 0.248 curvature mean = 0.065, std = 0.369 curvature mean = 0.029, std = 0.304 curvature mean = 0.033, std = 0.574 curvature mean = 0.028, std = 0.331 curvature mean = 0.017, std = 0.724 curvature mean = 0.028, std = 0.342 curvature mean = 0.005, std = 0.829 MRISregister() return, current seed 0 -01: dt=0.0000, 66 negative triangles 124: dt=0.9900, 66 negative triangles 125: dt=0.9900, 58 negative triangles 126: dt=0.9900, 51 negative triangles 127: dt=0.9900, 54 negative triangles 128: dt=0.9900, 48 negative triangles 129: dt=0.9900, 55 negative triangles 130: dt=0.9900, 60 negative triangles 131: dt=0.9900, 51 negative triangles 132: dt=0.9900, 48 negative triangles 133: dt=0.9900, 47 negative triangles 134: dt=0.9900, 49 negative triangles 135: dt=0.9900, 47 negative triangles 136: dt=0.9900, 47 negative triangles 137: dt=0.9900, 49 negative triangles 138: dt=0.9900, 47 negative triangles 139: dt=0.9900, 46 negative triangles 140: dt=0.9900, 46 negative triangles 141: dt=0.9900, 52 negative triangles 142: dt=0.9900, 55 negative triangles 143: dt=0.9900, 53 negative triangles 144: dt=0.9900, 49 negative triangles 145: dt=0.9900, 50 negative triangles 146: dt=0.9900, 50 negative triangles 147: dt=0.9900, 52 negative triangles 148: dt=0.9900, 47 negative triangles 149: dt=0.9405, 46 negative triangles 150: dt=0.9405, 43 negative triangles 151: dt=0.9405, 47 negative triangles 152: dt=0.9405, 47 negative triangles 153: dt=0.9405, 47 negative triangles 154: dt=0.9405, 46 negative triangles 155: dt=0.9405, 42 negative triangles 156: dt=0.9405, 45 negative triangles 157: dt=0.9405, 46 negative triangles 158: dt=0.9405, 54 negative triangles 159: dt=0.9405, 50 negative triangles 160: dt=0.9405, 44 negative triangles 161: dt=0.9405, 48 negative triangles 162: dt=0.9405, 42 negative triangles 163: dt=0.9405, 44 negative triangles 164: dt=0.9405, 45 negative triangles 165: dt=0.8935, 48 negative triangles 166: dt=0.8935, 43 negative triangles 167: dt=0.8935, 42 negative triangles 168: dt=0.8935, 41 negative triangles 169: dt=0.8935, 43 negative triangles 170: dt=0.8935, 44 negative triangles 171: dt=0.8935, 40 negative triangles 172: dt=0.8935, 42 negative triangles 173: dt=0.8935, 41 negative triangles 174: dt=0.8935, 46 negative triangles 175: dt=0.8935, 47 negative triangles 176: dt=0.8935, 44 negative triangles 177: dt=0.8935, 48 negative triangles 178: dt=0.8935, 48 negative triangles 179: dt=0.8935, 48 negative triangles 180: dt=0.8935, 44 negative triangles 181: dt=0.8488, 45 negative triangles 182: dt=0.8488, 47 negative triangles 183: dt=0.8488, 43 negative triangles 184: dt=0.8488, 49 negative triangles 185: dt=0.8488, 47 negative triangles 186: dt=0.8488, 48 negative triangles 187: dt=0.8488, 50 negative triangles 188: dt=0.8488, 45 negative triangles 189: dt=0.8488, 39 negative triangles 190: dt=0.8488, 41 negative triangles 191: dt=0.8488, 37 negative triangles 192: dt=0.8488, 39 negative triangles 193: dt=0.8488, 35 negative triangles 194: dt=0.8488, 42 negative triangles 195: dt=0.8488, 38 negative triangles 196: dt=0.8488, 44 negative triangles 197: dt=0.8488, 38 negative triangles 198: dt=0.8488, 39 negative triangles 199: dt=0.8488, 34 negative triangles 200: dt=0.8488, 36 negative triangles 201: dt=0.8488, 35 negative triangles 202: dt=0.8488, 31 negative triangles 203: dt=0.8488, 37 negative triangles 204: dt=0.8488, 37 negative triangles 205: dt=0.8488, 39 negative triangles 206: dt=0.8488, 32 negative triangles 207: dt=0.8488, 34 negative triangles 208: dt=0.8488, 33 negative triangles 209: dt=0.8488, 32 negative triangles 210: dt=0.8488, 35 negative triangles 211: dt=0.8488, 33 negative triangles 212: dt=0.8064, 33 negative triangles 213: dt=0.8064, 31 negative triangles 214: dt=0.8064, 31 negative triangles 215: dt=0.8064, 31 negative triangles 216: dt=0.8064, 34 negative triangles 217: dt=0.8064, 34 negative triangles 218: dt=0.8064, 33 negative triangles 219: dt=0.8064, 27 negative triangles 220: dt=0.8064, 29 negative triangles 221: dt=0.8064, 28 negative triangles 222: dt=0.8064, 25 negative triangles 223: dt=0.8064, 27 negative triangles 224: dt=0.8064, 22 negative triangles 225: dt=0.8064, 22 negative triangles 226: dt=0.8064, 22 negative triangles 227: dt=0.8064, 25 negative triangles 228: dt=0.8064, 23 negative triangles 229: dt=0.8064, 23 negative triangles 230: dt=0.8064, 23 negative triangles 231: dt=0.8064, 19 negative triangles 232: dt=0.8064, 16 negative triangles 233: dt=0.8064, 14 negative triangles 234: dt=0.8064, 20 negative triangles 235: dt=0.8064, 14 negative triangles 236: dt=0.8064, 12 negative triangles 237: dt=0.8064, 6 negative triangles 238: dt=0.8064, 8 negative triangles 239: dt=0.8064, 9 negative triangles 240: dt=0.8064, 5 negative triangles 241: dt=0.8064, 5 negative triangles 242: dt=0.8064, 7 negative triangles 243: dt=0.8064, 6 negative triangles 244: dt=0.8064, 3 negative triangles 245: dt=0.8064, 2 negative triangles 246: dt=0.8064, 2 negative triangles 247: dt=0.8064, 1 negative triangles 248: dt=0.8064, 2 negative triangles 249: dt=0.8064, 2 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.26 hours mris_register utimesec 4527.410485 mris_register stimesec 2.062474 mris_register ru_maxrss 276408 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 36042 mris_register ru_majflt 3 mris_register ru_nswap 0 mris_register ru_inblock 376 mris_register ru_oublock 12272 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 4 mris_register ru_nivcsw 398883 FSRUNTIME@ mris_register 1.2591 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Tue Jan 16 04:41:41 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_register -curv -rusage /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /usr/local/freesurfer-6.0.0//average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts cmdline mris_register -curv -rusage /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /usr/local/freesurfer-6.0.0//average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer-6.0.0//average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=kapla, 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=kapla, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = -0.000, std = 5.845 curvature mean = 0.030, std = 0.805 curvature mean = 0.024, std = 0.850 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 16.00) sse = 397125.5, tmin=1.5656 d=32.00 min @ (-8.00, -8.00, 0.00) sse = 322386.9, tmin=3.1801 d=16.00 min @ (4.00, 4.00, 4.00) sse = 303857.4, tmin=4.8004 d=8.00 min @ (-2.00, -2.00, 0.00) sse = 286198.8, tmin=6.4887 d=4.00 min @ (0.00, 0.00, -1.00) sse = 282575.1, tmin=8.1471 d=2.00 min @ (-0.50, -0.50, 0.00) sse = 282441.8, tmin=9.8047 d=1.00 min @ (0.25, 0.25, 0.00) sse = 282216.7, tmin=11.4357 tol=1.0e+00, sigma=0.5, host=kapla, 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 13.05 min curvature mean = -0.013, std = 0.817 curvature mean = 0.012, std = 0.943 curvature mean = -0.021, std = 0.821 curvature mean = 0.005, std = 0.977 curvature mean = -0.024, std = 0.822 curvature mean = 0.001, std = 0.990 2 Reading smoothwm curvature mean = -0.030, std = 0.268 curvature mean = 0.029, std = 0.241 curvature mean = 0.065, std = 0.355 curvature mean = 0.024, std = 0.299 curvature mean = 0.032, std = 0.539 curvature mean = 0.023, std = 0.326 curvature mean = 0.017, std = 0.679 curvature mean = 0.023, std = 0.338 curvature mean = 0.005, std = 0.779 MRISregister() return, current seed 0 -01: dt=0.0000, 47 negative triangles 120: dt=0.9900, 47 negative triangles expanding nbhd size to 1 121: dt=0.9900, 58 negative triangles 122: dt=0.9900, 33 negative triangles 123: dt=0.9900, 37 negative triangles 124: dt=0.9900, 39 negative triangles 125: dt=0.9900, 32 negative triangles 126: dt=0.9900, 28 negative triangles 127: dt=0.9900, 28 negative triangles 128: dt=0.9900, 27 negative triangles 129: dt=0.9900, 22 negative triangles 130: dt=0.9900, 17 negative triangles 131: dt=0.9900, 14 negative triangles 132: dt=0.9900, 11 negative triangles 133: dt=0.9900, 10 negative triangles 134: dt=0.9900, 7 negative triangles 135: dt=0.9900, 7 negative triangles 136: dt=0.9900, 6 negative triangles 137: dt=0.9900, 5 negative triangles 138: dt=0.9900, 7 negative triangles 139: dt=0.9900, 5 negative triangles 140: dt=0.9900, 6 negative triangles 141: dt=0.9900, 4 negative triangles 142: dt=0.9900, 5 negative triangles 143: dt=0.9900, 5 negative triangles 144: dt=0.9900, 3 negative triangles 145: dt=0.9900, 2 negative triangles 146: dt=0.9900, 2 negative triangles 147: dt=0.9900, 3 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.28 hours mris_register utimesec 4586.695465 mris_register stimesec 0.819313 mris_register ru_maxrss 278728 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 39179 mris_register ru_majflt 6 mris_register ru_nswap 0 mris_register ru_inblock 6256 mris_register ru_oublock 12400 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 26 mris_register ru_nivcsw 418550 FSRUNTIME@ mris_register 1.2754 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Tue Jan 16 05:58:13 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Tue Jan 16 05:58:15 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Tue Jan 16 05:58:17 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mrisp_paint -a 5 /usr/local/freesurfer-6.0.0//average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer-6.0.0//average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh Tue Jan 16 05:58:19 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mrisp_paint -a 5 /usr/local/freesurfer-6.0.0//average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer-6.0.0//average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Tue Jan 16 05:58:21 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 icbm-205 lh ../surf/lh.sphere.reg /usr/local/freesurfer-6.0.0//average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer-6.0.0//average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1316 labels changed using aseg relabeling using gibbs priors... 000: 3667 changed, 174418 examined... 001: 881 changed, 15315 examined... 002: 230 changed, 4959 examined... 003: 84 changed, 1352 examined... 004: 32 changed, 486 examined... 005: 13 changed, 187 examined... 006: 7 changed, 80 examined... 007: 4 changed, 35 examined... 008: 0 changed, 29 examined... 260 labels changed using aseg 000: 128 total segments, 80 labels (442 vertices) changed 001: 47 total segments, 7 labels (19 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1750 vertices marked for relabeling... 1750 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 17 seconds. #----------------------------------------- #@# Cortical Parc rh Tue Jan 16 05:58:38 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 icbm-205 rh ../surf/rh.sphere.reg /usr/local/freesurfer-6.0.0//average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer-6.0.0//average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1241 labels changed using aseg relabeling using gibbs priors... 000: 3325 changed, 176232 examined... 001: 832 changed, 14168 examined... 002: 211 changed, 4576 examined... 003: 50 changed, 1273 examined... 004: 14 changed, 308 examined... 005: 5 changed, 89 examined... 006: 1 changed, 34 examined... 007: 0 changed, 6 examined... 207 labels changed using aseg 000: 113 total segments, 69 labels (301 vertices) changed 001: 45 total segments, 1 labels (2 vertices) changed 002: 44 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 1 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2002 vertices marked for relabeling... 2002 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 17 seconds. #-------------------------------------------- #@# Make Pial Surf lh Tue Jan 16 05:58:56 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs icbm-205 lh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/filled.mgz... reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/brain.finalsurfs.mgz... reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/../mri/aseg.presurf.mgz... reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/wm.mgz... 15250 bright wm thresholded. 1356 bright non-wm voxels segmented. reading original surface position from /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.orig... computing class statistics... border white: 337784 voxels (2.01%) border gray 364708 voxels (2.17%) WM (99.0): 99.8 +- 5.5 [70.0 --> 110.0] GM (84.0) : 83.0 +- 8.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 72.1 (was 70) setting MAX_BORDER_WHITE to 107.5 (was 105) setting MIN_BORDER_WHITE to 81.0 (was 85) setting MAX_CSF to 63.1 (was 40) setting MAX_GRAY to 96.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 72.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 54.2 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-4.3, GM=81+-7.0 mean inside = 96.7, mean outside = 86.1 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.88 +- 0.25 (0.03-->4.02) (max @ vno 87519 --> 88822) face area 0.32 +- 0.15 (0.00-->2.64) mean absolute distance = 0.86 +- 1.02 4447 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown deleting segment 6 with 77 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 17 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown mean border=88.8, 76 (76) missing vertices, mean dist 0.5 [1.0 (%14.9)->0.8 (%85.1))] %54 local maxima, %42 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=kapla, 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 0.92 +- 0.26 (0.10-->4.47) (max @ vno 87519 --> 88822) face area 0.32 +- 0.15 (0.00-->3.72) mean absolute distance = 0.51 +- 0.89 7888 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2088076.1, rms=6.171 001: dt: 0.5000, sse=1415918.6, rms=4.254 (31.074%) 002: dt: 0.5000, sse=1114942.1, rms=3.042 (28.475%) 003: dt: 0.5000, sse=980432.5, rms=2.317 (23.838%) 004: dt: 0.5000, sse=917414.1, rms=1.867 (19.425%) 005: dt: 0.5000, sse=887751.3, rms=1.591 (14.772%) 006: dt: 0.5000, sse=869010.1, rms=1.414 (11.147%) 007: dt: 0.5000, sse=860077.2, rms=1.310 (7.359%) 008: dt: 0.5000, sse=856479.8, rms=1.253 (4.329%) rms = 1.23, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=854092.0, rms=1.233 (1.580%) 010: dt: 0.2500, sse=839365.1, rms=0.931 (24.495%) rms = 0.90, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=837557.4, rms=0.904 (2.902%) rms = 0.90, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=837282.6, rms=0.898 (0.722%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 1 with 36 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 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown mean border=90.7, 34 (6) missing vertices, mean dist -0.3 [0.7 (%65.6)->0.2 (%34.4))] %64 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=kapla, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.06-->4.54) (max @ vno 87519 --> 88822) face area 0.36 +- 0.17 (0.00-->3.25) mean absolute distance = 0.45 +- 0.61 6804 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1244091.4, rms=3.214 013: dt: 0.5000, sse=1037203.0, rms=2.043 (36.422%) 014: dt: 0.5000, sse=974456.1, rms=1.542 (24.541%) 015: dt: 0.5000, sse=949133.6, rms=1.296 (15.940%) 016: dt: 0.5000, sse=936514.4, rms=1.142 (11.891%) 017: dt: 0.5000, sse=931316.9, rms=1.074 (5.907%) rms = 1.03, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=928222.9, rms=1.031 (4.024%) 019: dt: 0.2500, sse=920034.5, rms=0.844 (18.171%) rms = 0.82, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=919366.2, rms=0.824 (2.316%) rms = 0.82, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=918241.4, rms=0.817 (0.830%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 2 with 59 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown mean border=92.8, 31 (3) missing vertices, mean dist -0.3 [0.5 (%70.7)->0.3 (%29.3))] %79 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=kapla, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.88 +- 0.25 (0.03-->4.59) (max @ vno 87519 --> 88822) face area 0.34 +- 0.16 (0.00-->3.36) mean absolute distance = 0.33 +- 0.45 6129 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1139539.4, rms=2.932 022: dt: 0.5000, sse=945617.9, rms=1.640 (44.075%) 023: dt: 0.5000, sse=900446.4, rms=1.124 (31.476%) 024: dt: 0.5000, sse=889403.1, rms=0.943 (16.111%) 025: dt: 0.5000, sse=888667.5, rms=0.883 (6.340%) rms = 0.92, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=878902.8, rms=0.795 (9.952%) rms = 0.76, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=881033.0, rms=0.764 (3.917%) rms = 0.76, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=878026.2, rms=0.761 (0.395%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown deleting segment 1 with 57 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 4 with 15 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown mean border=93.7, 34 (2) missing vertices, mean dist -0.1 [0.4 (%60.1)->0.3 (%39.9))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=kapla, 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-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=897359.4, rms=1.451 029: dt: 0.5000, sse=857841.2, rms=0.731 (49.629%) rms = 0.74, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=846066.1, rms=0.676 (7.534%) rms = 0.64, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=846979.0, rms=0.643 (4.796%) rms = 0.64, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=851957.5, rms=0.636 (1.163%) positioning took 0.6 minutes generating cortex label... 5 non-cortical segments detected only using segment with 9326 vertices erasing segment 1 (vno[0] = 119817) erasing segment 2 (vno[0] = 124745) erasing segment 3 (vno[0] = 125865) erasing segment 4 (vno[0] = 127863) writing cortex label to /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/lh.cortex.label... writing curvature file /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.curv writing smoothed area to lh.area writing curvature file /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.area vertex spacing 0.88 +- 0.26 (0.03-->4.47) (max @ vno 87519 --> 88822) face area 0.33 +- 0.16 (0.00-->3.35) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 36 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 53 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown deleting segment 9 with 7 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=69.9, 73 (73) missing vertices, mean dist 2.0 [0.0 (%0.0)->3.0 (%100.0))] %20 local maxima, %43 large gradients and %32 min vals, 489 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=kapla, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=21191856.0, rms=24.702 001: dt: 0.0500, sse=19521652.0, rms=23.669 (4.181%) 002: dt: 0.0500, sse=18339570.0, rms=22.909 (3.208%) 003: dt: 0.0500, sse=17427190.0, rms=22.305 (2.636%) 004: dt: 0.0500, sse=16676302.0, rms=21.796 (2.285%) 005: dt: 0.0500, sse=16030072.0, rms=21.347 (2.058%) 006: dt: 0.0500, sse=15457306.0, rms=20.942 (1.900%) 007: dt: 0.0500, sse=14938209.0, rms=20.567 (1.788%) 008: dt: 0.0500, sse=14459695.0, rms=20.216 (1.709%) 009: dt: 0.0500, sse=14013174.0, rms=19.882 (1.650%) 010: dt: 0.0500, sse=13592913.0, rms=19.563 (1.606%) positioning took 1.2 minutes mean border=69.7, 30 (19) missing vertices, mean dist 1.6 [0.0 (%0.0)->2.4 (%100.0))] %21 local maxima, %44 large gradients and %32 min vals, 446 gradients ignored tol=1.0e-04, sigma=2.0, host=kapla, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=14330776.0, rms=20.115 011: dt: 0.0500, sse=13931552.0, rms=19.816 (1.489%) 012: dt: 0.0500, sse=13551590.0, rms=19.526 (1.461%) 013: dt: 0.0500, sse=13188781.0, rms=19.246 (1.436%) 014: dt: 0.0500, sse=12841483.0, rms=18.973 (1.416%) 015: dt: 0.0500, sse=12508562.0, rms=18.708 (1.396%) 016: dt: 0.0500, sse=12188998.0, rms=18.450 (1.379%) 017: dt: 0.0500, sse=11882396.0, rms=18.199 (1.360%) 018: dt: 0.0500, sse=11588178.0, rms=17.955 (1.342%) 019: dt: 0.0500, sse=11305555.0, rms=17.717 (1.325%) 020: dt: 0.0500, sse=11034027.0, rms=17.486 (1.307%) positioning took 1.2 minutes mean border=69.6, 34 (10) missing vertices, mean dist 1.4 [0.1 (%0.3)->2.0 (%99.7))] %21 local maxima, %44 large gradients and %31 min vals, 448 gradients ignored tol=1.0e-04, sigma=2.0, host=kapla, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=11139236.0, rms=17.579 021: dt: 0.0500, sse=10872117.0, rms=17.349 (1.307%) 022: dt: 0.0500, sse=10615658.0, rms=17.125 (1.288%) 023: dt: 0.0500, sse=10368324.0, rms=16.907 (1.275%) 024: dt: 0.0500, sse=10130931.0, rms=16.695 (1.256%) 025: dt: 0.0500, sse=9903004.0, rms=16.488 (1.237%) 026: dt: 0.0500, sse=9683581.0, rms=16.287 (1.221%) 027: dt: 0.0500, sse=9471550.0, rms=16.090 (1.210%) 028: dt: 0.0500, sse=9264975.0, rms=15.895 (1.208%) 029: dt: 0.0500, sse=9063450.0, rms=15.703 (1.208%) 030: dt: 0.0500, sse=8866831.0, rms=15.514 (1.208%) positioning took 1.2 minutes mean border=69.5, 49 (6) missing vertices, mean dist 1.1 [0.1 (%6.5)->1.8 (%93.5))] %21 local maxima, %44 large gradients and %30 min vals, 432 gradients ignored tol=1.0e-04, sigma=2.0, host=kapla, 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=8932156.0, rms=15.575 031: dt: 0.5000, sse=7482232.5, rms=14.104 (9.447%) 032: dt: 0.5000, sse=6269283.5, rms=12.739 (9.677%) 033: dt: 0.5000, sse=5197566.0, rms=11.400 (10.511%) 034: dt: 0.5000, sse=4248434.0, rms=10.062 (11.737%) 035: dt: 0.5000, sse=3455585.0, rms=8.791 (12.632%) 036: dt: 0.5000, sse=2818951.2, rms=7.614 (13.390%) 037: dt: 0.5000, sse=2331404.0, rms=6.575 (13.644%) 038: dt: 0.5000, sse=1999992.9, rms=5.755 (12.470%) 039: dt: 0.5000, sse=1778557.5, rms=5.139 (10.708%) 040: dt: 0.5000, sse=1639376.1, rms=4.703 (8.476%) 041: dt: 0.5000, sse=1540035.0, rms=4.372 (7.047%) 042: dt: 0.5000, sse=1478608.5, rms=4.147 (5.139%) 043: dt: 0.5000, sse=1433756.9, rms=3.981 (4.012%) 044: dt: 0.5000, sse=1406620.1, rms=3.870 (2.777%) 045: dt: 0.5000, sse=1386472.8, rms=3.794 (1.959%) rms = 3.74, time step reduction 1 of 3 to 0.250... 046: dt: 0.5000, sse=1375307.9, rms=3.745 (1.307%) 047: dt: 0.2500, sse=1250943.4, rms=3.135 (16.272%) 048: dt: 0.2500, sse=1221746.0, rms=2.987 (4.736%) rms = 2.96, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=1217232.2, rms=2.960 (0.905%) 050: dt: 0.1250, sse=1205665.4, rms=2.895 (2.179%) rms = 2.89, time step reduction 3 of 3 to 0.062... 051: dt: 0.1250, sse=1203707.8, rms=2.885 (0.354%) positioning took 3.4 minutes mean border=68.5, 1930 (3) missing vertices, mean dist 0.1 [0.2 (%43.1)->0.4 (%56.9))] %39 local maxima, %29 large gradients and %27 min vals, 285 gradients ignored tol=1.0e-04, sigma=1.0, host=kapla, 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=1509359.9, rms=3.482 052: dt: 0.5000, sse=1431750.2, rms=3.138 (9.887%) rms = 3.09, time step reduction 1 of 3 to 0.250... 053: dt: 0.5000, sse=1417454.6, rms=3.094 (1.394%) 054: dt: 0.2500, sse=1302441.0, rms=2.399 (22.477%) 055: dt: 0.2500, sse=1278666.0, rms=2.236 (6.803%) 056: dt: 0.2500, sse=1270542.6, rms=2.179 (2.517%) rms = 2.15, time step reduction 2 of 3 to 0.125... 057: dt: 0.2500, sse=1266073.8, rms=2.150 (1.329%) 058: dt: 0.1250, sse=1255181.0, rms=2.065 (3.991%) rms = 2.05, time step reduction 3 of 3 to 0.062... 059: dt: 0.1250, sse=1253411.6, rms=2.053 (0.571%) positioning took 1.7 minutes mean border=67.8, 2424 (2) missing vertices, mean dist 0.1 [0.1 (%43.8)->0.3 (%56.2))] %49 local maxima, %20 large gradients and %26 min vals, 257 gradients ignored tol=1.0e-04, sigma=0.5, host=kapla, 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=1287278.4, rms=2.328 rms = 2.38, time step reduction 1 of 3 to 0.250... 060: dt: 0.2500, sse=1258397.1, rms=2.125 (8.717%) 061: dt: 0.2500, sse=1244012.8, rms=2.019 (5.014%) rms = 1.99, time step reduction 2 of 3 to 0.125... 062: dt: 0.2500, sse=1239393.8, rms=1.989 (1.483%) rms = 1.96, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1236539.2, rms=1.962 (1.328%) positioning took 1.0 minutes mean border=67.4, 4566 (1) missing vertices, mean dist 0.0 [0.1 (%46.4)->0.2 (%53.6))] %52 local maxima, %16 large gradients and %25 min vals, 264 gradients ignored tol=1.0e-04, sigma=0.2, host=kapla, 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-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1246663.4, rms=2.049 rms = 2.13, time step reduction 1 of 3 to 0.250... 064: dt: 0.2500, sse=1234589.9, rms=1.953 (4.698%) 065: dt: 0.2500, sse=1226465.1, rms=1.897 (2.857%) rms = 1.87, time step reduction 2 of 3 to 0.125... 066: dt: 0.2500, sse=1222765.8, rms=1.874 (1.181%) rms = 1.85, time step reduction 3 of 3 to 0.062... 067: dt: 0.1250, sse=1220093.4, rms=1.849 (1.376%) positioning took 1.1 minutes writing curvature file /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.area.pial vertex spacing 0.98 +- 0.42 (0.07-->7.82) (max @ vno 112616 --> 112632) face area 0.38 +- 0.29 (0.00-->6.90) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 174418 vertices processed 25000 of 174418 vertices processed 50000 of 174418 vertices processed 75000 of 174418 vertices processed 100000 of 174418 vertices processed 125000 of 174418 vertices processed 150000 of 174418 vertices processed 0 of 174418 vertices processed 25000 of 174418 vertices processed 50000 of 174418 vertices processed 75000 of 174418 vertices processed 100000 of 174418 vertices processed 125000 of 174418 vertices processed 150000 of 174418 vertices processed thickness calculation complete, 1229:2312 truncations. 49830 vertices at 0 distance 127182 vertices at 1 distance 92407 vertices at 2 distance 40349 vertices at 3 distance 15293 vertices at 4 distance 5588 vertices at 5 distance 2013 vertices at 6 distance 740 vertices at 7 distance 288 vertices at 8 distance 137 vertices at 9 distance 94 vertices at 10 distance 48 vertices at 11 distance 50 vertices at 12 distance 19 vertices at 13 distance 14 vertices at 14 distance 18 vertices at 15 distance 15 vertices at 16 distance 20 vertices at 17 distance 13 vertices at 18 distance 10 vertices at 19 distance 6 vertices at 20 distance writing curvature file /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.thickness positioning took 20.2 minutes #-------------------------------------------- #@# Make Pial Surf rh Tue Jan 16 06:19:07 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs icbm-205 rh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/filled.mgz... reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/brain.finalsurfs.mgz... reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/../mri/aseg.presurf.mgz... reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/wm.mgz... 15250 bright wm thresholded. 1356 bright non-wm voxels segmented. reading original surface position from /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.orig... computing class statistics... border white: 337784 voxels (2.01%) border gray 364708 voxels (2.17%) WM (99.0): 99.8 +- 5.5 [70.0 --> 110.0] GM (84.0) : 83.0 +- 8.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 72.1 (was 70) setting MAX_BORDER_WHITE to 107.5 (was 105) setting MIN_BORDER_WHITE to 81.0 (was 85) setting MAX_CSF to 63.1 (was 40) setting MAX_GRAY to 96.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 72.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 54.2 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-4.3, GM=81+-7.0 mean inside = 96.7, mean outside = 86.0 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.88 +- 0.25 (0.04-->4.36) (max @ vno 106094 --> 108719) face area 0.32 +- 0.15 (0.00-->3.69) mean absolute distance = 0.85 +- 1.03 4750 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 3 with 124 points - only 0.00% unknown deleting segment 5 with 28 points - only 0.00% unknown mean border=89.1, 95 (95) missing vertices, mean dist 0.5 [1.0 (%16.0)->0.8 (%84.0))] %54 local maxima, %41 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=kapla, 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 0.92 +- 0.25 (0.12-->4.51) (max @ vno 108719 --> 106094) face area 0.32 +- 0.15 (0.00-->3.63) mean absolute distance = 0.51 +- 0.90 7917 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2079018.5, rms=6.093 001: dt: 0.5000, sse=1421465.1, rms=4.231 (30.549%) 002: dt: 0.5000, sse=1126421.6, rms=3.055 (27.806%) 003: dt: 0.5000, sse=993501.1, rms=2.339 (23.419%) 004: dt: 0.5000, sse=930476.2, rms=1.900 (18.780%) 005: dt: 0.5000, sse=898508.8, rms=1.625 (14.494%) 006: dt: 0.5000, sse=882473.1, rms=1.460 (10.126%) 007: dt: 0.5000, sse=873470.4, rms=1.366 (6.466%) rms = 1.32, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=869449.4, rms=1.322 (3.221%) 009: dt: 0.2500, sse=855262.6, rms=1.018 (22.971%) rms = 0.98, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=850551.1, rms=0.977 (4.056%) rms = 0.97, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=850235.7, rms=0.965 (1.199%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 2 with 111 points - only 0.00% unknown deleting segment 3 with 45 points - only 15.56% unknown removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown mean border=90.9, 38 (10) missing vertices, mean dist -0.3 [0.7 (%64.4)->0.2 (%35.6))] %63 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=kapla, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.07-->4.62) (max @ vno 108719 --> 106094) face area 0.35 +- 0.17 (0.00-->4.20) mean absolute distance = 0.45 +- 0.62 6931 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1242170.9, rms=3.173 012: dt: 0.5000, sse=1038190.8, rms=2.029 (36.058%) 013: dt: 0.5000, sse=978546.3, rms=1.525 (24.849%) 014: dt: 0.5000, sse=953572.2, rms=1.288 (15.500%) 015: dt: 0.5000, sse=940244.3, rms=1.143 (11.259%) 016: dt: 0.5000, sse=935889.1, rms=1.090 (4.648%) rms = 1.05, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=932599.8, rms=1.054 (3.317%) 018: dt: 0.2500, sse=924687.2, rms=0.868 (17.645%) rms = 0.85, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=925738.2, rms=0.851 (1.917%) rms = 0.85, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=924245.6, rms=0.846 (0.645%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown deleting segment 1 with 97 points - only 0.00% unknown deleting segment 2 with 48 points - only 2.08% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown mean border=92.9, 32 (8) missing vertices, mean dist -0.3 [0.5 (%68.7)->0.3 (%31.3))] %77 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=kapla, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.88 +- 0.25 (0.02-->4.71) (max @ vno 114271 --> 112847) face area 0.34 +- 0.16 (0.00-->4.23) mean absolute distance = 0.35 +- 0.47 5783 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1135708.4, rms=2.857 021: dt: 0.5000, sse=964446.4, rms=1.622 (43.200%) 022: dt: 0.5000, sse=907114.0, rms=1.127 (30.564%) 023: dt: 0.5000, sse=899133.0, rms=0.962 (14.637%) 024: dt: 0.5000, sse=893543.6, rms=0.904 (5.999%) rms = 0.94, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=887376.3, rms=0.817 (9.653%) rms = 0.79, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=887889.1, rms=0.789 (3.362%) rms = 0.79, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=886972.6, rms=0.787 (0.253%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown deleting segment 1 with 65 points - only 0.00% unknown deleting segment 2 with 53 points - only 1.89% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown mean border=93.8, 70 (6) missing vertices, mean dist -0.1 [0.4 (%59.7)->0.3 (%40.3))] %84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=kapla, 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-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=912696.9, rms=1.511 028: dt: 0.5000, sse=860531.4, rms=0.766 (49.302%) rms = 0.77, time step reduction 1 of 3 to 0.250... 029: dt: 0.5000, sse=860248.7, rms=0.766 (0.040%) 030: dt: 0.2500, sse=854142.2, rms=0.664 (13.325%) rms = 0.66, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=870078.7, rms=0.658 (0.905%) rms = 0.65, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=851193.2, rms=0.654 (0.528%) positioning took 0.7 minutes generating cortex label... 6 non-cortical segments detected only using segment with 9292 vertices erasing segment 1 (vno[0] = 109655) erasing segment 2 (vno[0] = 109668) erasing segment 3 (vno[0] = 120272) erasing segment 4 (vno[0] = 125013) erasing segment 5 (vno[0] = 175670) writing cortex label to /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/rh.cortex.label... writing curvature file /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.curv writing smoothed area to rh.area writing curvature file /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.area vertex spacing 0.87 +- 0.26 (0.04-->4.77) (max @ vno 112844 --> 114269) face area 0.33 +- 0.16 (0.00-->3.97) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 5 with 67 points - only 0.00% unknown deleting segment 6 with 16 points - only 0.00% unknown deleting segment 7 with 9 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown deleting segment 9 with 9 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=70.0, 95 (95) missing vertices, mean dist 1.9 [4.5 (%0.0)->2.9 (%100.0))] %20 local maxima, %44 large gradients and %32 min vals, 515 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=kapla, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=21202288.0, rms=24.596 001: dt: 0.0500, sse=19589646.0, rms=23.604 (4.034%) 002: dt: 0.0500, sse=18434632.0, rms=22.867 (3.123%) 003: dt: 0.0500, sse=17533470.0, rms=22.275 (2.590%) 004: dt: 0.0500, sse=16786598.0, rms=21.771 (2.259%) 005: dt: 0.0500, sse=16140938.0, rms=21.327 (2.042%) 006: dt: 0.0500, sse=15566648.0, rms=20.923 (1.892%) 007: dt: 0.0500, sse=15044154.0, rms=20.549 (1.788%) 008: dt: 0.0500, sse=14561275.0, rms=20.197 (1.712%) 009: dt: 0.0500, sse=14109218.0, rms=19.862 (1.659%) 010: dt: 0.0500, sse=13682938.0, rms=19.541 (1.618%) positioning took 1.3 minutes mean border=69.9, 46 (35) missing vertices, mean dist 1.6 [2.7 (%0.0)->2.4 (%100.0))] %20 local maxima, %44 large gradients and %31 min vals, 490 gradients ignored tol=1.0e-04, sigma=2.0, host=kapla, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=14446659.0, rms=20.109 011: dt: 0.0500, sse=14039913.0, rms=19.806 (1.505%) 012: dt: 0.0500, sse=13652233.0, rms=19.513 (1.479%) 013: dt: 0.0500, sse=13281318.0, rms=19.229 (1.458%) 014: dt: 0.0500, sse=12925481.0, rms=18.952 (1.440%) 015: dt: 0.0500, sse=12583635.0, rms=18.682 (1.425%) 016: dt: 0.0500, sse=12255084.0, rms=18.419 (1.409%) 017: dt: 0.0500, sse=11939362.0, rms=18.162 (1.393%) 018: dt: 0.0500, sse=11636108.0, rms=17.912 (1.377%) 019: dt: 0.0500, sse=11344545.0, rms=17.668 (1.361%) 020: dt: 0.0500, sse=11064232.0, rms=17.430 (1.345%) positioning took 1.2 minutes mean border=69.7, 60 (30) missing vertices, mean dist 1.4 [0.1 (%0.4)->2.0 (%99.6))] %20 local maxima, %45 large gradients and %31 min vals, 500 gradients ignored tol=1.0e-04, sigma=2.0, host=kapla, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=11172007.0, rms=17.525 021: dt: 0.0500, sse=10894961.0, rms=17.288 (1.352%) 022: dt: 0.0500, sse=10629096.0, rms=17.057 (1.333%) 023: dt: 0.0500, sse=10372398.0, rms=16.832 (1.323%) 024: dt: 0.0500, sse=10126267.0, rms=16.613 (1.303%) 025: dt: 0.0500, sse=9889985.0, rms=16.399 (1.284%) 026: dt: 0.0500, sse=9662795.0, rms=16.191 (1.267%) 027: dt: 0.0500, sse=9443497.0, rms=15.988 (1.255%) 028: dt: 0.0500, sse=9230065.0, rms=15.788 (1.253%) 029: dt: 0.0500, sse=9021901.0, rms=15.590 (1.254%) 030: dt: 0.0500, sse=8819004.0, rms=15.394 (1.254%) positioning took 1.2 minutes mean border=69.6, 67 (21) missing vertices, mean dist 1.1 [0.1 (%7.5)->1.8 (%92.5))] %21 local maxima, %45 large gradients and %30 min vals, 478 gradients ignored tol=1.0e-04, sigma=2.0, host=kapla, 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=8890862.0, rms=15.462 031: dt: 0.5000, sse=7403060.5, rms=13.952 (9.762%) 032: dt: 0.5000, sse=6184873.5, rms=12.578 (9.848%) 033: dt: 0.5000, sse=5126340.0, rms=11.251 (10.553%) 034: dt: 0.5000, sse=4211011.0, rms=9.956 (11.508%) 035: dt: 0.5000, sse=3445743.8, rms=8.729 (12.323%) 036: dt: 0.5000, sse=2830630.2, rms=7.596 (12.983%) 037: dt: 0.5000, sse=2356223.2, rms=6.593 (13.199%) 038: dt: 0.5000, sse=2036387.8, rms=5.814 (11.820%) 039: dt: 0.5000, sse=1814531.4, rms=5.211 (10.371%) 040: dt: 0.5000, sse=1682110.6, rms=4.806 (7.766%) 041: dt: 0.5000, sse=1582171.2, rms=4.484 (6.695%) 042: dt: 0.5000, sse=1527226.4, rms=4.290 (4.343%) 043: dt: 0.5000, sse=1479076.1, rms=4.120 (3.948%) 044: dt: 0.5000, sse=1455599.2, rms=4.029 (2.227%) 045: dt: 0.5000, sse=1427542.6, rms=3.926 (2.551%) rms = 3.88, time step reduction 1 of 3 to 0.250... 046: dt: 0.5000, sse=1417859.0, rms=3.883 (1.093%) 047: dt: 0.2500, sse=1287307.0, rms=3.275 (15.650%) 048: dt: 0.2500, sse=1255798.5, rms=3.123 (4.650%) rms = 3.09, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=1249369.1, rms=3.088 (1.124%) 050: dt: 0.1250, sse=1238767.4, rms=3.031 (1.841%) rms = 3.02, time step reduction 3 of 3 to 0.062... 051: dt: 0.1250, sse=1236453.8, rms=3.019 (0.384%) positioning took 3.4 minutes mean border=68.7, 1757 (2) missing vertices, mean dist 0.1 [0.2 (%44.4)->0.4 (%55.6))] %38 local maxima, %31 large gradients and %26 min vals, 240 gradients ignored tol=1.0e-04, sigma=1.0, host=kapla, 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=1529037.8, rms=3.558 052: dt: 0.5000, sse=1446488.6, rms=3.205 (9.919%) 053: dt: 0.5000, sse=1427307.6, rms=3.138 (2.089%) rms = 3.19, time step reduction 1 of 3 to 0.250... 054: dt: 0.2500, sse=1326290.6, rms=2.558 (18.471%) 055: dt: 0.2500, sse=1289429.1, rms=2.315 (9.525%) 056: dt: 0.2500, sse=1278577.1, rms=2.240 (3.209%) rms = 2.20, time step reduction 2 of 3 to 0.125... 057: dt: 0.2500, sse=1272985.8, rms=2.204 (1.639%) 058: dt: 0.1250, sse=1264910.4, rms=2.141 (2.865%) rms = 2.13, time step reduction 3 of 3 to 0.062... 059: dt: 0.1250, sse=1262858.6, rms=2.127 (0.613%) positioning took 1.8 minutes mean border=68.1, 2408 (1) missing vertices, mean dist 0.1 [0.1 (%45.7)->0.3 (%54.3))] %47 local maxima, %22 large gradients and %25 min vals, 274 gradients ignored tol=1.0e-04, sigma=0.5, host=kapla, 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=1288195.8, rms=2.326 rms = 2.39, time step reduction 1 of 3 to 0.250... 060: dt: 0.2500, sse=1261592.2, rms=2.141 (7.939%) 061: dt: 0.2500, sse=1248537.8, rms=2.049 (4.317%) rms = 2.02, time step reduction 2 of 3 to 0.125... 062: dt: 0.2500, sse=1243687.2, rms=2.020 (1.413%) rms = 1.99, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1240839.5, rms=1.993 (1.301%) positioning took 1.1 minutes mean border=67.7, 4488 (1) missing vertices, mean dist 0.1 [0.1 (%47.8)->0.3 (%52.2))] %51 local maxima, %18 large gradients and %24 min vals, 262 gradients ignored tol=1.0e-04, sigma=0.2, host=kapla, 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-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1248016.5, rms=2.050 rms = 2.13, time step reduction 1 of 3 to 0.250... 064: dt: 0.2500, sse=1236946.4, rms=1.963 (4.216%) rms = 1.91, time step reduction 2 of 3 to 0.125... 065: dt: 0.2500, sse=1229377.4, rms=1.914 (2.487%) rms = 1.89, time step reduction 3 of 3 to 0.062... 066: dt: 0.1250, sse=1226576.9, rms=1.888 (1.361%) positioning took 0.8 minutes writing curvature file /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.area.pial vertex spacing 0.98 +- 0.41 (0.05-->7.30) (max @ vno 108651 --> 107303) face area 0.38 +- 0.29 (0.00-->8.66) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 176232 vertices processed 25000 of 176232 vertices processed 50000 of 176232 vertices processed 75000 of 176232 vertices processed 100000 of 176232 vertices processed 125000 of 176232 vertices processed 150000 of 176232 vertices processed 175000 of 176232 vertices processed 0 of 176232 vertices processed 25000 of 176232 vertices processed 50000 of 176232 vertices processed 75000 of 176232 vertices processed 100000 of 176232 vertices processed 125000 of 176232 vertices processed 150000 of 176232 vertices processed 175000 of 176232 vertices processed thickness calculation complete, 967:2298 truncations. 50986 vertices at 0 distance 126899 vertices at 1 distance 92640 vertices at 2 distance 41550 vertices at 3 distance 15832 vertices at 4 distance 5627 vertices at 5 distance 1987 vertices at 6 distance 774 vertices at 7 distance 317 vertices at 8 distance 194 vertices at 9 distance 87 vertices at 10 distance 66 vertices at 11 distance 37 vertices at 12 distance 28 vertices at 13 distance 16 vertices at 14 distance 16 vertices at 15 distance 5 vertices at 16 distance 6 vertices at 17 distance 7 vertices at 18 distance 5 vertices at 19 distance 15 vertices at 20 distance writing curvature file /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.thickness positioning took 20.2 minutes #-------------------------------------------- #@# Surf Volume lh Tue Jan 16 06:39:16 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume icbm-205 lh /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.volume masking with /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/lh.cortex.label Total face volume 316003 Total vertex volume 310659 (mask=0) #@# icbm-205 lh 310659 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Tue Jan 16 06:39:19 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume icbm-205 rh /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.volume masking with /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/rh.cortex.label Total face volume 313059 Total vertex volume 308521 (mask=0) #@# icbm-205 rh 308521 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Tue Jan 16 06:39:23 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon icbm-205 SUBJECTS_DIR is /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 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 = 44 writing volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/ribbon.mgz mris_volmask took 16.68 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Tue Jan 16 06:56:04 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab icbm-205 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/wm.mgz... reading input surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white... reading input pial surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.pial... reading input white surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 316003 Total vertex volume 310659 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 2128430 mm^3 (det: 0.915278 ) lhCtxGM: 310211.420 309855.000 diff= 356.4 pctdiff= 0.115 rhCtxGM: 307783.078 307377.000 diff= 406.1 pctdiff= 0.132 lhCtxWM: 317493.011 318337.500 diff= -844.5 pctdiff=-0.266 rhCtxWM: 320511.394 320670.500 diff= -159.1 pctdiff=-0.050 SubCortGMVol 76355.000 SupraTentVol 1367122.903 (1364345.000) diff=2777.903 pctdiff=0.203 SupraTentVolNotVent 1335388.903 (1332611.000) diff=2777.903 pctdiff=0.208 BrainSegVol 1558906.000 (1555798.000) diff=3108.000 pctdiff=0.199 BrainSegVolNotVent 1522258.000 (1521753.903) diff=504.097 pctdiff=0.033 BrainSegVolNotVent 1522258.000 CerebellumVol 189384.000 VentChorVol 31734.000 3rd4th5thCSF 4914.000 CSFVol 1806.000, OptChiasmVol 263.000 MaskVol 2206782.000 2092 1443 3869 2.591 0.489 0.101 0.016 16 1.3 bankssts 1215 766 2593 3.354 0.729 0.139 0.033 19 1.5 caudalanteriorcingulate 5308 3044 9083 2.828 0.624 0.099 0.024 36 5.0 caudalmiddlefrontal 2831 1831 3422 1.901 0.466 0.139 0.033 32 3.7 cuneus 859 599 2364 3.139 0.775 0.104 0.028 5 0.9 entorhinal 5117 3457 12101 3.042 0.760 0.125 0.029 54 5.8 fusiform 8977 5875 17004 2.583 0.572 0.116 0.027 88 10.0 inferiorparietal 5595 3878 13364 2.904 0.676 0.129 0.033 68 7.8 inferiortemporal 1767 1139 3210 2.537 0.902 0.120 0.025 19 1.7 isthmuscingulate 9274 5832 13774 2.207 0.612 0.133 0.033 108 12.1 lateraloccipital 4183 2947 9300 3.014 0.792 0.134 0.037 48 6.1 lateralorbitofrontal 5655 3750 7208 1.883 0.508 0.133 0.030 65 7.0 lingual 2975 2069 6912 3.005 0.857 0.135 0.037 40 4.5 medialorbitofrontal 6292 4265 15272 2.947 0.690 0.125 0.030 69 7.7 middletemporal 1080 720 2497 2.865 0.859 0.102 0.021 8 0.9 parahippocampal 3021 1903 5315 2.633 0.618 0.099 0.021 19 2.5 paracentral 2942 1994 6123 2.736 0.556 0.118 0.027 27 3.1 parsopercularis 1001 700 2534 2.815 0.660 0.149 0.040 15 1.6 parsorbitalis 2257 1441 4630 2.861 0.798 0.114 0.029 19 2.7 parstriangularis 2531 1689 2213 1.517 0.318 0.147 0.036 33 4.0 pericalcarine 8968 5218 12973 2.284 0.792 0.098 0.022 65 8.1 postcentral 1878 1304 3946 2.761 0.741 0.121 0.024 21 1.7 posteriorcingulate 10668 6471 16938 2.534 0.736 0.100 0.021 70 9.6 precentral 7719 5149 13121 2.324 0.671 0.117 0.027 74 8.1 precuneus 1338 913 3657 3.440 0.718 0.128 0.033 18 1.6 rostralanteriorcingulate 11891 7365 20769 2.582 0.660 0.119 0.030 122 14.1 rostralmiddlefrontal 14561 8989 30415 3.040 0.684 0.109 0.027 127 15.5 superiorfrontal 11501 6867 17306 2.319 0.597 0.107 0.024 93 10.9 superiorparietal 7863 5309 19909 3.150 0.716 0.111 0.024 70 7.5 superiortemporal 7273 4732 13694 2.696 0.602 0.119 0.029 80 8.0 supramarginal 473 238 1076 3.126 0.527 0.120 0.040 7 0.7 frontalpole 806 530 3403 4.247 0.740 0.120 0.038 10 1.1 temporalpole 746 467 1279 2.633 0.433 0.114 0.023 7 0.6 transversetemporal 3817 2587 9241 3.376 0.821 0.107 0.025 27 3.5 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab icbm-205 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/wm.mgz... reading input surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.pial... reading input pial surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.pial... reading input white surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 316003 Total vertex volume 310659 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 2128430 mm^3 (det: 0.915278 ) lhCtxGM: 310211.420 309855.000 diff= 356.4 pctdiff= 0.115 rhCtxGM: 307783.078 307377.000 diff= 406.1 pctdiff= 0.132 lhCtxWM: 317493.011 318337.500 diff= -844.5 pctdiff=-0.266 rhCtxWM: 320511.394 320670.500 diff= -159.1 pctdiff=-0.050 SubCortGMVol 76355.000 SupraTentVol 1367122.903 (1364345.000) diff=2777.903 pctdiff=0.203 SupraTentVolNotVent 1335388.903 (1332611.000) diff=2777.903 pctdiff=0.208 BrainSegVol 1558906.000 (1555798.000) diff=3108.000 pctdiff=0.199 BrainSegVolNotVent 1522258.000 (1521753.903) diff=504.097 pctdiff=0.033 BrainSegVolNotVent 1522258.000 CerebellumVol 189384.000 VentChorVol 31734.000 3rd4th5thCSF 4914.000 CSFVol 1806.000, OptChiasmVol 263.000 MaskVol 2206782.000 2092 1509 3869 2.591 0.489 0.106 0.023 26 2.0 bankssts 1215 876 2593 3.354 0.729 0.149 0.057 35 3.1 caudalanteriorcingulate 5308 3440 9083 2.828 0.624 0.096 0.019 55 4.6 caudalmiddlefrontal 2831 2003 3422 1.901 0.466 0.118 0.027 37 3.3 cuneus 859 890 2364 3.139 0.775 0.147 0.030 10 1.3 entorhinal 5117 4315 12101 3.042 0.760 0.131 0.029 57 6.6 fusiform 8977 7028 17004 2.583 0.572 0.122 0.023 80 9.2 inferiorparietal 5595 5216 13364 2.904 0.676 0.150 0.031 76 8.2 inferiortemporal 1767 1365 3210 2.537 0.902 0.126 0.026 25 1.8 isthmuscingulate 9274 6757 13774 2.207 0.612 0.118 0.027 119 10.9 lateraloccipital 4183 3167 9300 3.014 0.792 0.126 0.030 55 5.5 lateralorbitofrontal 5655 4111 7208 1.883 0.508 0.117 0.027 110 7.0 lingual 2975 2581 6912 3.005 0.857 0.146 0.036 44 4.5 medialorbitofrontal 6292 5744 15272 2.947 0.690 0.146 0.031 81 9.3 middletemporal 1080 976 2497 2.865 0.859 0.126 0.025 8 1.2 parahippocampal 3021 2151 5315 2.633 0.618 0.099 0.019 21 2.4 paracentral 2942 2419 6123 2.736 0.556 0.131 0.028 32 3.4 parsopercularis 1001 995 2534 2.815 0.660 0.174 0.049 13 1.8 parsorbitalis 2257 1770 4630 2.861 0.798 0.138 0.029 28 3.2 parstriangularis 2531 1369 2213 1.517 0.318 0.106 0.037 100 3.8 pericalcarine 8968 6312 12973 2.284 0.792 0.099 0.018 65 6.6 postcentral 1878 1492 3946 2.761 0.741 0.136 0.029 44 2.0 posteriorcingulate 10668 6952 16938 2.534 0.736 0.086 0.015 86 7.0 precentral 7719 5912 13121 2.324 0.671 0.131 0.027 89 8.9 precuneus 1338 1240 3657 3.440 0.718 0.141 0.030 21 1.5 rostralanteriorcingulate 11891 8503 20769 2.582 0.660 0.121 0.025 123 13.4 rostralmiddlefrontal 14561 10750 30415 3.040 0.684 0.113 0.024 138 15.2 superiorfrontal 11501 8009 17306 2.319 0.597 0.109 0.020 97 9.3 superiorparietal 7863 6820 19909 3.150 0.716 0.129 0.024 76 8.7 superiortemporal 7273 5388 13694 2.696 0.602 0.119 0.024 77 7.8 supramarginal 473 445 1076 3.126 0.527 0.135 0.019 3 0.4 frontalpole 806 1026 3403 4.247 0.740 0.185 0.032 7 1.3 temporalpole 746 550 1279 2.633 0.433 0.104 0.021 6 0.6 transversetemporal 3817 2526 9241 3.376 0.821 0.119 0.028 43 4.5 insula #----------------------------------------- #@# Parcellation Stats rh Tue Jan 16 06:57:27 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab icbm-205 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/wm.mgz... reading input surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white... reading input pial surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.pial... reading input white surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 313059 Total vertex volume 308521 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 2128430 mm^3 (det: 0.915278 ) lhCtxGM: 310211.420 309855.000 diff= 356.4 pctdiff= 0.115 rhCtxGM: 307783.078 307377.000 diff= 406.1 pctdiff= 0.132 lhCtxWM: 317493.011 318337.500 diff= -844.5 pctdiff=-0.266 rhCtxWM: 320511.394 320670.500 diff= -159.1 pctdiff=-0.050 SubCortGMVol 76355.000 SupraTentVol 1367122.903 (1364345.000) diff=2777.903 pctdiff=0.203 SupraTentVolNotVent 1335388.903 (1332611.000) diff=2777.903 pctdiff=0.208 BrainSegVol 1558906.000 (1555798.000) diff=3108.000 pctdiff=0.199 BrainSegVolNotVent 1522258.000 (1521753.903) diff=504.097 pctdiff=0.033 BrainSegVolNotVent 1522258.000 CerebellumVol 189384.000 VentChorVol 31734.000 3rd4th5thCSF 4914.000 CSFVol 1806.000, OptChiasmVol 263.000 MaskVol 2206782.000 1336 941 2498 2.690 0.541 0.090 0.015 6 0.8 bankssts 1303 875 3268 3.171 0.728 0.126 0.025 19 1.3 caudalanteriorcingulate 5108 3138 7912 2.553 0.622 0.108 0.029 37 6.4 caudalmiddlefrontal 3032 1893 3523 1.788 0.478 0.135 0.030 35 3.7 cuneus 894 577 2160 3.063 0.853 0.116 0.031 7 1.2 entorhinal 5498 3670 12304 2.857 0.749 0.125 0.033 59 7.3 fusiform 10520 6720 19433 2.602 0.699 0.113 0.026 94 10.7 inferiorparietal 7012 4784 16815 2.898 0.727 0.135 0.038 94 11.4 inferiortemporal 1548 1015 3211 2.689 0.799 0.132 0.030 20 1.6 isthmuscingulate 8551 5489 13124 2.344 0.677 0.136 0.033 91 11.7 lateraloccipital 4599 3034 9380 2.950 0.788 0.135 0.041 56 8.2 lateralorbitofrontal 5959 3778 7774 2.001 0.545 0.134 0.032 70 8.1 lingual 3054 2139 7070 2.977 0.819 0.136 0.038 46 4.7 medialorbitofrontal 6728 4743 17198 2.936 0.716 0.125 0.033 73 8.9 middletemporal 1117 715 2239 2.630 0.851 0.098 0.018 8 0.7 parahippocampal 3757 2241 5515 2.371 0.667 0.098 0.021 23 3.3 paracentral 2819 1785 5719 2.777 0.707 0.116 0.029 26 3.1 parsopercularis 1385 922 3813 3.134 0.744 0.139 0.041 16 2.5 parsorbitalis 2224 1413 3920 2.558 0.615 0.107 0.024 18 2.0 parstriangularis 2533 1803 2270 1.455 0.329 0.140 0.033 30 3.5 pericalcarine 8774 5240 12651 2.197 0.721 0.105 0.024 68 8.5 postcentral 1892 1343 4083 2.635 0.796 0.131 0.026 27 2.0 posteriorcingulate 11500 7086 17679 2.430 0.691 0.102 0.025 78 11.8 precentral 7544 4956 12750 2.380 0.641 0.118 0.027 74 7.8 precuneus 1084 748 3357 3.507 0.813 0.141 0.038 16 1.7 rostralanteriorcingulate 11292 6839 19184 2.558 0.640 0.118 0.033 110 15.1 rostralmiddlefrontal 13684 8207 28609 3.098 0.671 0.106 0.027 117 14.8 superiorfrontal 11634 6939 16994 2.223 0.650 0.103 0.024 90 11.1 superiorparietal 7130 4676 16786 3.098 0.760 0.102 0.024 56 6.5 superiortemporal 6664 4343 12157 2.577 0.667 0.116 0.028 56 7.4 supramarginal 580 326 1401 3.049 0.840 0.153 0.058 8 1.6 frontalpole 940 650 2907 3.254 0.986 0.155 0.052 11 2.0 temporalpole 586 336 990 2.590 0.457 0.092 0.018 4 0.4 transversetemporal 4220 2864 9794 3.273 0.931 0.117 0.037 39 6.1 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab icbm-205 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/wm.mgz... reading input surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.pial... reading input pial surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.pial... reading input white surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 313059 Total vertex volume 308521 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 2128430 mm^3 (det: 0.915278 ) lhCtxGM: 310211.420 309855.000 diff= 356.4 pctdiff= 0.115 rhCtxGM: 307783.078 307377.000 diff= 406.1 pctdiff= 0.132 lhCtxWM: 317493.011 318337.500 diff= -844.5 pctdiff=-0.266 rhCtxWM: 320511.394 320670.500 diff= -159.1 pctdiff=-0.050 SubCortGMVol 76355.000 SupraTentVol 1367122.903 (1364345.000) diff=2777.903 pctdiff=0.203 SupraTentVolNotVent 1335388.903 (1332611.000) diff=2777.903 pctdiff=0.208 BrainSegVol 1558906.000 (1555798.000) diff=3108.000 pctdiff=0.199 BrainSegVolNotVent 1522258.000 (1521753.903) diff=504.097 pctdiff=0.033 BrainSegVolNotVent 1522258.000 CerebellumVol 189384.000 VentChorVol 31734.000 3rd4th5thCSF 4914.000 CSFVol 1806.000, OptChiasmVol 263.000 MaskVol 2206782.000 1336 909 2498 2.690 0.541 0.113 0.026 13 1.4 bankssts 1303 1180 3268 3.171 0.728 0.159 0.040 45 2.0 caudalanteriorcingulate 5108 3156 7912 2.553 0.622 0.090 0.018 38 4.0 caudalmiddlefrontal 3032 2210 3523 1.788 0.478 0.120 0.026 31 3.4 cuneus 894 810 2160 3.063 0.853 0.136 0.030 9 1.4 entorhinal 5498 4787 12304 2.857 0.749 0.138 0.031 69 8.1 fusiform 10520 8020 19433 2.602 0.699 0.121 0.028 135 15.5 inferiorparietal 7012 6611 16815 2.898 0.727 0.155 0.036 102 11.4 inferiortemporal 1548 1315 3211 2.689 0.799 0.146 0.034 40 2.1 isthmuscingulate 8551 5786 13124 2.344 0.677 0.112 0.028 112 9.8 lateraloccipital 4599 3326 9380 2.950 0.788 0.124 0.029 66 6.0 lateralorbitofrontal 5959 4264 7774 2.001 0.545 0.120 0.028 80 7.4 lingual 3054 2660 7070 2.977 0.819 0.149 0.035 38 4.7 medialorbitofrontal 6728 6566 17198 2.936 0.716 0.153 0.031 92 10.3 middletemporal 1117 899 2239 2.630 0.851 0.114 0.022 17 1.0 parahippocampal 3757 2441 5515 2.371 0.667 0.091 0.017 35 2.5 paracentral 2819 2220 5719 2.777 0.707 0.121 0.024 25 2.9 parsopercularis 1385 1467 3813 3.134 0.744 0.167 0.031 23 2.0 parsorbitalis 2224 1646 3920 2.558 0.615 0.131 0.027 25 2.8 parstriangularis 2533 1553 2270 1.455 0.329 0.102 0.026 33 2.7 pericalcarine 8774 6378 12651 2.197 0.721 0.105 0.019 64 7.1 postcentral 1892 1668 4083 2.635 0.796 0.142 0.028 26 2.4 posteriorcingulate 11500 7420 17679 2.430 0.691 0.087 0.016 80 7.8 precentral 7544 5479 12750 2.380 0.641 0.125 0.028 84 9.2 precuneus 1084 1113 3357 3.507 0.813 0.180 0.038 35 1.9 rostralanteriorcingulate 11292 8123 19184 2.558 0.640 0.124 0.026 130 13.6 rostralmiddlefrontal 13684 9779 28609 3.098 0.671 0.107 0.022 123 12.6 superiorfrontal 11634 8233 16994 2.223 0.650 0.106 0.021 100 9.1 superiorparietal 7130 5892 16786 3.098 0.760 0.118 0.023 61 7.1 superiortemporal 6664 4875 12157 2.577 0.667 0.114 0.023 61 6.3 supramarginal 580 558 1401 3.049 0.840 0.160 0.034 6 1.1 frontalpole 940 1007 2907 3.254 0.986 0.153 0.036 22 1.4 temporalpole 586 419 990 2.590 0.457 0.087 0.016 3 0.3 transversetemporal 4220 2822 9794 3.273 0.931 0.129 0.036 63 6.8 insula #----------------------------------------- #@# Cortical Parc 2 lh Tue Jan 16 06:58:50 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 icbm-205 lh ../surf/lh.sphere.reg /usr/local/freesurfer-6.0.0//average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer-6.0.0//average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 2.9 using min determinant for regularization = 0.086 0 singular and 762 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 14 labels changed using aseg relabeling using gibbs priors... 000: 11078 changed, 174418 examined... 001: 2597 changed, 42602 examined... 002: 725 changed, 13632 examined... 003: 305 changed, 4225 examined... 004: 127 changed, 1779 examined... 005: 63 changed, 752 examined... 006: 33 changed, 338 examined... 007: 11 changed, 181 examined... 008: 5 changed, 66 examined... 009: 6 changed, 27 examined... 010: 3 changed, 34 examined... 011: 1 changed, 20 examined... 012: 1 changed, 5 examined... 013: 1 changed, 7 examined... 014: 0 changed, 7 examined... 4 labels changed using aseg 000: 322 total segments, 230 labels (2813 vertices) changed 001: 105 total segments, 13 labels (25 vertices) changed 002: 92 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 43 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1070 vertices marked for relabeling... 1070 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 21 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Tue Jan 16 06:59:10 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 icbm-205 rh ../surf/rh.sphere.reg /usr/local/freesurfer-6.0.0//average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer-6.0.0//average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 719 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 22 labels changed using aseg relabeling using gibbs priors... 000: 10816 changed, 176232 examined... 001: 2432 changed, 42154 examined... 002: 653 changed, 12762 examined... 003: 274 changed, 3712 examined... 004: 124 changed, 1567 examined... 005: 63 changed, 702 examined... 006: 23 changed, 332 examined... 007: 15 changed, 134 examined... 008: 9 changed, 93 examined... 009: 2 changed, 47 examined... 010: 2 changed, 11 examined... 011: 1 changed, 10 examined... 012: 1 changed, 7 examined... 013: 1 changed, 9 examined... 014: 1 changed, 5 examined... 015: 0 changed, 8 examined... 9 labels changed using aseg 000: 274 total segments, 190 labels (3486 vertices) changed 001: 98 total segments, 14 labels (180 vertices) changed 002: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 43 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1079 vertices marked for relabeling... 1079 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 21 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Tue Jan 16 06:59:31 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab icbm-205 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/wm.mgz... reading input surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white... reading input pial surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.pial... reading input white surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 316003 Total vertex volume 310659 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 2128430 mm^3 (det: 0.915278 ) lhCtxGM: 310211.420 309855.000 diff= 356.4 pctdiff= 0.115 rhCtxGM: 307783.078 307377.000 diff= 406.1 pctdiff= 0.132 lhCtxWM: 317493.011 318337.500 diff= -844.5 pctdiff=-0.266 rhCtxWM: 320511.394 320670.500 diff= -159.1 pctdiff=-0.050 SubCortGMVol 76355.000 SupraTentVol 1367122.903 (1364345.000) diff=2777.903 pctdiff=0.203 SupraTentVolNotVent 1335388.903 (1332611.000) diff=2777.903 pctdiff=0.208 BrainSegVol 1558906.000 (1555798.000) diff=3108.000 pctdiff=0.199 BrainSegVolNotVent 1522258.000 (1521753.903) diff=504.097 pctdiff=0.033 BrainSegVolNotVent 1522258.000 CerebellumVol 189384.000 VentChorVol 31734.000 3rd4th5thCSF 4914.000 CSFVol 1806.000, OptChiasmVol 263.000 MaskVol 2206782.000 1407 967 3017 2.805 0.698 0.137 0.032 17 1.7 G&S_frontomargin 1612 1040 3087 2.709 0.651 0.132 0.031 18 2.0 G&S_occipital_inf 2133 1261 3341 2.322 0.669 0.098 0.021 14 1.8 G&S_paracentral 2100 1297 4591 3.130 0.591 0.114 0.026 19 2.3 G&S_subcentral 1101 701 2391 2.603 0.630 0.150 0.043 16 2.0 G&S_transv_frontopol 2560 1780 6073 3.124 0.684 0.121 0.032 27 2.9 G&S_cingul-Ant 1680 1180 3729 3.233 0.591 0.136 0.030 20 2.0 G&S_cingul-Mid-Ant 1629 1149 3331 2.730 0.549 0.108 0.022 11 1.4 G&S_cingul-Mid-Post 672 462 2144 3.157 0.665 0.153 0.037 10 1.0 G_cingul-Post-dorsal 326 207 713 3.067 0.689 0.154 0.032 5 0.4 G_cingul-Post-ventral 2664 1702 3290 1.850 0.496 0.140 0.035 31 3.7 G_cuneus 1561 1007 3804 2.882 0.596 0.130 0.033 20 2.0 G_front_inf-Opercular 500 332 1463 3.106 0.527 0.137 0.046 8 0.9 G_front_inf-Orbital 1341 824 3390 3.004 0.773 0.119 0.037 14 2.0 G_front_inf-Triangul 7938 4090 13820 2.702 0.699 0.107 0.032 81 10.4 G_front_middle 10483 6100 23445 3.156 0.715 0.113 0.031 108 12.5 G_front_sup 680 459 1859 3.579 0.743 0.121 0.030 8 0.7 G_Ins_lg&S_cent_ins 903 571 3426 4.114 0.691 0.116 0.032 9 1.1 G_insular_short 3307 2055 6852 2.596 0.582 0.135 0.034 44 4.4 G_occipital_middle 2387 1337 3686 2.321 0.619 0.119 0.034 21 3.3 G_occipital_sup 2014 1325 5220 3.146 0.631 0.141 0.036 29 2.9 G_oc-temp_lat-fusifor 3950 2564 4982 1.806 0.478 0.142 0.035 51 5.5 G_oc-temp_med-Lingual 1695 1114 4894 3.172 0.867 0.116 0.032 14 2.0 G_oc-temp_med-Parahip 2623 1835 6862 2.954 0.758 0.146 0.043 40 4.4 G_orbital 3712 2279 8282 2.817 0.603 0.131 0.039 52 5.7 G_pariet_inf-Angular 3970 2477 8371 2.793 0.634 0.121 0.033 52 4.9 G_pariet_inf-Supramar 4748 2665 7440 2.359 0.662 0.097 0.022 36 4.2 G_parietal_sup 3816 1919 5455 2.367 0.729 0.092 0.025 29 3.8 G_postcentral 4410 2271 7149 2.608 0.785 0.094 0.024 31 4.4 G_precentral 4041 2568 8394 2.507 0.696 0.128 0.036 54 5.4 G_precuneus 1049 713 3009 3.037 0.729 0.140 0.047 19 1.8 G_rectus 444 323 1028 3.550 0.882 0.156 0.048 7 0.9 G_subcallosal 621 363 1273 2.762 0.501 0.113 0.028 7 0.5 G_temp_sup-G_T_transv 2806 1847 9180 3.482 0.691 0.132 0.031 37 3.6 G_temp_sup-Lateral 936 645 2944 3.869 0.781 0.081 0.018 5 0.6 G_temp_sup-Plan_polar 1331 854 3077 2.973 0.603 0.098 0.024 11 1.2 G_temp_sup-Plan_tempo 3167 2188 9078 3.085 0.695 0.148 0.044 52 5.7 G_temporal_inf 3414 2255 10170 3.112 0.698 0.136 0.037 49 5.1 G_temporal_middle 354 238 578 2.422 0.511 0.105 0.016 2 0.2 Lat_Fis-ant-Horizont 388 287 644 2.446 0.454 0.103 0.016 2 0.2 Lat_Fis-ant-Vertical 1162 795 1603 2.548 0.547 0.112 0.026 7 1.2 Lat_Fis-post 2750 1663 3256 1.891 0.515 0.143 0.038 37 4.5 Pole_occipital 1911 1312 7237 3.678 0.953 0.131 0.038 23 2.8 Pole_temporal 2856 1924 2862 1.767 0.659 0.139 0.032 35 3.8 S_calcarine 4510 2974 5097 1.934 0.655 0.106 0.021 28 4.0 S_central 1458 1022 2196 2.350 0.547 0.093 0.014 7 0.8 S_cingul-Marginalis 511 367 910 3.280 0.460 0.097 0.016 2 0.3 S_circular_insula_ant 1610 1115 2719 2.984 0.607 0.080 0.013 5 0.9 S_circular_insula_inf 1925 1339 3028 2.815 0.517 0.099 0.017 8 1.3 S_circular_insula_sup 1099 754 2118 2.925 0.634 0.094 0.014 5 0.7 S_collat_transv_ant 646 455 707 2.014 0.325 0.128 0.027 5 0.7 S_collat_transv_post 2970 2034 4898 2.566 0.609 0.111 0.022 22 2.4 S_front_inf 2158 1460 3092 2.438 0.562 0.109 0.022 12 1.8 S_front_middle 3634 2470 6210 2.755 0.482 0.098 0.019 20 2.6 S_front_sup 578 429 854 2.673 0.536 0.141 0.022 5 0.7 S_interm_prim-Jensen 3444 2327 4689 2.170 0.514 0.110 0.019 24 2.6 S_intrapariet&P_trans 1204 823 1464 2.059 0.395 0.118 0.026 10 1.1 S_oc_middle&Lunatus 1952 1314 2491 2.154 0.452 0.116 0.023 16 1.8 S_oc_sup&transversal 914 624 1452 2.464 0.462 0.131 0.031 11 1.1 S_occipital_ant 903 628 1517 2.653 0.442 0.109 0.018 6 0.6 S_oc-temp_lat 2582 1784 3804 2.297 0.554 0.102 0.016 18 1.7 S_oc-temp_med&Lingual 545 382 988 2.769 1.007 0.135 0.024 5 0.6 S_orbital_lateral 704 496 1013 2.180 0.734 0.120 0.023 6 0.6 S_orbital_med-olfact 1531 1069 3252 3.183 0.789 0.136 0.039 16 2.4 S_orbital-H_Shaped 2578 1707 3223 2.050 0.562 0.110 0.022 18 2.3 S_parieto_occipital 1577 927 1535 2.332 1.114 0.104 0.023 21 1.1 S_pericallosal 3166 2145 4553 2.295 0.543 0.104 0.020 21 2.5 S_postcentral 2206 1507 3544 2.652 0.501 0.098 0.018 12 1.5 S_precentral-inf-part 1909 1307 2901 2.610 0.521 0.098 0.015 8 1.4 S_precentral-sup-part 893 620 1848 3.171 0.913 0.118 0.020 6 0.8 S_suborbital 1689 1192 2509 2.287 0.528 0.115 0.020 11 1.5 S_subparietal 1937 1375 2881 2.568 0.425 0.106 0.016 11 1.4 S_temporal_inf 8020 5561 13920 2.612 0.511 0.103 0.018 53 5.7 S_temporal_sup 526 357 805 2.747 0.441 0.099 0.014 4 0.3 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Tue Jan 16 07:00:13 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab icbm-205 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/wm.mgz... reading input surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white... reading input pial surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.pial... reading input white surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 313059 Total vertex volume 308521 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 2128430 mm^3 (det: 0.915278 ) lhCtxGM: 310211.420 309855.000 diff= 356.4 pctdiff= 0.115 rhCtxGM: 307783.078 307377.000 diff= 406.1 pctdiff= 0.132 lhCtxWM: 317493.011 318337.500 diff= -844.5 pctdiff=-0.266 rhCtxWM: 320511.394 320670.500 diff= -159.1 pctdiff=-0.050 SubCortGMVol 76355.000 SupraTentVol 1367122.903 (1364345.000) diff=2777.903 pctdiff=0.203 SupraTentVolNotVent 1335388.903 (1332611.000) diff=2777.903 pctdiff=0.208 BrainSegVol 1558906.000 (1555798.000) diff=3108.000 pctdiff=0.199 BrainSegVolNotVent 1522258.000 (1521753.903) diff=504.097 pctdiff=0.033 BrainSegVolNotVent 1522258.000 CerebellumVol 189384.000 VentChorVol 31734.000 3rd4th5thCSF 4914.000 CSFVol 1806.000, OptChiasmVol 263.000 MaskVol 2206782.000 1277 827 2221 2.469 0.582 0.149 0.045 17 2.5 G&S_frontomargin 1375 940 2402 2.605 0.615 0.145 0.032 15 1.9 G&S_occipital_inf 2306 1292 3240 2.212 0.669 0.099 0.023 15 2.2 G&S_paracentral 1688 1134 3295 2.581 0.654 0.129 0.030 17 2.0 G&S_subcentral 1471 862 3174 2.832 0.707 0.131 0.040 19 2.5 G&S_transv_frontopol 3334 2303 8604 3.207 0.750 0.121 0.032 36 4.3 G&S_cingul-Ant 1836 1283 4321 3.185 0.668 0.104 0.019 14 1.3 G&S_cingul-Mid-Ant 1613 1110 3246 2.739 0.566 0.114 0.024 13 1.5 G&S_cingul-Mid-Post 595 418 2047 3.249 0.532 0.167 0.038 10 0.8 G_cingul-Post-dorsal 371 220 837 2.888 0.699 0.140 0.040 6 0.5 G_cingul-Post-ventral 2877 1788 3427 1.782 0.505 0.136 0.031 35 3.5 G_cuneus 1718 1037 4315 3.032 0.674 0.130 0.040 23 2.6 G_front_inf-Opercular 363 233 1096 3.136 0.462 0.126 0.030 4 0.4 G_front_inf-Orbital 982 559 2047 2.737 0.647 0.117 0.034 12 1.3 G_front_inf-Triangul 5657 3056 9901 2.636 0.681 0.115 0.038 61 9.3 G_front_middle 9815 5505 21878 3.184 0.686 0.112 0.031 103 12.4 G_front_sup 687 477 2184 3.690 1.123 0.128 0.047 8 1.2 G_Ins_lg&S_cent_ins 627 386 2545 3.979 0.763 0.124 0.052 9 1.2 G_insular_short 3090 1913 7135 2.982 0.713 0.136 0.035 40 4.1 G_occipital_middle 2537 1494 3497 2.021 0.574 0.118 0.029 24 3.1 G_occipital_sup 2471 1565 6030 2.981 0.666 0.138 0.037 34 3.6 G_oc-temp_lat-fusifor 3690 2219 4925 1.972 0.559 0.132 0.032 45 5.0 G_oc-temp_med-Lingual 1996 1255 4616 3.008 0.922 0.127 0.038 21 3.0 G_oc-temp_med-Parahip 3314 2136 8430 3.019 0.876 0.148 0.053 51 7.4 G_orbital 4405 2589 9259 2.708 0.744 0.123 0.037 51 6.2 G_pariet_inf-Angular 3196 1953 6821 2.787 0.673 0.123 0.035 35 4.2 G_pariet_inf-Supramar 3783 2000 6177 2.382 0.706 0.099 0.027 33 4.1 G_parietal_sup 3518 1795 5502 2.411 0.686 0.098 0.026 27 3.7 G_postcentral 5255 2854 8086 2.413 0.724 0.106 0.030 43 6.7 G_precentral 3408 2075 7129 2.631 0.621 0.117 0.030 38 4.0 G_precuneus 884 616 2315 2.739 0.735 0.165 0.061 21 2.4 G_rectus 643 435 1233 3.187 1.122 0.106 0.035 7 0.6 G_subcallosal 518 295 937 2.551 0.422 0.087 0.016 3 0.3 G_temp_sup-G_T_transv 2523 1644 7756 3.436 0.708 0.134 0.041 34 3.8 G_temp_sup-Lateral 1193 754 2852 3.278 0.750 0.087 0.026 7 1.0 G_temp_sup-Plan_polar 955 639 1781 2.526 0.660 0.091 0.017 5 0.7 G_temp_sup-Plan_tempo 3985 2671 11260 2.986 0.710 0.150 0.047 69 7.9 G_temporal_inf 3652 2589 11044 3.035 0.738 0.135 0.042 50 5.7 G_temporal_middle 422 283 628 2.317 0.527 0.085 0.012 2 0.2 Lat_Fis-ant-Horizont 256 186 359 2.439 0.455 0.096 0.012 1 0.1 Lat_Fis-ant-Vertical 1458 1013 2124 2.575 0.644 0.105 0.019 7 1.1 Lat_Fis-post 4041 2608 5195 1.966 0.582 0.146 0.041 47 7.2 Pole_occipital 2368 1646 8543 3.415 0.897 0.155 0.053 34 5.4 Pole_temporal 2623 1803 2716 1.722 0.680 0.123 0.025 27 2.6 S_calcarine 4511 3042 5313 1.970 0.635 0.100 0.020 24 3.8 S_central 1604 1113 2200 2.065 0.565 0.083 0.011 7 0.7 S_cingul-Marginalis 563 389 919 3.064 0.579 0.095 0.018 2 0.5 S_circular_insula_ant 1546 1037 2629 3.055 0.780 0.080 0.016 6 1.1 S_circular_insula_inf 1596 1068 2714 2.868 0.651 0.099 0.020 6 1.4 S_circular_insula_sup 1557 1111 2908 2.844 0.744 0.104 0.018 9 1.2 S_collat_transv_ant 528 357 602 2.050 0.493 0.128 0.022 6 0.5 S_collat_transv_post 3122 2065 4474 2.321 0.529 0.108 0.021 20 2.7 S_front_inf 2987 1931 4340 2.405 0.602 0.111 0.026 21 3.0 S_front_middle 3508 2304 5674 2.714 0.493 0.095 0.018 18 2.6 S_front_sup 653 458 907 2.360 0.518 0.123 0.024 4 0.7 S_interm_prim-Jensen 4238 2795 5654 2.224 0.602 0.098 0.018 25 2.9 S_intrapariet&P_trans 643 467 1003 2.650 0.835 0.141 0.031 6 0.8 S_oc_middle&Lunatus 2281 1550 3135 2.217 0.488 0.130 0.027 21 2.4 S_oc_sup&transversal 1052 736 1556 2.472 0.371 0.107 0.020 6 0.8 S_occipital_ant 1205 814 1711 2.411 0.633 0.110 0.030 11 1.8 S_oc-temp_lat 2614 1809 3743 2.348 0.558 0.103 0.019 18 2.0 S_oc-temp_med&Lingual 571 407 916 2.484 0.595 0.123 0.025 3 0.7 S_orbital_lateral 818 575 1308 2.563 0.648 0.118 0.026 7 0.8 S_orbital_med-olfact 1875 1244 3618 3.087 0.652 0.128 0.035 19 2.7 S_orbital-H_Shaped 3004 1963 3779 2.055 0.558 0.112 0.021 22 2.6 S_parieto_occipital 1590 1004 1778 2.422 0.888 0.127 0.022 26 1.2 S_pericallosal 3588 2391 4437 2.093 0.600 0.104 0.020 23 3.1 S_postcentral 2605 1718 4338 2.748 0.638 0.101 0.018 16 1.9 S_precentral-inf-part 1643 1127 2404 2.487 0.461 0.094 0.020 7 1.3 S_precentral-sup-part 397 298 794 3.085 0.941 0.154 0.023 4 0.5 S_suborbital 1808 1297 2877 2.287 0.563 0.130 0.029 17 2.1 S_subparietal 2017 1416 3003 2.534 0.541 0.113 0.023 13 1.8 S_temporal_inf 7237 5022 12183 2.614 0.553 0.094 0.015 36 4.3 S_temporal_sup 292 197 473 2.688 0.517 0.111 0.013 2 0.2 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Tue Jan 16 07:00:56 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 icbm-205 lh ../surf/lh.sphere.reg /usr/local/freesurfer-6.0.0//average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer-6.0.0//average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1390 labels changed using aseg relabeling using gibbs priors... 000: 2354 changed, 174418 examined... 001: 543 changed, 10669 examined... 002: 143 changed, 3013 examined... 003: 50 changed, 835 examined... 004: 18 changed, 313 examined... 005: 11 changed, 113 examined... 006: 6 changed, 78 examined... 007: 1 changed, 42 examined... 008: 1 changed, 7 examined... 009: 1 changed, 7 examined... 010: 0 changed, 7 examined... 206 labels changed using aseg 000: 49 total segments, 16 labels (161 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 786 vertices marked for relabeling... 786 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 16 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Tue Jan 16 07:01:12 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 icbm-205 rh ../surf/rh.sphere.reg /usr/local/freesurfer-6.0.0//average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /usr/local/freesurfer-6.0.0//average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1657 labels changed using aseg relabeling using gibbs priors... 000: 2345 changed, 176232 examined... 001: 553 changed, 10736 examined... 002: 174 changed, 3142 examined... 003: 62 changed, 1012 examined... 004: 42 changed, 363 examined... 005: 26 changed, 213 examined... 006: 16 changed, 138 examined... 007: 7 changed, 83 examined... 008: 11 changed, 44 examined... 009: 8 changed, 56 examined... 010: 3 changed, 38 examined... 011: 4 changed, 18 examined... 012: 2 changed, 27 examined... 013: 1 changed, 12 examined... 014: 1 changed, 7 examined... 015: 2 changed, 8 examined... 016: 2 changed, 7 examined... 017: 3 changed, 13 examined... 018: 5 changed, 16 examined... 019: 5 changed, 21 examined... 020: 5 changed, 26 examined... 021: 3 changed, 19 examined... 022: 1 changed, 13 examined... 023: 1 changed, 6 examined... 024: 2 changed, 10 examined... 025: 1 changed, 12 examined... 026: 2 changed, 7 examined... 027: 5 changed, 12 examined... 028: 5 changed, 21 examined... 029: 4 changed, 23 examined... 030: 1 changed, 20 examined... 031: 2 changed, 7 examined... 032: 1 changed, 12 examined... 033: 0 changed, 7 examined... 367 labels changed using aseg 000: 59 total segments, 26 labels (444 vertices) changed 001: 35 total segments, 2 labels (8 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 667 vertices marked for relabeling... 667 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 17 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Tue Jan 16 07:01:29 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab icbm-205 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/wm.mgz... reading input surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white... reading input pial surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.pial... reading input white surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 316003 Total vertex volume 310659 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 2128430 mm^3 (det: 0.915278 ) lhCtxGM: 310211.420 309855.000 diff= 356.4 pctdiff= 0.115 rhCtxGM: 307783.078 307377.000 diff= 406.1 pctdiff= 0.132 lhCtxWM: 317493.011 318337.500 diff= -844.5 pctdiff=-0.266 rhCtxWM: 320511.394 320670.500 diff= -159.1 pctdiff=-0.050 SubCortGMVol 76355.000 SupraTentVol 1367122.903 (1364345.000) diff=2777.903 pctdiff=0.203 SupraTentVolNotVent 1335388.903 (1332611.000) diff=2777.903 pctdiff=0.208 BrainSegVol 1558906.000 (1555798.000) diff=3108.000 pctdiff=0.199 BrainSegVolNotVent 1522258.000 (1521753.903) diff=504.097 pctdiff=0.033 BrainSegVolNotVent 1522258.000 CerebellumVol 189384.000 VentChorVol 31734.000 3rd4th5thCSF 4914.000 CSFVol 1806.000, OptChiasmVol 263.000 MaskVol 2206782.000 1913 1263 4204 3.272 0.693 0.138 0.033 28 2.5 caudalanteriorcingulate 5760 3314 9754 2.812 0.625 0.099 0.024 40 5.4 caudalmiddlefrontal 3896 2491 4930 1.951 0.499 0.129 0.031 39 4.8 cuneus 751 525 2170 3.109 0.813 0.107 0.030 5 0.8 entorhinal 4687 3148 10296 2.912 0.659 0.123 0.028 48 5.1 fusiform 9082 5912 17132 2.595 0.578 0.119 0.028 91 10.2 inferiorparietal 5557 3837 14013 3.033 0.778 0.128 0.033 66 7.8 inferiortemporal 1771 1122 3171 2.529 0.928 0.123 0.031 22 1.8 isthmuscingulate 9341 5819 13946 2.227 0.607 0.133 0.033 108 12.3 lateraloccipital 4731 3338 10827 3.026 0.830 0.141 0.039 62 7.4 lateralorbitofrontal 5839 3872 7379 1.874 0.504 0.133 0.030 67 7.3 lingual 2457 1672 5936 2.976 0.862 0.131 0.037 34 3.6 medialorbitofrontal 8367 5717 19611 2.887 0.673 0.123 0.028 90 9.6 middletemporal 1196 793 2755 2.838 0.860 0.104 0.022 9 1.0 parahippocampal 3581 2284 6238 2.597 0.615 0.101 0.020 23 3.0 paracentral 2689 1814 5583 2.733 0.551 0.121 0.028 26 3.0 parsopercularis 941 678 2300 2.884 0.576 0.123 0.031 10 1.2 parsorbitalis 2731 1762 5528 2.872 0.752 0.111 0.027 22 3.0 parstriangularis 2490 1670 2170 1.513 0.318 0.147 0.036 32 3.9 pericalcarine 10188 6013 14707 2.286 0.758 0.100 0.022 75 9.3 postcentral 2165 1518 4442 2.717 0.734 0.122 0.025 23 2.1 posteriorcingulate 10385 6308 16704 2.550 0.739 0.101 0.021 67 9.3 precentral 7712 5112 13246 2.327 0.670 0.117 0.028 76 8.2 precuneus 1789 1223 4389 3.374 0.695 0.128 0.032 22 2.0 rostralanteriorcingulate 8775 5381 15188 2.592 0.667 0.118 0.030 89 10.3 rostralmiddlefrontal 16139 9815 33114 2.971 0.710 0.109 0.028 147 17.9 superiorfrontal 9025 5391 13433 2.328 0.616 0.108 0.023 74 8.1 superiorparietal 10148 6845 25917 3.149 0.788 0.108 0.025 90 9.7 superiortemporal 6512 4228 12281 2.700 0.602 0.117 0.029 69 7.1 supramarginal 768 485 1310 2.632 0.434 0.114 0.023 7 0.6 transversetemporal 3145 2156 7984 3.446 0.798 0.104 0.023 21 2.8 insula #----------------------------------------- #@# Parcellation Stats 3 rh Tue Jan 16 07:02:10 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab icbm-205 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/wm.mgz... reading input surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white... reading input pial surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.pial... reading input white surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 313059 Total vertex volume 308521 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 2128430 mm^3 (det: 0.915278 ) lhCtxGM: 310211.420 309855.000 diff= 356.4 pctdiff= 0.115 rhCtxGM: 307783.078 307377.000 diff= 406.1 pctdiff= 0.132 lhCtxWM: 317493.011 318337.500 diff= -844.5 pctdiff=-0.266 rhCtxWM: 320511.394 320670.500 diff= -159.1 pctdiff=-0.050 SubCortGMVol 76355.000 SupraTentVol 1367122.903 (1364345.000) diff=2777.903 pctdiff=0.203 SupraTentVolNotVent 1335388.903 (1332611.000) diff=2777.903 pctdiff=0.208 BrainSegVol 1558906.000 (1555798.000) diff=3108.000 pctdiff=0.199 BrainSegVolNotVent 1522258.000 (1521753.903) diff=504.097 pctdiff=0.033 BrainSegVolNotVent 1522258.000 CerebellumVol 189384.000 VentChorVol 31734.000 3rd4th5thCSF 4914.000 CSFVol 1806.000, OptChiasmVol 263.000 MaskVol 2206782.000 1359 915 3341 3.132 0.750 0.126 0.025 19 1.4 caudalanteriorcingulate 5437 3312 8299 2.549 0.610 0.108 0.029 40 6.7 caudalmiddlefrontal 3851 2391 4543 1.818 0.474 0.128 0.028 40 4.3 cuneus 839 539 1960 2.940 0.845 0.128 0.041 8 1.6 entorhinal 4960 3290 10587 2.834 0.702 0.118 0.029 49 5.6 fusiform 10582 6717 19695 2.617 0.698 0.114 0.027 97 11.2 inferiorparietal 7659 5220 18954 2.909 0.766 0.137 0.040 104 13.1 inferiortemporal 1572 1027 3208 2.673 0.797 0.133 0.030 21 1.7 isthmuscingulate 8664 5588 13175 2.312 0.681 0.137 0.033 92 11.8 lateraloccipital 5450 3576 11111 2.921 0.782 0.142 0.047 73 10.8 lateralorbitofrontal 5858 3716 7660 2.009 0.545 0.134 0.032 70 7.8 lingual 2482 1735 5782 2.940 0.888 0.142 0.043 39 4.3 medialorbitofrontal 7846 5535 19343 2.906 0.692 0.121 0.031 80 9.7 middletemporal 1218 778 2437 2.680 0.890 0.096 0.018 8 0.9 parahippocampal 3929 2335 5828 2.405 0.687 0.100 0.022 26 3.4 paracentral 3121 1959 6109 2.734 0.734 0.115 0.028 29 3.3 parsopercularis 1121 768 2863 2.948 0.762 0.117 0.028 10 1.3 parsorbitalis 2239 1440 3894 2.506 0.591 0.109 0.025 18 2.3 parstriangularis 2543 1808 2281 1.457 0.326 0.142 0.034 31 3.7 pericalcarine 9692 5792 14151 2.218 0.727 0.104 0.024 75 9.2 postcentral 1973 1402 4198 2.658 0.775 0.131 0.026 27 2.0 posteriorcingulate 11035 6815 16930 2.415 0.682 0.104 0.025 76 11.6 precentral 7692 5030 13164 2.378 0.654 0.116 0.026 73 7.7 precuneus 1464 1001 4061 3.397 0.851 0.129 0.032 19 1.9 rostralanteriorcingulate 7902 4775 14136 2.652 0.643 0.116 0.033 74 10.6 rostralmiddlefrontal 17476 10537 35595 2.990 0.719 0.108 0.028 155 19.8 superiorfrontal 9444 5620 13635 2.232 0.643 0.104 0.024 75 9.2 superiorparietal 9098 6031 21407 3.066 0.779 0.107 0.027 74 9.2 superiortemporal 6200 4057 11107 2.566 0.672 0.113 0.027 48 6.7 supramarginal 604 355 1015 2.560 0.448 0.093 0.018 4 0.4 transversetemporal 3119 2107 8052 3.470 0.859 0.114 0.034 26 4.2 insula #----------------------------------------- #@# WM/GM Contrast lh Tue Jan 16 07:02:51 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts pctsurfcon --s icbm-205 --lh-only Log file is /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts/pctsurfcon.log Tue Jan 16 07:02:51 EST 2018 setenv SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 cd /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts /usr/local/freesurfer-6.0.0//bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux kaplan 3.13.0-137-generic #186-Ubuntu SMP Mon Dec 4 19:09:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer-6.0.0/ mri_vol2surf --mov /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/tmp.pctsurfcon.30088/lh.wm.mgh --regheader icbm-205 --cortex srcvol = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/lh.cortex.label Reading surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 = 95799 Masking with /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/lh.cortex.label Writing to /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/tmp.pctsurfcon.30088/lh.wm.mgh Dim: 174418 1 1 mri_vol2surf --mov /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/tmp.pctsurfcon.30088/lh.gm.mgh --projfrac 0.3 --regheader icbm-205 --cortex srcvol = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/lh.cortex.label Reading surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Done reading source surface Reading thickness /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 = 111198 Masking with /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/lh.cortex.label Writing to /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/tmp.pctsurfcon.30088/lh.gm.mgh Dim: 174418 1 1 mri_concat /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/tmp.pctsurfcon.30088/lh.wm.mgh /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/tmp.pctsurfcon.30088/lh.gm.mgh --paired-diff-norm --mul 100 --o /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.w-g.pct.mgh mri_segstats --in /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.w-g.pct.mgh --annot icbm-205 lh aparc --sum /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.w-g.pct.mgh --annot icbm-205 lh aparc --sum /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/stats/lh.w-g.pct.stats --snr sysname Linux hostname kaplan machine x86_64 user trisanna UseRobust 0 Constructing seg from annotation Reading annotation /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.w-g.pct.mgh Vertex Area is 0.642343 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# WM/GM Contrast rh Tue Jan 16 07:02:57 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts pctsurfcon --s icbm-205 --rh-only Log file is /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts/pctsurfcon.log Tue Jan 16 07:02:57 EST 2018 setenv SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 cd /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/scripts /usr/local/freesurfer-6.0.0//bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux kaplan 3.13.0-137-generic #186-Ubuntu SMP Mon Dec 4 19:09:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer-6.0.0/ mri_vol2surf --mov /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/tmp.pctsurfcon.30144/rh.wm.mgh --regheader icbm-205 --cortex srcvol = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/rh.cortex.label Reading surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 = 97085 Masking with /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/rh.cortex.label Writing to /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/tmp.pctsurfcon.30144/rh.wm.mgh Dim: 176232 1 1 mri_vol2surf --mov /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/tmp.pctsurfcon.30144/rh.gm.mgh --projfrac 0.3 --regheader icbm-205 --cortex srcvol = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/orig.mgz as target reference. -------- original matrix ----------- -1.00000 0.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/rh.cortex.label Reading surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white Done reading source surface Reading thickness /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 = 112442 Masking with /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/rh.cortex.label Writing to /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/tmp.pctsurfcon.30144/rh.gm.mgh Dim: 176232 1 1 mri_concat /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/tmp.pctsurfcon.30144/rh.wm.mgh /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/tmp.pctsurfcon.30144/rh.gm.mgh --paired-diff-norm --mul 100 --o /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.w-g.pct.mgh mri_segstats --in /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.w-g.pct.mgh --annot icbm-205 rh aparc --sum /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --in /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.w-g.pct.mgh --annot icbm-205 rh aparc --sum /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/stats/rh.w-g.pct.stats --snr sysname Linux hostname kaplan machine x86_64 user trisanna UseRobust 0 Constructing seg from annotation Reading annotation /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.w-g.pct.mgh Vertex Area is 0.639602 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# Relabel Hypointensities Tue Jan 16 07:03:04 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 12217 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 7700 voxels changed to hypointensity... 19344 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Tue Jan 16 07:03:29 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205 mri_aparc2aseg --s icbm-205 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer-6.0.0//average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /usr/local/freesurfer-6.0.0//average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 subject icbm-205 outvol /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading lh pial surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.pial Loading lh annotations from /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white Reading rh pial surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.pial Loading rh annotations from /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 9.58 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 105 rescaling Left_Cerebral_Cortex from 61 --> 79 rescaling Left_Lateral_Ventricle from 13 --> 23 rescaling Left_Inf_Lat_Vent from 34 --> 40 rescaling Left_Cerebellum_White_Matter from 86 --> 91 rescaling Left_Cerebellum_Cortex from 60 --> 70 rescaling Left_Thalamus from 94 --> 105 rescaling Left_Thalamus_Proper from 84 --> 90 rescaling Left_Caudate from 75 --> 74 rescaling Left_Putamen from 80 --> 83 rescaling Left_Pallidum from 98 --> 95 rescaling Third_Ventricle from 25 --> 25 rescaling Fourth_Ventricle from 22 --> 25 rescaling Brain_Stem from 81 --> 86 rescaling Left_Hippocampus from 57 --> 70 rescaling Left_Amygdala from 56 --> 76 rescaling CSF from 32 --> 47 rescaling Left_Accumbens_area from 62 --> 68 rescaling Left_VentralDC from 87 --> 91 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 75 rescaling Right_Lateral_Ventricle from 13 --> 18 rescaling Right_Inf_Lat_Vent from 25 --> 29 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 68 rescaling Right_Thalamus_Proper from 85 --> 90 rescaling Right_Caudate from 62 --> 77 rescaling Right_Putamen from 80 --> 86 rescaling Right_Pallidum from 97 --> 91 rescaling Right_Hippocampus from 53 --> 71 rescaling Right_Amygdala from 55 --> 73 rescaling Right_Accumbens_area from 65 --> 75 rescaling Right_VentralDC from 86 --> 94 rescaling Fifth_Ventricle from 40 --> 41 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 77 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 = 616402 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 169 changed. pass 2: 6 changed. pass 3: 3 changed. pass 4: 2 changed. pass 5: 2 changed. pass 6: 2 changed. pass 7: 2 changed. pass 8: 2 changed. pass 9: 2 changed. pass 10: 2 changed. pass 11: 2 changed. nchanged = 0 Writing output aseg to /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Tue Jan 16 07:09:44 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205 mri_aparc2aseg --s icbm-205 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer-6.0.0//average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /usr/local/freesurfer-6.0.0//average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 subject icbm-205 outvol /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading lh pial surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.pial Loading lh annotations from /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white Reading rh pial surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.pial Loading rh annotations from /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 9.58 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 105 rescaling Left_Cerebral_Cortex from 61 --> 79 rescaling Left_Lateral_Ventricle from 13 --> 23 rescaling Left_Inf_Lat_Vent from 34 --> 40 rescaling Left_Cerebellum_White_Matter from 86 --> 91 rescaling Left_Cerebellum_Cortex from 60 --> 70 rescaling Left_Thalamus from 94 --> 105 rescaling Left_Thalamus_Proper from 84 --> 90 rescaling Left_Caudate from 75 --> 74 rescaling Left_Putamen from 80 --> 83 rescaling Left_Pallidum from 98 --> 95 rescaling Third_Ventricle from 25 --> 25 rescaling Fourth_Ventricle from 22 --> 25 rescaling Brain_Stem from 81 --> 86 rescaling Left_Hippocampus from 57 --> 70 rescaling Left_Amygdala from 56 --> 76 rescaling CSF from 32 --> 47 rescaling Left_Accumbens_area from 62 --> 68 rescaling Left_VentralDC from 87 --> 91 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 75 rescaling Right_Lateral_Ventricle from 13 --> 18 rescaling Right_Inf_Lat_Vent from 25 --> 29 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 68 rescaling Right_Thalamus_Proper from 85 --> 90 rescaling Right_Caudate from 62 --> 77 rescaling Right_Putamen from 80 --> 86 rescaling Right_Pallidum from 97 --> 91 rescaling Right_Hippocampus from 53 --> 71 rescaling Right_Amygdala from 55 --> 73 rescaling Right_Accumbens_area from 65 --> 75 rescaling Right_VentralDC from 86 --> 94 rescaling Fifth_Ventricle from 40 --> 41 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 77 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 = 616395 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 169 changed. pass 2: 6 changed. pass 3: 3 changed. pass 4: 2 changed. pass 5: 2 changed. pass 6: 2 changed. pass 7: 2 changed. pass 8: 2 changed. pass 9: 2 changed. pass 10: 2 changed. pass 11: 2 changed. nchanged = 0 Writing output aseg to /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Tue Jan 16 07:16:01 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205 mri_aparc2aseg --s icbm-205 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer-6.0.0//average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /usr/local/freesurfer-6.0.0//average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 subject icbm-205 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading lh pial surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.pial Loading lh annotations from /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/lh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white Reading rh pial surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.pial Loading rh annotations from /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/rh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter setting orig areas to linear transform determinant scaled 9.58 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 105 rescaling Left_Cerebral_Cortex from 61 --> 79 rescaling Left_Lateral_Ventricle from 13 --> 23 rescaling Left_Inf_Lat_Vent from 34 --> 40 rescaling Left_Cerebellum_White_Matter from 86 --> 91 rescaling Left_Cerebellum_Cortex from 60 --> 70 rescaling Left_Thalamus from 94 --> 105 rescaling Left_Thalamus_Proper from 84 --> 90 rescaling Left_Caudate from 75 --> 74 rescaling Left_Putamen from 80 --> 83 rescaling Left_Pallidum from 98 --> 95 rescaling Third_Ventricle from 25 --> 25 rescaling Fourth_Ventricle from 22 --> 25 rescaling Brain_Stem from 81 --> 86 rescaling Left_Hippocampus from 57 --> 70 rescaling Left_Amygdala from 56 --> 76 rescaling CSF from 32 --> 47 rescaling Left_Accumbens_area from 62 --> 68 rescaling Left_VentralDC from 87 --> 91 rescaling Right_Cerebral_White_Matter from 105 --> 103 rescaling Right_Cerebral_Cortex from 58 --> 75 rescaling Right_Lateral_Ventricle from 13 --> 18 rescaling Right_Inf_Lat_Vent from 25 --> 29 rescaling Right_Cerebellum_White_Matter from 87 --> 90 rescaling Right_Cerebellum_Cortex from 59 --> 68 rescaling Right_Thalamus_Proper from 85 --> 90 rescaling Right_Caudate from 62 --> 77 rescaling Right_Putamen from 80 --> 86 rescaling Right_Pallidum from 97 --> 91 rescaling Right_Hippocampus from 53 --> 71 rescaling Right_Amygdala from 55 --> 73 rescaling Right_Accumbens_area from 65 --> 75 rescaling Right_VentralDC from 86 --> 94 rescaling Fifth_Ventricle from 40 --> 41 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 77 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 = 616395 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 169 changed. pass 2: 6 changed. pass 3: 3 changed. pass 4: 2 changed. pass 5: 2 changed. pass 6: 2 changed. pass 7: 2 changed. pass 8: 2 changed. pass 9: 2 changed. pass 10: 2 changed. pass 11: 2 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Tue Jan 16 07:22:18 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Tue Jan 16 07:22:18 EST 2018 setenv SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 cd /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri /usr/local/freesurfer-6.0.0//bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux kaplan 3.13.0-137-generic #186-Ubuntu SMP Mon Dec 4 19:09:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri cmdline mri_binarize.bin --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 sysname Linux hostname kaplan machine x86_64 user trisanna input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done Started at Tue Jan 16 07:22:18 EST 2018 Ended at Tue Jan 16 07:22:23 EST 2018 Apas2aseg-Run-Time-Sec 5 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Tue Jan 16 07:22:23 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205 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 /usr/local/freesurfer-6.0.0//ASegStatsLUT.txt --subject icbm-205 $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer-6.0.0//ASegStatsLUT.txt --subject icbm-205 sysname Linux hostname kaplan machine x86_64 user trisanna UseRobust 0 atlas_icv (eTIV) = 2128430 mm^3 (det: 0.915278 ) Computing euler number orig.nofix lheno = -70, rheno = -62 orig.nofix lhholes = 36, rhholes = 32 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 310211.420 309855.000 diff= 356.4 pctdiff= 0.115 rhCtxGM: 307783.078 307377.000 diff= 406.1 pctdiff= 0.132 lhCtxWM: 317493.011 318337.500 diff= -844.5 pctdiff=-0.266 rhCtxWM: 320511.394 320670.500 diff= -159.1 pctdiff=-0.050 SubCortGMVol 76355.000 SupraTentVol 1367122.903 (1364345.000) diff=2777.903 pctdiff=0.203 SupraTentVolNotVent 1335388.903 (1332611.000) diff=2777.903 pctdiff=0.208 BrainSegVol 1558906.000 (1555798.000) diff=3108.000 pctdiff=0.199 BrainSegVolNotVent 1522258.000 (1521753.903) diff=504.097 pctdiff=0.033 BrainSegVolNotVent 1522258.000 CerebellumVol 189384.000 VentChorVol 31734.000 3rd4th5thCSF 4914.000 CSFVol 1806.000, OptChiasmVol 263.000 MaskVol 2206782.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Tue Jan 16 07:24:35 EST 2018 /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205 mri_aparc2aseg --s icbm-205 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 subject icbm-205 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/aparc+aseg.mgz Reading lh white surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading lh pial surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.pial Loading lh annotations from /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white Reading rh pial surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.pial Loading rh annotations from /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/ribbon.mgz Loading filled from /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 9944 vertices from left hemi Ripped 9731 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-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/aseg.mgz Loading Ctx Seg File /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1253181 Used brute-force search on 994 voxels Fixing Parahip LH WM Found 3 clusters 0 k 4.000000 1 k 19.000000 2 k 1693.000000 Fixing Parahip RH WM Found 7 clusters 0 k 34.000000 1 k 1.000000 2 k 3.000000 3 k 2.000000 4 k 1.000000 5 k 1.000000 6 k 1737.000000 Writing output aseg to mri/wmparc.mgz mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject icbm-205 --surf-wm-vol --ctab /usr/local/freesurfer-6.0.0//WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject icbm-205 --surf-wm-vol --ctab /usr/local/freesurfer-6.0.0//WMParcStatsLUT.txt --etiv sysname Linux hostname kaplan machine x86_64 user trisanna UseRobust 0 atlas_icv (eTIV) = 2128430 mm^3 (det: 0.915278 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 310211.420 309855.000 diff= 356.4 pctdiff= 0.115 rhCtxGM: 307783.078 307377.000 diff= 406.1 pctdiff= 0.132 lhCtxWM: 317493.011 318337.500 diff= -844.5 pctdiff=-0.266 rhCtxWM: 320511.394 320670.500 diff= -159.1 pctdiff=-0.050 SubCortGMVol 76355.000 SupraTentVol 1367122.903 (1364345.000) diff=2777.903 pctdiff=0.203 SupraTentVolNotVent 1335388.903 (1332611.000) diff=2777.903 pctdiff=0.208 BrainSegVol 1558906.000 (1555798.000) diff=3108.000 pctdiff=0.199 BrainSegVolNotVent 1522258.000 (1521753.903) diff=504.097 pctdiff=0.033 BrainSegVolNotVent 1522258.000 CerebellumVol 189384.000 VentChorVol 31734.000 3rd4th5thCSF 4914.000 CSFVol 1806.000, OptChiasmVol 263.000 MaskVol 2206782.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label #-------------------------------------------- #@# BA_exvivo Labels lh Tue Jan 16 07:34:48 EST 2018 mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA1_exvivo.label --trgsubject icbm-205 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 1049 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 5178 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA2_exvivo.label --trgsubject icbm-205 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 1485 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 9394 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA3a_exvivo.label --trgsubject icbm-205 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 515 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4592 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA3b_exvivo.label --trgsubject icbm-205 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 1024 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 7007 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA4a_exvivo.label --trgsubject icbm-205 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 1178 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6962 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA4p_exvivo.label --trgsubject icbm-205 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 732 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4802 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA6_exvivo.label --trgsubject icbm-205 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 3966 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 17555 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA44_exvivo.label --trgsubject icbm-205 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 746 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4927 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA45_exvivo.label --trgsubject icbm-205 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 1217 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4639 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.V1_exvivo.label --trgsubject icbm-205 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 2397 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 7038 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.V2_exvivo.label --trgsubject icbm-205 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 4592 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 12706 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.MT_exvivo.label --trgsubject icbm-205 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 770 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2788 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject icbm-205 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 174418 Number of reverse mapping hits = 181 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1471 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject icbm-205 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 173 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1372 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject icbm-205 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.BA1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 285 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1299 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject icbm-205 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.BA2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 556 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2648 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject icbm-205 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.BA3a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 178 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1682 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject icbm-205 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.BA3b_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 416 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2412 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject icbm-205 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.BA4a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 456 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2775 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject icbm-205 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.BA4p_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 283 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1832 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject icbm-205 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.BA6_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 1950 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 8985 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject icbm-205 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.BA44_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 215 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2127 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject icbm-205 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.BA45_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 485 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1636 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject icbm-205 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.V1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 1683 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 5088 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject icbm-205 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.V2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 2132 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 5466 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject icbm-205 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.MT_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 174418 Number of reverse mapping hits = 186 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 699 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject icbm-205 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 174418 Number of reverse mapping hits = 87 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 557 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject icbm-205 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./lh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 174418 Number of reverse mapping hits = 72 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 522 mri_label2label: Done mris_label2annot --s icbm-205 --hemi lh --ctab /usr/local/freesurfer-6.0.0//average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer-6.0.0//average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label cmdline mris_label2annot --s icbm-205 --hemi lh --ctab /usr/local/freesurfer-6.0.0//average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname kaplan machine x86_64 user trisanna subject icbm-205 hemi lh SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 ColorTable /usr/local/freesurfer-6.0.0//average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 119270 unhit vertices Writing annot to /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/lh.BA_exvivo.annot mris_label2annot --s icbm-205 --hemi lh --ctab /usr/local/freesurfer-6.0.0//average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer-6.0.0//average/colortable_BA.txt Number of ctab entries 15 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label cmdline mris_label2annot --s icbm-205 --hemi lh --ctab /usr/local/freesurfer-6.0.0//average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname kaplan machine x86_64 user trisanna subject icbm-205 hemi lh SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 ColorTable /usr/local/freesurfer-6.0.0//average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 141107 unhit vertices Writing annot to /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/label/lh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab icbm-205 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/wm.mgz... reading input surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white... reading input pial surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.pial... reading input white surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 316003 Total vertex volume 310659 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer-6.0.0//average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 2128430 mm^3 (det: 0.915278 ) lhCtxGM: 310211.420 309855.000 diff= 356.4 pctdiff= 0.115 rhCtxGM: 307783.078 307377.000 diff= 406.1 pctdiff= 0.132 lhCtxWM: 317493.011 318337.500 diff= -844.5 pctdiff=-0.266 rhCtxWM: 320511.394 320670.500 diff= -159.1 pctdiff=-0.050 SubCortGMVol 76355.000 SupraTentVol 1367122.903 (1364345.000) diff=2777.903 pctdiff=0.203 SupraTentVolNotVent 1335388.903 (1332611.000) diff=2777.903 pctdiff=0.208 BrainSegVol 1558906.000 (1555798.000) diff=3108.000 pctdiff=0.199 BrainSegVolNotVent 1522258.000 (1521753.903) diff=504.097 pctdiff=0.033 BrainSegVolNotVent 1522258.000 CerebellumVol 189384.000 VentChorVol 31734.000 3rd4th5thCSF 4914.000 CSFVol 1806.000, OptChiasmVol 263.000 MaskVol 2206782.000 1694 840 2493 2.396 0.608 0.090 0.025 12 1.6 BA1_exvivo 5012 3041 7584 2.454 0.654 0.103 0.023 38 4.6 BA2_exvivo 1473 987 1329 1.701 0.418 0.133 0.029 14 1.6 BA3a_exvivo 3319 2020 4369 2.032 0.827 0.105 0.025 27 3.3 BA3b_exvivo 2378 1463 3892 2.552 0.784 0.096 0.022 14 2.1 BA4a_exvivo 1952 1208 2925 2.471 0.677 0.090 0.019 9 1.6 BA4p_exvivo 13924 7967 25966 2.893 0.712 0.096 0.023 100 13.0 BA6_exvivo 2768 1850 5586 2.758 0.531 0.113 0.023 25 2.6 BA44_exvivo 3734 2438 7604 2.705 0.796 0.121 0.032 35 4.8 BA45_exvivo 4479 2937 4436 1.579 0.371 0.139 0.034 53 6.5 V1_exvivo 10289 6501 13141 1.982 0.546 0.142 0.036 130 15.1 V2_exvivo 2579 1693 4440 2.524 0.513 0.117 0.028 24 2.7 MT_exvivo 742 482 2005 3.048 0.747 0.091 0.023 4 0.6 perirhinal_exvivo 805 579 2295 3.397 0.750 0.122 0.030 7 0.9 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab icbm-205 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/mri/wm.mgz... reading input surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white... reading input pial surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.pial... reading input white surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 316003 Total vertex volume 310659 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer-6.0.0//average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 2128430 mm^3 (det: 0.915278 ) lhCtxGM: 310211.420 309855.000 diff= 356.4 pctdiff= 0.115 rhCtxGM: 307783.078 307377.000 diff= 406.1 pctdiff= 0.132 lhCtxWM: 317493.011 318337.500 diff= -844.5 pctdiff=-0.266 rhCtxWM: 320511.394 320670.500 diff= -159.1 pctdiff=-0.050 SubCortGMVol 76355.000 SupraTentVol 1367122.903 (1364345.000) diff=2777.903 pctdiff=0.203 SupraTentVolNotVent 1335388.903 (1332611.000) diff=2777.903 pctdiff=0.208 BrainSegVol 1558906.000 (1555798.000) diff=3108.000 pctdiff=0.199 BrainSegVolNotVent 1522258.000 (1521753.903) diff=504.097 pctdiff=0.033 BrainSegVolNotVent 1522258.000 CerebellumVol 189384.000 VentChorVol 31734.000 3rd4th5thCSF 4914.000 CSFVol 1806.000, OptChiasmVol 263.000 MaskVol 2206782.000 1098 508 1617 2.477 0.623 0.088 0.023 7 1.0 BA1_exvivo 2254 1296 3281 2.457 0.716 0.093 0.022 15 1.9 BA2_exvivo 1299 868 1128 1.661 0.366 0.135 0.029 13 1.4 BA3a_exvivo 2122 1350 2246 1.661 0.531 0.104 0.020 15 1.8 BA3b_exvivo 2324 1446 3638 2.493 0.772 0.089 0.020 10 2.0 BA4a_exvivo 1578 960 2314 2.465 0.638 0.090 0.020 7 1.3 BA4p_exvivo 7911 4561 13690 2.697 0.693 0.099 0.023 56 7.5 BA6_exvivo 1657 1169 3335 2.648 0.502 0.121 0.025 17 1.6 BA44_exvivo 1536 954 3537 2.858 0.749 0.120 0.035 16 2.3 BA45_exvivo 4774 3101 4716 1.578 0.363 0.137 0.034 55 6.9 V1_exvivo 5253 3311 6392 1.911 0.526 0.152 0.038 76 8.5 V2_exvivo 664 427 1427 2.639 0.550 0.115 0.032 7 0.7 MT_exvivo 391 253 988 2.955 0.673 0.069 0.015 1 0.2 perirhinal_exvivo 450 338 1268 3.279 0.910 0.131 0.030 4 0.5 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Tue Jan 16 07:40:12 EST 2018 mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.BA1_exvivo.label --trgsubject icbm-205 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 176232 Number of reverse mapping hits = 1261 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 5223 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.BA2_exvivo.label --trgsubject icbm-205 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 176232 Number of reverse mapping hits = 1552 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 8239 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.BA3a_exvivo.label --trgsubject icbm-205 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 176232 Number of reverse mapping hits = 547 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4527 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.BA3b_exvivo.label --trgsubject icbm-205 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 176232 Number of reverse mapping hits = 950 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 5472 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.BA4a_exvivo.label --trgsubject icbm-205 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 176232 Number of reverse mapping hits = 1725 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 7472 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.BA4p_exvivo.label --trgsubject icbm-205 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 176232 Number of reverse mapping hits = 968 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 5441 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.BA6_exvivo.label --trgsubject icbm-205 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 176232 Number of reverse mapping hits = 4067 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 16323 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.BA44_exvivo.label --trgsubject icbm-205 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 176232 Number of reverse mapping hits = 2046 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 8958 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.BA45_exvivo.label --trgsubject icbm-205 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 176232 Number of reverse mapping hits = 1504 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6859 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.V1_exvivo.label --trgsubject icbm-205 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 176232 Number of reverse mapping hits = 2306 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 7033 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.V2_exvivo.label --trgsubject icbm-205 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 176232 Number of reverse mapping hits = 4392 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 12408 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.MT_exvivo.label --trgsubject icbm-205 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = icbm-205 trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305 FREESURFER_HOME /usr/local/freesurfer-6.0.0/ Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/surf/rh.white Reading target registration /data-01/trisanna/freesurfer/freesurfer_6.0/ICBM_305/icbm-205/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 176232 Number of reverse mapping hits = 844 Checking for and removing duplicates /usr/local/freesurfer-6.0.0//bin/mri_label2label: line 3: 31598 Aborted (core dumped) mri_label2label.bin "$@" Linux kaplan 3.13.0-137-generic #186-Ubuntu SMP Mon Dec 4 19:09:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s icbm-205 exited with ERRORS at Tue Jan 16 07:42:26 EST 2018 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting