Mon Dec 19 10:27:44 GMT 2016 /usr/local/freesurfer/subjects/SynthN /usr/local/freesurfer/bin/recon-all -subjid SynthN -i w_MniNick.nii -all subjid SynthN setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20161130-24fa2c9 Linux stefano-Q170M-C 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 127934 maxlocks unlimited maxsignal 127934 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 32797824 7085292 7671708 225524 18040824 25008764 Swap: 10257404 88 10257316 ######################################## program versions used $Id: recon-all,v 1.597 2016/10/18 14:38:18 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: $ TimeStamp: 2016/12/19-10:27:44-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: tkregister2.c,v 1.133 2016/08/02 21:17:11 greve Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-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: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_normalize.c,v 1.89 2016/07/29 22:15:21 zkaufman Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_segment.c,v 1.44 2016/10/22 17:29:37 fischl Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_label2label.c,v 1.49 2016/08/02 20:18:11 zkaufman Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_em_register.c,v 1.106 2016/10/22 17:31:12 fischl Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_ca_normalize.c,v 1.69 2016/10/22 17:30:57 fischl Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_ca_register.c,v 1.99 2016/10/22 17:31:24 fischl Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_ca_label.c,v 1.115 2016/10/22 17:31:36 fischl Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_tessellate.c,v 1.39 2016/07/20 21:05:04 zkaufman Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mris_fix_topology.c,v 1.51 2016/10/27 19:43:58 fischl Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mris_make_surfaces.c,v 1.165 2016/11/21 03:01:42 fischl Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mris_volmask.cpp,v 1.28 2016/11/18 19:19:29 fischl Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mris_calc.c,v 1.55 2016/09/27 18:50:16 greve Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-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: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-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: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/12/19-10:27:45-GMT BuildTimeStamp: Nov 30 2016 01:21:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: stefano Machine: stefano-Q170M-C Platform: Linux PlatformVersion: 4.4.0-53-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/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/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /usr/local/freesurfer/subjects/SynthN mri_convert /mnt/8E74B1C874B1B377/Desktop/Synth_Nick/w_MniNick.nii /usr/local/freesurfer/subjects/SynthN/mri/orig/001.mgz mri_convert.bin /mnt/8E74B1C874B1B377/Desktop/Synth_Nick/w_MniNick.nii /usr/local/freesurfer/subjects/SynthN/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mnt/8E74B1C874B1B377/Desktop/Synth_Nick/w_MniNick.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /usr/local/freesurfer/subjects/SynthN/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon Dec 19 10:27:46 GMT 2016 Found 1 runs /usr/local/freesurfer/subjects/SynthN/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 /usr/local/freesurfer/subjects/SynthN/mri/orig/001.mgz /usr/local/freesurfer/subjects/SynthN/mri/rawavg.mgz /usr/local/freesurfer/subjects/SynthN mri_convert /usr/local/freesurfer/subjects/SynthN/mri/rawavg.mgz /usr/local/freesurfer/subjects/SynthN/mri/orig.mgz --conform mri_convert.bin /usr/local/freesurfer/subjects/SynthN/mri/rawavg.mgz /usr/local/freesurfer/subjects/SynthN/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /usr/local/freesurfer/subjects/SynthN/mri/rawavg.mgz... TR=1000.00, 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 float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/SynthN/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/SynthN/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/SynthN/mri/orig.mgz /usr/local/freesurfer/subjects/SynthN/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Dec 19 10:27:52 GMT 2016 /usr/local/freesurfer/subjects/SynthN/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /usr/local/freesurfer/subjects/SynthN/mri /usr/local/freesurfer/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 stefano-Q170M-C 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Mon Dec 19 10:27:52 GMT 2016 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.2118 /usr/local/freesurfer/subjects/SynthN/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2118/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.2118/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=1000.00, 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.2118/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Dec 19 10:27:54 GMT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.2118/nu0.mnc ./tmp.mri_nu_correct.mni.2118/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.2118/0/ -iterations 1000 -distance 50 [stefano@stefano-Q170M-C:/usr/local/freesurfer/subjects/SynthN/mri/] [2016-12-19 10:27:54] running: /usr/local/freesurfer/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.2118/0/ ./tmp.mri_nu_correct.mni.2118/nu0.mnc ./tmp.mri_nu_correct.mni.2118/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 Number of iterations: 18 CV of field change: 0.000932032 mri_convert ./tmp.mri_nu_correct.mni.2118/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.2118/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.2118/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 Dec 19 10:28:30 GMT 2016 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 Dec 19 10:28:30 GMT 2016 Ended at Mon Dec 19 10:28:59 GMT 2016 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Dec 19 10:29:01 GMT 2016 /usr/local/freesurfer/subjects/SynthN/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6483, pval=0.3663 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/SynthN/mri/transforms/talairach_avi.log tal_QC_AZS /usr/local/freesurfer/subjects/SynthN/mri/transforms/talairach_avi.log TalAviQA: 0.95887 z-score: -4 #-------------------------------------------- #@# Nu Intensity Correction Mon Dec 19 10:29:01 GMT 2016 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /usr/local/freesurfer/subjects/SynthN/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux stefano-Q170M-C 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Mon Dec 19 10:29:01 GMT 2016 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.3476 /usr/local/freesurfer/subjects/SynthN/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3476/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.3476/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=1000.00, 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.3476/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Dec 19 10:29:03 GMT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.3476/nu0.mnc ./tmp.mri_nu_correct.mni.3476/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.3476/0/ [stefano@stefano-Q170M-C:/usr/local/freesurfer/subjects/SynthN/mri/] [2016-12-19 10:29:03] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.3476/0/ ./tmp.mri_nu_correct.mni.3476/nu0.mnc ./tmp.mri_nu_correct.mni.3476/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 Number of iterations: 15 CV of field change: 0.000926241 -------------------------------------------------------- Iteration 2 Mon Dec 19 10:29:31 GMT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.3476/nu1.mnc ./tmp.mri_nu_correct.mni.3476/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.3476/1/ [stefano@stefano-Q170M-C:/usr/local/freesurfer/subjects/SynthN/mri/] [2016-12-19 10:29:31] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.3476/1/ ./tmp.mri_nu_correct.mni.3476/nu1.mnc ./tmp.mri_nu_correct.mni.3476/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 6 CV of field change: 0.00085949 mri_binarize --i ./tmp.mri_nu_correct.mni.3476/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.3476/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /usr/local/freesurfer/subjects/SynthN/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.3476/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.3476/ones.mgz sysname Linux hostname stefano-Q170M-C machine x86_64 user stefano input ./tmp.mri_nu_correct.mni.3476/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.3476/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.3476/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.3476/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3476/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.3476/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.3476/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3476/input.mean.dat sysname Linux hostname stefano-Q170M-C machine x86_64 user stefano UseRobust 0 Loading ./tmp.mri_nu_correct.mni.3476/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.3476/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.3476/ones.mgz --i ./tmp.mri_nu_correct.mni.3476/nu2.mnc --sum ./tmp.mri_nu_correct.mni.3476/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3476/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.3476/ones.mgz --i ./tmp.mri_nu_correct.mni.3476/nu2.mnc --sum ./tmp.mri_nu_correct.mni.3476/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3476/output.mean.dat sysname Linux hostname stefano-Q170M-C machine x86_64 user stefano UseRobust 0 Loading ./tmp.mri_nu_correct.mni.3476/ones.mgz Loading ./tmp.mri_nu_correct.mni.3476/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.3476/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.3476/nu2.mnc ./tmp.mri_nu_correct.mni.3476/nu2.mnc mul 1.00497087550188976262 Saving result to './tmp.mri_nu_correct.mni.3476/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.3476/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.3476/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.3476/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 7 seconds. mapping (44, 173) to ( 3, 110) Mon Dec 19 10:30:28 GMT 2016 mri_nu_correct.mni done mri_add_xform_to_header -c /usr/local/freesurfer/subjects/SynthN/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Mon Dec 19 10:30:29 GMT 2016 /usr/local/freesurfer/subjects/SynthN/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 1.07582 0.01333 0.01652 -1.01294; -0.00324 1.21004 -0.07136 3.90367; 0.03400 -0.22146 1.25583 -9.35475; 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 = 23 Starting OpenSpline(): npoints = 23 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 70 (70), valley at 0 (-1) csf peak at 35, 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 66 (66), valley at 0 (-1) csf peak at 33, setting threshold to 55 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 7 seconds. #-------------------------------------------- #@# Skull Stripping Mon Dec 19 10:32:37 GMT 2016 /usr/local/freesurfer/subjects/SynthN/mri mri_em_register -rusage /usr/local/freesurfer/subjects/SynthN/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /usr/local/freesurfer/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/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=28.0 skull bounding box = (55, 64, 43) --> (196, 193, 217) using (102, 107, 130) as brain centroid... mean wm in atlas = 108, using box (85,91,109) --> (119, 122,151) to find MRI wm before smoothing, mri peak at 95 robust fit to distribution - 95 +- 6.4 after smoothing, mri peak at 95, scaling input intensities by 1.137 scaling channel 0 by 1.13684 initial log_p = -4.755 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.711870 @ (9.091, -9.091, -9.091) max log p = -4.515606 @ (-13.636, -4.545, -4.545) max log p = -4.515606 @ (0.000, 0.000, 0.000) max log p = -4.502019 @ (1.136, -3.409, 1.136) max log p = -4.490089 @ (1.705, 0.568, -0.568) max log p = -4.490089 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -16.5, -13.1): log p = -4.490 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.394, old_max_log_p =-4.490 (thresh=-4.5) 1.15000 0.00000 0.00000 -20.69151; 0.00000 1.23625 0.00000 -46.45869; 0.00000 0.00000 1.15000 -39.16689; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.394, old_max_log_p =-4.394 (thresh=-4.4) 1.15000 0.00000 0.00000 -20.69151; 0.00000 1.23625 0.00000 -46.45869; 0.00000 0.00000 1.15000 -39.16689; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.346, old_max_log_p =-4.394 (thresh=-4.4) 1.16843 0.08680 0.02658 -37.98785; -0.07521 1.22305 -0.14978 -15.37523; -0.03755 0.15261 1.09714 -52.67356; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.346, old_max_log_p =-4.346 (thresh=-4.3) 1.16843 0.08680 0.02658 -37.98785; -0.07521 1.22305 -0.14978 -15.37523; -0.03755 0.15261 1.09714 -52.67356; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.335, old_max_log_p =-4.346 (thresh=-4.3) 1.16843 0.08680 0.02658 -37.98785; -0.07561 1.22569 -0.14095 -16.89768; -0.03706 0.14312 1.10219 -52.42197; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.335, old_max_log_p =-4.335 (thresh=-4.3) 1.16843 0.08680 0.02658 -37.98785; -0.07561 1.22569 -0.14095 -16.89768; -0.03706 0.14312 1.10219 -52.42197; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3243 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.16843 0.08680 0.02658 -37.98785; -0.07561 1.22569 -0.14095 -16.89768; -0.03706 0.14312 1.10219 -52.42197; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.16843 0.08680 0.02658 -37.98785; -0.07561 1.22569 -0.14095 -16.89768; -0.03706 0.14312 1.10219 -52.42197; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.16843 0.08680 0.02658 -37.98785; -0.07561 1.22569 -0.14095 -16.89768; -0.03706 0.14312 1.10219 -52.42197; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.335 (old=-4.755) transform before final EM align: 1.16843 0.08680 0.02658 -37.98785; -0.07561 1.22569 -0.14095 -16.89768; -0.03706 0.14312 1.10219 -52.42197; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364799 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.16843 0.08680 0.02658 -37.98785; -0.07561 1.22569 -0.14095 -16.89768; -0.03706 0.14312 1.10219 -52.42197; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.16843 0.08680 0.02658 -37.98785; -0.07561 1.22569 -0.14095 -16.89768; -0.03706 0.14312 1.10219 -52.42197; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 4.8 tol 0.000000 final transform: 1.16843 0.08680 0.02658 -37.98785; -0.07561 1.22569 -0.14095 -16.89768; -0.03706 0.14312 1.10219 -52.42197; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 755.628000 mri_em_register stimesec 1.464000 mri_em_register ru_maxrss 614088 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 156666 mri_em_register ru_majflt 1 mri_em_register ru_nswap 0 mri_em_register ru_inblock 168 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 21 mri_em_register ru_nivcsw 15174 registration took 12 minutes and 38 seconds. mri_watershed -rusage /usr/local/freesurfer/subjects/SynthN/touch/rusage.mri_watershed.dat -T1 -brain_atlas /usr/local/freesurfer/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=131 z=137 r=62 first estimation of the main basin volume: 1025165 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=103, y=113, z=107, Imax=255 CSF=14, 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=675191390 voxels, voxel volume =1.000 = 675191390 mmm3 = 675191.360 cm3 done. PostAnalyze...Basin Prior 110 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=126,y=137, z=124, r=9457 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 44774 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1036468348 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1044773735 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1066101405 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1051548740 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1079170668 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 3, 3, 9, 90 after analyzing : 3, 17, 25, 35 RIGHT_CER before analyzing : 3, 14, 84, 90 after analyzing : 3, 60, 84, 67 LEFT_CER before analyzing : 3, 3, 40, 89 after analyzing : 3, 27, 40, 42 RIGHT_BRAIN before analyzing : 3, 3, 25, 64 after analyzing : 3, 17, 25, 28 LEFT_BRAIN before analyzing : 3, 3, 27, 56 after analyzing : 3, 19, 27, 28 OTHER before analyzing : 3, 4, 58, 92 after analyzing : 3, 40, 58, 53 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...78 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.011 curvature mean = 74.632, std = 8.215 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 5.15, sigma = 8.10 after rotation: sse = 5.15, sigma = 8.10 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 6.03, its var is 10.56 before Erosion-Dilatation 3.11% of inacurate vertices after Erosion-Dilatation 6.15% 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...33 iterations mri_strip_skull: done peeling brain Brain Size = 2004498 voxels, voxel volume = 1.000 mm3 = 2004498 mmm3 = 2004.498 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 18.504000 mri_watershed stimesec 0.236000 mri_watershed ru_maxrss 822048 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 207619 mri_watershed ru_majflt 1 mri_watershed ru_nswap 0 mri_watershed ru_inblock 144 mri_watershed ru_oublock 2872 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 1 mri_watershed ru_nivcsw 528 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Mon Dec 19 10:45:35 GMT 2016 /usr/local/freesurfer/subjects/SynthN/mri mri_em_register -rusage /usr/local/freesurfer/subjects/SynthN/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/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/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=28.0 skull bounding box = (55, 69, 43) --> (196, 193, 217) using (102, 110, 130) as brain centroid... mean wm in atlas = 107, using box (85,95,109) --> (119, 125,151) to find MRI wm before smoothing, mri peak at 95 robust fit to distribution - 95 +- 5.9 after smoothing, mri peak at 95, scaling input intensities by 1.126 scaling channel 0 by 1.12632 initial log_p = -4.517 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.319199 @ (-9.091, -9.091, -9.091) max log p = -4.124527 @ (4.545, -4.545, -4.545) max log p = -3.957756 @ (2.273, -6.818, -6.818) max log p = -3.945356 @ (-1.136, 3.409, 3.409) max log p = -3.927642 @ (0.568, -0.568, -0.568) max log p = -3.927642 @ (0.000, 0.000, 0.000) Found translation: (-2.8, -17.6, -17.6): log p = -3.928 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.928, old_max_log_p =-3.928 (thresh=-3.9) 1.00000 0.00000 0.00000 -2.84091; 0.00000 1.00000 0.00000 -17.61364; 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=-3.885, old_max_log_p =-3.928 (thresh=-3.9) 0.97915 0.06404 -0.00404 -6.53417; -0.06418 0.97705 -0.06164 1.42888; 0.00000 0.06418 0.94243 -21.19036; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.885, old_max_log_p =-3.885 (thresh=-3.9) 0.97915 0.06404 -0.00404 -6.53417; -0.06418 0.97705 -0.06164 1.42888; 0.00000 0.06418 0.94243 -21.19036; 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=-3.877, old_max_log_p =-3.885 (thresh=-3.9) 0.98259 0.06426 -0.00405 -7.00306; -0.06410 0.97591 -0.06157 1.56700; 0.00000 0.06418 0.94243 -21.19036; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.877, old_max_log_p =-3.877 (thresh=-3.9) 0.98259 0.06426 -0.00405 -7.00306; -0.06410 0.97591 -0.06157 1.56700; 0.00000 0.06418 0.94243 -21.19036; 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 0.98259 0.06426 -0.00405 -7.00306; -0.06410 0.97591 -0.06157 1.56700; 0.00000 0.06418 0.94243 -21.19036; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.98259 0.06426 -0.00405 -7.00306; -0.06410 0.97591 -0.06157 1.56700; 0.00000 0.06418 0.94243 -21.19036; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.98259 0.06426 -0.00405 -7.00306; -0.06410 0.97591 -0.06157 1.56700; 0.00000 0.06418 0.94243 -21.19036; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.877 (old=-4.517) transform before final EM align: 0.98259 0.06426 -0.00405 -7.00306; -0.06410 0.97591 -0.06157 1.56700; 0.00000 0.06418 0.94243 -21.19036; 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 0.98259 0.06426 -0.00405 -7.00306; -0.06410 0.97591 -0.06157 1.56700; 0.00000 0.06418 0.94243 -21.19036; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.98259 0.06426 -0.00405 -7.00306; -0.06410 0.97591 -0.06157 1.56700; 0.00000 0.06418 0.94243 -21.19036; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = 4.2 tol 0.000000 final transform: 0.98259 0.06426 -0.00405 -7.00306; -0.06410 0.97591 -0.06157 1.56700; 0.00000 0.06418 0.94243 -21.19036; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 526.712000 mri_em_register stimesec 1.312000 mri_em_register ru_maxrss 603204 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 158414 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 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 11 mri_em_register ru_nivcsw 6906 registration took 8 minutes and 49 seconds. #-------------------------------------- #@# CA Normalize Mon Dec 19 10:54:24 GMT 2016 /usr/local/freesurfer/subjects/SynthN/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/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/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=28.0 skull bounding box = (55, 69, 43) --> (196, 193, 217) using (102, 110, 130) as brain centroid... mean wm in atlas = 107, using box (85,95,109) --> (119, 125,151) to find MRI wm before smoothing, mri peak at 95 robust fit to distribution - 95 +- 5.9 after smoothing, mri peak at 95, scaling input intensities by 1.126 scaling channel 0 by 1.12632 using 246344 sample points... INFO: compute sample coordinates transform 0.98259 0.06426 -0.00405 -7.00306; -0.06410 0.97591 -0.06157 1.56700; 0.00000 0.06418 0.94243 -21.19036; 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 (125, 68, 40) --> (195, 194, 219) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 132.0 1 of 4240 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (61, 67, 41) --> (130, 190, 219) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 4584 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (126, 154, 61) --> (174, 199, 119) Left_Cerebellum_White_Matter: limiting intensities to 99.0 --> 132.0 1 of 112 (0.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (79, 154, 59) --> (126, 196, 121) Right_Cerebellum_White_Matter: limiting intensities to 104.0 --> 132.0 0 of 145 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (108, 147, 96) --> (144, 218, 132) Brain_Stem: limiting intensities to 113.0 --> 132.0 13 of 63 (20.6%) samples deleted using 9144 total control points for intensity normalization... bias field = 0.962 +- 0.070 21 of 9129 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (125, 68, 40) --> (195, 194, 219) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 214 of 5163 (4.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (61, 67, 41) --> (130, 190, 219) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 114.0 88 of 5372 (1.6%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (126, 154, 61) --> (174, 199, 119) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 21 of 224 (9.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (79, 154, 59) --> (126, 196, 121) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 16 of 221 (7.2%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (108, 147, 96) --> (144, 218, 132) Brain_Stem: limiting intensities to 91.0 --> 132.0 30 of 119 (25.2%) samples deleted using 11099 total control points for intensity normalization... bias field = 1.087 +- 0.076 19 of 10641 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (125, 68, 40) --> (195, 194, 219) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 119 of 5291 (2.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (61, 67, 41) --> (130, 190, 219) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 118.0 24 of 5811 (0.4%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (126, 154, 61) --> (174, 199, 119) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 185 of 274 (67.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (79, 154, 59) --> (126, 196, 121) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 195 of 258 (75.6%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (108, 147, 96) --> (144, 218, 132) Brain_Stem: limiting intensities to 92.0 --> 132.0 145 of 192 (75.5%) samples deleted using 11826 total control points for intensity normalization... bias field = 1.086 +- 0.066 10 of 11030 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 10 seconds. #-------------------------------------- #@# CA Reg Mon Dec 19 10:55:34 GMT 2016 /usr/local/freesurfer/subjects/SynthN/mri mri_ca_register -rusage /usr/local/freesurfer/subjects/SynthN/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/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/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 0.91 (predicted orig area = 8.8) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.020, neg=0, invalid=4512 0001: dt=297.847174, rms=0.929 (8.934%), neg=0, invalid=4512 0002: dt=271.942515, rms=0.908 (2.256%), neg=0, invalid=4512 0003: dt=221.952000, rms=0.898 (1.103%), neg=0, invalid=4512 0004: dt=369.920000, rms=0.888 (1.107%), neg=0, invalid=4512 0005: dt=170.252427, rms=0.881 (0.747%), neg=0, invalid=4512 0006: dt=517.888000, rms=0.872 (1.052%), neg=0, invalid=4512 0007: dt=151.436620, rms=0.868 (0.459%), neg=0, invalid=4512 0008: dt=1183.744000, rms=0.861 (0.777%), neg=0, invalid=4512 0009: dt=129.472000, rms=0.856 (0.576%), neg=0, invalid=4512 0010: dt=1775.616000, rms=0.851 (0.590%), neg=0, invalid=4512 0011: dt=221.952000, rms=0.849 (0.291%), neg=0, invalid=4512 0012: dt=221.952000, rms=0.848 (0.111%), neg=0, invalid=4512 0013: dt=221.952000, rms=0.847 (0.085%), neg=0, invalid=4512 0014: dt=221.952000, rms=0.846 (0.131%), neg=0, invalid=4512 0015: dt=221.952000, rms=0.845 (0.178%), neg=0, invalid=4512 0016: dt=221.952000, rms=0.843 (0.207%), neg=0, invalid=4512 0017: dt=221.952000, rms=0.841 (0.252%), neg=0, invalid=4512 0018: dt=221.952000, rms=0.839 (0.259%), neg=0, invalid=4512 0019: dt=221.952000, rms=0.836 (0.277%), neg=0, invalid=4512 0020: dt=221.952000, rms=0.834 (0.224%), neg=0, invalid=4512 0021: dt=221.952000, rms=0.833 (0.212%), neg=0, invalid=4512 0022: dt=221.952000, rms=0.831 (0.180%), neg=0, invalid=4512 0023: dt=221.952000, rms=0.830 (0.174%), neg=0, invalid=4512 0024: dt=221.952000, rms=0.829 (0.143%), neg=0, invalid=4512 0025: dt=221.952000, rms=0.827 (0.171%), neg=0, invalid=4512 0026: dt=221.952000, rms=0.826 (0.148%), neg=0, invalid=4512 0027: dt=221.952000, rms=0.825 (0.154%), neg=0, invalid=4512 0028: dt=221.952000, rms=0.823 (0.154%), neg=0, invalid=4512 0029: dt=221.952000, rms=0.822 (0.199%), neg=0, invalid=4512 0030: dt=221.952000, rms=0.820 (0.176%), neg=0, invalid=4512 0031: dt=221.952000, rms=0.819 (0.150%), neg=0, invalid=4512 0032: dt=221.952000, rms=0.818 (0.114%), neg=0, invalid=4512 0033: dt=221.952000, rms=0.817 (0.121%), neg=0, invalid=4512 0034: dt=221.952000, rms=0.816 (0.113%), neg=0, invalid=4512 0035: dt=369.920000, rms=0.816 (0.041%), neg=0, invalid=4512 0036: dt=369.920000, rms=0.816 (-0.025%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.817, neg=0, invalid=4512 0037: dt=92.480000, rms=0.816 (0.154%), neg=0, invalid=4512 0038: dt=8.092000, rms=0.816 (-0.001%), neg=0, invalid=4512 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.825, neg=0, invalid=4512 0039: dt=272.589833, rms=0.811 (1.764%), neg=0, invalid=4512 0040: dt=133.948365, rms=0.801 (1.191%), neg=0, invalid=4512 0041: dt=89.291280, rms=0.797 (0.517%), neg=0, invalid=4512 0042: dt=248.832000, rms=0.791 (0.767%), neg=0, invalid=4512 0043: dt=71.634757, rms=0.787 (0.446%), neg=0, invalid=4512 0044: dt=497.664000, rms=0.781 (0.821%), neg=0, invalid=4512 0045: dt=75.428571, rms=0.777 (0.493%), neg=0, invalid=4512 0046: dt=145.152000, rms=0.775 (0.245%), neg=0, invalid=4512 0047: dt=145.152000, rms=0.775 (-0.066%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.776, neg=0, invalid=4512 0048: dt=64.338624, rms=0.774 (0.319%), neg=0, invalid=4512 0049: dt=36.288000, rms=0.774 (0.016%), neg=0, invalid=4512 0050: dt=36.288000, rms=0.773 (0.009%), neg=0, invalid=4512 0051: dt=36.288000, rms=0.773 (0.006%), neg=0, invalid=4512 0052: dt=36.288000, rms=0.773 (0.005%), neg=0, invalid=4512 0053: dt=497.664000, rms=0.772 (0.228%), neg=0, invalid=4512 0054: dt=78.840580, rms=0.771 (0.110%), neg=0, invalid=4512 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.793, neg=0, invalid=4512 0055: dt=25.600000, rms=0.788 (0.623%), neg=0, invalid=4512 0056: dt=89.895954, rms=0.779 (1.145%), neg=0, invalid=4512 0057: dt=102.720617, rms=0.768 (1.430%), neg=0, invalid=4512 0058: dt=11.200000, rms=0.766 (0.249%), neg=0, invalid=4512 0059: dt=11.200000, rms=0.766 (0.061%), neg=0, invalid=4512 0060: dt=11.200000, rms=0.766 (-0.098%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.766, neg=0, invalid=4512 0061: dt=0.000000, rms=0.766 (0.093%), neg=0, invalid=4512 0062: dt=0.000000, rms=0.766 (0.000%), neg=0, invalid=4512 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.815, neg=0, invalid=4512 0063: dt=0.000000, rms=0.814 (0.082%), neg=0, invalid=4512 0064: dt=0.000000, rms=0.814 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.815, neg=0, invalid=4512 0065: dt=0.000000, rms=0.814 (0.082%), neg=0, invalid=4512 0066: dt=0.000000, rms=0.814 (0.000%), neg=0, invalid=4512 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.909, neg=0, invalid=4512 0067: dt=1.387560, rms=0.895 (1.501%), neg=0, invalid=4512 0068: dt=0.782051, rms=0.893 (0.210%), neg=0, invalid=4512 0069: dt=0.782051, rms=0.893 (0.075%), neg=0, invalid=4512 0070: dt=0.782051, rms=0.893 (-0.264%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.893, neg=0, invalid=4512 0071: dt=0.448000, rms=0.892 (0.117%), neg=0, invalid=4512 0072: dt=0.320000, rms=0.892 (0.012%), neg=0, invalid=4512 0073: dt=0.320000, rms=0.892 (-0.002%), neg=0, invalid=4512 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.803, neg=0, invalid=4512 0074: dt=1.074993, rms=0.770 (4.038%), neg=0, invalid=4512 0075: dt=0.096000, rms=0.769 (0.166%), neg=0, invalid=4512 0076: dt=0.096000, rms=0.769 (-0.100%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.770, neg=0, invalid=4512 0077: dt=0.028000, rms=0.769 (0.108%), neg=0, invalid=4512 0078: dt=0.001750, rms=0.769 (-0.001%), neg=0, invalid=4512 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.12632 (10) Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (1100 voxels, overlap=0.006) Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (1100 voxels, peak = 9), gca=8.9 gca peak = 0.15565 (16) mri peak = 0.10141 (13) Right_Lateral_Ventricle (43): linear fit = 0.69 x + 0.0 (1176 voxels, overlap=0.443) Right_Lateral_Ventricle (43): linear fit = 0.69 x + 0.0 (1176 voxels, peak = 11), gca=11.0 gca peak = 0.26829 (96) mri peak = 0.08856 (97) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1469 voxels, overlap=1.001) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1469 voxels, peak = 96), gca=95.5 gca peak = 0.20183 (93) mri peak = 0.08220 (98) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (1268 voxels, overlap=1.004) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (1268 voxels, peak = 95), gca=95.3 gca peak = 0.21683 (55) mri peak = 0.06853 (58) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (1720 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (1720 voxels, peak = 57), gca=57.5 gca peak = 0.30730 (58) mri peak = 0.07060 (54) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (1126 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (1126 voxels, peak = 54), gca=54.2 gca peak = 0.11430 (101) mri peak = 0.07212 (100) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (85410 voxels, overlap=0.959) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (85410 voxels, peak = 102), gca=101.5 gca peak = 0.12076 (102) mri peak = 0.07693 (97) Left_Cerebral_White_Matter (2): linear fit = 0.98 x + 0.0 (85263 voxels, overlap=0.976) Left_Cerebral_White_Matter (2): linear fit = 0.98 x + 0.0 (85263 voxels, peak = 99), gca=99.5 gca peak = 0.14995 (59) mri peak = 0.02734 (63) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (28227 voxels, overlap=0.670) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (28227 voxels, peak = 60), gca=60.5 gca peak = 0.15082 (58) mri peak = 0.02304 (84) Right_Cerebral_Cortex (42): linear fit = 1.48 x + 0.0 (36659 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.48 x + 0.0 (36659 voxels, peak = 86), gca=85.6 gca peak = 0.14161 (67) mri peak = 0.09825 (66) Right_Caudate (50): linear fit = 0.95 x + 0.0 (1090 voxels, overlap=0.973) Right_Caudate (50): linear fit = 0.95 x + 0.0 (1090 voxels, peak = 64), gca=64.0 gca peak = 0.15243 (71) mri peak = 0.06798 (75) Left_Caudate (11): linear fit = 1.03 x + 0.0 (1575 voxels, overlap=0.997) Left_Caudate (11): linear fit = 1.03 x + 0.0 (1575 voxels, peak = 73), gca=73.5 gca peak = 0.13336 (57) mri peak = 0.03030 (60) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (28841 voxels, overlap=0.416) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (28841 voxels, peak = 64), gca=63.6 gca peak = 0.13252 (56) mri peak = 0.03298 (83) Right_Cerebellum_Cortex (47): linear fit = 1.47 x + 0.0 (37357 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.47 x + 0.0 (37357 voxels, peak = 82), gca=82.0 gca peak = 0.18181 (84) mri peak = 0.05572 (82) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (13635 voxels, overlap=0.932) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (13635 voxels, peak = 84), gca=83.6 gca peak = 0.20573 (83) mri peak = 0.06521 (84) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (11607 voxels, overlap=0.858) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (11607 voxels, peak = 85), gca=85.1 gca peak = 0.21969 (57) mri peak = 0.08457 (64) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (691 voxels, overlap=0.960) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (691 voxels, peak = 64), gca=64.1 gca peak = 0.39313 (56) mri peak = 0.08382 (59) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (816 voxels, overlap=0.999) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (816 voxels, peak = 59), gca=58.5 gca peak = 0.14181 (85) mri peak = 0.06200 (94) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (7707 voxels, overlap=0.682) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (7707 voxels, peak = 91), gca=90.5 gca peak = 0.11978 (83) mri peak = 0.07157 (88) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5332 voxels, overlap=0.540) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5332 voxels, peak = 93), gca=92.5 gca peak = 0.13399 (79) mri peak = 0.05126 (80) Left_Putamen (12): linear fit = 1.04 x + 0.0 (3491 voxels, overlap=0.921) Left_Putamen (12): linear fit = 1.04 x + 0.0 (3491 voxels, peak = 83), gca=82.6 gca peak = 0.14159 (79) mri peak = 0.05354 (82) Right_Putamen (51): linear fit = 1.02 x + 0.0 (3722 voxels, overlap=1.001) Right_Putamen (51): linear fit = 1.02 x + 0.0 (3722 voxels, peak = 81), gca=81.0 gca peak = 0.10025 (80) mri peak = 0.06902 (85) Brain_Stem (16): linear fit = 1.10 x + 0.0 (15076 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (15076 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.06552 (103) Right_VentralDC (60): linear fit = 1.17 x + 0.0 (1983 voxels, overlap=0.236) Right_VentralDC (60): linear fit = 1.17 x + 0.0 (1983 voxels, peak = 101), gca=101.0 gca peak = 0.12801 (89) mri peak = 0.06111 (99) Left_VentralDC (28): linear fit = 1.14 x + 0.0 (2049 voxels, overlap=0.624) Left_VentralDC (28): linear fit = 1.14 x + 0.0 (2049 voxels, peak = 102), gca=101.9 gca peak = 0.20494 (23) mri peak = 0.17026 (18) gca peak = 0.15061 (21) mri peak = 0.09079 ( 8) Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (90 voxels, overlap=0.011) Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (90 voxels, peak = 6), gca=6.0 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.11 x + 0.0 estimating mean wm scale to be 0.99 x + 0.0 estimating mean csf scale to be 0.56 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=0.772, neg=0, invalid=4512 0079: dt=102.759076, rms=0.758 (1.803%), neg=0, invalid=4512 0080: dt=136.861538, rms=0.755 (0.374%), neg=0, invalid=4512 0081: dt=369.920000, rms=0.752 (0.370%), neg=0, invalid=4512 0082: dt=443.904000, rms=0.750 (0.315%), neg=0, invalid=4512 0083: dt=110.976000, rms=0.749 (0.145%), neg=0, invalid=4512 0084: dt=221.952000, rms=0.748 (0.057%), neg=0, invalid=4512 0085: dt=221.952000, rms=0.748 (0.089%), neg=0, invalid=4512 0086: dt=110.976000, rms=0.747 (0.041%), neg=0, invalid=4512 0087: dt=110.976000, rms=0.747 (0.038%), neg=0, invalid=4512 0088: dt=110.976000, rms=0.747 (0.058%), neg=0, invalid=4512 0089: dt=110.976000, rms=0.746 (0.066%), neg=0, invalid=4512 0090: dt=110.976000, rms=0.746 (0.064%), neg=0, invalid=4512 0091: dt=110.976000, rms=0.745 (0.060%), neg=0, invalid=4512 0092: dt=110.976000, rms=0.745 (0.047%), neg=0, invalid=4512 0093: dt=110.976000, rms=0.745 (0.030%), neg=0, invalid=4512 0094: dt=110.976000, rms=0.744 (0.023%), neg=0, invalid=4512 0095: dt=110.976000, rms=0.744 (0.031%), neg=0, invalid=4512 0096: dt=110.976000, rms=0.744 (0.029%), neg=0, invalid=4512 0097: dt=110.976000, rms=0.744 (0.027%), neg=0, invalid=4512 0098: dt=110.976000, rms=0.744 (0.028%), neg=0, invalid=4512 0099: dt=110.976000, rms=0.743 (0.032%), neg=0, invalid=4512 0100: dt=110.976000, rms=0.743 (0.037%), neg=0, invalid=4512 0101: dt=110.976000, rms=0.743 (0.043%), neg=0, invalid=4512 0102: dt=110.976000, rms=0.742 (0.050%), neg=0, invalid=4512 0103: dt=110.976000, rms=0.742 (0.054%), neg=0, invalid=4512 0104: dt=110.976000, rms=0.742 (0.051%), neg=0, invalid=4512 0105: dt=110.976000, rms=0.741 (0.056%), neg=0, invalid=4512 0106: dt=110.976000, rms=0.741 (0.062%), neg=0, invalid=4512 0107: dt=110.976000, rms=0.740 (0.073%), neg=0, invalid=4512 0108: dt=110.976000, rms=0.740 (0.073%), neg=0, invalid=4512 0109: dt=110.976000, rms=0.739 (0.059%), neg=0, invalid=4512 0110: dt=110.976000, rms=0.739 (0.044%), neg=0, invalid=4512 0111: dt=110.976000, rms=0.739 (0.042%), neg=0, invalid=4512 0112: dt=110.976000, rms=0.738 (0.043%), neg=0, invalid=4512 0113: dt=110.976000, rms=0.738 (0.043%), neg=0, invalid=4512 0114: dt=110.976000, rms=0.738 (0.042%), neg=0, invalid=4512 0115: dt=110.976000, rms=0.737 (0.039%), neg=0, invalid=4512 0116: dt=110.976000, rms=0.737 (0.035%), neg=0, invalid=4512 0117: dt=110.976000, rms=0.737 (0.033%), neg=0, invalid=4512 0118: dt=110.976000, rms=0.737 (0.030%), neg=0, invalid=4512 0119: dt=110.976000, rms=0.736 (0.029%), neg=0, invalid=4512 0120: dt=110.976000, rms=0.736 (0.026%), neg=0, invalid=4512 0121: dt=110.976000, rms=0.736 (0.023%), neg=0, invalid=4512 0122: dt=110.976000, rms=0.736 (0.020%), neg=0, invalid=4512 0123: dt=1479.680000, rms=0.736 (0.038%), neg=0, invalid=4512 0124: dt=55.488000, rms=0.736 (0.008%), neg=0, invalid=4512 0125: dt=55.488000, rms=0.736 (0.002%), neg=0, invalid=4512 0126: dt=55.488000, rms=0.736 (-0.004%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.736, neg=0, invalid=4512 0127: dt=110.976000, rms=0.735 (0.158%), neg=0, invalid=4512 0128: dt=295.936000, rms=0.735 (0.056%), neg=0, invalid=4512 0129: dt=517.888000, rms=0.734 (0.146%), neg=0, invalid=4512 0130: dt=32.368000, rms=0.734 (0.003%), neg=0, invalid=4512 0131: dt=32.368000, rms=0.734 (0.003%), neg=0, invalid=4512 0132: dt=32.368000, rms=0.734 (-0.001%), neg=0, invalid=4512 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.735, neg=0, invalid=4512 0133: dt=113.098507, rms=0.730 (0.654%), neg=0, invalid=4512 0134: dt=187.193676, rms=0.722 (1.135%), neg=0, invalid=4512 0135: dt=58.181818, rms=0.718 (0.489%), neg=0, invalid=4512 0136: dt=145.152000, rms=0.714 (0.597%), neg=0, invalid=4512 0137: dt=124.416000, rms=0.712 (0.296%), neg=0, invalid=4512 0138: dt=86.936416, rms=0.709 (0.385%), neg=0, invalid=4512 0139: dt=67.018868, rms=0.708 (0.195%), neg=0, invalid=4512 0140: dt=36.288000, rms=0.707 (0.126%), neg=0, invalid=4512 0141: dt=31.104000, rms=0.706 (0.082%), neg=0, invalid=4512 0142: dt=2.268000, rms=0.706 (0.004%), neg=0, invalid=4512 0143: dt=1.134000, rms=0.706 (0.003%), neg=0, invalid=4512 0144: dt=0.567000, rms=0.706 (0.001%), neg=0, invalid=4512 0145: dt=0.070875, rms=0.706 (0.000%), neg=0, invalid=4512 0146: dt=0.035437, rms=0.706 (0.000%), neg=0, invalid=4512 0147: dt=0.008859, rms=0.706 (-0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.707, neg=0, invalid=4512 0148: dt=0.008859, rms=0.706 (0.115%), neg=0, invalid=4512 0149: dt=0.008859, rms=0.706 (0.000%), neg=0, invalid=4512 0150: dt=0.001107, rms=0.706 (0.000%), neg=0, invalid=4512 0151: dt=0.000277, rms=0.706 (0.000%), neg=0, invalid=4512 0152: dt=0.000069, rms=0.706 (0.000%), neg=0, invalid=4512 0153: dt=0.000000, rms=0.706 (0.000%), neg=0, invalid=4512 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.711, neg=0, invalid=4512 0154: dt=0.000000, rms=0.710 (0.114%), neg=0, invalid=4512 0155: dt=0.000000, rms=0.710 (0.000%), neg=0, invalid=4512 0156: dt=0.000061, rms=0.710 (0.000%), neg=0, invalid=4512 0157: dt=0.000008, rms=0.710 (0.000%), neg=0, invalid=4512 0158: dt=0.000001, rms=0.710 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.711, neg=0, invalid=4512 0159: dt=44.800000, rms=0.688 (3.157%), neg=0, invalid=4512 0160: dt=44.800000, rms=0.676 (1.800%), neg=0, invalid=4512 0161: dt=11.200000, rms=0.673 (0.447%), neg=0, invalid=4512 0162: dt=11.200000, rms=0.671 (0.341%), neg=0, invalid=4512 0163: dt=0.700000, rms=0.670 (0.016%), neg=0, invalid=4512 0164: dt=0.700000, rms=0.670 (0.020%), neg=0, invalid=4512 0165: dt=0.087500, rms=0.670 (0.002%), neg=0, invalid=4512 0166: dt=0.043750, rms=0.670 (0.002%), neg=0, invalid=4512 0167: dt=0.010937, rms=0.670 (0.000%), neg=0, invalid=4512 0168: dt=0.002734, rms=0.670 (0.000%), neg=0, invalid=4512 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.683, neg=0, invalid=4512 0169: dt=13.824000, rms=0.655 (4.035%), neg=0, invalid=4512 0170: dt=16.128000, rms=0.643 (1.890%), neg=0, invalid=4512 0171: dt=16.128000, rms=0.638 (0.717%), neg=0, invalid=4512 0172: dt=11.520000, rms=0.636 (0.428%), neg=0, invalid=4512 0173: dt=16.128000, rms=0.634 (0.329%), neg=0, invalid=4512 0174: dt=12.742515, rms=0.632 (0.249%), neg=0, invalid=4512 0175: dt=11.520000, rms=0.631 (0.197%), neg=0, invalid=4512 0176: dt=2.880000, rms=0.630 (0.068%), neg=0, invalid=4512 0177: dt=0.011250, rms=0.630 (0.000%), neg=0, invalid=4512 0178: dt=0.000352, rms=0.630 (0.000%), neg=0, invalid=4512 0179: dt=0.000088, rms=0.630 (0.000%), neg=0, invalid=4512 0180: dt=0.000011, rms=0.630 (0.000%), neg=0, invalid=4512 0181: dt=0.000000, rms=0.630 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.631, neg=0, invalid=4512 0182: dt=1.008000, rms=0.630 (0.115%), neg=0, invalid=4512 0183: dt=0.864000, rms=0.630 (0.001%), neg=0, invalid=4512 0184: dt=0.864000, rms=0.630 (0.000%), neg=0, invalid=4512 0185: dt=0.864000, rms=0.630 (-0.008%), neg=0, invalid=4512 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.657, neg=0, invalid=4512 0186: dt=0.000000, rms=0.656 (0.100%), neg=0, invalid=4512 0187: dt=0.000000, rms=0.656 (0.000%), neg=0, invalid=4512 0188: dt=0.100000, rms=0.656 (-0.084%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.657, neg=0, invalid=4512 0189: dt=0.000000, rms=0.656 (0.100%), neg=0, invalid=4512 0190: dt=0.000000, rms=0.656 (0.000%), neg=0, invalid=4512 0191: dt=0.100000, rms=0.656 (-0.060%), neg=0, invalid=4512 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.613, neg=0, invalid=4512 0192: dt=0.448000, rms=0.592 (3.369%), neg=0, invalid=4512 0193: dt=0.448000, rms=0.587 (0.894%), neg=0, invalid=4512 0194: dt=0.320000, rms=0.585 (0.298%), neg=0, invalid=4512 0195: dt=0.384000, rms=0.584 (0.269%), neg=0, invalid=4512 0196: dt=0.320000, rms=0.583 (0.124%), neg=0, invalid=4512 0197: dt=0.320000, rms=0.582 (0.120%), neg=0, invalid=4512 0198: dt=0.384000, rms=0.582 (0.079%), neg=0, invalid=4512 0199: dt=0.384000, rms=0.581 (0.090%), neg=0, invalid=4512 0200: dt=0.384000, rms=0.581 (0.052%), neg=0, invalid=4512 0201: dt=0.384000, rms=0.581 (0.060%), neg=0, invalid=4512 0202: dt=0.320000, rms=0.580 (0.031%), neg=0, invalid=4512 0203: dt=0.320000, rms=0.580 (0.050%), neg=0, invalid=4512 0204: dt=0.320000, rms=0.580 (0.063%), neg=0, invalid=4512 0205: dt=0.320000, rms=0.579 (0.061%), neg=0, invalid=4512 0206: dt=0.320000, rms=0.579 (0.075%), neg=0, invalid=4512 0207: dt=0.320000, rms=0.579 (0.084%), neg=0, invalid=4512 0208: dt=0.320000, rms=0.578 (0.068%), neg=0, invalid=4512 0209: dt=0.160000, rms=0.578 (-0.002%), neg=0, invalid=4512 0210: dt=0.048000, rms=0.578 (0.001%), neg=0, invalid=4512 0211: dt=0.112000, rms=0.578 (-0.001%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.579, neg=0, invalid=4512 0212: dt=0.112000, rms=0.577 (0.398%), neg=0, invalid=4512 0213: dt=0.320000, rms=0.573 (0.600%), neg=0, invalid=4512 0214: dt=0.384000, rms=0.572 (0.262%), neg=0, invalid=4512 0215: dt=0.320000, rms=0.571 (0.080%), neg=0, invalid=4512 0216: dt=0.320000, rms=0.571 (0.020%), neg=0, invalid=4512 0217: dt=0.320000, rms=0.571 (0.028%), neg=0, invalid=4512 0218: dt=0.320000, rms=0.571 (0.019%), neg=0, invalid=4512 0219: dt=0.320000, rms=0.571 (-0.003%), neg=0, invalid=4512 0220: dt=0.000000, rms=0.571 (0.000%), neg=0, invalid=4512 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=0.569, neg=0, invalid=4512 0221: dt=0.000000, rms=0.568 (0.141%), neg=0, invalid=4512 0222: dt=0.000000, rms=0.568 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.569, neg=0, invalid=4512 0223: dt=3.468000, rms=0.568 (0.141%), neg=0, invalid=4512 0224: dt=1.734000, rms=0.568 (0.001%), neg=0, invalid=4512 0225: dt=1.734000, rms=0.568 (-0.001%), neg=0, invalid=4512 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.569, neg=0, invalid=4512 0226: dt=9.072000, rms=0.568 (0.147%), neg=0, invalid=4512 0227: dt=9.072000, rms=0.568 (0.004%), neg=0, invalid=4512 0228: dt=9.072000, rms=0.568 (0.001%), neg=0, invalid=4512 0229: dt=9.072000, rms=0.568 (-0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.569, neg=0, invalid=4512 0230: dt=36.288000, rms=0.567 (0.290%), neg=0, invalid=4512 0231: dt=145.152000, rms=0.566 (0.253%), neg=0, invalid=4512 0232: dt=31.104000, rms=0.566 (0.050%), neg=0, invalid=4512 0233: dt=31.104000, rms=0.565 (0.053%), neg=0, invalid=4512 0234: dt=31.104000, rms=0.565 (0.076%), neg=0, invalid=4512 0235: dt=31.104000, rms=0.564 (0.087%), neg=0, invalid=4512 0236: dt=31.104000, rms=0.564 (0.093%), neg=0, invalid=4512 0237: dt=31.104000, rms=0.563 (0.097%), neg=0, invalid=4512 0238: dt=31.104000, rms=0.563 (0.100%), neg=0, invalid=4512 0239: dt=31.104000, rms=0.562 (0.086%), neg=0, invalid=4512 0240: dt=31.104000, rms=0.562 (0.076%), neg=0, invalid=4512 0241: dt=82.944000, rms=0.562 (0.021%), neg=0, invalid=4512 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.563, neg=0, invalid=4512 0242: dt=22.114286, rms=0.560 (0.497%), neg=0, invalid=4512 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0243: dt=58.389610, rms=0.557 (0.595%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0244: dt=11.200000, rms=0.556 (0.204%), neg=0, invalid=4512 0245: dt=11.200000, rms=0.555 (0.064%), neg=0, invalid=4512 0246: dt=11.200000, rms=0.555 (0.097%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0247: dt=11.200000, rms=0.554 (0.141%), neg=0, invalid=4512 0248: dt=11.200000, rms=0.553 (0.197%), neg=0, invalid=4512 iter 0, gcam->neg = 4 after 9 iterations, nbhd size=1, neg = 0 0249: dt=11.200000, rms=0.552 (0.193%), neg=0, invalid=4512 iter 0, gcam->neg = 10 after 3 iterations, nbhd size=0, neg = 0 0250: dt=11.200000, rms=0.551 (0.155%), neg=0, invalid=4512 iter 0, gcam->neg = 8 after 3 iterations, nbhd size=0, neg = 0 0251: dt=11.200000, rms=0.550 (0.111%), neg=0, invalid=4512 iter 0, gcam->neg = 13 after 4 iterations, nbhd size=0, neg = 0 0252: dt=11.200000, rms=0.550 (0.066%), neg=0, invalid=4512 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0253: dt=44.800000, rms=0.549 (0.085%), neg=0, invalid=4512 iter 0, gcam->neg = 3 after 4 iterations, nbhd size=0, neg = 0 0254: dt=76.800000, rms=0.548 (0.177%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0255: dt=11.200000, rms=0.548 (0.025%), neg=0, invalid=4512 0256: dt=11.200000, rms=0.548 (0.012%), neg=0, invalid=4512 0257: dt=11.200000, rms=0.548 (0.008%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 4 iterations, nbhd size=0, neg = 0 0258: dt=11.200000, rms=0.548 (0.018%), neg=0, invalid=4512 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0259: dt=11.200000, rms=0.548 (0.043%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 0260: dt=11.200000, rms=0.547 (0.063%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0261: dt=11.200000, rms=0.547 (0.061%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.548, neg=0, invalid=4512 0262: dt=38.400000, rms=0.543 (0.863%), neg=0, invalid=4512 0263: dt=23.176955, rms=0.542 (0.163%), neg=0, invalid=4512 0264: dt=23.176955, rms=0.541 (0.169%), neg=0, invalid=4512 0265: dt=23.176955, rms=0.541 (0.173%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0266: dt=23.176955, rms=0.540 (0.134%), neg=0, invalid=4512 0267: dt=23.176955, rms=0.539 (0.071%), neg=0, invalid=4512 0268: dt=23.176955, rms=0.539 (0.101%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0269: dt=23.176955, rms=0.538 (0.105%), neg=0, invalid=4512 0270: dt=23.176955, rms=0.538 (0.120%), neg=0, invalid=4512 0271: dt=23.176955, rms=0.537 (0.107%), neg=0, invalid=4512 0272: dt=38.400000, rms=0.537 (0.083%), neg=0, invalid=4512 0273: dt=38.400000, rms=0.537 (-0.047%), neg=0, invalid=4512 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.542, neg=0, invalid=4512 0274: dt=4.342857, rms=0.541 (0.257%), neg=0, invalid=4512 0275: dt=4.032000, rms=0.541 (0.044%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0276: dt=4.032000, rms=0.541 (0.027%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0277: dt=4.032000, rms=0.541 (-0.020%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.542, neg=0, invalid=4512 0278: dt=6.571429, rms=0.540 (0.240%), neg=0, invalid=4512 0279: dt=20.615385, rms=0.539 (0.239%), neg=0, invalid=4512 iter 0, gcam->neg = 7 after 5 iterations, nbhd size=0, neg = 0 0280: dt=20.615385, rms=0.538 (0.195%), neg=0, invalid=4512 iter 0, gcam->neg = 31 after 10 iterations, nbhd size=1, neg = 0 0281: dt=20.615385, rms=0.534 (0.738%), neg=0, invalid=4512 iter 0, gcam->neg = 13 after 9 iterations, nbhd size=1, neg = 0 0282: dt=20.615385, rms=0.533 (0.255%), neg=0, invalid=4512 iter 0, gcam->neg = 39 after 2 iterations, nbhd size=0, neg = 0 0283: dt=20.615385, rms=0.530 (0.530%), neg=0, invalid=4512 iter 0, gcam->neg = 80 after 15 iterations, nbhd size=1, neg = 0 0284: dt=20.615385, rms=0.527 (0.418%), neg=0, invalid=4512 iter 0, gcam->neg = 78 after 14 iterations, nbhd size=1, neg = 0 0285: dt=20.615385, rms=0.528 (-0.030%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=0, neg = 0 0286: dt=5.830508, rms=0.526 (0.350%), neg=0, invalid=4512 iter 0, gcam->neg = 7 after 12 iterations, nbhd size=1, neg = 0 0287: dt=10.400000, rms=0.525 (0.098%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0288: dt=10.400000, rms=0.525 (-0.081%), neg=0, invalid=4512 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.532, neg=0, invalid=4512 0289: dt=0.000000, rms=0.532 (0.137%), neg=0, invalid=4512 0290: dt=0.000000, rms=0.532 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.532, neg=0, invalid=4512 0291: dt=0.000000, rms=0.532 (0.137%), neg=0, invalid=4512 0292: dt=0.000000, rms=0.532 (0.000%), neg=0, invalid=4512 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.522, neg=0, invalid=4512 iter 0, gcam->neg = 1847 after 14 iterations, nbhd size=1, neg = 0 0293: dt=1.781784, rms=0.491 (5.827%), neg=0, invalid=4512 0294: dt=0.003000, rms=0.491 (0.008%), neg=0, invalid=4512 0295: dt=0.003000, rms=0.491 (0.001%), neg=0, invalid=4512 0296: dt=0.003000, rms=0.491 (-0.001%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.492, neg=0, invalid=4512 0297: dt=0.064000, rms=0.491 (0.223%), neg=0, invalid=4512 0298: dt=0.007000, rms=0.491 (0.003%), neg=0, invalid=4512 0299: dt=0.007000, rms=0.491 (0.000%), neg=0, invalid=4512 0300: dt=0.007000, rms=0.491 (-0.001%), neg=0, invalid=4512 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=0.477, neg=0, invalid=4512 0301: dt=0.000000, rms=0.477 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.477, neg=0, invalid=4512 0302: dt=4.624000, rms=0.477 (0.000%), neg=0, invalid=4512 0303: dt=0.433500, rms=0.477 (0.000%), neg=0, invalid=4512 0304: dt=0.433500, rms=0.477 (-0.000%), neg=0, invalid=4512 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.477, neg=0, invalid=4512 0305: dt=2.268000, rms=0.477 (0.001%), neg=0, invalid=4512 0306: dt=1.296000, rms=0.477 (0.000%), neg=0, invalid=4512 0307: dt=1.296000, rms=0.477 (-0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.477, neg=0, invalid=4512 0308: dt=25.920000, rms=0.477 (0.019%), neg=0, invalid=4512 0309: dt=36.288000, rms=0.477 (0.014%), neg=0, invalid=4512 0310: dt=36.288000, rms=0.476 (0.019%), neg=0, invalid=4512 0311: dt=36.288000, rms=0.476 (0.024%), neg=0, invalid=4512 0312: dt=36.288000, rms=0.476 (0.022%), neg=0, invalid=4512 0313: dt=36.288000, rms=0.476 (0.022%), neg=0, invalid=4512 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.477, neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0314: dt=11.200000, rms=0.476 (0.147%), neg=0, invalid=4512 iter 0, gcam->neg = 6 after 11 iterations, nbhd size=1, neg = 0 0315: dt=11.200000, rms=0.476 (0.064%), neg=0, invalid=4512 iter 0, gcam->neg = 7 after 2 iterations, nbhd size=0, neg = 0 0316: dt=11.200000, rms=0.476 (0.043%), neg=0, invalid=4512 iter 0, gcam->neg = 20 after 10 iterations, nbhd size=1, neg = 0 0317: dt=11.200000, rms=0.476 (-0.038%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.476, neg=0, invalid=4512 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0318: dt=38.400000, rms=0.473 (0.523%), neg=0, invalid=4512 0319: dt=11.200000, rms=0.473 (0.113%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0320: dt=11.200000, rms=0.472 (0.054%), neg=0, invalid=4512 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0321: dt=11.200000, rms=0.472 (0.076%), neg=0, invalid=4512 iter 0, gcam->neg = 9 after 10 iterations, nbhd size=1, neg = 0 0322: dt=11.200000, rms=0.472 (0.065%), neg=0, invalid=4512 iter 0, gcam->neg = 11 after 1 iterations, nbhd size=0, neg = 0 0323: dt=11.200000, rms=0.471 (0.123%), neg=0, invalid=4512 iter 0, gcam->neg = 10 after 1 iterations, nbhd size=0, neg = 0 0324: dt=11.200000, rms=0.470 (0.130%), neg=0, invalid=4512 iter 0, gcam->neg = 12 after 11 iterations, nbhd size=1, neg = 0 0325: dt=11.200000, rms=0.470 (0.046%), neg=0, invalid=4512 iter 0, gcam->neg = 10 after 8 iterations, nbhd size=1, neg = 0 0326: dt=11.200000, rms=0.470 (0.032%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0327: dt=38.400000, rms=0.470 (0.033%), neg=0, invalid=4512 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0328: dt=44.800000, rms=0.470 (0.081%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0329: dt=11.200000, rms=0.470 (0.009%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0330: dt=11.200000, rms=0.469 (0.008%), neg=0, invalid=4512 0331: dt=11.200000, rms=0.469 (0.014%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 0332: dt=11.200000, rms=0.469 (0.024%), neg=0, invalid=4512 iter 0, gcam->neg = 3 after 5 iterations, nbhd size=0, neg = 0 0333: dt=11.200000, rms=0.469 (0.033%), neg=0, invalid=4512 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0334: dt=11.200000, rms=0.469 (0.044%), neg=0, invalid=4512 iter 0, gcam->neg = 3 after 5 iterations, nbhd size=0, neg = 0 0335: dt=11.200000, rms=0.469 (0.044%), neg=0, invalid=4512 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0336: dt=11.200000, rms=0.469 (0.039%), neg=0, invalid=4512 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.472, neg=0, invalid=4512 iter 0, gcam->neg = 13 after 2 iterations, nbhd size=0, neg = 0 0337: dt=5.777778, rms=0.472 (0.093%), neg=0, invalid=4512 iter 0, gcam->neg = 12 after 9 iterations, nbhd size=1, neg = 0 0338: dt=3.555556, rms=0.472 (0.006%), neg=0, invalid=4512 iter 0, gcam->neg = 9 after 10 iterations, nbhd size=1, neg = 0 0339: dt=3.555556, rms=0.472 (-0.023%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.472, neg=0, invalid=4512 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0340: dt=10.562092, rms=0.471 (0.209%), neg=0, invalid=4512 iter 0, gcam->neg = 21 after 9 iterations, nbhd size=1, neg = 0 0341: dt=30.822400, rms=0.469 (0.392%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0342: dt=5.111111, rms=0.469 (0.094%), neg=0, invalid=4512 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0343: dt=5.111111, rms=0.468 (0.053%), neg=0, invalid=4512 iter 0, gcam->neg = 8 after 4 iterations, nbhd size=0, neg = 0 0344: dt=5.111111, rms=0.468 (0.077%), neg=0, invalid=4512 iter 0, gcam->neg = 8 after 2 iterations, nbhd size=0, neg = 0 0345: dt=5.111111, rms=0.467 (0.103%), neg=0, invalid=4512 iter 0, gcam->neg = 9 after 5 iterations, nbhd size=0, neg = 0 0346: dt=5.111111, rms=0.467 (0.120%), neg=0, invalid=4512 iter 0, gcam->neg = 12 after 2 iterations, nbhd size=0, neg = 0 0347: dt=5.111111, rms=0.466 (0.121%), neg=0, invalid=4512 iter 0, gcam->neg = 11 after 8 iterations, nbhd size=1, neg = 0 0348: dt=5.111111, rms=0.466 (0.083%), neg=0, invalid=4512 iter 0, gcam->neg = 14 after 5 iterations, nbhd size=0, neg = 0 0349: dt=5.111111, rms=0.466 (0.093%), neg=0, invalid=4512 iter 0, gcam->neg = 21 after 11 iterations, nbhd size=1, neg = 0 0350: dt=5.111111, rms=0.465 (0.045%), neg=0, invalid=4512 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0351: dt=11.555556, rms=0.465 (0.024%), neg=0, invalid=4512 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.472, neg=0, invalid=4512 0352: dt=0.000050, rms=0.472 (0.000%), neg=0, invalid=4512 0353: dt=0.000000, rms=0.472 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.472, neg=0, invalid=4512 0354: dt=0.000000, rms=0.472 (0.000%), neg=0, invalid=4512 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.461, neg=0, invalid=4512 iter 0, gcam->neg = 929 after 14 iterations, nbhd size=1, neg = 0 0355: dt=1.108026, rms=0.450 (2.400%), neg=0, invalid=4512 0356: dt=0.000027, rms=0.450 (0.000%), neg=0, invalid=4512 0357: dt=0.000027, rms=0.450 (-0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.450, neg=0, invalid=4512 0358: dt=0.112000, rms=0.449 (0.108%), neg=0, invalid=4512 0359: dt=0.112000, rms=0.449 (0.052%), neg=0, invalid=4512 0360: dt=0.112000, rms=0.449 (0.047%), neg=0, invalid=4512 0361: dt=0.112000, rms=0.449 (0.006%), neg=0, invalid=4512 0362: dt=0.112000, rms=0.449 (-0.091%), neg=0, invalid=4512 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 57 minutes and 20 seconds. mri_ca_register utimesec 6984.652000 mri_ca_register stimesec 9.344000 mri_ca_register ru_maxrss 1337168 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4414580 mri_ca_register ru_majflt 1 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 152 mri_ca_register ru_oublock 62968 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 45 mri_ca_register ru_nivcsw 289258 FSRUNTIME@ mri_ca_register 1.9554 hours 1 threads #-------------------------------------- #@# SubCort Seg Mon Dec 19 12:52:53 GMT 2016 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname stefano-Q170M-C machine x86_64 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/SynthN/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/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/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 8.78 Atlas used for the 3D morph was /usr/local/freesurfer/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 = 0.11451 (13) Left_Lateral_Ventricle (4): linear fit = 0.56 x + 0.0 (1462 voxels, overlap=0.037) Left_Lateral_Ventricle (4): linear fit = 0.56 x + 0.0 (1462 voxels, peak = 11), gca=11.1 gca peak = 0.17677 (13) mri peak = 0.11956 ( 5) Right_Lateral_Ventricle (43): linear fit = 0.31 x + 0.0 (2551 voxels, overlap=0.425) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (2551 voxels, peak = 4), gca=5.2 gca peak = 0.28129 (95) mri peak = 0.09892 (97) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (1112 voxels, overlap=1.019) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (1112 voxels, peak = 96), gca=96.4 gca peak = 0.16930 (96) mri peak = 0.10458 (94) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (1219 voxels, overlap=1.005) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (1219 voxels, peak = 97), gca=97.4 gca peak = 0.24553 (55) mri peak = 0.08257 (58) Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (1146 voxels, overlap=1.009) Right_Hippocampus (53): linear fit = 0.96 x + 0.0 (1146 voxels, peak = 53), gca=53.1 gca peak = 0.30264 (59) mri peak = 0.07497 (54) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (1061 voxels, overlap=1.015) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (1061 voxels, peak = 56), gca=55.8 gca peak = 0.07580 (103) mri peak = 0.08528 (93) Right_Cerebral_White_Matter (41): linear fit = 0.96 x + 0.0 (46031 voxels, overlap=0.620) Right_Cerebral_White_Matter (41): linear fit = 0.96 x + 0.0 (46031 voxels, peak = 99), gca=99.4 gca peak = 0.07714 (104) mri peak = 0.06838 (97) Left_Cerebral_White_Matter (2): linear fit = 0.98 x + 0.0 (72086 voxels, overlap=0.871) Left_Cerebral_White_Matter (2): linear fit = 0.98 x + 0.0 (72086 voxels, peak = 101), gca=101.4 gca peak = 0.09712 (58) mri peak = 0.02898 (63) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (31399 voxels, overlap=0.764) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (31399 voxels, peak = 59), gca=59.4 gca peak = 0.11620 (58) mri peak = 0.02775 (83) Right_Cerebral_Cortex (42): linear fit = 1.41 x + 0.0 (40926 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.41 x + 0.0 (40926 voxels, peak = 82), gca=82.1 gca peak = 0.30970 (66) mri peak = 0.10448 (69) Right_Caudate (50): linear fit = 1.00 x + 0.0 (2029 voxels, overlap=1.008) Right_Caudate (50): linear fit = 1.00 x + 0.0 (2029 voxels, peak = 66), gca=66.0 gca peak = 0.15280 (69) mri peak = 0.09222 (74) Left_Caudate (11): linear fit = 1.03 x + 0.0 (1735 voxels, overlap=1.006) Left_Caudate (11): linear fit = 1.03 x + 0.0 (1735 voxels, peak = 71), gca=71.4 gca peak = 0.13902 (56) mri peak = 0.03073 (66) Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (30186 voxels, overlap=0.219) Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (30186 voxels, peak = 65), gca=64.7 gca peak = 0.14777 (55) mri peak = 0.04343 (83) Right_Cerebellum_Cortex (47): linear fit = 1.47 x + 0.0 (26624 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.47 x + 0.0 (26624 voxels, peak = 81), gca=80.6 gca peak = 0.16765 (84) mri peak = 0.06833 (82) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (8331 voxels, overlap=0.937) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (8331 voxels, peak = 85), gca=85.3 gca peak = 0.18739 (84) mri peak = 0.09463 (85) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (4412 voxels, overlap=0.944) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (4412 voxels, peak = 85), gca=85.3 gca peak = 0.29869 (57) mri peak = 0.10790 (66) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (516 voxels, overlap=0.508) Left_Amygdala (18): linear fit = 1.12 x + 0.0 (516 voxels, peak = 64), gca=63.6 gca peak = 0.33601 (57) mri peak = 0.07121 (56) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (512 voxels, overlap=0.760) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (512 voxels, peak = 60), gca=59.6 gca peak = 0.11131 (90) mri peak = 0.06809 (93) Left_Thalamus_Proper (10): linear fit = 1.04 x + 0.0 (5751 voxels, overlap=0.953) Left_Thalamus_Proper (10): linear fit = 1.04 x + 0.0 (5751 voxels, peak = 94), gca=94.0 gca peak = 0.11793 (83) mri peak = 0.08446 (95) Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (5568 voxels, overlap=0.426) Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (5568 voxels, peak = 92), gca=91.7 gca peak = 0.08324 (81) mri peak = 0.09189 (79) Left_Putamen (12): linear fit = 1.03 x + 0.0 (2785 voxels, overlap=0.757) Left_Putamen (12): linear fit = 1.03 x + 0.0 (2785 voxels, peak = 84), gca=83.8 gca peak = 0.10360 (77) mri peak = 0.06542 (74) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2697 voxels, overlap=0.988) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2697 voxels, peak = 77), gca=76.6 gca peak = 0.08424 (78) mri peak = 0.06903 (87) Brain_Stem (16): linear fit = 1.12 x + 0.0 (13310 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.12 x + 0.0 (13310 voxels, peak = 88), gca=87.8 gca peak = 0.12631 (89) mri peak = 0.07320 (103) Right_VentralDC (60): linear fit = 1.18 x + 0.0 (2130 voxels, overlap=0.330) Right_VentralDC (60): linear fit = 1.18 x + 0.0 (2130 voxels, peak = 105), gca=105.5 gca peak = 0.14500 (87) mri peak = 0.06463 (99) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (2106 voxels, overlap=0.477) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (2106 voxels, peak = 99), gca=98.7 gca peak = 0.14975 (24) mri peak = 0.17394 (13) Third_Ventricle (14): linear fit = 0.49 x + 0.0 (82 voxels, overlap=0.074) Third_Ventricle (14): linear fit = 0.49 x + 0.0 (82 voxels, peak = 12), gca=11.6 gca peak = 0.19357 (14) mri peak = 0.18607 ( 3) Fourth_Ventricle (15): linear fit = 0.12 x + 0.0 (98 voxels, overlap=0.020) Fourth_Ventricle (15): linear fit = 0.12 x + 0.0 (98 voxels, peak = 2), gca=1.8 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.09 x + 0.0 estimating mean wm scale to be 0.97 x + 0.0 estimating mean csf scale to be 0.48 x + 0.0 Left_Pallidum too bright - rescaling by 0.999 (from 1.015) to 97.4 (was 97.4) Right_Pallidum too bright - rescaling by 1.010 (from 1.015) to 97.4 (was 96.4) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.24360 (11) mri peak = 0.11451 (13) Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (1462 voxels, overlap=0.958) Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (1462 voxels, peak = 11), gca=11.5 gca peak = 0.30173 ( 5) mri peak = 0.11956 ( 5) Right_Lateral_Ventricle (43): linear fit = 0.88 x + 0.0 (2551 voxels, overlap=0.997) Right_Lateral_Ventricle (43): linear fit = 0.88 x + 0.0 (2551 voxels, peak = 4), gca=4.4 gca peak = 0.31232 (98) mri peak = 0.09892 (97) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (1112 voxels, overlap=1.017) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (1112 voxels, peak = 97), gca=96.5 gca peak = 0.17752 (96) mri peak = 0.10458 (94) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (1219 voxels, overlap=1.002) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (1219 voxels, peak = 95), gca=94.6 gca peak = 0.24047 (54) mri peak = 0.08257 (58) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (1146 voxels, overlap=0.989) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (1146 voxels, peak = 55), gca=54.8 gca peak = 0.29597 (53) mri peak = 0.07497 (54) Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (1061 voxels, overlap=1.010) Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (1061 voxels, peak = 55), gca=55.4 gca peak = 0.08039 (99) mri peak = 0.08528 (93) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (46031 voxels, overlap=0.769) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (46031 voxels, peak = 99), gca=99.5 gca peak = 0.07997 (102) mri peak = 0.06838 (97) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (72086 voxels, overlap=0.864) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (72086 voxels, peak = 103), gca=102.5 gca peak = 0.09406 (59) mri peak = 0.02898 (63) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (31399 voxels, overlap=0.652) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (31399 voxels, peak = 60), gca=60.5 gca peak = 0.08280 (82) mri peak = 0.02775 (83) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (40926 voxels, overlap=0.156) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (40926 voxels, peak = 80), gca=80.0 gca peak = 0.30977 (66) mri peak = 0.10448 (69) Right_Caudate (50): linear fit = 1.00 x + 0.0 (2029 voxels, overlap=1.008) Right_Caudate (50): linear fit = 1.00 x + 0.0 (2029 voxels, peak = 66), gca=66.0 gca peak = 0.16703 (80) mri peak = 0.09222 (74) Left_Caudate (11): linear fit = 0.99 x + 0.0 (1735 voxels, overlap=1.006) Left_Caudate (11): linear fit = 0.99 x + 0.0 (1735 voxels, peak = 79), gca=78.8 gca peak = 0.12086 (65) mri peak = 0.03073 (66) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (30186 voxels, overlap=0.847) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (30186 voxels, peak = 67), gca=66.6 gca peak = 0.10792 (80) mri peak = 0.04343 (83) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (26624 voxels, overlap=0.922) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (26624 voxels, peak = 80), gca=80.0 gca peak = 0.16360 (86) mri peak = 0.06833 (82) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (8331 voxels, overlap=0.963) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (8331 voxels, peak = 86), gca=85.6 gca peak = 0.16947 (86) mri peak = 0.09463 (85) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4412 voxels, overlap=0.990) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4412 voxels, peak = 85), gca=84.7 gca peak = 0.24256 (65) mri peak = 0.10790 (66) Left_Amygdala (18): linear fit = 1.03 x + 0.0 (516 voxels, overlap=1.010) Left_Amygdala (18): linear fit = 1.03 x + 0.0 (516 voxels, peak = 67), gca=67.3 gca peak = 0.23019 (60) mri peak = 0.07121 (56) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (512 voxels, overlap=0.938) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (512 voxels, peak = 62), gca=61.5 gca peak = 0.11735 (94) mri peak = 0.06809 (93) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5751 voxels, overlap=0.993) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5751 voxels, peak = 94), gca=93.5 gca peak = 0.09369 (89) mri peak = 0.08446 (95) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5568 voxels, overlap=0.912) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5568 voxels, peak = 89), gca=88.6 gca peak = 0.08281 (84) mri peak = 0.09189 (79) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2785 voxels, overlap=0.845) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2785 voxels, peak = 84), gca=84.0 gca peak = 0.11090 (75) mri peak = 0.06542 (74) Right_Putamen (51): linear fit = 0.99 x + 0.0 (2697 voxels, overlap=0.999) Right_Putamen (51): linear fit = 0.99 x + 0.0 (2697 voxels, peak = 74), gca=73.9 gca peak = 0.07728 (88) mri peak = 0.06903 (87) Brain_Stem (16): linear fit = 0.99 x + 0.0 (13310 voxels, overlap=0.819) Brain_Stem (16): linear fit = 0.99 x + 0.0 (13310 voxels, peak = 87), gca=86.7 gca peak = 0.11797 (104) mri peak = 0.07320 (103) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (2130 voxels, overlap=0.899) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (2130 voxels, peak = 104), gca=104.0 gca peak = 0.17128 (97) mri peak = 0.06463 (99) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (2106 voxels, overlap=0.951) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (2106 voxels, peak = 97), gca=97.5 gca peak = 0.31441 (12) mri peak = 0.17394 (13) Third_Ventricle (14): linear fit = 1.03 x + 0.0 (82 voxels, overlap=1.004) Third_Ventricle (14): linear fit = 1.03 x + 0.0 (82 voxels, peak = 12), gca=12.4 gca peak = 0.33705 ( 7) mri peak = 0.18607 ( 3) Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (98 voxels, overlap=0.664) Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (98 voxels, peak = 2), gca=1.9 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.19706 (30) gca peak Left_Thalamus = 0.64095 (98) gca peak Fourth_Ventricle = 0.33705 ( 7) gca peak CSF = 0.32890 (17) gca peak Left_Accumbens_area = 0.64467 (64) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.76046 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.21178 (22) gca peak Right_Accumbens_area = 0.33354 (67) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.92269 (15) gca peak WM_hypointensities = 0.08195 (74) gca peak non_WM_hypointensities = 0.09744 (42) gca peak Optic_Chiasm = 0.61050 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.02 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.99 x + 0.0 Right_Pallidum too bright - rescaling by 1.015 (from 0.985) to 98.0 (was 96.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 108465 voxels changed in iteration 0 of unlikely voxel relabeling 703 voxels changed in iteration 1 of unlikely voxel relabeling 129 voxels changed in iteration 2 of unlikely voxel relabeling 13 voxels changed in iteration 3 of unlikely voxel relabeling 5 voxels changed in iteration 4 of unlikely voxel relabeling 109979 gm and wm labels changed (%20 to gray, %80 to white out of all changed labels) 640 hippocampal voxels changed. 1 amygdala voxels changed. pass 1: 101212 changed. image ll: -2.279, PF=0.500 pass 2: 30572 changed. image ll: -2.278, PF=0.500 pass 3: 10795 changed. pass 4: 4361 changed. 112659 voxels changed in iteration 0 of unlikely voxel relabeling 1111 voxels changed in iteration 1 of unlikely voxel relabeling 53 voxels changed in iteration 2 of unlikely voxel relabeling 2 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 13890 voxels changed in iteration 0 of unlikely voxel relabeling 176 voxels changed in iteration 1 of unlikely voxel relabeling 94 voxels changed in iteration 2 of unlikely voxel relabeling 3 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 10627 voxels changed in iteration 0 of unlikely voxel relabeling 119 voxels changed in iteration 1 of unlikely voxel relabeling 4 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 9883 voxels changed in iteration 0 of unlikely voxel relabeling 78 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 4252.720000 mri_ca_label stimesec 3.216000 mri_ca_label ru_maxrss 2107780 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 644919 mri_ca_label ru_majflt 1 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 152 mri_ca_label ru_oublock 600 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 35 mri_ca_label ru_nivcsw 235265 auto-labeling took 71 minutes and 8 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /usr/local/freesurfer/subjects/SynthN/mri/transforms/cc_up.lta SynthN will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /usr/local/freesurfer/subjects/SynthN/mri/transforms/cc_up.lta reading aseg from /usr/local/freesurfer/subjects/SynthN/mri/aseg.auto_noCCseg.mgz reading norm from /usr/local/freesurfer/subjects/SynthN/mri/norm.mgz 44563 voxels in left wm, 62971 in right wm, xrange [120, 131] searching rotation angles z=[-7 7], y=[-9 5] searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.7 global minimum found at slice 126.0, rotations (-1.66, -0.06) final transformation (x=126.0, yr=-1.663, zr=-0.060): 0.99958 0.00105 -0.02902 5.55642; -0.00105 1.00000 0.00003 9.12803; 0.02902 0.00000 0.99958 -0.60413; 0.00000 0.00000 0.00000 1.00000; updating x range to be [124, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 119 125 eigenvectors: 0.00038 -0.00302 1.00000; 0.17536 -0.98450 -0.00304; 0.98450 0.17536 0.00015; error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /usr/local/freesurfer/subjects/SynthN/mri/aseg.auto.mgz... corpus callosum segmentation took 0.9 minutes #-------------------------------------- #@# Merge ASeg Mon Dec 19 14:04:54 GMT 2016 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Mon Dec 19 14:04:54 GMT 2016 /usr/local/freesurfer/subjects/SynthN/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... 2184 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 64 (64), valley at 19 (19) csf peak at 32, setting threshold to 53 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 64 (64), valley at 19 (19) csf peak at 32, setting threshold to 53 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 0 seconds. #-------------------------------------------- #@# Mask BFS Mon Dec 19 14:07:56 GMT 2016 /usr/local/freesurfer/subjects/SynthN/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1834391 voxels in mask (pct= 10.93) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Dec 19 14:07:58 GMT 2016 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 105.0 +- 5.2 [79.0 --> 125.0] GM (70.0) : 68.2 +- 10.3 [30.0 --> 95.0] setting bottom of white matter range to 78.4 setting top of gray matter range to 88.7 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 5806 sparsely connected voxels removed... thickening thin strands.... 20 segments, 2719 filled 4908 bright non-wm voxels segmented. 3182 diagonally connected voxels added... white matter segmentation took 1.6 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 0.52 minutes reading wm segmentation from wm.seg.mgz... 646 voxels added to wm to prevent paths from MTL structures to cortex 6141 additional wm voxels added 0 additional wm voxels added SEG EDIT: 63129 voxels turned on, 68901 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+): 44 found - 44 modified | TOTAL: 44 pass 2 (xy+): 0 found - 44 modified | TOTAL: 44 pass 1 (xy-): 30 found - 30 modified | TOTAL: 74 pass 2 (xy-): 0 found - 30 modified | TOTAL: 74 pass 1 (yz+): 37 found - 37 modified | TOTAL: 111 pass 2 (yz+): 0 found - 37 modified | TOTAL: 111 pass 1 (yz-): 45 found - 45 modified | TOTAL: 156 pass 2 (yz-): 0 found - 45 modified | TOTAL: 156 pass 1 (xz+): 27 found - 27 modified | TOTAL: 183 pass 2 (xz+): 0 found - 27 modified | TOTAL: 183 pass 1 (xz-): 24 found - 24 modified | TOTAL: 207 pass 2 (xz-): 0 found - 24 modified | TOTAL: 207 Iteration Number : 1 pass 1 (+++): 51 found - 51 modified | TOTAL: 51 pass 2 (+++): 0 found - 51 modified | TOTAL: 51 pass 1 (+++): 73 found - 73 modified | TOTAL: 124 pass 2 (+++): 0 found - 73 modified | TOTAL: 124 pass 1 (+++): 48 found - 48 modified | TOTAL: 172 pass 2 (+++): 0 found - 48 modified | TOTAL: 172 pass 1 (+++): 50 found - 50 modified | TOTAL: 222 pass 2 (+++): 0 found - 50 modified | TOTAL: 222 Iteration Number : 1 pass 1 (++): 57 found - 57 modified | TOTAL: 57 pass 2 (++): 0 found - 57 modified | TOTAL: 57 pass 1 (+-): 154 found - 154 modified | TOTAL: 211 pass 2 (+-): 1 found - 155 modified | TOTAL: 212 pass 3 (+-): 0 found - 155 modified | TOTAL: 212 pass 1 (--): 61 found - 61 modified | TOTAL: 273 pass 2 (--): 1 found - 62 modified | TOTAL: 274 pass 3 (--): 0 found - 62 modified | TOTAL: 274 pass 1 (-+): 113 found - 113 modified | TOTAL: 387 pass 2 (-+): 0 found - 113 modified | TOTAL: 387 Iteration Number : 2 pass 1 (xy+): 15 found - 15 modified | TOTAL: 15 pass 2 (xy+): 0 found - 15 modified | TOTAL: 15 pass 1 (xy-): 15 found - 15 modified | TOTAL: 30 pass 2 (xy-): 0 found - 15 modified | TOTAL: 30 pass 1 (yz+): 6 found - 6 modified | TOTAL: 36 pass 2 (yz+): 0 found - 6 modified | TOTAL: 36 pass 1 (yz-): 20 found - 20 modified | TOTAL: 56 pass 2 (yz-): 0 found - 20 modified | TOTAL: 56 pass 1 (xz+): 11 found - 11 modified | TOTAL: 67 pass 2 (xz+): 0 found - 11 modified | TOTAL: 67 pass 1 (xz-): 12 found - 12 modified | TOTAL: 79 pass 2 (xz-): 0 found - 12 modified | TOTAL: 79 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 14 found - 14 modified | TOTAL: 14 pass 2 (+++): 0 found - 14 modified | TOTAL: 14 pass 1 (+++): 0 found - 0 modified | TOTAL: 14 pass 1 (+++): 2 found - 2 modified | TOTAL: 16 pass 2 (+++): 0 found - 2 modified | TOTAL: 16 Iteration Number : 2 pass 1 (++): 5 found - 5 modified | TOTAL: 5 pass 2 (++): 0 found - 5 modified | TOTAL: 5 pass 1 (+-): 4 found - 4 modified | TOTAL: 9 pass 2 (+-): 0 found - 4 modified | TOTAL: 9 pass 1 (--): 8 found - 8 modified | TOTAL: 17 pass 2 (--): 0 found - 8 modified | TOTAL: 17 pass 1 (-+): 4 found - 4 modified | TOTAL: 21 pass 2 (-+): 0 found - 4 modified | TOTAL: 21 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 0 found - 0 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 1 found - 1 modified | TOTAL: 5 pass 2 (xz-): 0 found - 1 modified | TOTAL: 5 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 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 938 (out of 769397: 0.121914) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Mon Dec 19 14:10:07 GMT 2016 /usr/local/freesurfer/subjects/SynthN/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 0.98259 0.06426 -0.00405 -7.00308; -0.06410 0.97591 -0.06157 1.56700; 0.00000 0.06418 0.94243 -21.19035; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 0.98259 0.06426 -0.00405 -7.00308; -0.06410 0.97591 -0.06157 1.56700; 0.00000 0.06418 0.94243 -21.19035; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1251 (min = 350, max = 1400), aspect = 0.53 (min = 0.10, max = 0.75) no need to search using seed (126, 118, 90), TAL = (2.0, -38.0, 10.0) talairach voxel to voxel transform 1.01336 -0.06673 0.00000 7.20122; 0.06628 1.01594 0.06665 0.28456; -0.00451 -0.06918 1.05655 22.46539; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 118, 90) --> (2.0, -38.0, 10.0) done. writing output to filled.mgz... filling took 0.6 minutes talairach cc position changed to (2.00, -38.00, 10.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -38.00, 10.00) SRC: (108.77, 133.32, 108.90) search lh wm seed point around talairach space (-16.00, -38.00, 10.00), SRC: (145.25, 135.71, 108.74) 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 Dec 19 14:10:44 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 6 found - 6 modified | TOTAL: 10 pass 2 (xy-): 0 found - 6 modified | TOTAL: 10 pass 1 (yz+): 1 found - 1 modified | TOTAL: 11 pass 2 (yz+): 0 found - 1 modified | TOTAL: 11 pass 1 (yz-): 10 found - 10 modified | TOTAL: 21 pass 2 (yz-): 0 found - 10 modified | TOTAL: 21 pass 1 (xz+): 1 found - 1 modified | TOTAL: 22 pass 2 (xz+): 0 found - 1 modified | TOTAL: 22 pass 1 (xz-): 3 found - 3 modified | TOTAL: 25 pass 2 (xz-): 0 found - 3 modified | TOTAL: 25 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 2 found - 2 modified | TOTAL: 3 pass 2 (--): 0 found - 2 modified | TOTAL: 3 pass 1 (-+): 0 found - 0 modified | TOTAL: 3 Iteration Number : 2 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-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 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 Iteration Number : 3 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 : 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 Total Number of Modified Voxels = 29 (out of 364631: 0.007953) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.39 2016/07/20 21:05:04 zkaufman Exp $ $Id: mrisurf.c,v 1.786 2016/11/21 03:01:17 fischl Exp $ slice 50: 1874 vertices, 2041 faces slice 60: 9656 vertices, 9981 faces slice 70: 21148 vertices, 21595 faces slice 80: 34669 vertices, 35173 faces slice 90: 49114 vertices, 49537 faces slice 100: 63033 vertices, 63479 faces slice 110: 78584 vertices, 79128 faces slice 120: 93477 vertices, 93982 faces slice 130: 108631 vertices, 109168 faces slice 140: 123671 vertices, 124195 faces slice 150: 138133 vertices, 138680 faces slice 160: 151418 vertices, 151871 faces slice 170: 162473 vertices, 162927 faces slice 180: 172143 vertices, 172476 faces slice 190: 180875 vertices, 181225 faces slice 200: 187760 vertices, 188059 faces slice 210: 192473 vertices, 192669 faces slice 220: 193134 vertices, 193214 faces slice 230: 193134 vertices, 193214 faces slice 240: 193134 vertices, 193214 faces slice 250: 193134 vertices, 193214 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... 193134 voxel in cpt #1: X=-80 [v=193134,e=579642,f=386428] located at (-29.513027, -5.587452, -1.929262) For the whole surface: X=-80 [v=193134,e=579642,f=386428] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Mon Dec 19 14:10:50 GMT 2016 /usr/local/freesurfer/subjects/SynthN/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-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 1 found - 1 modified | TOTAL: 3 pass 2 (yz+): 0 found - 1 modified | TOTAL: 3 pass 1 (yz-): 2 found - 2 modified | TOTAL: 5 pass 2 (yz-): 0 found - 2 modified | TOTAL: 5 pass 1 (xz+): 1 found - 1 modified | TOTAL: 6 pass 2 (xz+): 0 found - 1 modified | TOTAL: 6 pass 1 (xz-): 0 found - 0 modified | TOTAL: 6 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 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 8 (out of 383607: 0.002085) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.39 2016/07/20 21:05:04 zkaufman Exp $ $Id: mrisurf.c,v 1.786 2016/11/21 03:01:17 fischl Exp $ slice 50: 1129 vertices, 1236 faces slice 60: 6337 vertices, 6544 faces slice 70: 14856 vertices, 15204 faces slice 80: 26177 vertices, 26581 faces slice 90: 39193 vertices, 39626 faces slice 100: 53986 vertices, 54475 faces slice 110: 68878 vertices, 69422 faces slice 120: 84894 vertices, 85476 faces slice 130: 102148 vertices, 102790 faces slice 140: 118613 vertices, 119191 faces slice 150: 133402 vertices, 134010 faces slice 160: 146555 vertices, 147052 faces slice 170: 158390 vertices, 158886 faces slice 180: 169293 vertices, 169771 faces slice 190: 178712 vertices, 179165 faces slice 200: 186750 vertices, 187159 faces slice 210: 192463 vertices, 192779 faces slice 220: 194248 vertices, 194400 faces slice 230: 194248 vertices, 194400 faces slice 240: 194248 vertices, 194400 faces slice 250: 194248 vertices, 194400 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... 194248 voxel in cpt #1: X=-152 [v=194248,e=583200,f=388800] located at (32.895264, -0.596403, -1.310855) For the whole surface: X=-152 [v=194248,e=583200,f=388800] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Mon Dec 19 14:10:56 GMT 2016 /usr/local/freesurfer/subjects/SynthN/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 Dec 19 14:11:03 GMT 2016 /usr/local/freesurfer/subjects/SynthN/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 Dec 19 14:11:10 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 51.2 mm, total surface area = 103983 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.151 (target=0.015) step 005: RMS=0.118 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.081 (target=0.015) step 020: RMS=0.071 (target=0.015) step 025: RMS=0.065 (target=0.015) step 030: RMS=0.060 (target=0.015) step 035: RMS=0.057 (target=0.015) step 040: RMS=0.055 (target=0.015) step 045: RMS=0.052 (target=0.015) step 050: RMS=0.050 (target=0.015) step 055: RMS=0.051 (target=0.015) step 060: RMS=0.050 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 44.360000 mris_inflate stimesec 0.036000 mris_inflate ru_maxrss 250596 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 30915 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 13592 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 2321 #-------------------------------------------- #@# Inflation1 rh Mon Dec 19 14:11:54 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 50.8 mm, total surface area = 103306 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.158 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.098 (target=0.015) step 015: RMS=0.089 (target=0.015) step 020: RMS=0.080 (target=0.015) step 025: RMS=0.074 (target=0.015) step 030: RMS=0.069 (target=0.015) step 035: RMS=0.067 (target=0.015) step 040: RMS=0.064 (target=0.015) step 045: RMS=0.061 (target=0.015) step 050: RMS=0.060 (target=0.015) step 055: RMS=0.061 (target=0.015) step 060: RMS=0.060 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 44.168000 mris_inflate stimesec 0.032000 mris_inflate ru_maxrss 251936 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 30795 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 13672 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 2219 #-------------------------------------------- #@# QSphere lh Mon Dec 19 14:12:39 GMT 2016 /usr/local/freesurfer/subjects/SynthN/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 1.786 2016/11/21 03:01:17 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.83 +- 0.52 (0.00-->6.65) (max @ vno 136296 --> 136317) face area 0.02 +- 0.03 (-0.08-->0.82) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.282... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.530, avgs=0 005/300: dt: 0.9000, rms radial error=175.271, avgs=0 010/300: dt: 0.9000, rms radial error=174.717, avgs=0 015/300: dt: 0.9000, rms radial error=173.989, avgs=0 020/300: dt: 0.9000, rms radial error=173.160, avgs=0 025/300: dt: 0.9000, rms radial error=172.274, avgs=0 030/300: dt: 0.9000, rms radial error=171.357, avgs=0 035/300: dt: 0.9000, rms radial error=170.423, avgs=0 040/300: dt: 0.9000, rms radial error=169.483, avgs=0 045/300: dt: 0.9000, rms radial error=168.540, avgs=0 050/300: dt: 0.9000, rms radial error=167.599, avgs=0 055/300: dt: 0.9000, rms radial error=166.660, avgs=0 060/300: dt: 0.9000, rms radial error=165.725, avgs=0 065/300: dt: 0.9000, rms radial error=164.795, avgs=0 070/300: dt: 0.9000, rms radial error=163.869, avgs=0 075/300: dt: 0.9000, rms radial error=162.948, avgs=0 080/300: dt: 0.9000, rms radial error=162.032, avgs=0 085/300: dt: 0.9000, rms radial error=161.121, avgs=0 090/300: dt: 0.9000, rms radial error=160.215, avgs=0 095/300: dt: 0.9000, rms radial error=159.314, avgs=0 100/300: dt: 0.9000, rms radial error=158.418, avgs=0 105/300: dt: 0.9000, rms radial error=157.527, avgs=0 110/300: dt: 0.9000, rms radial error=156.640, avgs=0 115/300: dt: 0.9000, rms radial error=155.759, avgs=0 120/300: dt: 0.9000, rms radial error=154.882, avgs=0 125/300: dt: 0.9000, rms radial error=154.010, avgs=0 130/300: dt: 0.9000, rms radial error=153.142, avgs=0 135/300: dt: 0.9000, rms radial error=152.280, avgs=0 140/300: dt: 0.9000, rms radial error=151.422, avgs=0 145/300: dt: 0.9000, rms radial error=150.571, avgs=0 150/300: dt: 0.9000, rms radial error=149.724, avgs=0 155/300: dt: 0.9000, rms radial error=148.881, avgs=0 160/300: dt: 0.9000, rms radial error=148.044, avgs=0 165/300: dt: 0.9000, rms radial error=147.210, avgs=0 170/300: dt: 0.9000, rms radial error=146.381, avgs=0 175/300: dt: 0.9000, rms radial error=145.557, avgs=0 180/300: dt: 0.9000, rms radial error=144.737, avgs=0 185/300: dt: 0.9000, rms radial error=143.921, avgs=0 190/300: dt: 0.9000, rms radial error=143.110, avgs=0 195/300: dt: 0.9000, rms radial error=142.303, avgs=0 200/300: dt: 0.9000, rms radial error=141.500, avgs=0 205/300: dt: 0.9000, rms radial error=140.702, avgs=0 210/300: dt: 0.9000, rms radial error=139.909, avgs=0 215/300: dt: 0.9000, rms radial error=139.119, avgs=0 220/300: dt: 0.9000, rms radial error=138.334, avgs=0 225/300: dt: 0.9000, rms radial error=137.553, avgs=0 230/300: dt: 0.9000, rms radial error=136.776, avgs=0 235/300: dt: 0.9000, rms radial error=136.003, avgs=0 240/300: dt: 0.9000, rms radial error=135.234, avgs=0 245/300: dt: 0.9000, rms radial error=134.470, avgs=0 250/300: dt: 0.9000, rms radial error=133.710, avgs=0 255/300: dt: 0.9000, rms radial error=132.960, avgs=0 260/300: dt: 0.9000, rms radial error=132.214, avgs=0 265/300: dt: 0.9000, rms radial error=131.472, avgs=0 270/300: dt: 0.9000, rms radial error=130.734, avgs=0 275/300: dt: 0.9000, rms radial error=130.001, avgs=0 280/300: dt: 0.9000, rms radial error=129.268, avgs=0 285/300: dt: 0.9000, rms radial error=128.543, avgs=0 290/300: dt: 0.9000, rms radial error=127.819, avgs=0 295/300: dt: 0.9000, rms radial error=127.100, avgs=0 300/300: dt: 0.9000, rms radial error=126.384, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 23272.94 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00004 epoch 2 (K=40.0), pass 1, starting sse = 4204.95 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00002 epoch 3 (K=160.0), pass 1, starting sse = 484.74 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/11 = 0.00454 epoch 4 (K=640.0), pass 1, starting sse = 37.99 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00365 final distance error %27.18 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 237.660000 mris_sphere stimesec 0.084000 mris_sphere ru_maxrss 250692 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 30417 mris_sphere ru_majflt 1 mris_sphere ru_nswap 0 mris_sphere ru_inblock 144 mris_sphere ru_oublock 13592 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 7 mris_sphere ru_nivcsw 11155 FSRUNTIME@ mris_sphere 0.0662 hours 1 threads #-------------------------------------------- #@# QSphere rh Mon Dec 19 14:16:37 GMT 2016 /usr/local/freesurfer/subjects/SynthN/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 1.786 2016/11/21 03:01:17 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.84 +- 0.53 (0.00-->8.02) (max @ vno 118844 --> 120436) face area 0.02 +- 0.03 (-0.24-->0.68) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.279... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.285, avgs=0 005/300: dt: 0.9000, rms radial error=176.024, avgs=0 010/300: dt: 0.9000, rms radial error=175.464, avgs=0 015/300: dt: 0.9000, rms radial error=174.728, avgs=0 020/300: dt: 0.9000, rms radial error=173.889, avgs=0 025/300: dt: 0.9000, rms radial error=172.991, avgs=0 030/300: dt: 0.9000, rms radial error=172.060, avgs=0 035/300: dt: 0.9000, rms radial error=171.112, avgs=0 040/300: dt: 0.9000, rms radial error=170.156, avgs=0 045/300: dt: 0.9000, rms radial error=169.200, avgs=0 050/300: dt: 0.9000, rms radial error=168.246, avgs=0 055/300: dt: 0.9000, rms radial error=167.294, avgs=0 060/300: dt: 0.9000, rms radial error=166.346, avgs=0 065/300: dt: 0.9000, rms radial error=165.401, avgs=0 070/300: dt: 0.9000, rms radial error=164.462, avgs=0 075/300: dt: 0.9000, rms radial error=163.529, avgs=0 080/300: dt: 0.9000, rms radial error=162.612, avgs=0 085/300: dt: 0.9000, rms radial error=161.700, avgs=0 090/300: dt: 0.9000, rms radial error=160.793, avgs=0 095/300: dt: 0.9000, rms radial error=159.891, avgs=0 100/300: dt: 0.9000, rms radial error=158.994, avgs=0 105/300: dt: 0.9000, rms radial error=158.102, avgs=0 110/300: dt: 0.9000, rms radial error=157.214, avgs=0 115/300: dt: 0.9000, rms radial error=156.332, avgs=0 120/300: dt: 0.9000, rms radial error=155.455, avgs=0 125/300: dt: 0.9000, rms radial error=154.583, avgs=0 130/300: dt: 0.9000, rms radial error=153.716, avgs=0 135/300: dt: 0.9000, rms radial error=152.854, avgs=0 140/300: dt: 0.9000, rms radial error=151.996, avgs=0 145/300: dt: 0.9000, rms radial error=151.143, avgs=0 150/300: dt: 0.9000, rms radial error=150.295, avgs=0 155/300: dt: 0.9000, rms radial error=149.451, avgs=0 160/300: dt: 0.9000, rms radial error=148.612, avgs=0 165/300: dt: 0.9000, rms radial error=147.777, avgs=0 170/300: dt: 0.9000, rms radial error=146.947, avgs=0 175/300: dt: 0.9000, rms radial error=146.122, avgs=0 180/300: dt: 0.9000, rms radial error=145.302, avgs=0 185/300: dt: 0.9000, rms radial error=144.484, avgs=0 190/300: dt: 0.9000, rms radial error=143.672, avgs=0 195/300: dt: 0.9000, rms radial error=142.865, avgs=0 200/300: dt: 0.9000, rms radial error=142.063, avgs=0 205/300: dt: 0.9000, rms radial error=141.265, avgs=0 210/300: dt: 0.9000, rms radial error=140.470, avgs=0 215/300: dt: 0.9000, rms radial error=139.681, avgs=0 220/300: dt: 0.9000, rms radial error=138.896, avgs=0 225/300: dt: 0.9000, rms radial error=138.116, avgs=0 230/300: dt: 0.9000, rms radial error=137.340, avgs=0 235/300: dt: 0.9000, rms radial error=136.568, avgs=0 240/300: dt: 0.9000, rms radial error=135.800, avgs=0 245/300: dt: 0.9000, rms radial error=135.037, avgs=0 250/300: dt: 0.9000, rms radial error=134.278, avgs=0 255/300: dt: 0.9000, rms radial error=133.523, avgs=0 260/300: dt: 0.9000, rms radial error=132.778, avgs=0 265/300: dt: 0.9000, rms radial error=132.027, avgs=0 270/300: dt: 0.9000, rms radial error=131.284, avgs=0 275/300: dt: 0.9000, rms radial error=130.546, avgs=0 280/300: dt: 0.9000, rms radial error=129.815, avgs=0 285/300: dt: 0.9000, rms radial error=129.083, avgs=0 290/300: dt: 0.9000, rms radial error=128.357, avgs=0 295/300: dt: 0.9000, rms radial error=127.633, avgs=0 300/300: dt: 0.9000, rms radial error=126.916, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 23494.71 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 2 (K=40.0), pass 1, starting sse = 4261.43 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 = 520.68 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00258 epoch 4 (K=640.0), pass 1, starting sse = 52.87 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00453 final distance error %28.07 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 237.844000 mris_sphere stimesec 0.108000 mris_sphere ru_maxrss 252412 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 30810 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 13672 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 6 mris_sphere ru_nivcsw 15640 FSRUNTIME@ mris_sphere 0.0663 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Mon Dec 19 14:20:36 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Mon Dec 19 14:20:36 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Mon Dec 19 14:20:36 GMT 2016 mris_fix_topology -rusage /usr/local/freesurfer/subjects/SynthN/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 SynthN 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 1.51 2016/10/27 19:43:58 fischl Exp $ $Id: mrisurf.c,v 1.786 2016/11/21 03:01:17 fischl Exp $ before topology correction, eno=-80 (nv=193134, nf=386428, ne=579642, g=41) 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... 16505 ambiguous faces found in tessellation segmenting defects... 59 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 9 into 8 -merging segment 48 into 45 -merging segment 49 into 47 56 defects to be corrected 0 vertices coincident reading input surface /usr/local/freesurfer/subjects/SynthN/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5774 (-4.7887) -vertex loglikelihood: -6.3474 (-3.1737) -normal dot loglikelihood: -3.5644 (-3.5644) -quad curv loglikelihood: -6.2855 (-3.1428) Total Loglikelihood : -25.7747 CORRECTING DEFECT 0 (vertices=134, convex hull=71, v0=187) After retessellation of defect 0 (v0=187), euler #=-51 (183688,548667,364928) : difference with theory (-53) = -2 CORRECTING DEFECT 1 (vertices=858, convex hull=268, v0=235) After retessellation of defect 1 (v0=235), euler #=-50 (183793,549120,365277) : difference with theory (-52) = -2 CORRECTING DEFECT 2 (vertices=95, convex hull=127, v0=16319) After retessellation of defect 2 (v0=16319), euler #=-49 (183834,549306,365423) : difference with theory (-51) = -2 CORRECTING DEFECT 3 (vertices=528, convex hull=253, v0=23653) After retessellation of defect 3 (v0=23653), euler #=-48 (183888,549585,365649) : difference with theory (-50) = -2 CORRECTING DEFECT 4 (vertices=7, convex hull=27, v0=26036) After retessellation of defect 4 (v0=26036), euler #=-47 (183890,549599,365662) : difference with theory (-49) = -2 CORRECTING DEFECT 5 (vertices=115, convex hull=145, v0=26586) After retessellation of defect 5 (v0=26586), euler #=-46 (183959,549870,365865) : difference with theory (-48) = -2 CORRECTING DEFECT 6 (vertices=251, convex hull=144, v0=32778) After retessellation of defect 6 (v0=32778), euler #=-45 (184017,550116,366054) : difference with theory (-47) = -2 CORRECTING DEFECT 7 (vertices=7, convex hull=27, v0=35761) After retessellation of defect 7 (v0=35761), euler #=-44 (184020,550133,366069) : difference with theory (-46) = -2 CORRECTING DEFECT 8 (vertices=243, convex hull=123, v0=44291) After retessellation of defect 8 (v0=44291), euler #=-42 (184055,550297,366200) : difference with theory (-45) = -3 CORRECTING DEFECT 9 (vertices=28, convex hull=70, v0=52305) After retessellation of defect 9 (v0=52305), euler #=-41 (184067,550359,366251) : difference with theory (-44) = -3 CORRECTING DEFECT 10 (vertices=32, convex hull=59, v0=53036) After retessellation of defect 10 (v0=53036), euler #=-40 (184083,550431,366308) : difference with theory (-43) = -3 CORRECTING DEFECT 11 (vertices=140, convex hull=40, v0=59163) After retessellation of defect 11 (v0=59163), euler #=-39 (184090,550464,366335) : difference with theory (-42) = -3 CORRECTING DEFECT 12 (vertices=212, convex hull=194, v0=60377) After retessellation of defect 12 (v0=60377), euler #=-38 (184158,550762,366566) : difference with theory (-41) = -3 CORRECTING DEFECT 13 (vertices=52, convex hull=31, v0=62680) After retessellation of defect 13 (v0=62680), euler #=-37 (184163,550785,366585) : difference with theory (-40) = -3 CORRECTING DEFECT 14 (vertices=149, convex hull=49, v0=63033) After retessellation of defect 14 (v0=63033), euler #=-36 (184172,550833,366625) : difference with theory (-39) = -3 CORRECTING DEFECT 15 (vertices=23, convex hull=20, v0=64476) After retessellation of defect 15 (v0=64476), euler #=-35 (184174,550844,366635) : difference with theory (-38) = -3 CORRECTING DEFECT 16 (vertices=42, convex hull=27, v0=77559) After retessellation of defect 16 (v0=77559), euler #=-34 (184178,550867,366655) : difference with theory (-37) = -3 CORRECTING DEFECT 17 (vertices=250, convex hull=103, v0=80600) After retessellation of defect 17 (v0=80600), euler #=-33 (184207,551001,366761) : difference with theory (-36) = -3 CORRECTING DEFECT 18 (vertices=141, convex hull=105, v0=81154) After retessellation of defect 18 (v0=81154), euler #=-32 (184225,551102,366845) : difference with theory (-35) = -3 CORRECTING DEFECT 19 (vertices=51, convex hull=72, v0=81315) After retessellation of defect 19 (v0=81315), euler #=-31 (184247,551203,366925) : difference with theory (-34) = -3 CORRECTING DEFECT 20 (vertices=42, convex hull=38, v0=85478) After retessellation of defect 20 (v0=85478), euler #=-30 (184251,551228,366947) : difference with theory (-33) = -3 CORRECTING DEFECT 21 (vertices=40, convex hull=90, v0=86083) After retessellation of defect 21 (v0=86083), euler #=-29 (184264,551302,367009) : difference with theory (-32) = -3 CORRECTING DEFECT 22 (vertices=163, convex hull=53, v0=86174) After retessellation of defect 22 (v0=86174), euler #=-29 (184278,551379,367072) : difference with theory (-31) = -2 CORRECTING DEFECT 23 (vertices=9, convex hull=26, v0=94525) After retessellation of defect 23 (v0=94525), euler #=-28 (184278,551388,367082) : difference with theory (-30) = -2 CORRECTING DEFECT 24 (vertices=17, convex hull=26, v0=95290) After retessellation of defect 24 (v0=95290), euler #=-27 (184279,551401,367095) : difference with theory (-29) = -2 CORRECTING DEFECT 25 (vertices=358, convex hull=199, v0=102289) After retessellation of defect 25 (v0=102289), euler #=-27 (184350,551717,367340) : difference with theory (-28) = -1 CORRECTING DEFECT 26 (vertices=44, convex hull=83, v0=102755) After retessellation of defect 26 (v0=102755), euler #=-26 (184370,551814,367418) : difference with theory (-27) = -1 CORRECTING DEFECT 27 (vertices=8, convex hull=35, v0=104082) After retessellation of defect 27 (v0=104082), euler #=-25 (184371,551828,367432) : difference with theory (-26) = -1 CORRECTING DEFECT 28 (vertices=34, convex hull=26, v0=106457) After retessellation of defect 28 (v0=106457), euler #=-24 (184373,551844,367447) : difference with theory (-25) = -1 CORRECTING DEFECT 29 (vertices=59, convex hull=21, v0=108609) After retessellation of defect 29 (v0=108609), euler #=-23 (184378,551864,367463) : difference with theory (-24) = -1 CORRECTING DEFECT 30 (vertices=63, convex hull=25, v0=110493) After retessellation of defect 30 (v0=110493), euler #=-22 (184385,551893,367486) : difference with theory (-23) = -1 CORRECTING DEFECT 31 (vertices=731, convex hull=481, v0=116054) L defect detected... After retessellation of defect 31 (v0=116054), euler #=-21 (184587,552737,368129) : difference with theory (-22) = -1 CORRECTING DEFECT 32 (vertices=30, convex hull=57, v0=117231) After retessellation of defect 32 (v0=117231), euler #=-20 (184602,552804,368182) : difference with theory (-21) = -1 CORRECTING DEFECT 33 (vertices=61, convex hull=72, v0=117326) After retessellation of defect 33 (v0=117326), euler #=-19 (184635,552932,368278) : difference with theory (-20) = -1 CORRECTING DEFECT 34 (vertices=189, convex hull=185, v0=118347) After retessellation of defect 34 (v0=118347), euler #=-18 (184710,553242,368514) : difference with theory (-19) = -1 CORRECTING DEFECT 35 (vertices=451, convex hull=175, v0=119211) After retessellation of defect 35 (v0=119211), euler #=-17 (184794,553582,368771) : difference with theory (-18) = -1 CORRECTING DEFECT 36 (vertices=7, convex hull=19, v0=121574) After retessellation of defect 36 (v0=121574), euler #=-16 (184795,553590,368779) : difference with theory (-17) = -1 CORRECTING DEFECT 37 (vertices=284, convex hull=99, v0=123671) After retessellation of defect 37 (v0=123671), euler #=-15 (184816,553700,368869) : difference with theory (-16) = -1 CORRECTING DEFECT 38 (vertices=69, convex hull=90, v0=125063) After retessellation of defect 38 (v0=125063), euler #=-14 (184841,553817,368962) : difference with theory (-15) = -1 CORRECTING DEFECT 39 (vertices=108, convex hull=72, v0=125829) After retessellation of defect 39 (v0=125829), euler #=-13 (184852,553879,369014) : difference with theory (-14) = -1 CORRECTING DEFECT 40 (vertices=36, convex hull=21, v0=127588) After retessellation of defect 40 (v0=127588), euler #=-13 (184854,553897,369030) : difference with theory (-13) = 0 CORRECTING DEFECT 41 (vertices=329, convex hull=332, v0=129781) After retessellation of defect 41 (v0=129781), euler #=-12 (185018,554550,369520) : difference with theory (-12) = 0 CORRECTING DEFECT 42 (vertices=45, convex hull=76, v0=132036) After retessellation of defect 42 (v0=132036), euler #=-11 (185041,554653,369601) : difference with theory (-11) = 0 CORRECTING DEFECT 43 (vertices=7, convex hull=17, v0=132295) After retessellation of defect 43 (v0=132295), euler #=-10 (185042,554660,369608) : difference with theory (-10) = 0 CORRECTING DEFECT 44 (vertices=258, convex hull=88, v0=134878) After retessellation of defect 44 (v0=134878), euler #=-8 (185057,554759,369694) : difference with theory (-9) = -1 CORRECTING DEFECT 45 (vertices=99, convex hull=92, v0=134891) After retessellation of defect 45 (v0=134891), euler #=-7 (185070,554841,369764) : difference with theory (-8) = -1 CORRECTING DEFECT 46 (vertices=57, convex hull=76, v0=137585) After retessellation of defect 46 (v0=137585), euler #=-5 (185092,554941,369844) : difference with theory (-7) = -2 CORRECTING DEFECT 47 (vertices=46, convex hull=60, v0=141138) After retessellation of defect 47 (v0=141138), euler #=-4 (185094,554970,369872) : difference with theory (-6) = -2 CORRECTING DEFECT 48 (vertices=9, convex hull=14, v0=142878) After retessellation of defect 48 (v0=142878), euler #=-3 (185094,554971,369874) : difference with theory (-5) = -2 CORRECTING DEFECT 49 (vertices=39, convex hull=68, v0=146138) After retessellation of defect 49 (v0=146138), euler #=-2 (185114,555054,369938) : difference with theory (-4) = -2 CORRECTING DEFECT 50 (vertices=1321, convex hull=161, v0=147603) After retessellation of defect 50 (v0=147603), euler #=-1 (185210,555414,370203) : difference with theory (-3) = -2 CORRECTING DEFECT 51 (vertices=239, convex hull=119, v0=153462) After retessellation of defect 51 (v0=153462), euler #=0 (185240,555560,370320) : difference with theory (-2) = -2 CORRECTING DEFECT 52 (vertices=739, convex hull=195, v0=153564) After retessellation of defect 52 (v0=153564), euler #=-1 (185329,555939,370609) : difference with theory (-1) = 0 CORRECTING DEFECT 53 (vertices=51, convex hull=36, v0=157248) After retessellation of defect 53 (v0=157248), euler #=0 (185338,555979,370641) : difference with theory (0) = 0 CORRECTING DEFECT 54 (vertices=34, convex hull=60, v0=160934) After retessellation of defect 54 (v0=160934), euler #=1 (185349,556036,370688) : difference with theory (1) = 0 CORRECTING DEFECT 55 (vertices=11, convex hull=23, v0=168442) After retessellation of defect 55 (v0=168442), euler #=2 (185351,556047,370698) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.25 (0.05-->28.59) (max @ vno 148737 --> 172989) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.25 (0.05-->28.59) (max @ vno 148737 --> 172989) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 182 mutations (33.8%), 357 crossovers (66.2%), 627 vertices were eliminated building final representation... 7783 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=185351, nf=370698, ne=556047, g=0) writing corrected surface to /usr/local/freesurfer/subjects/SynthN/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 53.4 minutes 0 defective edges removing intersecting faces 000: 797 intersecting 001: 95 intersecting 002: 80 intersecting 003: 42 intersecting expanding nbhd size to 2 004: 45 intersecting 005: 28 intersecting 006: 10 intersecting mris_fix_topology utimesec 3189.640000 mris_fix_topology stimesec 2.620000 mris_fix_topology ru_maxrss 597396 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 65283 mris_fix_topology ru_majflt 1 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 152 mris_fix_topology ru_oublock 17576 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 172300 FSRUNTIME@ mris_fix_topology lh 0.8905 hours 1 threads #@# Fix Topology rh Mon Dec 19 15:14:01 GMT 2016 mris_fix_topology -rusage /usr/local/freesurfer/subjects/SynthN/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 SynthN 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 1.51 2016/10/27 19:43:58 fischl Exp $ $Id: mrisurf.c,v 1.786 2016/11/21 03:01:17 fischl Exp $ before topology correction, eno=-152 (nv=194248, nf=388800, ne=583200, g=77) 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... 27118 ambiguous faces found in tessellation segmenting defects... 83 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 3 into 2 -merging segment 42 into 5 -merging segment 27 into 23 -merging segment 37 into 36 -merging segment 64 into 63 -merging segment 70 into 67 -merging segment 71 into 67 -merging segment 78 into 75 -merging segment 81 into 80 74 defects to be corrected 0 vertices coincident reading input surface /usr/local/freesurfer/subjects/SynthN/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5629 (-4.7814) -vertex loglikelihood: -6.3869 (-3.1935) -normal dot loglikelihood: -3.5532 (-3.5532) -quad curv loglikelihood: -5.9308 (-2.9654) Total Loglikelihood : -25.4338 CORRECTING DEFECT 0 (vertices=43, convex hull=27, v0=28115) After retessellation of defect 0 (v0=28115), euler #=-74 (178411,530544,352059) : difference with theory (-71) = 3 CORRECTING DEFECT 1 (vertices=52, convex hull=41, v0=36108) After retessellation of defect 1 (v0=36108), euler #=-73 (178418,530579,352088) : difference with theory (-70) = 3 CORRECTING DEFECT 2 (vertices=138, convex hull=207, v0=37091) After retessellation of defect 2 (v0=37091), euler #=-71 (178507,530941,352363) : difference with theory (-69) = 2 CORRECTING DEFECT 3 (vertices=622, convex hull=270, v0=39085) After retessellation of defect 3 (v0=39085), euler #=-70 (178593,531334,352671) : difference with theory (-68) = 2 CORRECTING DEFECT 4 (vertices=760, convex hull=379, v0=40070) normal vector of length zero at vertex 180004 with 3 faces normal vector of length zero at vertex 180004 with 3 faces After retessellation of defect 4 (v0=40070), euler #=-68 (178693,531820,353059) : difference with theory (-67) = 1 CORRECTING DEFECT 5 (vertices=109, convex hull=113, v0=40281) After retessellation of defect 5 (v0=40281), euler #=-67 (178747,532030,353216) : difference with theory (-66) = 1 CORRECTING DEFECT 6 (vertices=11, convex hull=28, v0=42621) After retessellation of defect 6 (v0=42621), euler #=-66 (178747,532041,353228) : difference with theory (-65) = 1 CORRECTING DEFECT 7 (vertices=32, convex hull=35, v0=49201) After retessellation of defect 7 (v0=49201), euler #=-65 (178749,532062,353248) : difference with theory (-64) = 1 CORRECTING DEFECT 8 (vertices=459, convex hull=245, v0=51287) After retessellation of defect 8 (v0=51287), euler #=-64 (178876,532569,353629) : difference with theory (-63) = 1 CORRECTING DEFECT 9 (vertices=298, convex hull=240, v0=51915) After retessellation of defect 9 (v0=51915), euler #=-63 (178954,532914,353897) : difference with theory (-62) = 1 CORRECTING DEFECT 10 (vertices=266, convex hull=168, v0=52161) After retessellation of defect 10 (v0=52161), euler #=-62 (179044,533262,354156) : difference with theory (-61) = 1 CORRECTING DEFECT 11 (vertices=191, convex hull=35, v0=52459) After retessellation of defect 11 (v0=52459), euler #=-61 (179051,533294,354182) : difference with theory (-60) = 1 CORRECTING DEFECT 12 (vertices=20, convex hull=34, v0=57546) After retessellation of defect 12 (v0=57546), euler #=-60 (179053,533313,354200) : difference with theory (-59) = 1 CORRECTING DEFECT 13 (vertices=122, convex hull=165, v0=59613) After retessellation of defect 13 (v0=59613), euler #=-59 (179128,533612,354425) : difference with theory (-58) = 1 CORRECTING DEFECT 14 (vertices=132, convex hull=107, v0=59731) After retessellation of defect 14 (v0=59731), euler #=-58 (179149,533721,354514) : difference with theory (-57) = 1 CORRECTING DEFECT 15 (vertices=1233, convex hull=311, v0=65538) After retessellation of defect 15 (v0=65538), euler #=-59 (179417,534696,355220) : difference with theory (-56) = 3 CORRECTING DEFECT 16 (vertices=96, convex hull=100, v0=65576) After retessellation of defect 16 (v0=65576), euler #=-58 (179469,534893,355366) : difference with theory (-55) = 3 CORRECTING DEFECT 17 (vertices=13, convex hull=25, v0=65580) After retessellation of defect 17 (v0=65580), euler #=-57 (179471,534907,355379) : difference with theory (-54) = 3 CORRECTING DEFECT 18 (vertices=10, convex hull=23, v0=65635) After retessellation of defect 18 (v0=65635), euler #=-56 (179472,534914,355386) : difference with theory (-53) = 3 CORRECTING DEFECT 19 (vertices=104, convex hull=112, v0=68580) After retessellation of defect 19 (v0=68580), euler #=-55 (179527,535128,355546) : difference with theory (-52) = 3 CORRECTING DEFECT 20 (vertices=21, convex hull=31, v0=70223) After retessellation of defect 20 (v0=70223), euler #=-54 (179530,535148,355564) : difference with theory (-51) = 3 CORRECTING DEFECT 21 (vertices=34, convex hull=62, v0=70919) After retessellation of defect 21 (v0=70919), euler #=-53 (179539,535200,355608) : difference with theory (-50) = 3 CORRECTING DEFECT 22 (vertices=49, convex hull=99, v0=71096) After retessellation of defect 22 (v0=71096), euler #=-51 (179560,535299,355688) : difference with theory (-49) = 2 CORRECTING DEFECT 23 (vertices=1234, convex hull=549, v0=71438) XL defect detected... After retessellation of defect 23 (v0=71438), euler #=-50 (179770,536212,356392) : difference with theory (-48) = 2 CORRECTING DEFECT 24 (vertices=5, convex hull=25, v0=71885) After retessellation of defect 24 (v0=71885), euler #=-49 (179770,536219,356400) : difference with theory (-47) = 2 CORRECTING DEFECT 25 (vertices=6, convex hull=11, v0=76645) After retessellation of defect 25 (v0=76645), euler #=-48 (179771,536224,356405) : difference with theory (-46) = 2 CORRECTING DEFECT 26 (vertices=12, convex hull=15, v0=80880) After retessellation of defect 26 (v0=80880), euler #=-47 (179772,536232,356413) : difference with theory (-45) = 2 CORRECTING DEFECT 27 (vertices=721, convex hull=290, v0=81731) After retessellation of defect 27 (v0=81731), euler #=-46 (179789,536426,356591) : difference with theory (-44) = 2 CORRECTING DEFECT 28 (vertices=264, convex hull=126, v0=81979) After retessellation of defect 28 (v0=81979), euler #=-45 (179828,536600,356727) : difference with theory (-43) = 2 CORRECTING DEFECT 29 (vertices=77, convex hull=112, v0=83806) After retessellation of defect 29 (v0=83806), euler #=-44 (179867,536769,356858) : difference with theory (-42) = 2 CORRECTING DEFECT 30 (vertices=165, convex hull=132, v0=86167) After retessellation of defect 30 (v0=86167), euler #=-43 (179925,537010,357042) : difference with theory (-41) = 2 CORRECTING DEFECT 31 (vertices=373, convex hull=194, v0=86629) After retessellation of defect 31 (v0=86629), euler #=-42 (179999,537338,357297) : difference with theory (-40) = 2 CORRECTING DEFECT 32 (vertices=85, convex hull=54, v0=87636) After retessellation of defect 32 (v0=87636), euler #=-41 (180013,537402,357348) : difference with theory (-39) = 2 CORRECTING DEFECT 33 (vertices=28, convex hull=24, v0=88230) After retessellation of defect 33 (v0=88230), euler #=-40 (180016,537418,357362) : difference with theory (-38) = 2 CORRECTING DEFECT 34 (vertices=671, convex hull=468, v0=91043) After retessellation of defect 34 (v0=91043), euler #=-38 (180205,538228,357985) : difference with theory (-37) = 1 CORRECTING DEFECT 35 (vertices=29, convex hull=29, v0=94816) After retessellation of defect 35 (v0=94816), euler #=-37 (180210,538253,358006) : difference with theory (-36) = 1 CORRECTING DEFECT 36 (vertices=50, convex hull=37, v0=96551) After retessellation of defect 36 (v0=96551), euler #=-36 (180226,538312,358050) : difference with theory (-35) = 1 CORRECTING DEFECT 37 (vertices=33, convex hull=30, v0=96881) After retessellation of defect 37 (v0=96881), euler #=-35 (180233,538343,358075) : difference with theory (-34) = 1 CORRECTING DEFECT 38 (vertices=30, convex hull=77, v0=97835) After retessellation of defect 38 (v0=97835), euler #=-34 (180242,538403,358127) : difference with theory (-33) = 1 CORRECTING DEFECT 39 (vertices=926, convex hull=688, v0=101025) XL defect detected... After retessellation of defect 39 (v0=101025), euler #=-34 (180561,539692,359097) : difference with theory (-32) = 2 CORRECTING DEFECT 40 (vertices=37, convex hull=65, v0=103796) After retessellation of defect 40 (v0=103796), euler #=-33 (180579,539770,359158) : difference with theory (-31) = 2 CORRECTING DEFECT 41 (vertices=16, convex hull=36, v0=104158) After retessellation of defect 41 (v0=104158), euler #=-32 (180580,539784,359172) : difference with theory (-30) = 2 CORRECTING DEFECT 42 (vertices=71, convex hull=51, v0=104948) After retessellation of defect 42 (v0=104948), euler #=-31 (180589,539828,359208) : difference with theory (-29) = 2 CORRECTING DEFECT 43 (vertices=280, convex hull=364, v0=105108) After retessellation of defect 43 (v0=105108), euler #=-30 (180743,540467,359694) : difference with theory (-28) = 2 CORRECTING DEFECT 44 (vertices=27, convex hull=31, v0=107828) After retessellation of defect 44 (v0=107828), euler #=-29 (180746,540492,359717) : difference with theory (-27) = 2 CORRECTING DEFECT 45 (vertices=80, convex hull=42, v0=108536) After retessellation of defect 45 (v0=108536), euler #=-28 (180759,540544,359757) : difference with theory (-26) = 2 CORRECTING DEFECT 46 (vertices=22, convex hull=26, v0=108630) After retessellation of defect 46 (v0=108630), euler #=-27 (180760,540554,359767) : difference with theory (-25) = 2 CORRECTING DEFECT 47 (vertices=28, convex hull=24, v0=109401) After retessellation of defect 47 (v0=109401), euler #=-26 (180760,540563,359777) : difference with theory (-24) = 2 CORRECTING DEFECT 48 (vertices=89, convex hull=26, v0=113256) After retessellation of defect 48 (v0=113256), euler #=-25 (180767,540591,359799) : difference with theory (-23) = 2 CORRECTING DEFECT 49 (vertices=39, convex hull=38, v0=113563) After retessellation of defect 49 (v0=113563), euler #=-24 (180772,540619,359823) : difference with theory (-22) = 2 CORRECTING DEFECT 50 (vertices=22, convex hull=25, v0=115653) After retessellation of defect 50 (v0=115653), euler #=-23 (180777,540641,359841) : difference with theory (-21) = 2 CORRECTING DEFECT 51 (vertices=343, convex hull=91, v0=116863) After retessellation of defect 51 (v0=116863), euler #=-22 (180822,540814,359970) : difference with theory (-20) = 2 CORRECTING DEFECT 52 (vertices=73, convex hull=45, v0=121366) After retessellation of defect 52 (v0=121366), euler #=-21 (180831,540856,360004) : difference with theory (-19) = 2 CORRECTING DEFECT 53 (vertices=46, convex hull=86, v0=123215) After retessellation of defect 53 (v0=123215), euler #=-20 (180859,540975,360096) : difference with theory (-18) = 2 CORRECTING DEFECT 54 (vertices=148, convex hull=148, v0=126132) After retessellation of defect 54 (v0=126132), euler #=-19 (180900,541167,360248) : difference with theory (-17) = 2 CORRECTING DEFECT 55 (vertices=112, convex hull=35, v0=126565) After retessellation of defect 55 (v0=126565), euler #=-18 (180909,541207,360280) : difference with theory (-16) = 2 CORRECTING DEFECT 56 (vertices=529, convex hull=210, v0=127413) After retessellation of defect 56 (v0=127413), euler #=-17 (181041,541700,360642) : difference with theory (-15) = 2 CORRECTING DEFECT 57 (vertices=50, convex hull=51, v0=128331) After retessellation of defect 57 (v0=128331), euler #=-16 (181055,541759,360688) : difference with theory (-14) = 2 CORRECTING DEFECT 58 (vertices=47, convex hull=69, v0=131524) After retessellation of defect 58 (v0=131524), euler #=-15 (181065,541815,360735) : difference with theory (-13) = 2 CORRECTING DEFECT 59 (vertices=317, convex hull=243, v0=131997) After retessellation of defect 59 (v0=131997), euler #=-13 (181144,542175,361018) : difference with theory (-12) = 1 CORRECTING DEFECT 60 (vertices=16, convex hull=34, v0=134459) After retessellation of defect 60 (v0=134459), euler #=-12 (181149,542203,361042) : difference with theory (-11) = 1 CORRECTING DEFECT 61 (vertices=6, convex hull=14, v0=134803) After retessellation of defect 61 (v0=134803), euler #=-11 (181150,542210,361049) : difference with theory (-10) = 1 CORRECTING DEFECT 62 (vertices=102, convex hull=109, v0=135695) After retessellation of defect 62 (v0=135695), euler #=-8 (181172,542337,361157) : difference with theory (-9) = -1 CORRECTING DEFECT 63 (vertices=29, convex hull=32, v0=138565) After retessellation of defect 63 (v0=138565), euler #=-7 (181178,542362,361177) : difference with theory (-8) = -1 CORRECTING DEFECT 64 (vertices=62, convex hull=83, v0=139943) After retessellation of defect 64 (v0=139943), euler #=-6 (181214,542507,361287) : difference with theory (-7) = -1 CORRECTING DEFECT 65 (vertices=255, convex hull=208, v0=143276) After retessellation of defect 65 (v0=143276), euler #=-6 (181256,542737,361475) : difference with theory (-6) = 0 CORRECTING DEFECT 66 (vertices=408, convex hull=292, v0=143337) After retessellation of defect 66 (v0=143337), euler #=-5 (181364,543205,361836) : difference with theory (-5) = 0 CORRECTING DEFECT 67 (vertices=49, convex hull=77, v0=146381) After retessellation of defect 67 (v0=146381), euler #=-4 (181387,543310,361919) : difference with theory (-4) = 0 CORRECTING DEFECT 68 (vertices=1115, convex hull=543, v0=146556) L defect detected... After retessellation of defect 68 (v0=146556), euler #=-2 (181587,544197,362608) : difference with theory (-3) = -1 CORRECTING DEFECT 69 (vertices=332, convex hull=121, v0=147251) After retessellation of defect 69 (v0=147251), euler #=-1 (181637,544407,362769) : difference with theory (-2) = -1 CORRECTING DEFECT 70 (vertices=41, convex hull=46, v0=154999) After retessellation of defect 70 (v0=154999), euler #=0 (181641,544439,362798) : difference with theory (-1) = -1 CORRECTING DEFECT 71 (vertices=397, convex hull=207, v0=155758) After retessellation of defect 71 (v0=155758), euler #=-1 (181752,544880,363127) : difference with theory (0) = 1 CORRECTING DEFECT 72 (vertices=1107, convex hull=706, v0=156291) XL defect detected... After retessellation of defect 72 (v0=156291), euler #=1 (182024,546060,364037) : difference with theory (1) = 0 CORRECTING DEFECT 73 (vertices=6, convex hull=25, v0=174917) After retessellation of defect 73 (v0=174917), euler #=2 (182025,546069,364046) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.90 +- 0.28 (0.03-->10.80) (max @ vno 134390 --> 134483) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.90 +- 0.28 (0.03-->10.80) (max @ vno 134390 --> 134483) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 221 mutations (35.1%), 409 crossovers (64.9%), 1228 vertices were eliminated building final representation... 12223 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=182025, nf=364046, ne=546069, g=0) writing corrected surface to /usr/local/freesurfer/subjects/SynthN/surf/rh.orig... defective orientation at vertex 134390(134394) with faces 265759 and 361441 defective orientation at vertex 134390(135403) with faces 265759 and 361436 defective orientation at vertex 134394(134390) with faces 265759 and 361441 defective orientation at vertex 134394(135403) with faces 265759 and 361440 defective orientation at vertex 135403(134390) with faces 265759 and 361436 defective orientation at vertex 135403(134394) with faces 265759 and 361440 0.003 % of the vertices (6 vertices) exhibit an orientation change topology fixing took 77.4 minutes 0 defective edges removing intersecting faces 000: 1558 intersecting 001: 87 intersecting 002: 14 intersecting 003: 9 intersecting mris_fix_topology utimesec 4621.836000 mris_fix_topology stimesec 4.288000 mris_fix_topology ru_maxrss 618128 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 75872 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 17360 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 5 mris_fix_topology ru_nivcsw 247986 FSRUNTIME@ mris_fix_topology rh 1.2898 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 185351 - 556047 + 370698 = 2 --> 0 holes F =2V-4: 370698 = 370702-4 (0) 2E=3F: 1112094 = 1112094 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 182025 - 546069 + 364046 = 2 --> 0 holes F =2V-4: 364046 = 364050-4 (0) 2E=3F: 1092138 = 1092138 (0) total defect index = 0 /usr/local/freesurfer/subjects/SynthN/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 248 intersecting 001: 77 intersecting 002: 67 intersecting 003: 42 intersecting 004: 37 intersecting 005: 13 intersecting expanding nbhd size to 2 006: 14 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /usr/local/freesurfer/subjects/SynthN/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 477 intersecting 001: 60 intersecting 002: 11 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Mon Dec 19 16:31:43 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs SynthN 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 1.165 2016/11/21 03:01:42 fischl Exp $ $Id: mrisurf.c,v 1.786 2016/11/21 03:01:17 fischl Exp $ reading volume /usr/local/freesurfer/subjects/SynthN/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/SynthN/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/SynthN/mri/../mri/aseg.presurf.mgz... reading volume /usr/local/freesurfer/subjects/SynthN/mri/wm.mgz... 18149 bright wm thresholded. 5002 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/SynthN/surf/lh.orig... computing class statistics... border white: 367032 voxels (2.19%) border gray 421357 voxels (2.51%) WM (96.0): 96.8 +- 8.6 [70.0 --> 110.0] GM (70.0) : 68.6 +- 11.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 50.2 (was 70) setting MAX_BORDER_WHITE to 111.6 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 38.5 (was 40) setting MAX_GRAY to 94.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 26.7 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.22 (0.01-->6.61) (max @ vno 141277 --> 184889) face area 0.29 +- 0.13 (0.00-->6.61) mean absolute distance = 0.66 +- 0.87 5426 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=103+-6.1, GM=62+-9.6 mean inside = 92.3, mean outside = 72.4 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=77.1, 156 (156) missing vertices, mean dist 0.3 [0.6 (%31.8)->0.7 (%68.2))] %68 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=stefa, 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 (0.08-->6.48) (max @ vno 141277 --> 184889) face area 0.29 +- 0.13 (0.00-->5.08) mean absolute distance = 0.39 +- 0.78 8290 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5203387.0, rms=11.098 001: dt: 0.5000, sse=2914979.8, rms=7.772 (29.967%) 002: dt: 0.5000, sse=1944097.5, rms=5.768 (25.790%) 003: dt: 0.5000, sse=1526498.8, rms=4.643 (19.503%) 004: dt: 0.5000, sse=1347525.1, rms=4.058 (12.598%) 005: dt: 0.5000, sse=1296921.6, rms=3.806 (6.205%) 006: dt: 0.5000, sse=1242367.0, rms=3.672 (3.518%) rms = 3.63, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=1244438.1, rms=3.632 (1.091%) 008: dt: 0.2500, sse=953178.2, rms=2.229 (38.640%) 009: dt: 0.2500, sse=902646.4, rms=1.882 (15.561%) 010: dt: 0.2500, sse=889813.2, rms=1.760 (6.451%) 011: dt: 0.2500, sse=879335.1, rms=1.685 (4.270%) rms = 1.66, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=875706.3, rms=1.656 (1.720%) 013: dt: 0.1250, sse=868591.6, rms=1.590 (4.010%) rms = 1.57, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=868253.8, rms=1.573 (1.091%) positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=80.0, 170 (44) missing vertices, mean dist -0.3 [0.5 (%69.1)->0.2 (%30.9))] %73 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=stefa, 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 0.91 +- 0.25 (0.06-->6.25) (max @ vno 141277 --> 184889) face area 0.35 +- 0.16 (0.00-->5.97) mean absolute distance = 0.34 +- 0.57 7417 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1797976.9, rms=4.887 015: dt: 0.5000, sse=1352901.0, rms=3.363 (31.170%) rms = 3.32, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=1335251.9, rms=3.321 (1.267%) 017: dt: 0.2500, sse=1099230.4, rms=2.048 (38.343%) 018: dt: 0.2500, sse=1061361.4, rms=1.782 (12.946%) 019: dt: 0.2500, sse=1052435.4, rms=1.668 (6.445%) 020: dt: 0.2500, sse=1037784.8, rms=1.589 (4.697%) 021: dt: 0.2500, sse=1031246.8, rms=1.539 (3.183%) rms = 1.50, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=1028764.1, rms=1.497 (2.717%) rms = 1.46, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=1024047.5, rms=1.456 (2.698%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group mean border=82.5, 171 (34) missing vertices, mean dist -0.2 [0.4 (%69.9)->0.2 (%30.1))] %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=stefa, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.09-->6.02) (max @ vno 141277 --> 184889) face area 0.34 +- 0.16 (0.00-->5.39) mean absolute distance = 0.29 +- 0.46 6288 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1490382.4, rms=3.986 024: dt: 0.5000, sse=1276532.8, rms=2.979 (25.256%) rms = 3.07, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=1099446.8, rms=2.159 (27.548%) 026: dt: 0.2500, sse=1017343.8, rms=1.606 (25.602%) 027: dt: 0.2500, sse=1001505.9, rms=1.421 (11.510%) 028: dt: 0.2500, sse=996818.4, rms=1.355 (4.623%) rms = 1.33, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=990871.3, rms=1.328 (2.032%) 030: dt: 0.1250, sse=981816.6, rms=1.264 (4.807%) rms = 1.25, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=988575.4, rms=1.249 (1.181%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=83.5, 233 (27) missing vertices, mean dist -0.1 [0.3 (%59.0)->0.2 (%41.0))] %86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=stefa, 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 /usr/local/freesurfer/subjects/SynthN/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=1100619.9, rms=2.296 032: dt: 0.5000, sse=1070662.2, rms=2.101 (8.497%) rms = 2.50, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=985431.2, rms=1.425 (32.197%) 034: dt: 0.2500, sse=965157.2, rms=1.261 (11.485%) 035: dt: 0.2500, sse=954122.1, rms=1.194 (5.330%) rms = 1.20, time step reduction 2 of 3 to 0.125... 036: dt: 0.1250, sse=947215.6, rms=1.135 (4.951%) 037: dt: 0.1250, sse=942214.6, rms=1.051 (7.378%) rms = 1.03, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=939202.6, rms=1.034 (1.597%) positioning took 0.9 minutes generating cortex label... 20 non-cortical segments detected only using segment with 8839 vertices erasing segment 0 (vno[0] = 39422) erasing segment 1 (vno[0] = 45335) erasing segment 2 (vno[0] = 46641) erasing segment 3 (vno[0] = 63006) erasing segment 4 (vno[0] = 64426) erasing segment 6 (vno[0] = 101896) erasing segment 7 (vno[0] = 106676) erasing segment 8 (vno[0] = 110209) erasing segment 9 (vno[0] = 112494) erasing segment 10 (vno[0] = 113239) erasing segment 11 (vno[0] = 119696) erasing segment 12 (vno[0] = 130535) erasing segment 13 (vno[0] = 133058) erasing segment 14 (vno[0] = 133899) erasing segment 15 (vno[0] = 134362) erasing segment 16 (vno[0] = 138020) erasing segment 17 (vno[0] = 143730) erasing segment 18 (vno[0] = 145135) erasing segment 19 (vno[0] = 163650) writing cortex label to /usr/local/freesurfer/subjects/SynthN/label/lh.cortex.label... writing curvature file /usr/local/freesurfer/subjects/SynthN/surf/lh.curv writing smoothed area to lh.area writing curvature file /usr/local/freesurfer/subjects/SynthN/surf/lh.area vertex spacing 0.89 +- 0.25 (0.02-->5.96) (max @ vno 141277 --> 184889) face area 0.33 +- 0.16 (0.00-->5.35) refinement took 6.9 minutes #-------------------------------------------- #@# Make White Surf rh Mon Dec 19 16:38:39 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs SynthN 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 1.165 2016/11/21 03:01:42 fischl Exp $ $Id: mrisurf.c,v 1.786 2016/11/21 03:01:17 fischl Exp $ reading volume /usr/local/freesurfer/subjects/SynthN/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/SynthN/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/SynthN/mri/../mri/aseg.presurf.mgz... reading volume /usr/local/freesurfer/subjects/SynthN/mri/wm.mgz... 18149 bright wm thresholded. 5002 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/SynthN/surf/rh.orig... computing class statistics... border white: 367032 voxels (2.19%) border gray 421357 voxels (2.51%) WM (96.0): 96.8 +- 8.6 [70.0 --> 110.0] GM (70.0) : 68.6 +- 11.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 51.2 (was 70) setting MAX_BORDER_WHITE to 110.6 (was 105) setting MIN_BORDER_WHITE to 63.0 (was 85) setting MAX_CSF to 39.5 (was 40) setting MAX_GRAY to 93.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 51.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 27.7 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.24 (0.03-->7.48) (max @ vno 180252 --> 180347) face area 0.29 +- 0.14 (0.00-->8.66) mean absolute distance = 0.72 +- 0.99 5156 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+-6.1, GM=63+-13.0 mean inside = 92.0, mean outside = 73.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=78.7, 420 (420) missing vertices, mean dist 0.2 [0.7 (%36.8)->0.7 (%63.2))] %68 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=stefa, 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 +- 0.27 (0.08-->7.54) (max @ vno 180252 --> 180347) face area 0.29 +- 0.15 (0.00-->7.59) mean absolute distance = 0.42 +- 0.81 7913 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4877051.0, rms=10.800 001: dt: 0.5000, sse=2828096.0, rms=7.682 (28.868%) 002: dt: 0.5000, sse=1913146.1, rms=5.727 (25.448%) 003: dt: 0.5000, sse=1495893.0, rms=4.592 (19.828%) 004: dt: 0.5000, sse=1333249.5, rms=4.041 (11.983%) 005: dt: 0.5000, sse=1261671.5, rms=3.784 (6.372%) 006: dt: 0.5000, sse=1248451.8, rms=3.687 (2.562%) 007: dt: 0.5000, sse=1236302.5, rms=3.625 (1.685%) rms = 3.61, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=1231375.1, rms=3.607 (0.489%) 009: dt: 0.2500, sse=976804.1, rms=2.374 (34.194%) 010: dt: 0.2500, sse=952229.3, rms=2.075 (12.601%) 011: dt: 0.2500, sse=925185.4, rms=2.016 (2.834%) rms = 1.98, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=918062.8, rms=1.980 (1.765%) 013: dt: 0.1250, sse=911465.9, rms=1.924 (2.832%) rms = 1.92, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=905828.9, rms=1.920 (0.229%) positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=81.1, 413 (149) missing vertices, mean dist -0.2 [0.5 (%66.8)->0.3 (%33.2))] %72 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=stefa, 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 0.91 +- 0.26 (0.06-->7.62) (max @ vno 180252 --> 180347) face area 0.35 +- 0.18 (0.00-->9.80) mean absolute distance = 0.37 +- 0.61 6784 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1730469.9, rms=4.722 015: dt: 0.5000, sse=1354827.9, rms=3.371 (28.611%) 016: dt: 0.5000, sse=1343097.4, rms=3.285 (2.565%) rms = 3.24, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=1321843.6, rms=3.242 (1.284%) 018: dt: 0.2500, sse=1148285.5, rms=2.130 (34.296%) 019: dt: 0.2500, sse=1069513.4, rms=1.854 (12.967%) 020: dt: 0.2500, sse=1061296.1, rms=1.769 (4.602%) 021: dt: 0.2500, sse=1052911.8, rms=1.704 (3.666%) rms = 1.68, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=1052894.9, rms=1.682 (1.298%) 023: dt: 0.1250, sse=1048333.5, rms=1.621 (3.627%) rms = 1.60, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=1036557.8, rms=1.598 (1.425%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=83.5, 393 (82) missing vertices, mean dist -0.2 [0.4 (%68.5)->0.3 (%31.5))] %81 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=stefa, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.26 (0.06-->7.51) (max @ vno 180252 --> 180347) face area 0.34 +- 0.18 (0.00-->9.89) mean absolute distance = 0.31 +- 0.49 5937 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1481673.5, rms=3.994 025: dt: 0.5000, sse=1237955.8, rms=2.966 (25.753%) rms = 3.01, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=1104942.9, rms=2.274 (23.305%) 027: dt: 0.2500, sse=1048875.9, rms=1.851 (18.600%) 028: dt: 0.2500, sse=1027074.1, rms=1.666 (10.014%) 029: dt: 0.2500, sse=1014937.4, rms=1.590 (4.559%) 030: dt: 0.2500, sse=1009453.3, rms=1.521 (4.367%) rms = 1.49, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=1009172.9, rms=1.494 (1.764%) 032: dt: 0.1250, sse=989757.0, rms=1.358 (9.081%) rms = 1.32, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=983962.3, rms=1.319 (2.877%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=84.5, 411 (64) missing vertices, mean dist -0.1 [0.3 (%59.4)->0.3 (%40.6))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=stefa, 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 /usr/local/freesurfer/subjects/SynthN/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=1097584.4, rms=2.373 034: dt: 0.5000, sse=1068903.9, rms=2.101 (11.464%) rms = 2.40, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=980886.5, rms=1.474 (29.859%) 036: dt: 0.2500, sse=970237.4, rms=1.345 (8.691%) 037: dt: 0.2500, sse=959554.3, rms=1.254 (6.803%) rms = 1.30, time step reduction 2 of 3 to 0.125... 038: dt: 0.1250, sse=949305.4, rms=1.181 (5.796%) 039: dt: 0.1250, sse=946312.1, rms=1.095 (7.302%) rms = 1.06, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=935889.4, rms=1.059 (3.313%) positioning took 0.9 minutes generating cortex label... 35 non-cortical segments detected only using segment with 7358 vertices erasing segment 0 (vno[0] = 41117) erasing segment 1 (vno[0] = 48148) erasing segment 2 (vno[0] = 51192) erasing segment 3 (vno[0] = 54084) erasing segment 5 (vno[0] = 59178) erasing segment 6 (vno[0] = 62219) erasing segment 7 (vno[0] = 64217) erasing segment 8 (vno[0] = 65842) erasing segment 9 (vno[0] = 65932) erasing segment 10 (vno[0] = 67319) erasing segment 11 (vno[0] = 68350) erasing segment 12 (vno[0] = 68361) erasing segment 13 (vno[0] = 71683) erasing segment 14 (vno[0] = 74078) erasing segment 15 (vno[0] = 75385) erasing segment 16 (vno[0] = 79228) erasing segment 17 (vno[0] = 90753) erasing segment 18 (vno[0] = 95779) erasing segment 19 (vno[0] = 98124) erasing segment 20 (vno[0] = 106708) erasing segment 21 (vno[0] = 110987) erasing segment 22 (vno[0] = 118067) erasing segment 23 (vno[0] = 119455) erasing segment 24 (vno[0] = 120472) erasing segment 25 (vno[0] = 122154) erasing segment 26 (vno[0] = 124610) erasing segment 27 (vno[0] = 126616) erasing segment 28 (vno[0] = 128326) erasing segment 29 (vno[0] = 132726) erasing segment 30 (vno[0] = 133020) erasing segment 31 (vno[0] = 142696) erasing segment 32 (vno[0] = 146440) erasing segment 33 (vno[0] = 179343) erasing segment 34 (vno[0] = 181215) writing cortex label to /usr/local/freesurfer/subjects/SynthN/label/rh.cortex.label... writing curvature file /usr/local/freesurfer/subjects/SynthN/surf/rh.curv writing smoothed area to rh.area writing curvature file /usr/local/freesurfer/subjects/SynthN/surf/rh.area vertex spacing 0.89 +- 0.27 (0.03-->7.34) (max @ vno 180252 --> 180347) face area 0.34 +- 0.18 (0.00-->9.82) refinement took 7.1 minutes #-------------------------------------------- #@# Smooth2 lh Mon Dec 19 16:45:42 GMT 2016 /usr/local/freesurfer/subjects/SynthN/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 Mon Dec 19 16:45:49 GMT 2016 /usr/local/freesurfer/subjects/SynthN/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 Mon Dec 19 16:45:55 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts mris_inflate -rusage /usr/local/freesurfer/subjects/SynthN/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 50.8 mm, total surface area = 112075 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.168 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.094 (target=0.015) step 015: RMS=0.079 (target=0.015) step 020: RMS=0.067 (target=0.015) step 025: RMS=0.057 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.042 (target=0.015) step 040: RMS=0.037 (target=0.015) step 045: RMS=0.033 (target=0.015) step 050: RMS=0.030 (target=0.015) step 055: RMS=0.028 (target=0.015) step 060: RMS=0.026 (target=0.015) inflation complete. inflation took 0.7 minutes mris_inflate utimesec 42.708000 mris_inflate stimesec 0.036000 mris_inflate ru_maxrss 241080 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 29029 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 40 mris_inflate ru_oublock 14496 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 1 mris_inflate ru_nivcsw 3053 #-------------------------------------------- #@# Inflation2 rh Mon Dec 19 16:46:38 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts mris_inflate -rusage /usr/local/freesurfer/subjects/SynthN/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 51.2 mm, total surface area = 109918 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.172 (target=0.015) step 005: RMS=0.124 (target=0.015) step 010: RMS=0.096 (target=0.015) step 015: RMS=0.080 (target=0.015) step 020: RMS=0.067 (target=0.015) step 025: RMS=0.057 (target=0.015) step 030: RMS=0.050 (target=0.015) step 035: RMS=0.043 (target=0.015) step 040: RMS=0.037 (target=0.015) step 045: RMS=0.032 (target=0.015) step 050: RMS=0.029 (target=0.015) step 055: RMS=0.027 (target=0.015) step 060: RMS=0.026 (target=0.015) inflation complete. inflation took 0.7 minutes mris_inflate utimesec 42.072000 mris_inflate stimesec 0.036000 mris_inflate ru_maxrss 237308 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 28609 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 14232 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 4217 #-------------------------------------------- #@# Curv .H and .K lh Mon Dec 19 16:47:20 GMT 2016 /usr/local/freesurfer/subjects/SynthN/surf mris_curvature -w lh.white.preaparc total integrated curvature = 23.216*4pi (291.741) --> -22 handles ICI = 226.9, FI = 2145.4, variation=34251.661 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 258 vertices thresholded to be in k1 ~ [-0.74 0.52], k2 ~ [-0.16 0.10] total integrated curvature = 0.132*4pi (1.654) --> 1 handles ICI = 1.7, FI = 12.7, variation=216.151 193 vertices thresholded to be in [-0.03 0.03] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 178 vertices thresholded to be in [-0.24 0.24] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.025 done. #-------------------------------------------- #@# Curv .H and .K rh Mon Dec 19 16:48:45 GMT 2016 /usr/local/freesurfer/subjects/SynthN/surf mris_curvature -w rh.white.preaparc total integrated curvature = 38.748*4pi (486.921) --> -38 handles ICI = 242.8, FI = 2126.9, variation=34343.991 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 271 vertices thresholded to be in k1 ~ [-0.52 0.46], k2 ~ [-0.18 0.10] total integrated curvature = 0.149*4pi (1.878) --> 1 handles ICI = 1.6, FI = 11.1, variation=195.614 198 vertices thresholded to be in [-0.03 0.03] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 194 vertices thresholded to be in [-0.24 0.18] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.023 done. #----------------------------------------- #@# Curvature Stats lh Mon Dec 19 16:50:09 GMT 2016 /usr/local/freesurfer/subjects/SynthN/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm SynthN 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 [ SynthN/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 [ 371 ] Gb_filter = 0 WARN: S lookup min: -1.827728 WARN: S explicit min: 0.000000 vertex = 706 #----------------------------------------- #@# Curvature Stats rh Mon Dec 19 16:50:13 GMT 2016 /usr/local/freesurfer/subjects/SynthN/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm SynthN 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 [ SynthN/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 [ 364 ] Gb_filter = 0 WARN: S lookup min: -0.737387 WARN: S explicit min: 0.000000 vertex = 407 #-------------------------------------------- #@# Sphere lh Mon Dec 19 16:50:17 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts mris_sphere -rusage /usr/local/freesurfer/subjects/SynthN/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 1.786 2016/11/21 03:01:17 fischl 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 0.268... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=stefa, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.69 pass 1: epoch 2 of 3 starting distance error %20.61 unfolding complete - removing small folds... starting distance error %20.47 removing remaining folds... final distance error %20.50 MRISunfold() return, current seed 1234 -01: dt=0.0000, 211 negative triangles 199: dt=0.9900, 211 negative triangles 200: dt=0.9900, 121 negative triangles 201: dt=0.9900, 90 negative triangles 202: dt=0.9900, 82 negative triangles 203: dt=0.9900, 77 negative triangles 204: dt=0.9900, 83 negative triangles 205: dt=0.9900, 95 negative triangles 206: dt=0.9900, 96 negative triangles 207: dt=0.9900, 105 negative triangles 208: dt=0.9900, 111 negative triangles 209: dt=0.9900, 112 negative triangles 210: dt=0.9900, 104 negative triangles 211: dt=0.9900, 113 negative triangles 212: dt=0.9900, 117 negative triangles 213: dt=0.9405, 113 negative triangles 214: dt=0.9405, 104 negative triangles 215: dt=0.9405, 116 negative triangles 216: dt=0.9405, 106 negative triangles 217: dt=0.9405, 116 negative triangles 218: dt=0.9405, 106 negative triangles 219: dt=0.9405, 102 negative triangles 220: dt=0.9405, 86 negative triangles 221: dt=0.9405, 99 negative triangles 222: dt=0.9405, 84 negative triangles 223: dt=0.8935, 85 negative triangles 224: dt=0.8935, 80 negative triangles 225: dt=0.8935, 77 negative triangles 226: dt=0.8935, 87 negative triangles 227: dt=0.8935, 88 negative triangles 228: dt=0.8935, 73 negative triangles 229: dt=0.8935, 79 negative triangles 230: dt=0.8935, 61 negative triangles 231: dt=0.8935, 77 negative triangles 232: dt=0.8935, 65 negative triangles 233: dt=0.8935, 68 negative triangles 234: dt=0.8935, 74 negative triangles 235: dt=0.8935, 70 negative triangles 236: dt=0.8935, 60 negative triangles 237: dt=0.8935, 63 negative triangles 238: dt=0.8935, 51 negative triangles 239: dt=0.8935, 57 negative triangles 240: dt=0.8935, 51 negative triangles 241: dt=0.8935, 53 negative triangles 242: dt=0.8935, 42 negative triangles 243: dt=0.8935, 47 negative triangles 244: dt=0.8935, 38 negative triangles 245: dt=0.8935, 37 negative triangles 246: dt=0.8935, 37 negative triangles 247: dt=0.8935, 35 negative triangles 248: dt=0.8935, 33 negative triangles 249: dt=0.8935, 36 negative triangles 250: dt=0.8935, 33 negative triangles 251: dt=0.8935, 31 negative triangles 252: dt=0.8935, 31 negative triangles 253: dt=0.8935, 29 negative triangles 254: dt=0.8935, 24 negative triangles 255: dt=0.8935, 25 negative triangles 256: dt=0.8935, 24 negative triangles 257: dt=0.8935, 19 negative triangles 258: dt=0.8935, 21 negative triangles 259: dt=0.8935, 20 negative triangles 260: dt=0.8935, 14 negative triangles 261: dt=0.8935, 8 negative triangles 262: dt=0.8935, 7 negative triangles 263: dt=0.8935, 3 negative triangles 264: dt=0.8935, 6 negative triangles 265: dt=0.8935, 3 negative triangles 266: dt=0.8935, 3 negative triangles 267: dt=0.8935, 3 negative triangles 268: dt=0.8935, 3 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.82 hours mris_sphere utimesec 2961.068000 mris_sphere stimesec 1.644000 mris_sphere ru_maxrss 330348 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 51809 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 13040 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 8 mris_sphere ru_nivcsw 127124 FSRUNTIME@ mris_sphere 0.8249 hours 1 threads #-------------------------------------------- #@# Sphere rh Mon Dec 19 17:39:47 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts mris_sphere -rusage /usr/local/freesurfer/subjects/SynthN/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 1.786 2016/11/21 03:01:17 fischl 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 0.266... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=stefa, 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 %21.08 pass 1: epoch 2 of 3 starting distance error %21.03 unfolding complete - removing small folds... starting distance error %20.85 removing remaining folds... final distance error %20.88 MRISunfold() return, current seed 1234 -01: dt=0.0000, 260 negative triangles 242: dt=0.9900, 260 negative triangles 243: dt=0.9900, 163 negative triangles 244: dt=0.9900, 146 negative triangles 245: dt=0.9900, 101 negative triangles 246: dt=0.9900, 93 negative triangles 247: dt=0.9900, 94 negative triangles 248: dt=0.9900, 89 negative triangles 249: dt=0.9900, 81 negative triangles 250: dt=0.9900, 71 negative triangles 251: dt=0.9900, 56 negative triangles 252: dt=0.9900, 48 negative triangles 253: dt=0.9900, 50 negative triangles 254: dt=0.9900, 38 negative triangles 255: dt=0.9900, 36 negative triangles 256: dt=0.9900, 39 negative triangles 257: dt=0.9900, 30 negative triangles 258: dt=0.9900, 34 negative triangles 259: dt=0.9900, 30 negative triangles 260: dt=0.9900, 43 negative triangles 261: dt=0.9900, 34 negative triangles 262: dt=0.9900, 33 negative triangles 263: dt=0.9900, 32 negative triangles 264: dt=0.9900, 36 negative triangles 265: dt=0.9900, 33 negative triangles 266: dt=0.9900, 37 negative triangles 267: dt=0.9405, 30 negative triangles 268: dt=0.9405, 31 negative triangles 269: dt=0.9405, 35 negative triangles 270: dt=0.9405, 35 negative triangles 271: dt=0.9405, 36 negative triangles 272: dt=0.9405, 36 negative triangles 273: dt=0.9405, 39 negative triangles 274: dt=0.9405, 38 negative triangles 275: dt=0.9405, 31 negative triangles 276: dt=0.9405, 36 negative triangles 277: dt=0.9405, 29 negative triangles 278: dt=0.9405, 31 negative triangles 279: dt=0.9405, 39 negative triangles 280: dt=0.9405, 29 negative triangles 281: dt=0.9405, 35 negative triangles 282: dt=0.9405, 32 negative triangles 283: dt=0.9405, 38 negative triangles 284: dt=0.9405, 40 negative triangles 285: dt=0.9405, 40 negative triangles 286: dt=0.9405, 33 negative triangles 287: dt=0.8935, 35 negative triangles 288: dt=0.8935, 30 negative triangles 289: dt=0.8935, 34 negative triangles 290: dt=0.8935, 32 negative triangles 291: dt=0.8935, 31 negative triangles 292: dt=0.8935, 32 negative triangles 293: dt=0.8935, 30 negative triangles 294: dt=0.8935, 34 negative triangles 295: dt=0.8935, 34 negative triangles 296: dt=0.8935, 25 negative triangles 297: dt=0.8935, 30 negative triangles 298: dt=0.8935, 26 negative triangles 299: dt=0.8935, 30 negative triangles 300: dt=0.8935, 26 negative triangles 301: dt=0.8935, 29 negative triangles 302: dt=0.8935, 30 negative triangles 303: dt=0.8935, 30 negative triangles 304: dt=0.8935, 25 negative triangles 305: dt=0.8935, 22 negative triangles 306: dt=0.8935, 22 negative triangles 307: dt=0.8935, 25 negative triangles 308: dt=0.8935, 24 negative triangles 309: dt=0.8935, 23 negative triangles 310: dt=0.8935, 22 negative triangles 311: dt=0.8935, 23 negative triangles 312: dt=0.8935, 28 negative triangles 313: dt=0.8935, 22 negative triangles 314: dt=0.8935, 15 negative triangles 315: dt=0.8935, 19 negative triangles 316: dt=0.8935, 17 negative triangles 317: dt=0.8935, 17 negative triangles 318: dt=0.8935, 13 negative triangles 319: dt=0.8935, 16 negative triangles 320: dt=0.8935, 17 negative triangles 321: dt=0.8935, 18 negative triangles 322: dt=0.8935, 8 negative triangles 323: dt=0.8935, 13 negative triangles 324: dt=0.8935, 5 negative triangles 325: dt=0.8935, 7 negative triangles 326: dt=0.8935, 6 negative triangles 327: dt=0.8935, 2 negative triangles 328: dt=0.8935, 1 negative triangles 329: dt=0.8935, 1 negative triangles 330: dt=0.8935, 1 negative triangles 331: dt=0.8935, 1 negative triangles 332: dt=0.8935, 1 negative triangles 333: dt=0.8935, 1 negative triangles 334: dt=0.8935, 1 negative triangles 335: dt=0.8935, 1 negative triangles 336: dt=0.8935, 1 negative triangles 337: dt=0.8935, 1 negative triangles 338: dt=0.8488, 1 negative triangles 339: dt=0.8488, 1 negative triangles 340: dt=0.8488, 1 negative triangles 341: dt=0.8488, 1 negative triangles 342: dt=0.8488, 1 negative triangles 343: dt=0.8488, 1 negative triangles 344: dt=0.8488, 1 negative triangles 345: dt=0.8488, 1 negative triangles 346: dt=0.8488, 1 negative triangles 347: dt=0.8488, 1 negative triangles 348: dt=0.8064, 1 negative triangles 349: dt=0.8064, 1 negative triangles 350: dt=0.8064, 1 negative triangles 351: dt=0.8064, 1 negative triangles 352: dt=0.8064, 1 negative triangles 353: dt=0.8064, 1 negative triangles 354: dt=0.8064, 1 negative triangles expanding nbhd size to 1 355: dt=0.9900, 1 negative triangles 356: dt=0.9900, 1 negative triangles 357: dt=0.9900, 1 negative triangles 358: dt=0.9405, 1 negative triangles 359: dt=0.9405, 1 negative triangles 360: dt=0.9405, 1 negative triangles 361: dt=0.9405, 1 negative triangles 362: dt=0.9405, 1 negative triangles 363: dt=0.9405, 1 negative triangles 364: dt=0.9405, 1 negative triangles 365: dt=0.9405, 1 negative triangles 366: dt=0.9405, 1 negative triangles 367: dt=0.9405, 1 negative triangles 368: dt=0.8935, 1 negative triangles 369: dt=0.8935, 1 negative triangles 370: dt=0.8935, 1 negative triangles 371: dt=0.8935, 1 negative triangles 372: dt=0.8935, 1 negative triangles 373: dt=0.8935, 1 negative triangles 374: dt=0.8935, 1 negative triangles 375: dt=0.8935, 1 negative triangles 376: dt=0.8935, 1 negative triangles 377: dt=0.8935, 1 negative triangles 378: dt=0.8488, 1 negative triangles 379: dt=0.8488, 1 negative triangles 380: dt=0.8488, 1 negative triangles 381: dt=0.8488, 1 negative triangles 382: dt=0.8488, 1 negative triangles 383: dt=0.8488, 1 negative triangles 384: dt=0.8488, 1 negative triangles 385: dt=0.8488, 1 negative triangles 386: dt=0.8488, 1 negative triangles 387: dt=0.8488, 1 negative triangles 388: dt=0.8064, 1 negative triangles 389: dt=0.8064, 1 negative triangles 390: dt=0.8064, 1 negative triangles 391: dt=0.8064, 1 negative triangles 392: dt=0.8064, 1 negative triangles 393: dt=0.8064, 1 negative triangles 394: dt=0.8064, 1 negative triangles 395: dt=0.8064, 1 negative triangles 396: dt=0.8064, 1 negative triangles 397: dt=0.8064, 1 negative triangles 398: dt=0.7660, 1 negative triangles 399: dt=0.7660, 1 negative triangles 400: dt=0.7660, 1 negative triangles 401: dt=0.7660, 1 negative triangles 402: dt=0.7660, 1 negative triangles 403: dt=0.7660, 1 negative triangles 404: dt=0.7660, 1 negative triangles 405: dt=0.7660, 1 negative triangles 406: dt=0.7660, 1 negative triangles 407: dt=0.7660, 1 negative triangles 408: dt=0.7277, 1 negative triangles 409: dt=0.7277, 1 negative triangles 410: dt=0.7277, 1 negative triangles 411: dt=0.7277, 1 negative triangles 412: dt=0.7277, 1 negative triangles 413: dt=0.7277, 1 negative triangles 414: dt=0.7277, 1 negative triangles 415: dt=0.7277, 1 negative triangles 416: dt=0.7277, 1 negative triangles 417: dt=0.7277, 1 negative triangles 418: dt=0.6914, 1 negative triangles 419: dt=0.6914, 1 negative triangles 420: dt=0.6914, 1 negative triangles 421: dt=0.6914, 1 negative triangles 422: dt=0.6914, 1 negative triangles 423: dt=0.6914, 1 negative triangles 424: dt=0.6914, 1 negative triangles 425: dt=0.6914, 1 negative triangles 426: dt=0.6914, 1 negative triangles 427: dt=0.6914, 1 negative triangles 428: dt=0.6568, 1 negative triangles 429: dt=0.6568, 1 negative triangles 430: dt=0.6568, 1 negative triangles 431: dt=0.6568, 1 negative triangles 432: dt=0.6568, 1 negative triangles 433: dt=0.6568, 1 negative triangles 434: dt=0.6568, 1 negative triangles 435: dt=0.6568, 1 negative triangles 436: dt=0.6568, 1 negative triangles 437: dt=0.6568, 1 negative triangles 438: dt=0.6239, 1 negative triangles 439: dt=0.6239, 1 negative triangles 440: dt=0.6239, 1 negative triangles 441: dt=0.6239, 1 negative triangles 442: dt=0.6239, 1 negative triangles 443: dt=0.6239, 1 negative triangles 444: dt=0.6239, 1 negative triangles 445: dt=0.6239, 1 negative triangles 446: dt=0.6239, 1 negative triangles 447: dt=0.6239, 1 negative triangles 448: dt=0.5927, 1 negative triangles 449: dt=0.5927, 1 negative triangles 450: dt=0.5927, 1 negative triangles 451: dt=0.5927, 1 negative triangles 452: dt=0.5927, 1 negative triangles 453: dt=0.5927, 1 negative triangles 454: dt=0.5927, 1 negative triangles 455: dt=0.5927, 1 negative triangles 456: dt=0.5927, 1 negative triangles 457: dt=0.5927, 1 negative triangles 458: dt=0.5631, 1 negative triangles 459: dt=0.5631, 1 negative triangles 460: dt=0.5631, 1 negative triangles 461: dt=0.5631, 1 negative triangles 462: dt=0.5631, 1 negative triangles 463: dt=0.5631, 1 negative triangles 464: dt=0.5631, 1 negative triangles 465: dt=0.5631, 1 negative triangles 466: dt=0.5631, 1 negative triangles 467: dt=0.5631, 1 negative triangles 468: dt=0.5350, 1 negative triangles 469: dt=0.5350, 1 negative triangles 470: dt=0.5350, 1 negative triangles 471: dt=0.5350, 1 negative triangles 472: dt=0.5350, 1 negative triangles 473: dt=0.5350, 1 negative triangles 474: dt=0.5350, 1 negative triangles 475: dt=0.5350, 1 negative triangles 476: dt=0.5350, 1 negative triangles 477: dt=0.5350, 1 negative triangles 478: dt=0.5082, 1 negative triangles 479: dt=0.5082, 1 negative triangles 480: dt=0.5082, 1 negative triangles 481: dt=0.5082, 1 negative triangles 482: dt=0.5082, 1 negative triangles 483: dt=0.5082, 1 negative triangles 484: dt=0.5082, 1 negative triangles 485: dt=0.5082, 1 negative triangles 486: dt=0.5082, 1 negative triangles 487: dt=0.5082, 1 negative triangles 488: dt=0.4828, 1 negative triangles 489: dt=0.4828, 1 negative triangles 490: dt=0.4828, 1 negative triangles 491: dt=0.4828, 1 negative triangles 492: dt=0.4828, 1 negative triangles 493: dt=0.4828, 1 negative triangles 494: dt=0.4828, 1 negative triangles 495: dt=0.4828, 1 negative triangles 496: dt=0.4828, 1 negative triangles 497: dt=0.4828, 1 negative triangles 498: dt=0.4587, 1 negative triangles 499: dt=0.4587, 1 negative triangles 500: dt=0.4587, 1 negative triangles 501: dt=0.4587, 1 negative triangles 502: dt=0.4587, 1 negative triangles 503: dt=0.4587, 1 negative triangles 504: dt=0.4587, 1 negative triangles 505: dt=0.4587, 1 negative triangles 506: dt=0.4587, 1 negative triangles 507: dt=0.4587, 1 negative triangles 508: dt=0.4357, 1 negative triangles 509: dt=0.4357, 1 negative triangles 510: dt=0.4357, 1 negative triangles 511: dt=0.4357, 1 negative triangles 512: dt=0.4357, 1 negative triangles 513: dt=0.4357, 1 negative triangles 514: dt=0.4357, 1 negative triangles 515: dt=0.4357, 1 negative triangles 516: dt=0.4357, 1 negative triangles 517: dt=0.4357, 1 negative triangles 518: dt=0.4139, 1 negative triangles 519: dt=0.4139, 1 negative triangles 520: dt=0.4139, 1 negative triangles 521: dt=0.4139, 1 negative triangles 522: dt=0.4139, 1 negative triangles 523: dt=0.4139, 1 negative triangles 524: dt=0.4139, 1 negative triangles 525: dt=0.4139, 1 negative triangles 526: dt=0.4139, 1 negative triangles 527: dt=0.4139, 1 negative triangles 528: dt=0.3932, 1 negative triangles 529: dt=0.3932, 1 negative triangles 530: dt=0.3932, 1 negative triangles 531: dt=0.3932, 1 negative triangles 532: dt=0.3932, 1 negative triangles 533: dt=0.3932, 1 negative triangles 534: dt=0.3932, 1 negative triangles 535: dt=0.3932, 1 negative triangles 536: dt=0.3932, 1 negative triangles 537: dt=0.3932, 1 negative triangles 538: dt=0.3736, 1 negative triangles 539: dt=0.3736, 1 negative triangles 540: dt=0.3736, 1 negative triangles 541: dt=0.3736, 1 negative triangles 542: dt=0.3736, 1 negative triangles 543: dt=0.3736, 1 negative triangles 544: dt=0.3736, 1 negative triangles 545: dt=0.3736, 1 negative triangles 546: dt=0.3736, 1 negative triangles 547: dt=0.3736, 1 negative triangles 548: dt=0.3549, 1 negative triangles 549: dt=0.3549, 1 negative triangles 550: dt=0.3549, 1 negative triangles 551: dt=0.3549, 1 negative triangles 552: dt=0.3549, 1 negative triangles 553: dt=0.3549, 1 negative triangles 554: dt=0.3549, 1 negative triangles 555: dt=0.3549, 1 negative triangles 556: dt=0.3549, 1 negative triangles 557: dt=0.3549, 1 negative triangles 558: dt=0.3372, 1 negative triangles 559: dt=0.3372, 1 negative triangles 560: dt=0.3372, 1 negative triangles 561: dt=0.3372, 1 negative triangles 562: dt=0.3372, 1 negative triangles 563: dt=0.3372, 1 negative triangles 564: dt=0.3372, 1 negative triangles 565: dt=0.3372, 1 negative triangles 566: dt=0.3372, 1 negative triangles 567: dt=0.3372, 1 negative triangles 568: dt=0.3203, 1 negative triangles 569: dt=0.3203, 1 negative triangles 570: dt=0.3203, 1 negative triangles 571: dt=0.3203, 1 negative triangles 572: dt=0.3203, 1 negative triangles 573: dt=0.3203, 1 negative triangles 574: dt=0.3203, 1 negative triangles 575: dt=0.3203, 1 negative triangles 576: dt=0.3203, 1 negative triangles 577: dt=0.3203, 1 negative triangles 578: dt=0.3043, 1 negative triangles 579: dt=0.3043, 1 negative triangles 580: dt=0.3043, 1 negative triangles 581: dt=0.3043, 1 negative triangles 582: dt=0.3043, 1 negative triangles 583: dt=0.3043, 1 negative triangles 584: dt=0.3043, 1 negative triangles 585: dt=0.3043, 1 negative triangles 586: dt=0.3043, 1 negative triangles 587: dt=0.3043, 1 negative triangles 588: dt=0.2891, 1 negative triangles 589: dt=0.2891, 1 negative triangles 590: dt=0.2891, 1 negative triangles 591: dt=0.2891, 1 negative triangles 592: dt=0.2891, 1 negative triangles 593: dt=0.2891, 1 negative triangles 594: dt=0.2891, 1 negative triangles 595: dt=0.2891, 1 negative triangles 596: dt=0.2891, 1 negative triangles 597: dt=0.2891, 1 negative triangles 598: dt=0.2746, 1 negative triangles 599: dt=0.2746, 1 negative triangles 600: dt=0.2746, 1 negative triangles 601: dt=0.2746, 1 negative triangles 602: dt=0.2746, 1 negative triangles 603: dt=0.2746, 1 negative triangles 604: dt=0.2746, 1 negative triangles 605: dt=0.2746, 1 negative triangles 606: dt=0.2746, 1 negative triangles 607: dt=0.2746, 1 negative triangles 608: dt=0.2609, 1 negative triangles 609: dt=0.2609, 1 negative triangles 610: dt=0.2609, 1 negative triangles 611: dt=0.2609, 1 negative triangles 612: dt=0.2609, 1 negative triangles 613: dt=0.2609, 1 negative triangles 614: dt=0.2609, 1 negative triangles 615: dt=0.2609, 1 negative triangles 616: dt=0.2609, 1 negative triangles 617: dt=0.2609, 1 negative triangles 618: dt=0.2478, 1 negative triangles 619: dt=0.2478, 1 negative triangles 620: dt=0.2478, 1 negative triangles 621: dt=0.2478, 1 negative triangles 622: dt=0.2478, 1 negative triangles 623: dt=0.2478, 1 negative triangles 624: dt=0.2478, 1 negative triangles 625: dt=0.2478, 1 negative triangles 626: dt=0.2478, 1 negative triangles 627: dt=0.2478, 1 negative triangles 628: dt=0.2354, 1 negative triangles 629: dt=0.2354, 1 negative triangles 630: dt=0.2354, 1 negative triangles 631: dt=0.2354, 1 negative triangles 632: dt=0.2354, 1 negative triangles 633: dt=0.2354, 1 negative triangles 634: dt=0.2354, 1 negative triangles 635: dt=0.2354, 1 negative triangles 636: dt=0.2354, 1 negative triangles 637: dt=0.2354, 1 negative triangles 638: dt=0.2237, 1 negative triangles 639: dt=0.2237, 1 negative triangles 640: dt=0.2237, 1 negative triangles 641: dt=0.2237, 1 negative triangles 642: dt=0.2237, 1 negative triangles 643: dt=0.2237, 1 negative triangles 644: dt=0.2237, 1 negative triangles 645: dt=0.2237, 1 negative triangles 646: dt=0.2237, 1 negative triangles 647: dt=0.2237, 1 negative triangles 648: dt=0.2125, 1 negative triangles 649: dt=0.2125, 1 negative triangles 650: dt=0.2125, 1 negative triangles 651: dt=0.2125, 1 negative triangles 652: dt=0.2125, 1 negative triangles 653: dt=0.2125, 1 negative triangles 654: dt=0.2125, 1 negative triangles 655: dt=0.2125, 1 negative triangles 656: dt=0.2125, 1 negative triangles 657: dt=0.2125, 1 negative triangles 658: dt=0.2019, 1 negative triangles 659: dt=0.2019, 1 negative triangles 660: dt=0.2019, 1 negative triangles 661: dt=0.2019, 1 negative triangles 662: dt=0.2019, 1 negative triangles 663: dt=0.2019, 1 negative triangles 664: dt=0.2019, 1 negative triangles 665: dt=0.2019, 1 negative triangles 666: dt=0.2019, 1 negative triangles 667: dt=0.2019, 1 negative triangles 668: dt=0.1918, 1 negative triangles 669: dt=0.1918, 1 negative triangles 670: dt=0.1918, 1 negative triangles 671: dt=0.1918, 1 negative triangles 672: dt=0.1918, 1 negative triangles 673: dt=0.1918, 1 negative triangles 674: dt=0.1918, 1 negative triangles 675: dt=0.1918, 1 negative triangles 676: dt=0.1918, 1 negative triangles 677: dt=0.1918, 1 negative triangles 678: dt=0.1822, 1 negative triangles 679: dt=0.1822, 1 negative triangles 680: dt=0.1822, 1 negative triangles 681: dt=0.1822, 1 negative triangles 682: dt=0.1822, 1 negative triangles 683: dt=0.1822, 1 negative triangles 684: dt=0.1822, 1 negative triangles 685: dt=0.1822, 1 negative triangles 686: dt=0.1822, 1 negative triangles 687: dt=0.1822, 1 negative triangles 688: dt=0.1731, 1 negative triangles 689: dt=0.1731, 1 negative triangles 690: dt=0.1731, 1 negative triangles 691: dt=0.1731, 1 negative triangles 692: dt=0.1731, 1 negative triangles 693: dt=0.1731, 1 negative triangles 694: dt=0.1731, 1 negative triangles 695: dt=0.1731, 1 negative triangles 696: dt=0.1731, 1 negative triangles 697: dt=0.1731, 1 negative triangles 698: dt=0.1644, 1 negative triangles 699: dt=0.1644, 1 negative triangles 700: dt=0.1644, 1 negative triangles 701: dt=0.1644, 1 negative triangles 702: dt=0.1644, 1 negative triangles 703: dt=0.1644, 1 negative triangles 704: dt=0.1644, 1 negative triangles 705: dt=0.1644, 1 negative triangles 706: dt=0.1644, 1 negative triangles 707: dt=0.1644, 1 negative triangles 708: dt=0.1562, 1 negative triangles 709: dt=0.1562, 1 negative triangles 710: dt=0.1562, 1 negative triangles 711: dt=0.1562, 1 negative triangles 712: dt=0.1562, 1 negative triangles 713: dt=0.1562, 1 negative triangles 714: dt=0.1562, 1 negative triangles 715: dt=0.1562, 1 negative triangles 716: dt=0.1562, 1 negative triangles 717: dt=0.1562, 1 negative triangles 718: dt=0.1484, 1 negative triangles 719: dt=0.1484, 1 negative triangles 720: dt=0.1484, 1 negative triangles 721: dt=0.1484, 1 negative triangles 722: dt=0.1484, 1 negative triangles 723: dt=0.1484, 1 negative triangles 724: dt=0.1484, 1 negative triangles 725: dt=0.1484, 1 negative triangles 726: dt=0.1484, 1 negative triangles 727: dt=0.1484, 1 negative triangles 728: dt=0.1410, 1 negative triangles 729: dt=0.1410, 1 negative triangles 730: dt=0.1410, 1 negative triangles 731: dt=0.1410, 1 negative triangles 732: dt=0.1410, 1 negative triangles 733: dt=0.1410, 1 negative triangles 734: dt=0.1410, 1 negative triangles 735: dt=0.1410, 1 negative triangles 736: dt=0.1410, 1 negative triangles 737: dt=0.1410, 1 negative triangles 738: dt=0.1339, 1 negative triangles 739: dt=0.1339, 1 negative triangles 740: dt=0.1339, 1 negative triangles 741: dt=0.1339, 1 negative triangles 742: dt=0.1339, 1 negative triangles 743: dt=0.1339, 1 negative triangles 744: dt=0.1339, 1 negative triangles 745: dt=0.1339, 1 negative triangles 746: dt=0.1339, 1 negative triangles 747: dt=0.1339, 1 negative triangles 748: dt=0.1272, 1 negative triangles 749: dt=0.1272, 1 negative triangles 750: dt=0.1272, 1 negative triangles 751: dt=0.1272, 1 negative triangles 752: dt=0.1272, 1 negative triangles 753: dt=0.1272, 1 negative triangles 754: dt=0.1272, 1 negative triangles 755: dt=0.1272, 1 negative triangles 756: dt=0.1272, 1 negative triangles 757: dt=0.1272, 1 negative triangles 758: dt=0.1209, 1 negative triangles 759: dt=0.1209, 1 negative triangles 760: dt=0.1209, 1 negative triangles 761: dt=0.1209, 1 negative triangles 762: dt=0.1209, 1 negative triangles 763: dt=0.1209, 1 negative triangles 764: dt=0.1209, 1 negative triangles 765: dt=0.1209, 1 negative triangles 766: dt=0.1209, 1 negative triangles 767: dt=0.1209, 1 negative triangles 768: dt=0.1148, 1 negative triangles 769: dt=0.1148, 1 negative triangles 770: dt=0.1148, 1 negative triangles 771: dt=0.1148, 1 negative triangles 772: dt=0.1148, 1 negative triangles 773: dt=0.1148, 1 negative triangles 774: dt=0.1148, 1 negative triangles 775: dt=0.1148, 1 negative triangles 776: dt=0.1148, 1 negative triangles 777: dt=0.1148, 1 negative triangles 778: dt=0.1091, 1 negative triangles 779: dt=0.1091, 1 negative triangles 780: dt=0.1091, 1 negative triangles 781: dt=0.1091, 1 negative triangles 782: dt=0.1091, 1 negative triangles 783: dt=0.1091, 1 negative triangles 784: dt=0.1091, 1 negative triangles 785: dt=0.1091, 1 negative triangles 786: dt=0.1091, 1 negative triangles 787: dt=0.1091, 1 negative triangles 788: dt=0.1036, 1 negative triangles 789: dt=0.1036, 1 negative triangles 790: dt=0.1036, 1 negative triangles 791: dt=0.1036, 1 negative triangles 792: dt=0.1036, 1 negative triangles 793: dt=0.1036, 1 negative triangles 794: dt=0.1036, 1 negative triangles 795: dt=0.1036, 1 negative triangles 796: dt=0.1036, 1 negative triangles 797: dt=0.1036, 1 negative triangles 798: dt=0.0984, 1 negative triangles 799: dt=0.0984, 1 negative triangles 800: dt=0.0984, 1 negative triangles 801: dt=0.0984, 1 negative triangles 802: dt=0.0984, 1 negative triangles 803: dt=0.0984, 1 negative triangles 804: dt=0.0984, 1 negative triangles 805: dt=0.0984, 1 negative triangles 806: dt=0.0984, 1 negative triangles 807: dt=0.0984, 1 negative triangles 808: dt=0.0935, 1 negative triangles 809: dt=0.0935, 1 negative triangles 810: dt=0.0935, 1 negative triangles 811: dt=0.0935, 1 negative triangles 812: dt=0.0935, 1 negative triangles 813: dt=0.0935, 1 negative triangles 814: dt=0.0935, 1 negative triangles 815: dt=0.0935, 1 negative triangles 816: dt=0.0935, 1 negative triangles 817: dt=0.0935, 1 negative triangles 818: dt=0.0888, 1 negative triangles 819: dt=0.0888, 1 negative triangles 820: dt=0.0888, 1 negative triangles 821: dt=0.0888, 1 negative triangles 822: dt=0.0888, 1 negative triangles 823: dt=0.0888, 1 negative triangles 824: dt=0.0888, 1 negative triangles 825: dt=0.0888, 1 negative triangles 826: dt=0.0888, 1 negative triangles 827: dt=0.0888, 1 negative triangles 828: dt=0.0844, 1 negative triangles 829: dt=0.0844, 1 negative triangles 830: dt=0.0844, 1 negative triangles 831: dt=0.0844, 1 negative triangles 832: dt=0.0844, 1 negative triangles 833: dt=0.0844, 1 negative triangles 834: dt=0.0844, 1 negative triangles 835: dt=0.0844, 1 negative triangles 836: dt=0.0844, 1 negative triangles 837: dt=0.0844, 1 negative triangles 838: dt=0.0802, 1 negative triangles 839: dt=0.0802, 1 negative triangles 840: dt=0.0802, 1 negative triangles 841: dt=0.0802, 1 negative triangles 842: dt=0.0802, 1 negative triangles 843: dt=0.0802, 1 negative triangles 844: dt=0.0802, 1 negative triangles 845: dt=0.0802, 1 negative triangles 846: dt=0.0802, 1 negative triangles 847: dt=0.0802, 1 negative triangles 848: dt=0.0762, 1 negative triangles 849: dt=0.0762, 1 negative triangles 850: dt=0.0762, 1 negative triangles 851: dt=0.0762, 1 negative triangles 852: dt=0.0762, 1 negative triangles 853: dt=0.0762, 1 negative triangles 854: dt=0.0762, 1 negative triangles 855: dt=0.0762, 1 negative triangles 856: dt=0.0762, 1 negative triangles 857: dt=0.0762, 1 negative triangles 858: dt=0.0724, 1 negative triangles 859: dt=0.0724, 1 negative triangles 860: dt=0.0724, 1 negative triangles 861: dt=0.0724, 1 negative triangles 862: dt=0.0724, 1 negative triangles 863: dt=0.0724, 1 negative triangles 864: dt=0.0724, 1 negative triangles 865: dt=0.0724, 1 negative triangles 866: dt=0.0724, 1 negative triangles 867: dt=0.0724, 1 negative triangles 868: dt=0.0687, 1 negative triangles 869: dt=0.0687, 1 negative triangles 870: dt=0.0687, 1 negative triangles 871: dt=0.0687, 1 negative triangles 872: dt=0.0687, 1 negative triangles 873: dt=0.0687, 1 negative triangles 874: dt=0.0687, 1 negative triangles 875: dt=0.0687, 1 negative triangles 876: dt=0.0687, 1 negative triangles 877: dt=0.0687, 1 negative triangles 878: dt=0.0653, 1 negative triangles 879: dt=0.0653, 1 negative triangles 880: dt=0.0653, 1 negative triangles 881: dt=0.0653, 1 negative triangles 882: dt=0.0653, 1 negative triangles 883: dt=0.0653, 1 negative triangles 884: dt=0.0653, 1 negative triangles 885: dt=0.0653, 1 negative triangles 886: dt=0.0653, 1 negative triangles 887: dt=0.0653, 1 negative triangles 888: dt=0.0620, 1 negative triangles 889: dt=0.0620, 1 negative triangles 890: dt=0.0620, 1 negative triangles 891: dt=0.0620, 1 negative triangles 892: dt=0.0620, 1 negative triangles 893: dt=0.0620, 1 negative triangles 894: dt=0.0620, 1 negative triangles 895: dt=0.0620, 1 negative triangles 896: dt=0.0620, 1 negative triangles 897: dt=0.0620, 1 negative triangles 898: dt=0.0589, 1 negative triangles 899: dt=0.0589, 1 negative triangles 900: dt=0.0589, 1 negative triangles 901: dt=0.0589, 1 negative triangles 902: dt=0.0589, 1 negative triangles 903: dt=0.0589, 1 negative triangles 904: dt=0.0589, 1 negative triangles 905: dt=0.0589, 1 negative triangles 906: dt=0.0589, 1 negative triangles 907: dt=0.0589, 1 negative triangles 908: dt=0.0560, 1 negative triangles 909: dt=0.0560, 1 negative triangles 910: dt=0.0560, 1 negative triangles 911: dt=0.0560, 1 negative triangles 912: dt=0.0560, 1 negative triangles 913: dt=0.0560, 1 negative triangles 914: dt=0.0560, 1 negative triangles 915: dt=0.0560, 1 negative triangles 916: dt=0.0560, 1 negative triangles 917: dt=0.0560, 1 negative triangles 918: dt=0.0532, 1 negative triangles 919: dt=0.0532, 1 negative triangles 920: dt=0.0532, 1 negative triangles 921: dt=0.0532, 1 negative triangles 922: dt=0.0532, 1 negative triangles 923: dt=0.0532, 1 negative triangles 924: dt=0.0532, 1 negative triangles 925: dt=0.0532, 1 negative triangles 926: dt=0.0532, 1 negative triangles 927: dt=0.0532, 1 negative triangles 928: dt=0.0505, 1 negative triangles 929: dt=0.0505, 1 negative triangles 930: dt=0.0505, 1 negative triangles 931: dt=0.0505, 1 negative triangles 932: dt=0.0505, 1 negative triangles 933: dt=0.0505, 1 negative triangles 934: dt=0.0505, 1 negative triangles 935: dt=0.0505, 1 negative triangles 936: dt=0.0505, 1 negative triangles 937: dt=0.0505, 1 negative triangles 938: dt=0.0480, 1 negative triangles 939: dt=0.0480, 1 negative triangles 940: dt=0.0480, 1 negative triangles 941: dt=0.0480, 1 negative triangles 942: dt=0.0480, 1 negative triangles 943: dt=0.0480, 1 negative triangles 944: dt=0.0480, 1 negative triangles 945: dt=0.0480, 1 negative triangles 946: dt=0.0480, 1 negative triangles 947: dt=0.0480, 1 negative triangles 948: dt=0.0456, 1 negative triangles 949: dt=0.0456, 1 negative triangles 950: dt=0.0456, 1 negative triangles 951: dt=0.0456, 1 negative triangles 952: dt=0.0456, 1 negative triangles 953: dt=0.0456, 1 negative triangles 954: dt=0.0456, 1 negative triangles 955: dt=0.0456, 1 negative triangles 956: dt=0.0456, 1 negative triangles 957: dt=0.0456, 1 negative triangles 958: dt=0.0433, 1 negative triangles 959: dt=0.0433, 1 negative triangles 960: dt=0.0433, 1 negative triangles 961: dt=0.0433, 1 negative triangles 962: dt=0.0433, 1 negative triangles 963: dt=0.0433, 1 negative triangles 964: dt=0.0433, 1 negative triangles 965: dt=0.0433, 1 negative triangles 966: dt=0.0433, 1 negative triangles 967: dt=0.0433, 1 negative triangles 968: dt=0.0412, 1 negative triangles 969: dt=0.0412, 1 negative triangles 970: dt=0.0412, 1 negative triangles 971: dt=0.0412, 1 negative triangles 972: dt=0.0412, 1 negative triangles 973: dt=0.0412, 1 negative triangles 974: dt=0.0412, 1 negative triangles 975: dt=0.0412, 1 negative triangles 976: dt=0.0412, 1 negative triangles 977: dt=0.0412, 1 negative triangles 978: dt=0.0391, 1 negative triangles 979: dt=0.0391, 1 negative triangles 980: dt=0.0391, 1 negative triangles 981: dt=0.0391, 1 negative triangles 982: dt=0.0391, 1 negative triangles 983: dt=0.0391, 1 negative triangles 984: dt=0.0391, 1 negative triangles 985: dt=0.0391, 1 negative triangles 986: dt=0.0391, 1 negative triangles 987: dt=0.0391, 1 negative triangles 988: dt=0.0371, 1 negative triangles 989: dt=0.0371, 1 negative triangles 990: dt=0.0371, 1 negative triangles 991: dt=0.0371, 1 negative triangles 992: dt=0.0371, 1 negative triangles 993: dt=0.0371, 1 negative triangles 994: dt=0.0371, 1 negative triangles 995: dt=0.0371, 1 negative triangles 996: dt=0.0371, 1 negative triangles 997: dt=0.0371, 1 negative triangles 998: dt=0.0353, 1 negative triangles 999: dt=0.0353, 1 negative triangles 1000: dt=0.0353, 1 negative triangles 1001: dt=0.0353, 1 negative triangles 1002: dt=0.0353, 1 negative triangles 1003: dt=0.0353, 1 negative triangles 1004: dt=0.0353, 1 negative triangles 1005: dt=0.0353, 1 negative triangles 1006: dt=0.0353, 1 negative triangles 1007: dt=0.0353, 1 negative triangles 1008: dt=0.0335, 1 negative triangles 1009: dt=0.0335, 1 negative triangles 1010: dt=0.0335, 1 negative triangles 1011: dt=0.0335, 1 negative triangles 1012: dt=0.0335, 1 negative triangles 1013: dt=0.0335, 1 negative triangles 1014: dt=0.0335, 1 negative triangles 1015: dt=0.0335, 1 negative triangles 1016: dt=0.0335, 1 negative triangles 1017: dt=0.0335, 1 negative triangles 1018: dt=0.0319, 1 negative triangles 1019: dt=0.0319, 1 negative triangles 1020: dt=0.0319, 1 negative triangles 1021: dt=0.0319, 1 negative triangles 1022: dt=0.0319, 1 negative triangles 1023: dt=0.0319, 1 negative triangles 1024: dt=0.0319, 1 negative triangles 1025: dt=0.0319, 1 negative triangles 1026: dt=0.0319, 1 negative triangles 1027: dt=0.0319, 1 negative triangles 1028: dt=0.0303, 1 negative triangles 1029: dt=0.0303, 1 negative triangles 1030: dt=0.0303, 1 negative triangles 1031: dt=0.0303, 1 negative triangles 1032: dt=0.0303, 1 negative triangles 1033: dt=0.0303, 1 negative triangles 1034: dt=0.0303, 1 negative triangles 1035: dt=0.0303, 1 negative triangles 1036: dt=0.0303, 1 negative triangles 1037: dt=0.0303, 1 negative triangles 1038: dt=0.0287, 1 negative triangles 1039: dt=0.0287, 1 negative triangles 1040: dt=0.0287, 1 negative triangles 1041: dt=0.0287, 1 negative triangles 1042: dt=0.0287, 1 negative triangles 1043: dt=0.0287, 1 negative triangles 1044: dt=0.0287, 1 negative triangles 1045: dt=0.0287, 1 negative triangles 1046: dt=0.0287, 1 negative triangles 1047: dt=0.0287, 1 negative triangles 1048: dt=0.0273, 1 negative triangles 1049: dt=0.0273, 1 negative triangles 1050: dt=0.0273, 1 negative triangles 1051: dt=0.0273, 1 negative triangles 1052: dt=0.0273, 1 negative triangles 1053: dt=0.0273, 1 negative triangles 1054: dt=0.0273, 1 negative triangles 1055: dt=0.0273, 1 negative triangles 1056: dt=0.0273, 1 negative triangles 1057: dt=0.0273, 1 negative triangles 1058: dt=0.0259, 1 negative triangles 1059: dt=0.0259, 1 negative triangles 1060: dt=0.0259, 1 negative triangles 1061: dt=0.0259, 1 negative triangles 1062: dt=0.0259, 1 negative triangles 1063: dt=0.0259, 1 negative triangles 1064: dt=0.0259, 1 negative triangles 1065: dt=0.0259, 1 negative triangles 1066: dt=0.0259, 1 negative triangles 1067: dt=0.0259, 1 negative triangles 1068: dt=0.0246, 1 negative triangles 1069: dt=0.0246, 1 negative triangles 1070: dt=0.0246, 1 negative triangles 1071: dt=0.0246, 1 negative triangles 1072: dt=0.0246, 1 negative triangles 1073: dt=0.0246, 1 negative triangles 1074: dt=0.0246, 1 negative triangles 1075: dt=0.0246, 1 negative triangles 1076: dt=0.0246, 1 negative triangles 1077: dt=0.0246, 1 negative triangles 1078: dt=0.0234, 1 negative triangles 1079: dt=0.0234, 1 negative triangles 1080: dt=0.0234, 1 negative triangles 1081: dt=0.0234, 1 negative triangles 1082: dt=0.0234, 1 negative triangles 1083: dt=0.0234, 1 negative triangles 1084: dt=0.0234, 1 negative triangles 1085: dt=0.0234, 1 negative triangles 1086: dt=0.0234, 1 negative triangles 1087: dt=0.0234, 1 negative triangles 1088: dt=0.0222, 1 negative triangles 1089: dt=0.0222, 1 negative triangles 1090: dt=0.0222, 1 negative triangles 1091: dt=0.0222, 1 negative triangles 1092: dt=0.0222, 1 negative triangles 1093: dt=0.0222, 1 negative triangles 1094: dt=0.0222, 1 negative triangles 1095: dt=0.0222, 1 negative triangles 1096: dt=0.0222, 1 negative triangles 1097: dt=0.0222, 1 negative triangles 1098: dt=0.0211, 1 negative triangles 1099: dt=0.0211, 1 negative triangles 1100: dt=0.0211, 1 negative triangles 1101: dt=0.0211, 1 negative triangles 1102: dt=0.0211, 1 negative triangles 1103: dt=0.0211, 1 negative triangles 1104: dt=0.0211, 1 negative triangles 1105: dt=0.0211, 1 negative triangles 1106: dt=0.0211, 1 negative triangles 1107: dt=0.0211, 1 negative triangles 1108: dt=0.0201, 1 negative triangles 1109: dt=0.0201, 1 negative triangles 1110: dt=0.0201, 1 negative triangles 1111: dt=0.0201, 1 negative triangles 1112: dt=0.0201, 1 negative triangles 1113: dt=0.0201, 1 negative triangles 1114: dt=0.0201, 1 negative triangles 1115: dt=0.0201, 1 negative triangles 1116: dt=0.0201, 1 negative triangles 1117: dt=0.0201, 1 negative triangles 1118: dt=0.0191, 1 negative triangles 1119: dt=0.0191, 1 negative triangles 1120: dt=0.0191, 1 negative triangles 1121: dt=0.0191, 1 negative triangles 1122: dt=0.0191, 1 negative triangles 1123: dt=0.0191, 1 negative triangles 1124: dt=0.0191, 1 negative triangles 1125: dt=0.0191, 1 negative triangles 1126: dt=0.0191, 1 negative triangles 1127: dt=0.0191, 1 negative triangles 1128: dt=0.0181, 1 negative triangles 1129: dt=0.0181, 1 negative triangles 1130: dt=0.0181, 1 negative triangles 1131: dt=0.0181, 1 negative triangles 1132: dt=0.0181, 1 negative triangles 1133: dt=0.0181, 1 negative triangles 1134: dt=0.0181, 1 negative triangles 1135: dt=0.0181, 1 negative triangles 1136: dt=0.0181, 1 negative triangles 1137: dt=0.0181, 1 negative triangles 1138: dt=0.0172, 1 negative triangles 1139: dt=0.0172, 1 negative triangles 1140: dt=0.0172, 1 negative triangles 1141: dt=0.0172, 1 negative triangles 1142: dt=0.0172, 1 negative triangles 1143: dt=0.0172, 1 negative triangles 1144: dt=0.0172, 1 negative triangles 1145: dt=0.0172, 1 negative triangles 1146: dt=0.0172, 1 negative triangles 1147: dt=0.0172, 1 negative triangles 1148: dt=0.0164, 1 negative triangles 1149: dt=0.0164, 1 negative triangles 1150: dt=0.0164, 1 negative triangles 1151: dt=0.0164, 1 negative triangles 1152: dt=0.0164, 1 negative triangles 1153: dt=0.0164, 1 negative triangles 1154: dt=0.0164, 1 negative triangles 1155: dt=0.0164, 1 negative triangles 1156: dt=0.0164, 1 negative triangles 1157: dt=0.0164, 1 negative triangles 1158: dt=0.0155, 1 negative triangles 1159: dt=0.0155, 1 negative triangles 1160: dt=0.0155, 1 negative triangles 1161: dt=0.0155, 1 negative triangles 1162: dt=0.0155, 1 negative triangles 1163: dt=0.0155, 1 negative triangles 1164: dt=0.0155, 1 negative triangles 1165: dt=0.0155, 1 negative triangles 1166: dt=0.0155, 1 negative triangles 1167: dt=0.0155, 1 negative triangles 1168: dt=0.0148, 1 negative triangles 1169: dt=0.0148, 1 negative triangles 1170: dt=0.0148, 1 negative triangles 1171: dt=0.0148, 1 negative triangles 1172: dt=0.0148, 1 negative triangles 1173: dt=0.0148, 1 negative triangles 1174: dt=0.0148, 1 negative triangles 1175: dt=0.0148, 1 negative triangles 1176: dt=0.0148, 1 negative triangles 1177: dt=0.0148, 1 negative triangles 1178: dt=0.0140, 1 negative triangles 1179: dt=0.0140, 1 negative triangles 1180: dt=0.0140, 1 negative triangles 1181: dt=0.0140, 1 negative triangles 1182: dt=0.0140, 1 negative triangles 1183: dt=0.0140, 1 negative triangles 1184: dt=0.0140, 1 negative triangles 1185: dt=0.0140, 1 negative triangles 1186: dt=0.0140, 1 negative triangles 1187: dt=0.0140, 1 negative triangles 1188: dt=0.0133, 1 negative triangles 1189: dt=0.0133, 1 negative triangles 1190: dt=0.0133, 1 negative triangles 1191: dt=0.0133, 1 negative triangles 1192: dt=0.0133, 1 negative triangles 1193: dt=0.0133, 1 negative triangles 1194: dt=0.0133, 1 negative triangles 1195: dt=0.0133, 1 negative triangles 1196: dt=0.0133, 1 negative triangles 1197: dt=0.0133, 1 negative triangles 1198: dt=0.0127, 1 negative triangles 1199: dt=0.0127, 1 negative triangles 1200: dt=0.0127, 1 negative triangles 1201: dt=0.0127, 1 negative triangles 1202: dt=0.0127, 1 negative triangles 1203: dt=0.0127, 1 negative triangles 1204: dt=0.0127, 1 negative triangles 1205: dt=0.0127, 1 negative triangles 1206: dt=0.0127, 1 negative triangles 1207: dt=0.0127, 1 negative triangles 1208: dt=0.0120, 1 negative triangles 1209: dt=0.0120, 1 negative triangles 1210: dt=0.0120, 1 negative triangles 1211: dt=0.0120, 1 negative triangles 1212: dt=0.0120, 1 negative triangles 1213: dt=0.0120, 1 negative triangles 1214: dt=0.0120, 1 negative triangles 1215: dt=0.0120, 1 negative triangles 1216: dt=0.0120, 1 negative triangles 1217: dt=0.0120, 1 negative triangles 1218: dt=0.0114, 1 negative triangles 1219: dt=0.0114, 1 negative triangles 1220: dt=0.0114, 1 negative triangles 1221: dt=0.0114, 1 negative triangles 1222: dt=0.0114, 1 negative triangles 1223: dt=0.0114, 1 negative triangles 1224: dt=0.0114, 1 negative triangles 1225: dt=0.0114, 1 negative triangles 1226: dt=0.0114, 1 negative triangles 1227: dt=0.0114, 1 negative triangles 1228: dt=0.0108, 1 negative triangles 1229: dt=0.0108, 1 negative triangles 1230: dt=0.0108, 1 negative triangles 1231: dt=0.0108, 1 negative triangles 1232: dt=0.0108, 1 negative triangles 1233: dt=0.0108, 1 negative triangles 1234: dt=0.0108, 1 negative triangles 1235: dt=0.0108, 1 negative triangles 1236: dt=0.0108, 1 negative triangles 1237: dt=0.0108, 1 negative triangles 1238: dt=0.0103, 1 negative triangles 1239: dt=0.0103, 1 negative triangles 1240: dt=0.0103, 1 negative triangles 1241: dt=0.0103, 1 negative triangles 1242: dt=0.0103, 1 negative triangles 1243: 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 1.52 hours mris_sphere utimesec 5458.820000 mris_sphere stimesec 2.208000 mris_sphere ru_maxrss 325412 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 50500 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 12808 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 9 mris_sphere ru_nivcsw 123292 FSRUNTIME@ mris_sphere 1.5188 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Mon Dec 19 19:10:55 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts mris_register -curv -rusage /usr/local/freesurfer/subjects/SynthN/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /usr/local/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /usr/local/freesurfer/subjects/SynthN/scripts cmdline mris_register -curv -rusage /usr/local/freesurfer/subjects/SynthN/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /usr/local/freesurfer/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 1.786 2016/11/21 03:01:17 fischl Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/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=stefa, 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=stefa, 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 = 5.934 curvature mean = 0.028, std = 0.817 curvature mean = 0.016, std = 0.835 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 16.00) sse = 469215.2, tmin=1.1250 d=32.00 min @ (8.00, 8.00, -8.00) sse = 415042.4, tmin=2.2775 d=16.00 min @ (-4.00, 0.00, 4.00) sse = 391845.3, tmin=3.4482 d=8.00 min @ (0.00, -2.00, -2.00) sse = 382703.2, tmin=4.6164 d=4.00 min @ (0.00, 0.00, 1.00) sse = 382663.3, tmin=5.7833 d=2.00 min @ (0.00, 0.00, -0.50) sse = 382353.8, tmin=6.9410 d=1.00 min @ (-0.25, 0.00, 0.00) sse = 382337.3, tmin=8.0788 d=0.50 min @ (0.12, 0.12, 0.00) sse = 382282.7, tmin=9.2289 tol=1.0e+00, sigma=0.5, host=stefa, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 9.23 min curvature mean = -0.014, std = 0.810 curvature mean = 0.004, std = 0.919 curvature mean = -0.027, std = 0.814 curvature mean = 0.002, std = 0.961 curvature mean = -0.032, std = 0.815 curvature mean = 0.001, std = 0.980 2 Reading smoothwm curvature mean = -0.028, std = 0.290 curvature mean = 0.032, std = 0.244 curvature mean = 0.051, std = 0.320 curvature mean = 0.031, std = 0.298 curvature mean = 0.036, std = 0.486 curvature mean = 0.031, std = 0.324 curvature mean = 0.022, std = 0.617 curvature mean = 0.031, std = 0.333 curvature mean = 0.009, std = 0.722 MRISregister() return, current seed 0 -01: dt=0.0000, 283 negative triangles 173: dt=0.9900, 283 negative triangles 174: dt=0.9900, 224 negative triangles 175: dt=0.9900, 214 negative triangles 176: dt=0.9900, 213 negative triangles 177: dt=0.9900, 197 negative triangles 178: dt=0.9900, 182 negative triangles 179: dt=0.9900, 181 negative triangles 180: dt=0.9900, 158 negative triangles 181: dt=0.9900, 164 negative triangles 182: dt=0.9900, 147 negative triangles 183: dt=0.9900, 155 negative triangles 184: dt=0.9900, 129 negative triangles 185: dt=0.9900, 127 negative triangles 186: dt=0.9900, 124 negative triangles 187: dt=0.9900, 102 negative triangles 188: dt=0.9900, 96 negative triangles 189: dt=0.9900, 98 negative triangles 190: dt=0.9900, 98 negative triangles 191: dt=0.9900, 90 negative triangles 192: dt=0.9900, 88 negative triangles 193: dt=0.9900, 96 negative triangles 194: dt=0.9900, 84 negative triangles 195: dt=0.9900, 89 negative triangles 196: dt=0.9900, 80 negative triangles 197: dt=0.9900, 78 negative triangles 198: dt=0.9900, 83 negative triangles 199: dt=0.9900, 79 negative triangles 200: dt=0.9900, 76 negative triangles 201: dt=0.9900, 70 negative triangles 202: dt=0.9900, 72 negative triangles 203: dt=0.9900, 70 negative triangles 204: dt=0.9900, 56 negative triangles 205: dt=0.9900, 56 negative triangles 206: dt=0.9900, 47 negative triangles 207: dt=0.9900, 40 negative triangles 208: dt=0.9900, 48 negative triangles 209: dt=0.9900, 42 negative triangles 210: dt=0.9900, 32 negative triangles 211: dt=0.9900, 47 negative triangles 212: dt=0.9900, 36 negative triangles 213: dt=0.9900, 43 negative triangles 214: dt=0.9900, 34 negative triangles 215: dt=0.9900, 35 negative triangles 216: dt=0.9900, 31 negative triangles 217: dt=0.9900, 28 negative triangles 218: dt=0.9900, 29 negative triangles 219: dt=0.9900, 28 negative triangles 220: dt=0.9900, 26 negative triangles 221: dt=0.9900, 28 negative triangles 222: dt=0.9900, 20 negative triangles 223: dt=0.9900, 21 negative triangles 224: dt=0.9900, 24 negative triangles 225: dt=0.9900, 20 negative triangles 226: dt=0.9900, 16 negative triangles 227: dt=0.9900, 17 negative triangles 228: dt=0.9900, 17 negative triangles 229: dt=0.9900, 12 negative triangles 230: dt=0.9900, 15 negative triangles 231: dt=0.9900, 14 negative triangles 232: dt=0.9900, 17 negative triangles 233: dt=0.9900, 12 negative triangles 234: dt=0.9900, 14 negative triangles 235: dt=0.9900, 11 negative triangles 236: dt=0.9900, 10 negative triangles 237: dt=0.9900, 11 negative triangles 238: dt=0.9900, 10 negative triangles 239: dt=0.9900, 10 negative triangles 240: dt=0.9900, 14 negative triangles 241: dt=0.9900, 9 negative triangles 242: dt=0.9900, 10 negative triangles 243: dt=0.9900, 10 negative triangles 244: dt=0.9900, 11 negative triangles 245: dt=0.9900, 12 negative triangles 246: dt=0.9900, 10 negative triangles 247: dt=0.9900, 10 negative triangles 248: dt=0.9900, 8 negative triangles 249: dt=0.9900, 6 negative triangles 250: dt=0.9900, 4 negative triangles 251: dt=0.9900, 9 negative triangles 252: dt=0.9900, 6 negative triangles 253: dt=0.9900, 5 negative triangles 254: dt=0.9900, 5 negative triangles 255: dt=0.9900, 2 negative triangles 256: dt=0.9900, 2 negative triangles 257: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.36 hours mris_register utimesec 4879.324000 mris_register stimesec 1.164000 mris_register ru_maxrss 295184 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 36233 mris_register ru_majflt 1 mris_register ru_nswap 0 mris_register ru_inblock 40 mris_register ru_oublock 13040 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 4 mris_register ru_nivcsw 67035 FSRUNTIME@ mris_register 1.3570 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Mon Dec 19 20:32:20 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts mris_register -curv -rusage /usr/local/freesurfer/subjects/SynthN/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /usr/local/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /usr/local/freesurfer/subjects/SynthN/scripts cmdline mris_register -curv -rusage /usr/local/freesurfer/subjects/SynthN/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /usr/local/freesurfer/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 1.786 2016/11/21 03:01:17 fischl Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/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=stefa, 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=stefa, 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 = 5.876 curvature mean = 0.020, std = 0.801 curvature mean = 0.019, std = 0.833 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 16.00) sse = 458305.0, tmin=1.1022 d=32.00 min @ (8.00, 8.00, 0.00) sse = 368447.8, tmin=2.2089 d=8.00 min @ (0.00, -2.00, 0.00) sse = 360719.0, tmin=4.4504 d=4.00 min @ (0.00, 0.00, -1.00) sse = 359213.0, tmin=5.5774 d=1.00 min @ (0.00, 0.25, 0.25) sse = 358986.2, tmin=7.8201 d=0.50 min @ (0.12, 0.00, -0.12) sse = 358968.5, tmin=8.9524 tol=1.0e+00, sigma=0.5, host=stefa, 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 8.95 min curvature mean = -0.027, std = 0.796 curvature mean = 0.010, std = 0.926 curvature mean = -0.039, std = 0.799 curvature mean = 0.005, std = 0.965 curvature mean = -0.042, std = 0.799 curvature mean = 0.001, std = 0.982 2 Reading smoothwm curvature mean = -0.028, std = 0.299 curvature mean = 0.026, std = 0.232 curvature mean = 0.059, std = 0.303 curvature mean = 0.023, std = 0.286 curvature mean = 0.037, std = 0.468 curvature mean = 0.022, std = 0.312 curvature mean = 0.021, std = 0.603 curvature mean = 0.022, std = 0.323 curvature mean = 0.008, std = 0.710 MRISregister() return, current seed 0 -01: dt=0.0000, 415 negative triangles 157: dt=0.9900, 415 negative triangles 158: dt=0.9900, 355 negative triangles 159: dt=0.9900, 341 negative triangles 160: dt=0.9900, 319 negative triangles 161: dt=0.9900, 276 negative triangles 162: dt=0.9900, 263 negative triangles 163: dt=0.9900, 251 negative triangles 164: dt=0.9900, 241 negative triangles 165: dt=0.9900, 218 negative triangles 166: dt=0.9900, 215 negative triangles 167: dt=0.9900, 169 negative triangles 168: dt=0.9900, 166 negative triangles 169: dt=0.9900, 132 negative triangles 170: dt=0.9900, 121 negative triangles 171: dt=0.9900, 128 negative triangles 172: dt=0.9900, 113 negative triangles 173: dt=0.9900, 103 negative triangles 174: dt=0.9900, 104 negative triangles 175: dt=0.9900, 87 negative triangles 176: dt=0.9900, 80 negative triangles 177: dt=0.9900, 98 negative triangles 178: dt=0.9900, 80 negative triangles 179: dt=0.9900, 81 negative triangles 180: dt=0.9900, 75 negative triangles 181: dt=0.9900, 77 negative triangles 182: dt=0.9900, 75 negative triangles 183: dt=0.9900, 64 negative triangles 184: dt=0.9900, 68 negative triangles 185: dt=0.9900, 57 negative triangles 186: dt=0.9900, 53 negative triangles 187: dt=0.9900, 57 negative triangles 188: dt=0.9900, 54 negative triangles 189: dt=0.9900, 45 negative triangles 190: dt=0.9900, 40 negative triangles 191: dt=0.9900, 33 negative triangles 192: dt=0.9900, 27 negative triangles 193: dt=0.9900, 25 negative triangles 194: dt=0.9900, 28 negative triangles 195: dt=0.9900, 22 negative triangles 196: dt=0.9900, 26 negative triangles 197: dt=0.9900, 20 negative triangles 198: dt=0.9900, 19 negative triangles 199: dt=0.9900, 20 negative triangles 200: dt=0.9900, 19 negative triangles 201: dt=0.9900, 20 negative triangles 202: dt=0.9900, 18 negative triangles 203: dt=0.9900, 21 negative triangles 204: dt=0.9900, 21 negative triangles 205: dt=0.9900, 20 negative triangles 206: dt=0.9900, 19 negative triangles 207: dt=0.9900, 21 negative triangles 208: dt=0.9900, 18 negative triangles 209: dt=0.9900, 15 negative triangles 210: dt=0.9900, 19 negative triangles 211: dt=0.9900, 20 negative triangles 212: dt=0.9900, 14 negative triangles 213: dt=0.9900, 17 negative triangles 214: dt=0.9900, 15 negative triangles 215: dt=0.9900, 16 negative triangles 216: dt=0.9900, 15 negative triangles 217: dt=0.9900, 17 negative triangles 218: dt=0.9900, 13 negative triangles 219: dt=0.9900, 16 negative triangles 220: dt=0.9900, 15 negative triangles 221: dt=0.9900, 13 negative triangles 222: dt=0.9900, 18 negative triangles 223: dt=0.9900, 13 negative triangles 224: dt=0.9900, 11 negative triangles 225: dt=0.9900, 13 negative triangles 226: dt=0.9900, 13 negative triangles 227: dt=0.9900, 11 negative triangles 228: dt=0.9900, 11 negative triangles 229: dt=0.9900, 14 negative triangles 230: dt=0.9900, 11 negative triangles 231: dt=0.9900, 10 negative triangles 232: dt=0.9900, 11 negative triangles 233: dt=0.9900, 12 negative triangles 234: dt=0.9900, 11 negative triangles 235: dt=0.9900, 8 negative triangles 236: dt=0.9900, 12 negative triangles 237: dt=0.9900, 6 negative triangles 238: dt=0.9900, 6 negative triangles 239: dt=0.9900, 7 negative triangles 240: dt=0.9900, 7 negative triangles 241: dt=0.9900, 7 negative triangles 242: dt=0.9900, 4 negative triangles 243: dt=0.9900, 8 negative triangles 244: dt=0.9900, 6 negative triangles 245: dt=0.9900, 3 negative triangles 246: dt=0.9900, 6 negative triangles 247: dt=0.9900, 5 negative triangles 248: dt=0.9900, 2 negative triangles 249: dt=0.9900, 1 negative triangles 250: dt=0.9900, 1 negative triangles 251: dt=0.9900, 1 negative triangles 252: dt=0.9900, 1 negative triangles 253: dt=0.9900, 1 negative triangles 254: dt=0.9900, 1 negative triangles 255: dt=0.9900, 1 negative triangles 256: dt=0.9900, 1 negative triangles 257: dt=0.9900, 1 negative triangles 258: dt=0.9900, 1 negative triangles 259: dt=0.9405, 1 negative triangles 260: dt=0.9405, 1 negative triangles 261: dt=0.9405, 1 negative triangles 262: dt=0.9405, 1 negative triangles 263: dt=0.9405, 1 negative triangles 264: dt=0.9405, 1 negative triangles 265: dt=0.9405, 1 negative triangles 266: dt=0.9405, 1 negative triangles 267: dt=0.9405, 1 negative triangles 268: dt=0.9405, 1 negative triangles 269: dt=0.8935, 1 negative triangles 270: dt=0.8935, 1 negative triangles 271: dt=0.8935, 1 negative triangles 272: dt=0.8935, 1 negative triangles 273: dt=0.8935, 1 negative triangles 274: dt=0.8935, 1 negative triangles 275: dt=0.8935, 1 negative triangles expanding nbhd size to 1 276: dt=0.9900, 1 negative triangles 277: dt=0.9900, 1 negative triangles 278: dt=0.9900, 1 negative triangles 279: dt=0.9405, 1 negative triangles 280: dt=0.9405, 1 negative triangles 281: dt=0.9405, 1 negative triangles 282: dt=0.9405, 1 negative triangles 283: dt=0.9405, 1 negative triangles 284: dt=0.9405, 1 negative triangles 285: dt=0.9405, 1 negative triangles 286: dt=0.9405, 1 negative triangles 287: dt=0.9405, 1 negative triangles 288: dt=0.9405, 1 negative triangles 289: dt=0.8935, 1 negative triangles 290: dt=0.8935, 1 negative triangles 291: dt=0.8935, 1 negative triangles 292: dt=0.8935, 1 negative triangles 293: dt=0.8935, 1 negative triangles 294: dt=0.8935, 1 negative triangles 295: dt=0.8935, 1 negative triangles 296: dt=0.8935, 1 negative triangles 297: dt=0.8935, 1 negative triangles 298: dt=0.8935, 1 negative triangles 299: dt=0.8488, 1 negative triangles 300: dt=0.8488, 1 negative triangles 301: dt=0.8488, 1 negative triangles 302: dt=0.8488, 1 negative triangles 303: dt=0.8488, 1 negative triangles 304: dt=0.8488, 1 negative triangles 305: dt=0.8488, 1 negative triangles 306: dt=0.8488, 1 negative triangles 307: dt=0.8488, 1 negative triangles 308: dt=0.8488, 1 negative triangles 309: dt=0.8064, 1 negative triangles 310: dt=0.8064, 1 negative triangles 311: dt=0.8064, 1 negative triangles 312: dt=0.8064, 1 negative triangles 313: dt=0.8064, 1 negative triangles 314: dt=0.8064, 1 negative triangles 315: dt=0.8064, 1 negative triangles 316: dt=0.8064, 1 negative triangles 317: dt=0.8064, 1 negative triangles 318: dt=0.8064, 1 negative triangles 319: dt=0.7660, 1 negative triangles 320: dt=0.7660, 1 negative triangles 321: dt=0.7660, 1 negative triangles 322: dt=0.7660, 1 negative triangles 323: dt=0.7660, 1 negative triangles 324: dt=0.7660, 1 negative triangles 325: dt=0.7660, 1 negative triangles 326: dt=0.7660, 1 negative triangles 327: dt=0.7660, 1 negative triangles 328: dt=0.7660, 1 negative triangles 329: dt=0.7277, 1 negative triangles 330: dt=0.7277, 1 negative triangles 331: dt=0.7277, 1 negative triangles 332: dt=0.7277, 1 negative triangles 333: dt=0.7277, 1 negative triangles 334: dt=0.7277, 1 negative triangles 335: dt=0.7277, 1 negative triangles 336: dt=0.7277, 1 negative triangles 337: dt=0.7277, 1 negative triangles 338: dt=0.7277, 1 negative triangles 339: dt=0.6914, 1 negative triangles 340: dt=0.6914, 1 negative triangles 341: dt=0.6914, 1 negative triangles 342: dt=0.6914, 1 negative triangles 343: dt=0.6914, 1 negative triangles 344: dt=0.6914, 1 negative triangles 345: dt=0.6914, 1 negative triangles 346: dt=0.6914, 1 negative triangles 347: dt=0.6914, 1 negative triangles 348: dt=0.6914, 1 negative triangles 349: dt=0.6568, 1 negative triangles 350: dt=0.6568, 1 negative triangles 351: dt=0.6568, 1 negative triangles 352: dt=0.6568, 1 negative triangles 353: dt=0.6568, 1 negative triangles 354: dt=0.6568, 1 negative triangles 355: dt=0.6568, 1 negative triangles 356: dt=0.6568, 1 negative triangles 357: dt=0.6568, 1 negative triangles 358: dt=0.6568, 1 negative triangles 359: dt=0.6239, 1 negative triangles 360: dt=0.6239, 1 negative triangles 361: dt=0.6239, 1 negative triangles 362: dt=0.6239, 1 negative triangles 363: dt=0.6239, 1 negative triangles 364: dt=0.6239, 1 negative triangles 365: dt=0.6239, 1 negative triangles 366: dt=0.6239, 1 negative triangles 367: dt=0.6239, 1 negative triangles 368: dt=0.6239, 1 negative triangles 369: dt=0.5927, 1 negative triangles 370: dt=0.5927, 1 negative triangles 371: dt=0.5927, 1 negative triangles 372: dt=0.5927, 1 negative triangles 373: dt=0.5927, 1 negative triangles 374: dt=0.5927, 1 negative triangles 375: dt=0.5927, 1 negative triangles 376: dt=0.5927, 1 negative triangles 377: dt=0.5927, 1 negative triangles 378: dt=0.5927, 1 negative triangles 379: dt=0.5631, 1 negative triangles 380: dt=0.5631, 1 negative triangles 381: dt=0.5631, 1 negative triangles 382: dt=0.5631, 1 negative triangles 383: dt=0.5631, 1 negative triangles 384: dt=0.5631, 1 negative triangles 385: dt=0.5631, 1 negative triangles 386: dt=0.5631, 1 negative triangles 387: dt=0.5631, 1 negative triangles 388: dt=0.5631, 1 negative triangles 389: dt=0.5350, 1 negative triangles 390: dt=0.5350, 1 negative triangles 391: dt=0.5350, 1 negative triangles 392: dt=0.5350, 1 negative triangles 393: dt=0.5350, 1 negative triangles 394: dt=0.5350, 1 negative triangles 395: dt=0.5350, 1 negative triangles 396: dt=0.5350, 1 negative triangles 397: dt=0.5350, 1 negative triangles 398: dt=0.5350, 1 negative triangles 399: dt=0.5082, 1 negative triangles 400: dt=0.5082, 1 negative triangles 401: dt=0.5082, 1 negative triangles 402: dt=0.5082, 1 negative triangles 403: dt=0.5082, 1 negative triangles 404: dt=0.5082, 1 negative triangles 405: dt=0.5082, 1 negative triangles 406: dt=0.5082, 1 negative triangles 407: dt=0.5082, 1 negative triangles 408: dt=0.5082, 1 negative triangles 409: dt=0.4828, 1 negative triangles 410: dt=0.4828, 1 negative triangles 411: dt=0.4828, 1 negative triangles 412: dt=0.4828, 1 negative triangles 413: dt=0.4828, 1 negative triangles 414: dt=0.4828, 1 negative triangles 415: dt=0.4828, 1 negative triangles 416: dt=0.4828, 1 negative triangles 417: dt=0.4828, 1 negative triangles 418: dt=0.4828, 1 negative triangles 419: dt=0.4587, 1 negative triangles 420: dt=0.4587, 1 negative triangles 421: dt=0.4587, 1 negative triangles 422: dt=0.4587, 1 negative triangles 423: dt=0.4587, 1 negative triangles 424: dt=0.4587, 1 negative triangles 425: dt=0.4587, 1 negative triangles 426: dt=0.4587, 1 negative triangles 427: dt=0.4587, 1 negative triangles 428: dt=0.4587, 1 negative triangles 429: dt=0.4357, 1 negative triangles 430: dt=0.4357, 1 negative triangles 431: dt=0.4357, 1 negative triangles 432: dt=0.4357, 1 negative triangles 433: dt=0.4357, 1 negative triangles 434: dt=0.4357, 1 negative triangles 435: dt=0.4357, 1 negative triangles 436: dt=0.4357, 1 negative triangles 437: dt=0.4357, 1 negative triangles 438: dt=0.4357, 1 negative triangles 439: dt=0.4139, 1 negative triangles 440: dt=0.4139, 1 negative triangles 441: dt=0.4139, 1 negative triangles 442: dt=0.4139, 1 negative triangles 443: dt=0.4139, 1 negative triangles 444: dt=0.4139, 1 negative triangles 445: dt=0.4139, 1 negative triangles 446: dt=0.4139, 1 negative triangles 447: dt=0.4139, 1 negative triangles 448: dt=0.4139, 1 negative triangles 449: dt=0.3932, 1 negative triangles 450: dt=0.3932, 1 negative triangles 451: dt=0.3932, 1 negative triangles 452: dt=0.3932, 1 negative triangles 453: dt=0.3932, 1 negative triangles 454: dt=0.3932, 1 negative triangles 455: dt=0.3932, 1 negative triangles 456: dt=0.3932, 1 negative triangles 457: dt=0.3932, 1 negative triangles 458: dt=0.3932, 1 negative triangles 459: dt=0.3736, 1 negative triangles 460: dt=0.3736, 1 negative triangles 461: dt=0.3736, 1 negative triangles 462: dt=0.3736, 1 negative triangles 463: dt=0.3736, 1 negative triangles 464: dt=0.3736, 1 negative triangles 465: dt=0.3736, 1 negative triangles 466: dt=0.3736, 1 negative triangles 467: dt=0.3736, 1 negative triangles 468: dt=0.3736, 1 negative triangles 469: dt=0.3549, 1 negative triangles 470: dt=0.3549, 1 negative triangles 471: dt=0.3549, 1 negative triangles 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985: dt=0.0259, 1 negative triangles 986: dt=0.0259, 1 negative triangles 987: dt=0.0259, 1 negative triangles 988: dt=0.0259, 1 negative triangles 989: dt=0.0246, 1 negative triangles 990: dt=0.0246, 1 negative triangles 991: dt=0.0246, 1 negative triangles 992: dt=0.0246, 1 negative triangles 993: dt=0.0246, 1 negative triangles 994: dt=0.0246, 1 negative triangles 995: dt=0.0246, 1 negative triangles 996: dt=0.0246, 1 negative triangles 997: dt=0.0246, 1 negative triangles 998: dt=0.0246, 1 negative triangles 999: dt=0.0234, 1 negative triangles 1000: dt=0.0234, 1 negative triangles 1001: dt=0.0234, 1 negative triangles 1002: dt=0.0234, 1 negative triangles 1003: dt=0.0234, 1 negative triangles 1004: dt=0.0234, 1 negative triangles 1005: dt=0.0234, 1 negative triangles 1006: dt=0.0234, 1 negative triangles 1007: dt=0.0234, 1 negative triangles 1008: dt=0.0234, 1 negative triangles 1009: dt=0.0222, 1 negative triangles 1010: dt=0.0222, 1 negative triangles 1011: dt=0.0222, 1 negative triangles 1012: dt=0.0222, 1 negative triangles 1013: dt=0.0222, 1 negative triangles 1014: dt=0.0222, 1 negative triangles 1015: dt=0.0222, 1 negative triangles 1016: dt=0.0222, 1 negative triangles 1017: dt=0.0222, 1 negative triangles 1018: dt=0.0222, 1 negative triangles 1019: dt=0.0211, 1 negative triangles 1020: dt=0.0211, 1 negative triangles 1021: dt=0.0211, 1 negative triangles 1022: dt=0.0211, 1 negative triangles 1023: dt=0.0211, 1 negative triangles 1024: dt=0.0211, 1 negative triangles 1025: dt=0.0211, 1 negative triangles 1026: dt=0.0211, 1 negative triangles 1027: dt=0.0211, 1 negative triangles 1028: dt=0.0211, 1 negative triangles 1029: dt=0.0201, 1 negative triangles 1030: dt=0.0201, 1 negative triangles 1031: dt=0.0201, 1 negative triangles 1032: dt=0.0201, 1 negative triangles 1033: dt=0.0201, 1 negative triangles 1034: dt=0.0201, 1 negative triangles 1035: dt=0.0201, 1 negative triangles 1036: dt=0.0201, 1 negative triangles 1037: dt=0.0201, 1 negative triangles 1038: dt=0.0201, 1 negative triangles 1039: dt=0.0191, 1 negative triangles 1040: dt=0.0191, 1 negative triangles 1041: dt=0.0191, 1 negative triangles 1042: dt=0.0191, 1 negative triangles 1043: dt=0.0191, 1 negative triangles 1044: dt=0.0191, 1 negative triangles 1045: dt=0.0191, 1 negative triangles 1046: dt=0.0191, 1 negative triangles 1047: dt=0.0191, 1 negative triangles 1048: dt=0.0191, 1 negative triangles 1049: dt=0.0181, 1 negative triangles 1050: dt=0.0181, 1 negative triangles 1051: dt=0.0181, 1 negative triangles 1052: dt=0.0181, 1 negative triangles 1053: dt=0.0181, 1 negative triangles 1054: dt=0.0181, 1 negative triangles 1055: dt=0.0181, 1 negative triangles 1056: dt=0.0181, 1 negative triangles 1057: dt=0.0181, 1 negative triangles 1058: dt=0.0181, 1 negative triangles 1059: dt=0.0172, 1 negative triangles 1060: dt=0.0172, 1 negative triangles 1061: dt=0.0172, 1 negative triangles 1062: dt=0.0172, 1 negative triangles 1063: dt=0.0172, 1 negative triangles 1064: dt=0.0172, 1 negative triangles 1065: dt=0.0172, 1 negative triangles 1066: dt=0.0172, 1 negative triangles 1067: dt=0.0172, 1 negative triangles 1068: dt=0.0172, 1 negative triangles 1069: dt=0.0164, 1 negative triangles 1070: dt=0.0164, 1 negative triangles 1071: dt=0.0164, 1 negative triangles 1072: dt=0.0164, 1 negative triangles 1073: dt=0.0164, 1 negative triangles 1074: dt=0.0164, 1 negative triangles 1075: dt=0.0164, 1 negative triangles 1076: dt=0.0164, 1 negative triangles 1077: dt=0.0164, 1 negative triangles 1078: dt=0.0164, 1 negative triangles 1079: dt=0.0155, 1 negative triangles 1080: dt=0.0155, 1 negative triangles 1081: dt=0.0155, 1 negative triangles 1082: dt=0.0155, 1 negative triangles 1083: dt=0.0155, 1 negative triangles 1084: dt=0.0155, 1 negative triangles 1085: dt=0.0155, 1 negative triangles 1086: dt=0.0155, 1 negative triangles 1087: dt=0.0155, 1 negative triangles 1088: dt=0.0155, 1 negative triangles 1089: dt=0.0148, 1 negative triangles 1090: dt=0.0148, 1 negative triangles 1091: dt=0.0148, 1 negative triangles 1092: dt=0.0148, 1 negative triangles 1093: dt=0.0148, 1 negative triangles 1094: dt=0.0148, 1 negative triangles 1095: dt=0.0148, 1 negative triangles 1096: dt=0.0148, 1 negative triangles 1097: dt=0.0148, 1 negative triangles 1098: dt=0.0148, 1 negative triangles 1099: dt=0.0140, 1 negative triangles 1100: dt=0.0140, 1 negative triangles 1101: dt=0.0140, 1 negative triangles 1102: dt=0.0140, 1 negative triangles 1103: dt=0.0140, 1 negative triangles 1104: dt=0.0140, 1 negative triangles 1105: dt=0.0140, 1 negative triangles 1106: dt=0.0140, 1 negative triangles 1107: dt=0.0140, 1 negative triangles 1108: dt=0.0140, 1 negative triangles 1109: dt=0.0133, 1 negative triangles 1110: dt=0.0133, 1 negative triangles 1111: dt=0.0133, 1 negative triangles 1112: dt=0.0133, 1 negative triangles 1113: dt=0.0133, 1 negative triangles 1114: dt=0.0133, 1 negative triangles 1115: dt=0.0133, 1 negative triangles 1116: dt=0.0133, 1 negative triangles 1117: dt=0.0133, 1 negative triangles 1118: dt=0.0133, 1 negative triangles 1119: dt=0.0127, 1 negative triangles 1120: dt=0.0127, 1 negative triangles 1121: dt=0.0127, 1 negative triangles 1122: dt=0.0127, 1 negative triangles 1123: dt=0.0127, 1 negative triangles 1124: dt=0.0127, 1 negative triangles 1125: dt=0.0127, 1 negative triangles 1126: dt=0.0127, 1 negative triangles 1127: dt=0.0127, 1 negative triangles 1128: dt=0.0127, 1 negative triangles 1129: dt=0.0120, 1 negative triangles 1130: dt=0.0120, 1 negative triangles 1131: dt=0.0120, 1 negative triangles 1132: dt=0.0120, 1 negative triangles 1133: dt=0.0120, 1 negative triangles 1134: dt=0.0120, 1 negative triangles 1135: dt=0.0120, 1 negative triangles 1136: dt=0.0120, 1 negative triangles 1137: dt=0.0120, 1 negative triangles 1138: dt=0.0120, 1 negative triangles 1139: dt=0.0114, 1 negative triangles 1140: dt=0.0114, 1 negative triangles 1141: dt=0.0114, 1 negative triangles 1142: dt=0.0114, 1 negative triangles 1143: dt=0.0114, 1 negative triangles 1144: dt=0.0114, 1 negative triangles 1145: dt=0.0114, 1 negative triangles 1146: dt=0.0114, 1 negative triangles 1147: dt=0.0114, 1 negative triangles 1148: dt=0.0114, 1 negative triangles 1149: dt=0.0108, 1 negative triangles 1150: dt=0.0108, 1 negative triangles 1151: dt=0.0108, 1 negative triangles 1152: dt=0.0108, 1 negative triangles 1153: dt=0.0108, 1 negative triangles 1154: dt=0.0108, 1 negative triangles 1155: dt=0.0108, 1 negative triangles 1156: dt=0.0108, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... 1157: dt=0.0108, 1 negative triangles 1158: 1 negative triangles registration took 1.51 hours mris_register utimesec 5445.708000 mris_register stimesec 1.188000 mris_register ru_maxrss 289804 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 34909 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 12808 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 3 mris_register ru_nivcsw 83926 FSRUNTIME@ mris_register 1.5146 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Mon Dec 19 22:03:12 GMT 2016 /usr/local/freesurfer/subjects/SynthN/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 Mon Dec 19 22:03:14 GMT 2016 /usr/local/freesurfer/subjects/SynthN/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 Mon Dec 19 22:03:16 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts mrisp_paint -a 5 /usr/local/freesurfer/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/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh Mon Dec 19 22:03:18 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts mrisp_paint -a 5 /usr/local/freesurfer/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/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Mon Dec 19 22:03:20 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 SynthN lh ../surf/lh.sphere.reg /usr/local/freesurfer/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 1.786 2016/11/21 03:01:17 fischl Exp $ reading atlas from /usr/local/freesurfer/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... 1814 labels changed using aseg relabeling using gibbs priors... 000: 3742 changed, 185351 examined... 001: 913 changed, 15732 examined... 002: 250 changed, 5002 examined... 003: 86 changed, 1471 examined... 004: 44 changed, 559 examined... 005: 19 changed, 230 examined... 006: 6 changed, 108 examined... 007: 1 changed, 40 examined... 008: 0 changed, 5 examined... 349 labels changed using aseg 000: 142 total segments, 101 labels (411 vertices) changed 001: 43 total segments, 3 labels (7 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2096 vertices marked for relabeling... 2096 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 13 seconds. #----------------------------------------- #@# Cortical Parc rh Mon Dec 19 22:03:33 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 SynthN rh ../surf/rh.sphere.reg /usr/local/freesurfer/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 1.786 2016/11/21 03:01:17 fischl Exp $ reading atlas from /usr/local/freesurfer/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... 1222 labels changed using aseg relabeling using gibbs priors... 000: 3399 changed, 182025 examined... 001: 769 changed, 14728 examined... 002: 189 changed, 4317 examined... 003: 65 changed, 1114 examined... 004: 27 changed, 406 examined... 005: 12 changed, 156 examined... 006: 5 changed, 68 examined... 007: 2 changed, 36 examined... 008: 1 changed, 13 examined... 009: 1 changed, 5 examined... 010: 0 changed, 6 examined... 208 labels changed using aseg 000: 110 total segments, 71 labels (434 vertices) changed 001: 40 total segments, 1 labels (1 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1818 vertices marked for relabeling... 1818 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 13 seconds. #-------------------------------------------- #@# Make Pial Surf lh Mon Dec 19 22:03:46 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs SynthN 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 1.165 2016/11/21 03:01:42 fischl Exp $ $Id: mrisurf.c,v 1.786 2016/11/21 03:01:17 fischl Exp $ reading volume /usr/local/freesurfer/subjects/SynthN/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/SynthN/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/SynthN/mri/../mri/aseg.presurf.mgz... reading volume /usr/local/freesurfer/subjects/SynthN/mri/wm.mgz... 18149 bright wm thresholded. 5002 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/SynthN/surf/lh.orig... computing class statistics... border white: 367032 voxels (2.19%) border gray 421357 voxels (2.51%) WM (96.0): 96.8 +- 8.6 [70.0 --> 110.0] GM (70.0) : 68.6 +- 11.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 50.2 (was 70) setting MAX_BORDER_WHITE to 111.6 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 38.5 (was 40) setting MAX_GRAY to 94.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 50.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 26.7 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-6.1, GM=62+-9.6 mean inside = 92.3, mean outside = 72.4 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.02-->5.96) (max @ vno 141277 --> 184889) face area 0.33 +- 0.16 (0.00-->5.28) mean absolute distance = 0.62 +- 0.89 5597 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 13 points - only 0.00% unknown deleting segment 1 with 17 points - only 0.00% unknown deleting segment 2 with 84 points - only 0.00% unknown deleting segment 3 with 7 points - only 0.00% unknown deleting segment 4 with 16 points - only 0.00% unknown deleting segment 7 with 84 points - only 0.00% unknown deleting segment 8 with 10 points - only 0.00% unknown deleting segment 9 with 156 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown deleting segment 14 with 60 points - only 1.67% unknown deleting segment 15 with 10 points - only 0.00% unknown deleting segment 16 with 6 points - only 0.00% unknown deleting segment 17 with 15 points - only 0.00% unknown deleting segment 18 with 159 points - only 0.00% unknown deleting segment 19 with 15 points - only 0.00% unknown deleting segment 20 with 106 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 21 with 2 points - only 0.00% unknown mean border=76.8, 228 (225) missing vertices, mean dist 0.4 [0.8 (%15.1)->0.6 (%84.9))] %66 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=stefa, 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 (0.08-->5.99) (max @ vno 141277 --> 184889) face area 0.33 +- 0.16 (0.00-->5.13) mean absolute distance = 0.40 +- 0.79 8397 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3725656.8, rms=8.914 001: dt: 0.5000, sse=2148733.5, rms=5.900 (33.809%) 002: dt: 0.5000, sse=1648158.1, rms=4.612 (21.841%) 003: dt: 0.5000, sse=1499867.5, rms=4.123 (10.593%) 004: dt: 0.5000, sse=1381717.4, rms=3.740 (9.298%) 005: dt: 0.5000, sse=1367844.4, rms=3.657 (2.200%) 006: dt: 0.5000, sse=1325621.9, rms=3.451 (5.630%) rms = 3.50, time step reduction 1 of 3 to 0.250... 007: dt: 0.2500, sse=1096224.4, rms=2.387 (30.830%) 008: dt: 0.2500, sse=1018251.4, rms=1.831 (23.298%) 009: dt: 0.2500, sse=996112.1, rms=1.655 (9.623%) 010: dt: 0.2500, sse=986409.5, rms=1.586 (4.190%) rms = 1.55, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=984007.6, rms=1.551 (2.190%) 012: dt: 0.1250, sse=980359.5, rms=1.492 (3.824%) rms = 1.47, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=973748.7, rms=1.471 (1.405%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 18 points - only 0.00% unknown deleting segment 1 with 80 points - only 0.00% unknown deleting segment 2 with 5 points - only 0.00% unknown deleting segment 3 with 19 points - only 0.00% unknown deleting segment 4 with 87 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 96 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 10 points - only 0.00% unknown deleting segment 9 with 33 points - only 6.06% unknown deleting segment 10 with 6 points - only 0.00% unknown deleting segment 11 with 11 points - only 0.00% unknown deleting segment 12 with 135 points - only 0.00% unknown deleting segment 13 with 19 points - only 21.05% unknown deleting segment 14 with 13 points - only 0.00% unknown deleting segment 15 with 89 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 16 with 2 points - only 0.00% unknown mean border=79.8, 143 (39) missing vertices, mean dist -0.3 [0.5 (%69.5)->0.2 (%30.5))] %73 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=stefa, 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 0.91 +- 0.25 (0.08-->5.86) (max @ vno 141277 --> 184889) face area 0.35 +- 0.17 (0.00-->5.44) mean absolute distance = 0.35 +- 0.57 7639 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1822749.6, rms=4.904 014: dt: 0.5000, sse=1386782.9, rms=3.391 (30.856%) 015: dt: 0.5000, sse=1346028.1, rms=3.277 (3.378%) rms = 3.27, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=1343811.5, rms=3.265 (0.353%) 017: dt: 0.2500, sse=1098807.1, rms=1.945 (40.426%) 018: dt: 0.2500, sse=1057616.5, rms=1.620 (16.709%) 019: dt: 0.2500, sse=1044829.9, rms=1.499 (7.452%) 020: dt: 0.2500, sse=1036413.6, rms=1.415 (5.613%) 021: dt: 0.2500, sse=1029280.6, rms=1.360 (3.867%) rms = 1.31, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=1030490.9, rms=1.314 (3.393%) 023: dt: 0.1250, sse=1020554.7, rms=1.248 (5.061%) rms = 1.23, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=1030575.7, rms=1.230 (1.453%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 7 points - only 0.00% unknown deleting segment 1 with 8 points - only 0.00% unknown deleting segment 2 with 87 points - only 0.00% unknown deleting segment 3 with 6 points - only 0.00% unknown deleting segment 4 with 22 points - only 0.00% unknown deleting segment 5 with 88 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 115 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 9 points - only 0.00% unknown deleting segment 10 with 43 points - only 4.65% unknown deleting segment 11 with 9 points - only 0.00% unknown deleting segment 12 with 15 points - only 0.00% unknown deleting segment 13 with 140 points - only 0.00% unknown deleting segment 14 with 13 points - only 0.00% unknown deleting segment 15 with 95 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 16 with 2 points - only 0.00% unknown mean border=82.5, 161 (20) missing vertices, mean dist -0.2 [0.4 (%70.3)->0.2 (%29.7))] %82 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=stefa, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.25 (0.04-->5.69) (max @ vno 141277 --> 184889) face area 0.34 +- 0.17 (0.00-->4.88) mean absolute distance = 0.29 +- 0.46 6464 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1510271.5, rms=3.984 025: dt: 0.5000, sse=1256951.8, rms=2.919 (26.726%) rms = 3.00, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=1093223.0, rms=2.086 (28.549%) 027: dt: 0.2500, sse=1026252.9, rms=1.523 (26.997%) 028: dt: 0.2500, sse=1003814.2, rms=1.313 (13.756%) 029: dt: 0.2500, sse=989356.6, rms=1.246 (5.089%) rms = 1.21, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=987114.9, rms=1.206 (3.243%) 031: dt: 0.1250, sse=980302.4, rms=1.138 (5.601%) rms = 1.13, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=982467.4, rms=1.126 (1.053%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 1 with 95 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown deleting segment 3 with 10 points - only 0.00% unknown deleting segment 4 with 87 points - only 0.00% unknown deleting segment 5 with 6 points - only 0.00% unknown deleting segment 6 with 116 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 9 points - only 0.00% unknown deleting segment 9 with 49 points - only 4.08% unknown deleting segment 10 with 9 points - only 0.00% unknown deleting segment 11 with 15 points - only 0.00% unknown deleting segment 12 with 137 points - only 0.00% unknown deleting segment 13 with 13 points - only 0.00% unknown deleting segment 14 with 89 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 15 with 2 points - only 0.00% unknown mean border=83.6, 169 (15) missing vertices, mean dist -0.1 [0.3 (%59.4)->0.2 (%40.6))] %86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=stefa, 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 /usr/local/freesurfer/subjects/SynthN/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=1100214.2, rms=2.275 033: dt: 0.5000, sse=1076179.0, rms=2.084 (8.379%) rms = 2.46, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=980513.4, rms=1.376 (33.981%) 035: dt: 0.2500, sse=971235.8, rms=1.196 (13.108%) 036: dt: 0.2500, sse=979340.4, rms=1.120 (6.291%) rms = 1.14, time step reduction 2 of 3 to 0.125... 037: dt: 0.1250, sse=953950.0, rms=1.053 (6.017%) 038: dt: 0.1250, sse=944053.7, rms=0.970 (7.926%) rms = 0.94, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=943194.3, rms=0.944 (2.648%) positioning took 0.8 minutes generating cortex label... 22 non-cortical segments detected only using segment with 8834 vertices erasing segment 0 (vno[0] = 40909) erasing segment 1 (vno[0] = 64426) erasing segment 3 (vno[0] = 67270) erasing segment 4 (vno[0] = 68749) erasing segment 5 (vno[0] = 101896) erasing segment 6 (vno[0] = 106676) erasing segment 7 (vno[0] = 110209) erasing segment 8 (vno[0] = 112494) erasing segment 9 (vno[0] = 113239) erasing segment 10 (vno[0] = 115397) erasing segment 11 (vno[0] = 116139) erasing segment 12 (vno[0] = 122292) erasing segment 13 (vno[0] = 123617) erasing segment 14 (vno[0] = 126698) erasing segment 15 (vno[0] = 130535) erasing segment 16 (vno[0] = 130547) erasing segment 17 (vno[0] = 135337) erasing segment 18 (vno[0] = 138020) erasing segment 19 (vno[0] = 143730) erasing segment 20 (vno[0] = 145135) erasing segment 21 (vno[0] = 162095) writing cortex label to /usr/local/freesurfer/subjects/SynthN/label/lh.cortex.label... writing curvature file /usr/local/freesurfer/subjects/SynthN/surf/lh.curv writing smoothed area to lh.area writing curvature file /usr/local/freesurfer/subjects/SynthN/surf/lh.area vertex spacing 0.89 +- 0.26 (0.02-->5.59) (max @ vno 141277 --> 184889) face area 0.33 +- 0.17 (0.00-->4.77) 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... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 3 with 26 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 6 with 6 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 17 points - only 0.00% unknown deleting segment 10 with 16 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=48.9, 317 (317) missing vertices, mean dist 1.4 [1.0 (%0.1)->2.5 (%99.9))] % 7 local maxima, %46 large gradients and %43 min vals, 952 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=stefa, 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=46011664.0, rms=35.628 001: dt: 0.0500, sse=41104532.0, rms=33.635 (5.594%) 002: dt: 0.0500, sse=37607460.0, rms=32.139 (4.447%) 003: dt: 0.0500, sse=34908772.0, rms=30.936 (3.745%) 004: dt: 0.0500, sse=32699240.0, rms=29.914 (3.303%) 005: dt: 0.0500, sse=30815874.0, rms=29.015 (3.006%) 006: dt: 0.0500, sse=29160670.0, rms=28.201 (2.806%) 007: dt: 0.0500, sse=27675248.0, rms=27.449 (2.664%) 008: dt: 0.0500, sse=26321712.0, rms=26.746 (2.561%) 009: dt: 0.0500, sse=25073960.0, rms=26.082 (2.486%) 010: dt: 0.0500, sse=23914266.0, rms=25.448 (2.429%) positioning took 1.1 minutes mean border=48.5, 206 (137) missing vertices, mean dist 1.1 [0.6 (%0.1)->2.0 (%99.9))] % 7 local maxima, %47 large gradients and %42 min vals, 920 gradients ignored tol=1.0e-04, sigma=2.0, host=stefa, 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=25525170.0, rms=26.312 011: dt: 0.0500, sse=24417332.0, rms=25.713 (2.276%) 012: dt: 0.0500, sse=23378236.0, rms=25.138 (2.235%) 013: dt: 0.0500, sse=22401472.0, rms=24.586 (2.198%) 014: dt: 0.0500, sse=21479550.0, rms=24.052 (2.169%) 015: dt: 0.0500, sse=20609968.0, rms=23.538 (2.137%) 016: dt: 0.0500, sse=19789512.0, rms=23.043 (2.106%) 017: dt: 0.0500, sse=19013930.0, rms=22.564 (2.077%) 018: dt: 0.0500, sse=18281700.0, rms=22.103 (2.045%) 019: dt: 0.0500, sse=17590162.0, rms=21.658 (2.013%) 020: dt: 0.0500, sse=16938420.0, rms=21.230 (1.976%) positioning took 1.1 minutes mean border=48.4, 215 (108) missing vertices, mean dist 0.9 [0.1 (%0.8)->1.6 (%99.2))] % 7 local maxima, %47 large gradients and %42 min vals, 902 gradients ignored tol=1.0e-04, sigma=2.0, host=stefa, 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=17070286.0, rms=21.319 021: dt: 0.0500, sse=16426683.0, rms=20.889 (2.014%) 022: dt: 0.0500, sse=15822835.0, rms=20.478 (1.968%) 023: dt: 0.0500, sse=15251677.0, rms=20.082 (1.937%) 024: dt: 0.0500, sse=14716629.0, rms=19.703 (1.887%) 025: dt: 0.0500, sse=14215083.0, rms=19.341 (1.837%) 026: dt: 0.0500, sse=13744892.0, rms=18.995 (1.787%) 027: dt: 0.0500, sse=13300661.0, rms=18.662 (1.751%) 028: dt: 0.0500, sse=12876334.0, rms=18.339 (1.733%) 029: dt: 0.0500, sse=12469255.0, rms=18.023 (1.722%) 030: dt: 0.0500, sse=12080623.0, rms=17.716 (1.702%) positioning took 1.1 minutes mean border=48.3, 239 (87) missing vertices, mean dist 0.7 [0.1 (%13.7)->1.5 (%86.3))] % 7 local maxima, %47 large gradients and %42 min vals, 912 gradients ignored tol=1.0e-04, sigma=2.0, host=stefa, 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=12278254.0, rms=17.870 031: dt: 0.5000, sse=9582908.0, rms=15.601 (12.699%) 032: dt: 0.5000, sse=7738216.5, rms=13.827 (11.367%) 033: dt: 0.5000, sse=6275086.0, rms=12.244 (11.451%) 034: dt: 0.5000, sse=5199846.0, rms=10.928 (10.751%) 035: dt: 0.5000, sse=4341704.5, rms=9.755 (10.731%) 036: dt: 0.5000, sse=3728364.2, rms=8.816 (9.629%) 037: dt: 0.5000, sse=3256528.0, rms=8.024 (8.978%) 038: dt: 0.5000, sse=2970791.2, rms=7.498 (6.559%) 039: dt: 0.5000, sse=2756092.5, rms=7.083 (5.531%) 040: dt: 0.5000, sse=2634106.8, rms=6.830 (3.573%) 041: dt: 0.5000, sse=2534884.5, rms=6.623 (3.028%) 042: dt: 0.5000, sse=2487628.5, rms=6.517 (1.605%) 043: dt: 0.5000, sse=2432316.5, rms=6.398 (1.826%) rms = 6.37, time step reduction 1 of 3 to 0.250... 044: dt: 0.5000, sse=2423106.0, rms=6.373 (0.398%) 045: dt: 0.2500, sse=2202431.2, rms=5.826 (8.574%) 046: dt: 0.2500, sse=2139727.5, rms=5.671 (2.666%) rms = 5.68, time step reduction 2 of 3 to 0.125... 047: dt: 0.1250, sse=2105563.8, rms=5.582 (1.565%) 048: dt: 0.1250, sse=2057990.1, rms=5.455 (2.269%) rms = 5.43, time step reduction 3 of 3 to 0.062... 049: dt: 0.1250, sse=2048477.0, rms=5.430 (0.474%) positioning took 2.5 minutes mean border=47.7, 4144 (24) missing vertices, mean dist 0.1 [0.2 (%59.4)->0.7 (%40.6))] %11 local maxima, %43 large gradients and %39 min vals, 347 gradients ignored tol=1.0e-04, sigma=1.0, host=stefa, 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=2316081.0, rms=5.617 rms = 5.71, time step reduction 1 of 3 to 0.250... 050: dt: 0.2500, sse=2140787.2, rms=5.144 (8.420%) 051: dt: 0.2500, sse=2087395.2, rms=4.986 (3.065%) rms = 5.06, time step reduction 2 of 3 to 0.125... 052: dt: 0.1250, sse=2047973.0, rms=4.869 (2.346%) 053: dt: 0.1250, sse=1998914.5, rms=4.720 (3.070%) 054: dt: 0.1250, sse=1981898.8, rms=4.669 (1.077%) rms = 4.66, time step reduction 3 of 3 to 0.062... 055: dt: 0.1250, sse=1977315.4, rms=4.656 (0.263%) positioning took 0.8 minutes mean border=47.0, 4659 (15) missing vertices, mean dist 0.1 [0.1 (%58.2)->0.6 (%41.8))] %21 local maxima, %34 large gradients and %38 min vals, 405 gradients ignored tol=1.0e-04, sigma=0.5, host=stefa, 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=2071617.5, rms=4.959 rms = 5.56, time step reduction 1 of 3 to 0.250... 056: dt: 0.2500, sse=2002448.5, rms=4.758 (4.061%) rms = 4.77, time step reduction 2 of 3 to 0.125... rms = 4.73, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1993156.2, rms=4.730 (0.593%) positioning took 0.4 minutes mean border=46.2, 8275 (14) missing vertices, mean dist 0.1 [0.1 (%51.8)->0.5 (%48.2))] %27 local maxima, %27 large gradients and %37 min vals, 468 gradients ignored tol=1.0e-04, sigma=0.2, host=stefa, 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 /usr/local/freesurfer/subjects/SynthN/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=2072273.4, rms=4.954 rms = 5.17, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1988565.5, rms=4.711 (4.912%) 059: dt: 0.2500, sse=1917021.1, rms=4.505 (4.371%) rms = 4.49, time step reduction 2 of 3 to 0.125... 060: dt: 0.2500, sse=1908166.2, rms=4.487 (0.404%) 061: dt: 0.1250, sse=1824368.5, rms=4.209 (6.182%) 062: dt: 0.1250, sse=1795441.0, rms=4.115 (2.237%) rms = 4.07, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1781682.0, rms=4.071 (1.081%) positioning took 0.7 minutes writing curvature file /usr/local/freesurfer/subjects/SynthN/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /usr/local/freesurfer/subjects/SynthN/surf/lh.area.pial vertex spacing 0.99 +- 0.42 (0.07-->6.64) (max @ vno 120205 --> 120181) face area 0.39 +- 0.29 (0.00-->6.51) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 185351 vertices processed 25000 of 185351 vertices processed 50000 of 185351 vertices processed 75000 of 185351 vertices processed 100000 of 185351 vertices processed 125000 of 185351 vertices processed 150000 of 185351 vertices processed 175000 of 185351 vertices processed 0 of 185351 vertices processed 25000 of 185351 vertices processed 50000 of 185351 vertices processed 75000 of 185351 vertices processed 100000 of 185351 vertices processed 125000 of 185351 vertices processed 150000 of 185351 vertices processed 175000 of 185351 vertices processed thickness calculation complete, 179:941 truncations. 64288 vertices at 0 distance 146344 vertices at 1 distance 90609 vertices at 2 distance 35551 vertices at 3 distance 12581 vertices at 4 distance 4294 vertices at 5 distance 1380 vertices at 6 distance 474 vertices at 7 distance 206 vertices at 8 distance 98 vertices at 9 distance 64 vertices at 10 distance 39 vertices at 11 distance 39 vertices at 12 distance 18 vertices at 13 distance 14 vertices at 14 distance 22 vertices at 15 distance 12 vertices at 16 distance 18 vertices at 17 distance 7 vertices at 18 distance 11 vertices at 19 distance 11 vertices at 20 distance writing curvature file /usr/local/freesurfer/subjects/SynthN/surf/lh.thickness positioning took 16.1 minutes #-------------------------------------------- #@# Make Pial Surf rh Mon Dec 19 22:19:52 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs SynthN 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 1.165 2016/11/21 03:01:42 fischl Exp $ $Id: mrisurf.c,v 1.786 2016/11/21 03:01:17 fischl Exp $ reading volume /usr/local/freesurfer/subjects/SynthN/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/SynthN/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/SynthN/mri/../mri/aseg.presurf.mgz... reading volume /usr/local/freesurfer/subjects/SynthN/mri/wm.mgz... 18149 bright wm thresholded. 5002 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/SynthN/surf/rh.orig... computing class statistics... border white: 367032 voxels (2.19%) border gray 421357 voxels (2.51%) WM (96.0): 96.8 +- 8.6 [70.0 --> 110.0] GM (70.0) : 68.6 +- 11.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 51.2 (was 70) setting MAX_BORDER_WHITE to 110.6 (was 105) setting MIN_BORDER_WHITE to 63.0 (was 85) setting MAX_CSF to 39.5 (was 40) setting MAX_GRAY to 93.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 51.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 27.7 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-6.1, GM=63+-13.0 mean inside = 92.0, mean outside = 73.3 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.27 (0.03-->7.34) (max @ vno 180252 --> 180347) face area 0.33 +- 0.18 (0.00-->9.68) mean absolute distance = 0.66 +- 0.98 4914 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 41 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown deleting segment 8 with 59 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 9 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown deleting segment 12 with 74 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 13 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 14 with 3 points - only 0.00% unknown deleting segment 15 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 16 with 2 points - only 0.00% unknown deleting segment 17 with 138 points - only 0.00% unknown deleting segment 18 with 17 points - only 0.00% unknown deleting segment 19 with 63 points - only 0.00% unknown deleting segment 20 with 49 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 21 with 3 points - only 0.00% unknown mean border=78.5, 727 (724) missing vertices, mean dist 0.3 [0.9 (%17.4)->0.6 (%82.6))] %66 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=stefa, 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 +- 0.27 (0.07-->7.35) (max @ vno 180252 --> 180347) face area 0.33 +- 0.18 (0.00-->8.94) mean absolute distance = 0.42 +- 0.82 7537 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3362941.0, rms=8.417 001: dt: 0.5000, sse=2033393.1, rms=5.706 (32.213%) 002: dt: 0.5000, sse=1580009.0, rms=4.456 (21.898%) 003: dt: 0.5000, sse=1436572.5, rms=3.962 (11.098%) 004: dt: 0.5000, sse=1327080.8, rms=3.571 (9.875%) 005: dt: 0.5000, sse=1312281.1, rms=3.505 (1.831%) 006: dt: 0.5000, sse=1276616.6, rms=3.304 (5.745%) rms = 3.36, time step reduction 1 of 3 to 0.250... 007: dt: 0.2500, sse=1073813.1, rms=2.324 (29.648%) 008: dt: 0.2500, sse=1010164.2, rms=1.843 (20.727%) 009: dt: 0.2500, sse=1002073.1, rms=1.714 (6.991%) 010: dt: 0.2500, sse=993411.9, rms=1.663 (2.951%) rms = 1.62, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=986528.4, rms=1.623 (2.413%) 012: dt: 0.1250, sse=974312.6, rms=1.558 (4.007%) rms = 1.54, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=972546.6, rms=1.537 (1.351%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 29 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 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 8 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 72 points - only 0.00% unknown deleting segment 7 with 12 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown deleting segment 11 with 114 points - only 0.00% unknown deleting segment 12 with 7 points - only 0.00% unknown deleting segment 13 with 6 points - only 0.00% unknown deleting segment 14 with 59 points - only 0.00% unknown deleting segment 15 with 49 points - only 0.00% unknown mean border=81.1, 378 (174) missing vertices, mean dist -0.3 [0.5 (%67.2)->0.2 (%32.8))] %72 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=stefa, 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 0.91 +- 0.27 (0.06-->7.18) (max @ vno 180252 --> 180347) face area 0.36 +- 0.19 (0.00-->9.89) mean absolute distance = 0.37 +- 0.61 6958 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1694492.1, rms=4.588 014: dt: 0.5000, sse=1331995.2, rms=3.206 (30.115%) 015: dt: 0.5000, sse=1296451.4, rms=3.094 (3.508%) rms = 3.09, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=1292451.9, rms=3.091 (0.094%) 017: dt: 0.2500, sse=1095216.8, rms=1.921 (37.853%) 018: dt: 0.2500, sse=1053148.4, rms=1.632 (15.044%) 019: dt: 0.2500, sse=1049681.5, rms=1.545 (5.308%) 020: dt: 0.2500, sse=1041195.9, rms=1.482 (4.091%) rms = 1.46, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=1041319.2, rms=1.455 (1.803%) 022: dt: 0.1250, sse=1024557.1, rms=1.385 (4.810%) rms = 1.36, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=1030712.7, rms=1.359 (1.878%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 24 points - only 0.00% unknown deleting segment 1 with 9 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 9 points - only 0.00% unknown deleting segment 4 with 9 points - only 0.00% unknown deleting segment 5 with 74 points - only 0.00% unknown deleting segment 6 with 16 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 110 points - only 0.00% unknown deleting segment 10 with 9 points - only 0.00% unknown deleting segment 11 with 61 points - only 0.00% unknown deleting segment 12 with 49 points - only 0.00% unknown mean border=83.5, 339 (90) missing vertices, mean dist -0.2 [0.4 (%68.9)->0.3 (%31.1))] %81 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=stefa, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.27 (0.06-->7.15) (max @ vno 180252 --> 180347) face area 0.34 +- 0.19 (0.00-->9.88) mean absolute distance = 0.31 +- 0.50 6132 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1480239.4, rms=3.943 024: dt: 0.5000, sse=1230742.0, rms=2.875 (27.082%) rms = 2.91, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=1095223.5, rms=2.153 (25.120%) 026: dt: 0.2500, sse=1037365.1, rms=1.697 (21.171%) 027: dt: 0.2500, sse=1019314.7, rms=1.512 (10.912%) 028: dt: 0.2500, sse=1020013.3, rms=1.458 (3.554%) rms = 1.42, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=1002511.8, rms=1.423 (2.423%) 030: dt: 0.1250, sse=988569.5, rms=1.295 (8.993%) rms = 1.27, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=982975.5, rms=1.265 (2.285%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 24 points - only 0.00% unknown deleting segment 1 with 11 points - only 0.00% unknown deleting segment 2 with 9 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown deleting segment 4 with 71 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown deleting segment 6 with 13 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 9 with 5 points - only 0.00% unknown deleting segment 10 with 107 points - only 0.00% unknown deleting segment 11 with 9 points - only 0.00% unknown deleting segment 12 with 59 points - only 0.00% unknown deleting segment 13 with 49 points - only 0.00% unknown mean border=84.6, 377 (74) missing vertices, mean dist -0.1 [0.3 (%59.6)->0.3 (%40.4))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=stefa, 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 /usr/local/freesurfer/subjects/SynthN/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=1100009.6, rms=2.363 032: dt: 0.5000, sse=1084567.0, rms=2.061 (12.765%) rms = 2.37, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=985250.0, rms=1.427 (30.760%) 034: dt: 0.2500, sse=970678.2, rms=1.299 (8.981%) 035: dt: 0.2500, sse=966557.9, rms=1.214 (6.532%) rms = 1.25, time step reduction 2 of 3 to 0.125... 036: dt: 0.1250, sse=951921.8, rms=1.139 (6.190%) 037: dt: 0.1250, sse=955052.0, rms=1.045 (8.271%) rms = 1.01, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=941840.0, rms=1.007 (3.598%) positioning took 0.7 minutes generating cortex label... 32 non-cortical segments detected only using segment with 7326 vertices erasing segment 0 (vno[0] = 42440) erasing segment 1 (vno[0] = 45211) erasing segment 2 (vno[0] = 52699) erasing segment 3 (vno[0] = 54072) erasing segment 5 (vno[0] = 58015) erasing segment 6 (vno[0] = 59178) erasing segment 7 (vno[0] = 62219) erasing segment 8 (vno[0] = 64217) erasing segment 9 (vno[0] = 64592) erasing segment 10 (vno[0] = 65932) erasing segment 11 (vno[0] = 67319) erasing segment 12 (vno[0] = 68350) erasing segment 13 (vno[0] = 68361) erasing segment 14 (vno[0] = 71683) erasing segment 15 (vno[0] = 74078) erasing segment 16 (vno[0] = 76642) erasing segment 17 (vno[0] = 90754) erasing segment 18 (vno[0] = 95779) erasing segment 19 (vno[0] = 97365) erasing segment 20 (vno[0] = 106708) erasing segment 21 (vno[0] = 110987) erasing segment 22 (vno[0] = 118067) erasing segment 23 (vno[0] = 119455) erasing segment 24 (vno[0] = 120472) erasing segment 25 (vno[0] = 122154) erasing segment 26 (vno[0] = 124610) erasing segment 27 (vno[0] = 128326) erasing segment 28 (vno[0] = 131668) erasing segment 29 (vno[0] = 133020) erasing segment 30 (vno[0] = 179343) erasing segment 31 (vno[0] = 181215) writing cortex label to /usr/local/freesurfer/subjects/SynthN/label/rh.cortex.label... writing curvature file /usr/local/freesurfer/subjects/SynthN/surf/rh.curv writing smoothed area to rh.area writing curvature file /usr/local/freesurfer/subjects/SynthN/surf/rh.area vertex spacing 0.89 +- 0.27 (0.03-->6.99) (max @ vno 180252 --> 180347) face area 0.34 +- 0.19 (0.00-->9.77) 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 43 points - only 0.00% unknown deleting segment 1 with 38 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown deleting segment 7 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown deleting segment 9 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown deleting segment 11 with 23 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown deleting segment 13 with 8 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 14 with 4 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=50.9, 751 (751) missing vertices, mean dist 1.3 [0.8 (%0.0)->2.6 (%100.0))] % 8 local maxima, %41 large gradients and %46 min vals, 962 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=stefa, 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=43180076.0, rms=34.801 001: dt: 0.0500, sse=38640864.0, rms=32.881 (5.518%) 002: dt: 0.0500, sse=35431024.0, rms=31.452 (4.345%) 003: dt: 0.0500, sse=32959878.0, rms=30.306 (3.643%) 004: dt: 0.0500, sse=30943514.0, rms=29.338 (3.195%) 005: dt: 0.0500, sse=29223312.0, rms=28.486 (2.904%) 006: dt: 0.0500, sse=27715394.0, rms=27.717 (2.698%) 007: dt: 0.0500, sse=26363302.0, rms=27.010 (2.553%) 008: dt: 0.0500, sse=25132634.0, rms=26.349 (2.446%) 009: dt: 0.0500, sse=23997974.0, rms=25.725 (2.369%) 010: dt: 0.0500, sse=22942556.0, rms=25.130 (2.312%) positioning took 1.1 minutes mean border=50.5, 445 (357) missing vertices, mean dist 1.1 [0.3 (%0.0)->2.0 (%100.0))] % 9 local maxima, %42 large gradients and %45 min vals, 869 gradients ignored tol=1.0e-04, sigma=2.0, host=stefa, 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=24684224.0, rms=26.077 011: dt: 0.0500, sse=23669414.0, rms=25.515 (2.157%) 012: dt: 0.0500, sse=22717914.0, rms=24.976 (2.112%) 013: dt: 0.0500, sse=21822444.0, rms=24.458 (2.074%) 014: dt: 0.0500, sse=20978558.0, rms=23.959 (2.038%) 015: dt: 0.0500, sse=20180968.0, rms=23.478 (2.007%) 016: dt: 0.0500, sse=19426740.0, rms=23.014 (1.977%) 017: dt: 0.0500, sse=18713454.0, rms=22.567 (1.945%) 018: dt: 0.0500, sse=18039696.0, rms=22.135 (1.911%) 019: dt: 0.0500, sse=17403518.0, rms=21.720 (1.876%) 020: dt: 0.0500, sse=16801674.0, rms=21.320 (1.843%) positioning took 1.1 minutes mean border=50.3, 402 (221) missing vertices, mean dist 0.9 [0.1 (%0.8)->1.7 (%99.2))] % 9 local maxima, %42 large gradients and %45 min vals, 847 gradients ignored tol=1.0e-04, sigma=2.0, host=stefa, 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=17010650.0, rms=21.456 021: dt: 0.0500, sse=16411110.0, rms=21.052 (1.880%) 022: dt: 0.0500, sse=15848618.0, rms=20.667 (1.832%) 023: dt: 0.0500, sse=15315120.0, rms=20.294 (1.803%) 024: dt: 0.0500, sse=14813947.0, rms=19.937 (1.757%) 025: dt: 0.0500, sse=14343455.0, rms=19.597 (1.709%) 026: dt: 0.0500, sse=13901895.0, rms=19.271 (1.660%) 027: dt: 0.0500, sse=13482869.0, rms=18.957 (1.629%) 028: dt: 0.0500, sse=13079714.0, rms=18.650 (1.620%) 029: dt: 0.0500, sse=12692223.0, rms=18.350 (1.609%) 030: dt: 0.0500, sse=12320270.0, rms=18.057 (1.596%) positioning took 1.1 minutes mean border=50.2, 431 (169) missing vertices, mean dist 0.7 [0.1 (%14.5)->1.6 (%85.5))] % 9 local maxima, %43 large gradients and %44 min vals, 818 gradients ignored tol=1.0e-04, sigma=2.0, host=stefa, 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=12506409.0, rms=18.201 031: dt: 0.5000, sse=9891185.0, rms=16.013 (12.019%) 032: dt: 0.5000, sse=8025693.5, rms=14.242 (11.061%) 033: dt: 0.5000, sse=6509359.5, rms=12.625 (11.356%) 034: dt: 0.5000, sse=5359679.5, rms=11.238 (10.984%) 035: dt: 0.5000, sse=4446645.5, rms=10.005 (10.971%) 036: dt: 0.5000, sse=3809304.2, rms=9.040 (9.643%) 037: dt: 0.5000, sse=3352306.0, rms=8.285 (8.360%) 038: dt: 0.5000, sse=3063176.0, rms=7.762 (6.302%) 039: dt: 0.5000, sse=2847354.5, rms=7.355 (5.254%) 040: dt: 0.5000, sse=2730309.0, rms=7.117 (3.228%) 041: dt: 0.5000, sse=2617362.0, rms=6.888 (3.221%) 042: dt: 0.5000, sse=2561899.8, rms=6.767 (1.757%) 043: dt: 0.5000, sse=2500966.5, rms=6.638 (1.898%) rms = 6.60, time step reduction 1 of 3 to 0.250... 044: dt: 0.5000, sse=2483167.2, rms=6.595 (0.653%) 045: dt: 0.2500, sse=2266386.0, rms=6.070 (7.964%) 046: dt: 0.2500, sse=2210280.5, rms=5.934 (2.238%) rms = 5.93, time step reduction 2 of 3 to 0.125... 047: dt: 0.2500, sse=2208801.0, rms=5.928 (0.103%) 048: dt: 0.1250, sse=2116027.2, rms=5.691 (3.991%) 049: dt: 0.1250, sse=2093595.4, rms=5.635 (0.998%) rms = 5.62, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=2089407.9, rms=5.623 (0.203%) positioning took 2.3 minutes mean border=49.7, 5028 (48) missing vertices, mean dist 0.1 [0.2 (%57.3)->0.7 (%42.7))] %12 local maxima, %40 large gradients and %42 min vals, 300 gradients ignored tol=1.0e-04, sigma=1.0, host=stefa, 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=2314277.2, rms=5.727 rms = 5.82, time step reduction 1 of 3 to 0.250... 051: dt: 0.2500, sse=2138907.8, rms=5.257 (8.198%) 052: dt: 0.2500, sse=2081294.9, rms=5.090 (3.181%) rms = 5.16, time step reduction 2 of 3 to 0.125... 053: dt: 0.1250, sse=2039005.0, rms=4.965 (2.451%) 054: dt: 0.1250, sse=1987055.2, rms=4.807 (3.183%) 055: dt: 0.1250, sse=1967685.1, rms=4.749 (1.206%) rms = 4.73, time step reduction 3 of 3 to 0.062... 056: dt: 0.1250, sse=1962255.5, rms=4.734 (0.310%) positioning took 0.8 minutes mean border=49.1, 5576 (43) missing vertices, mean dist 0.1 [0.1 (%57.8)->0.6 (%42.2))] %19 local maxima, %33 large gradients and %41 min vals, 374 gradients ignored tol=1.0e-04, sigma=0.5, host=stefa, 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=2040977.5, rms=5.001 rms = 5.59, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=1976204.6, rms=4.812 (3.775%) rms = 4.85, time step reduction 2 of 3 to 0.125... rms = 4.78, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1967031.0, rms=4.784 (0.581%) positioning took 0.4 minutes mean border=48.5, 9615 (41) missing vertices, mean dist 0.1 [0.1 (%51.8)->0.5 (%48.2))] %25 local maxima, %27 large gradients and %39 min vals, 424 gradients ignored tol=1.0e-04, sigma=0.2, host=stefa, 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 /usr/local/freesurfer/subjects/SynthN/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=2041673.9, rms=4.998 rms = 5.27, time step reduction 1 of 3 to 0.250... 059: dt: 0.2500, sse=1957024.9, rms=4.751 (4.934%) 060: dt: 0.2500, sse=1892878.6, rms=4.570 (3.821%) rms = 4.57, time step reduction 2 of 3 to 0.125... 061: dt: 0.2500, sse=1888455.9, rms=4.566 (0.072%) 062: dt: 0.1250, sse=1796236.4, rms=4.262 (6.677%) 063: dt: 0.1250, sse=1765557.2, rms=4.161 (2.356%) rms = 4.12, time step reduction 3 of 3 to 0.062... 064: dt: 0.1250, sse=1752284.6, rms=4.118 (1.030%) positioning took 0.7 minutes writing curvature file /usr/local/freesurfer/subjects/SynthN/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /usr/local/freesurfer/subjects/SynthN/surf/rh.area.pial vertex spacing 0.99 +- 0.42 (0.05-->7.74) (max @ vno 108712 --> 108695) face area 0.38 +- 0.30 (0.00-->13.16) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 182025 vertices processed 25000 of 182025 vertices processed 50000 of 182025 vertices processed 75000 of 182025 vertices processed 100000 of 182025 vertices processed 125000 of 182025 vertices processed 150000 of 182025 vertices processed 175000 of 182025 vertices processed 0 of 182025 vertices processed 25000 of 182025 vertices processed 50000 of 182025 vertices processed 75000 of 182025 vertices processed 100000 of 182025 vertices processed 125000 of 182025 vertices processed 150000 of 182025 vertices processed 175000 of 182025 vertices processed thickness calculation complete, 673:1392 truncations. 61344 vertices at 0 distance 138765 vertices at 1 distance 91859 vertices at 2 distance 37188 vertices at 3 distance 13669 vertices at 4 distance 4832 vertices at 5 distance 1654 vertices at 6 distance 608 vertices at 7 distance 305 vertices at 8 distance 156 vertices at 9 distance 74 vertices at 10 distance 38 vertices at 11 distance 35 vertices at 12 distance 21 vertices at 13 distance 11 vertices at 14 distance 29 vertices at 15 distance 18 vertices at 16 distance 14 vertices at 17 distance 23 vertices at 18 distance 17 vertices at 19 distance 36 vertices at 20 distance writing curvature file /usr/local/freesurfer/subjects/SynthN/surf/rh.thickness positioning took 15.7 minutes #-------------------------------------------- #@# Surf Volume lh Mon Dec 19 22:35:34 GMT 2016 /usr/local/freesurfer/subjects/SynthN/surf /usr/local/freesurfer/subjects/SynthN/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 SynthN lh /usr/local/freesurfer/subjects/SynthN/surf/lh.volume masking with /usr/local/freesurfer/subjects/SynthN/label/lh.cortex.label Total face volume 308895 Total vertex volume 305343 (mask=0) #@# SynthN lh 305343 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Mon Dec 19 22:35:37 GMT 2016 /usr/local/freesurfer/subjects/SynthN/surf /usr/local/freesurfer/subjects/SynthN/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 SynthN rh /usr/local/freesurfer/subjects/SynthN/surf/rh.volume masking with /usr/local/freesurfer/subjects/SynthN/label/rh.cortex.label Total face volume 301678 Total vertex volume 298678 (mask=0) #@# SynthN rh 298678 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Mon Dec 19 22:35:40 GMT 2016 /usr/local/freesurfer/subjects/SynthN/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 SynthN SUBJECTS_DIR is /usr/local/freesurfer/subjects 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 = 67 writing volume /usr/local/freesurfer/subjects/SynthN/mri/ribbon.mgz mris_volmask took 12.99 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Mon Dec 19 22:48:39 GMT 2016 /usr/local/freesurfer/subjects/SynthN/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 SynthN lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /usr/local/freesurfer/subjects/SynthN/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/SynthN/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthN/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 308895 Total vertex volume 305343 (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) = 1204641 mm^3 (det: 1.617166 ) lhCtxGM: 303353.998 302860.000 diff= 494.0 pctdiff= 0.163 rhCtxGM: 296110.746 296782.000 diff= -671.3 pctdiff=-0.227 lhCtxWM: 316500.382 317449.500 diff= -949.1 pctdiff=-0.300 rhCtxWM: 330165.226 332241.500 diff=-2076.3 pctdiff=-0.629 SubCortGMVol 71549.000 SupraTentVol 1343879.351 (1341199.000) diff=2680.351 pctdiff=0.199 SupraTentVolNotVent 1323563.351 (1320883.000) diff=2680.351 pctdiff=0.203 BrainSegVol 1492481.000 (1489239.000) diff=3242.000 pctdiff=0.217 BrainSegVolNotVent 1467905.000 (1464577.351) diff=3327.649 pctdiff=0.227 BrainSegVolNotVent 1467905.000 CerebellumVol 146897.000 VentChorVol 20316.000 3rd4th5thCSF 4260.000 CSFVol 1018.000, OptChiasmVol 125.000 MaskVol 1847800.000 1438 1003 2057 2.034 0.457 0.082 0.012 5 0.6 bankssts 1254 808 2735 3.212 0.749 0.144 0.026 20 1.4 caudalanteriorcingulate 5741 3795 8098 2.088 0.549 0.120 0.029 62 7.7 caudalmiddlefrontal 2329 1628 3342 2.072 0.468 0.164 0.035 37 3.4 cuneus 598 456 1796 2.900 0.964 0.083 0.018 3 0.4 entorhinal 5337 3950 10172 2.311 0.622 0.138 0.028 79 6.6 fusiform 10788 6708 15723 2.272 0.641 0.109 0.026 90 12.0 inferiorparietal 7191 4852 13771 2.551 0.760 0.125 0.030 90 8.9 inferiortemporal 2054 1299 3805 2.651 0.903 0.119 0.027 26 2.0 isthmuscingulate 10174 6698 14680 2.053 0.638 0.133 0.029 121 12.8 lateraloccipital 4493 3158 10402 2.949 0.725 0.134 0.032 64 5.9 lateralorbitofrontal 4938 3416 8596 2.331 0.740 0.136 0.032 56 6.8 lingual 3153 2235 6119 2.507 0.796 0.139 0.039 48 5.0 medialorbitofrontal 7841 4900 15172 2.690 0.808 0.126 0.044 112 16.1 middletemporal 965 604 1912 2.637 0.847 0.076 0.016 5 0.4 parahippocampal 2601 1728 4162 2.185 0.611 0.104 0.018 16 1.9 paracentral 2765 1933 5372 2.483 0.682 0.111 0.018 26 1.9 parsopercularis 1146 788 3270 3.145 0.599 0.138 0.029 16 1.3 parsorbitalis 2205 1541 4381 2.413 0.667 0.111 0.018 20 1.7 parstriangularis 1566 1055 1770 1.841 0.435 0.120 0.022 16 1.3 pericalcarine 11809 7536 16429 1.969 0.668 0.111 0.025 107 13.0 postcentral 2287 1574 4146 2.382 0.996 0.156 0.038 41 4.0 posteriorcingulate 10700 6854 17439 2.373 0.702 0.104 0.025 90 11.4 precentral 7443 5092 12588 2.389 0.577 0.124 0.025 77 7.7 precuneus 1163 817 2458 2.816 0.811 0.146 0.029 19 1.4 rostralanteriorcingulate 12226 7911 20223 2.319 0.617 0.125 0.027 129 13.8 rostralmiddlefrontal 15053 9929 28694 2.606 0.696 0.121 0.029 153 19.0 superiorfrontal 14063 8945 19874 2.054 0.599 0.110 0.022 112 13.2 superiorparietal 9408 6323 19638 2.713 0.726 0.119 0.027 110 11.1 superiortemporal 7377 4907 12555 2.449 0.639 0.126 0.032 87 10.3 supramarginal 552 390 1534 2.956 0.604 0.191 0.067 12 1.6 frontalpole 721 527 2632 3.624 0.621 0.110 0.021 7 0.5 temporalpole 973 667 2205 2.773 0.596 0.123 0.029 11 1.0 transversetemporal 3782 2560 7488 2.884 0.762 0.110 0.037 35 7.6 insula mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab SynthN lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /usr/local/freesurfer/subjects/SynthN/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthN/surf/lh.pial... reading input pial surface /usr/local/freesurfer/subjects/SynthN/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthN/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 308895 Total vertex volume 305343 (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) = 1204641 mm^3 (det: 1.617166 ) lhCtxGM: 303353.998 302860.000 diff= 494.0 pctdiff= 0.163 rhCtxGM: 296110.746 296782.000 diff= -671.3 pctdiff=-0.227 lhCtxWM: 316500.382 317449.500 diff= -949.1 pctdiff=-0.300 rhCtxWM: 330165.226 332241.500 diff=-2076.3 pctdiff=-0.629 SubCortGMVol 71549.000 SupraTentVol 1343879.351 (1341199.000) diff=2680.351 pctdiff=0.199 SupraTentVolNotVent 1323563.351 (1320883.000) diff=2680.351 pctdiff=0.203 BrainSegVol 1492481.000 (1489239.000) diff=3242.000 pctdiff=0.217 BrainSegVolNotVent 1467905.000 (1464577.351) diff=3327.649 pctdiff=0.227 BrainSegVolNotVent 1467905.000 CerebellumVol 146897.000 VentChorVol 20316.000 3rd4th5thCSF 4260.000 CSFVol 1018.000, OptChiasmVol 125.000 MaskVol 1847800.000 1438 963 2057 2.034 0.457 0.098 0.017 11 1.0 bankssts 1254 977 2735 3.212 0.749 0.168 0.044 73 2.3 caudalanteriorcingulate 5741 4097 8098 2.088 0.549 0.109 0.027 57 7.3 caudalmiddlefrontal 2329 1737 3342 2.072 0.468 0.150 0.035 52 4.0 cuneus 598 783 1796 2.900 0.964 0.150 0.028 3 0.7 entorhinal 5337 4741 10172 2.311 0.622 0.165 0.038 85 9.9 fusiform 10788 7456 15723 2.272 0.641 0.106 0.022 94 10.5 inferiorparietal 7191 5814 13771 2.551 0.760 0.134 0.031 98 10.8 inferiortemporal 2054 1543 3805 2.651 0.903 0.140 0.038 33 3.5 isthmuscingulate 10174 8090 14680 2.053 0.638 0.133 0.029 151 14.1 lateraloccipital 4493 3977 10402 2.949 0.725 0.166 0.045 76 9.3 lateralorbitofrontal 4938 4171 8596 2.331 0.740 0.157 0.048 84 11.4 lingual 3153 2687 6119 2.507 0.796 0.173 0.047 51 7.0 medialorbitofrontal 7841 6126 15172 2.690 0.808 0.121 0.027 110 9.9 middletemporal 965 886 1912 2.637 0.847 0.179 0.047 13 2.1 parahippocampal 2601 2102 4162 2.185 0.611 0.120 0.022 22 2.3 paracentral 2765 2421 5372 2.483 0.682 0.152 0.035 34 4.3 parsopercularis 1146 1238 3270 3.145 0.599 0.176 0.033 16 1.8 parsorbitalis 2205 1990 4381 2.413 0.667 0.158 0.035 26 3.9 parstriangularis 1566 941 1770 1.841 0.435 0.107 0.024 29 1.5 pericalcarine 11809 9249 16429 1.969 0.668 0.122 0.025 108 13.8 postcentral 2287 1979 4146 2.382 0.996 0.180 0.047 55 5.3 posteriorcingulate 10700 7774 17439 2.373 0.702 0.111 0.024 102 12.0 precentral 7443 5455 12588 2.389 0.577 0.127 0.029 89 9.4 precuneus 1163 1067 2458 2.816 0.811 0.181 0.046 38 2.4 rostralanteriorcingulate 12226 9474 20223 2.319 0.617 0.131 0.028 135 16.3 rostralmiddlefrontal 15053 12047 28694 2.606 0.696 0.139 0.036 204 26.8 superiorfrontal 14063 10425 19874 2.054 0.599 0.118 0.023 140 15.0 superiorparietal 9408 7912 19638 2.713 0.726 0.148 0.036 122 16.2 superiortemporal 7377 5493 12555 2.449 0.639 0.126 0.041 140 15.9 supramarginal 552 616 1534 2.956 0.604 0.180 0.034 5 0.9 frontalpole 721 949 2632 3.624 0.621 0.172 0.034 5 1.1 temporalpole 973 1002 2205 2.773 0.596 0.180 0.044 12 2.0 transversetemporal 3782 2627 7488 2.884 0.762 0.163 0.050 64 9.1 insula #----------------------------------------- #@# Parcellation Stats rh Mon Dec 19 22:49:47 GMT 2016 /usr/local/freesurfer/subjects/SynthN/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 SynthN rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /usr/local/freesurfer/subjects/SynthN/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/SynthN/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthN/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 301678 Total vertex volume 298678 (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) = 1204641 mm^3 (det: 1.617166 ) lhCtxGM: 303353.998 302860.000 diff= 494.0 pctdiff= 0.163 rhCtxGM: 296110.746 296782.000 diff= -671.3 pctdiff=-0.227 lhCtxWM: 316500.382 317449.500 diff= -949.1 pctdiff=-0.300 rhCtxWM: 330165.226 332241.500 diff=-2076.3 pctdiff=-0.629 SubCortGMVol 71549.000 SupraTentVol 1343879.351 (1341199.000) diff=2680.351 pctdiff=0.199 SupraTentVolNotVent 1323563.351 (1320883.000) diff=2680.351 pctdiff=0.203 BrainSegVol 1492481.000 (1489239.000) diff=3242.000 pctdiff=0.217 BrainSegVolNotVent 1467905.000 (1464577.351) diff=3327.649 pctdiff=0.227 BrainSegVolNotVent 1467905.000 CerebellumVol 146897.000 VentChorVol 20316.000 3rd4th5thCSF 4260.000 CSFVol 1018.000, OptChiasmVol 125.000 MaskVol 1847800.000 1737 1203 2831 2.448 0.676 0.109 0.018 12 1.3 bankssts 1159 793 2570 2.728 0.664 0.135 0.021 17 1.1 caudalanteriorcingulate 5272 3488 7810 2.159 0.515 0.116 0.027 44 6.3 caudalmiddlefrontal 2390 1672 3603 1.982 0.623 0.147 0.027 32 2.7 cuneus 495 356 2091 3.697 0.805 0.107 0.023 4 0.5 entorhinal 5078 3580 9931 2.662 0.556 0.131 0.027 60 6.0 fusiform 13557 8803 22526 2.266 0.688 0.111 0.024 132 12.9 inferiorparietal 8865 6031 14961 2.432 0.873 0.145 0.054 127 22.6 inferiortemporal 1170 764 2068 2.535 0.933 0.122 0.033 16 1.4 isthmuscingulate 9662 6322 14572 2.216 0.545 0.135 0.031 104 12.3 lateraloccipital 4096 2831 8315 2.571 0.681 0.142 0.036 59 6.7 lateralorbitofrontal 4926 3478 8045 2.151 0.682 0.145 0.037 65 8.1 lingual 2787 2062 5525 2.329 0.759 0.140 0.039 46 4.5 medialorbitofrontal 6876 4833 13504 2.737 0.832 0.139 0.039 87 12.7 middletemporal 1094 772 1992 2.510 0.724 0.154 0.051 24 2.6 parahippocampal 2891 1908 4885 2.360 0.599 0.103 0.016 20 1.9 paracentral 2384 1622 4624 2.557 0.624 0.122 0.031 25 3.3 parsopercularis 1771 1169 4438 3.135 0.720 0.139 0.038 28 2.3 parsorbitalis 3373 2128 5856 2.520 0.596 0.120 0.030 35 4.1 parstriangularis 1822 1260 1944 1.668 0.379 0.116 0.027 17 2.2 pericalcarine 7860 5111 9429 1.746 0.561 0.106 0.026 89 9.5 postcentral 1937 1338 4238 2.907 0.744 0.146 0.030 27 2.5 posteriorcingulate 10782 7041 16634 2.228 0.712 0.110 0.026 110 12.4 precentral 8489 5693 14230 2.400 0.582 0.124 0.022 88 7.7 precuneus 926 667 1689 2.517 0.627 0.149 0.029 16 1.1 rostralanteriorcingulate 13763 8977 23688 2.381 0.617 0.128 0.029 156 17.1 rostralmiddlefrontal 16077 10111 28932 2.587 0.855 0.125 0.034 263 25.6 superiorfrontal 12108 7694 16429 1.975 0.576 0.112 0.023 112 11.6 superiorparietal 7006 4474 14666 2.964 0.708 0.106 0.025 58 7.1 superiortemporal 7888 5342 12865 2.247 0.626 0.137 0.036 110 12.9 supramarginal 578 351 1592 3.192 0.610 0.150 0.039 10 1.0 frontalpole 753 545 2924 3.835 0.771 0.136 0.034 9 1.1 temporalpole 556 363 1080 2.574 0.742 0.139 0.037 9 0.8 transversetemporal 4166 2838 8140 2.844 0.937 0.123 0.037 47 6.9 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 SynthN rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /usr/local/freesurfer/subjects/SynthN/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthN/surf/rh.pial... reading input pial surface /usr/local/freesurfer/subjects/SynthN/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthN/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 301678 Total vertex volume 298678 (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) = 1204641 mm^3 (det: 1.617166 ) lhCtxGM: 303353.998 302860.000 diff= 494.0 pctdiff= 0.163 rhCtxGM: 296110.746 296782.000 diff= -671.3 pctdiff=-0.227 lhCtxWM: 316500.382 317449.500 diff= -949.1 pctdiff=-0.300 rhCtxWM: 330165.226 332241.500 diff=-2076.3 pctdiff=-0.629 SubCortGMVol 71549.000 SupraTentVol 1343879.351 (1341199.000) diff=2680.351 pctdiff=0.199 SupraTentVolNotVent 1323563.351 (1320883.000) diff=2680.351 pctdiff=0.203 BrainSegVol 1492481.000 (1489239.000) diff=3242.000 pctdiff=0.217 BrainSegVolNotVent 1467905.000 (1464577.351) diff=3327.649 pctdiff=0.227 BrainSegVolNotVent 1467905.000 CerebellumVol 146897.000 VentChorVol 20316.000 3rd4th5thCSF 4260.000 CSFVol 1018.000, OptChiasmVol 125.000 MaskVol 1847800.000 1737 1135 2831 2.448 0.676 0.134 0.036 22 3.0 bankssts 1159 1065 2570 2.728 0.664 0.192 0.053 41 2.9 caudalanteriorcingulate 5272 3916 7810 2.159 0.515 0.118 0.033 70 9.3 caudalmiddlefrontal 2390 1976 3603 1.982 0.623 0.154 0.034 40 3.8 cuneus 495 736 2091 3.697 0.805 0.199 0.039 3 1.0 entorhinal 5078 3878 9931 2.662 0.556 0.151 0.036 99 9.1 fusiform 13557 10803 22526 2.266 0.688 0.129 0.025 138 16.5 inferiorparietal 8865 6554 14961 2.432 0.873 0.118 0.036 218 13.9 inferiortemporal 1170 894 2068 2.535 0.933 0.137 0.054 28 2.9 isthmuscingulate 9662 7113 14572 2.216 0.545 0.125 0.030 132 13.0 lateraloccipital 4096 3650 8315 2.571 0.681 0.178 0.045 72 8.4 lateralorbitofrontal 4926 4178 8045 2.151 0.682 0.154 0.041 83 9.9 lingual 2787 2734 5525 2.329 0.759 0.187 0.068 67 10.8 medialorbitofrontal 6876 5321 13504 2.737 0.832 0.121 0.030 239 10.1 middletemporal 1094 894 1992 2.510 0.724 0.162 0.043 19 2.3 parahippocampal 2891 2202 4885 2.360 0.599 0.123 0.024 28 3.1 paracentral 2384 1951 4624 2.557 0.624 0.156 0.046 35 5.4 parsopercularis 1771 1686 4438 3.135 0.720 0.173 0.039 52 3.3 parsorbitalis 3373 2547 5856 2.520 0.596 0.132 0.033 42 5.1 parstriangularis 1822 1177 1944 1.668 0.379 0.115 0.026 23 2.2 pericalcarine 7860 5924 9429 1.746 0.561 0.116 0.025 73 8.8 postcentral 1937 1570 4238 2.907 0.744 0.170 0.046 64 3.9 posteriorcingulate 10782 7844 16634 2.228 0.712 0.110 0.024 106 11.8 precentral 8489 6225 14230 2.400 0.582 0.131 0.028 119 10.6 precuneus 926 738 1689 2.517 0.627 0.168 0.048 45 1.7 rostralanteriorcingulate 13763 11040 23688 2.381 0.617 0.140 0.032 189 20.8 rostralmiddlefrontal 16077 11927 28932 2.587 0.855 0.130 0.032 205 23.8 superiorfrontal 12108 8999 16429 1.975 0.576 0.119 0.023 112 11.8 superiorparietal 7006 5610 14666 2.964 0.708 0.149 0.038 104 12.6 superiortemporal 7888 6219 12865 2.247 0.626 0.145 0.038 123 14.5 supramarginal 578 628 1592 3.192 0.610 0.188 0.041 7 1.2 frontalpole 753 958 2924 3.835 0.771 0.197 0.038 9 1.5 temporalpole 556 511 1080 2.574 0.742 0.193 0.061 9 1.6 transversetemporal 4166 2837 8140 2.844 0.937 0.166 0.066 245 14.3 insula #----------------------------------------- #@# Cortical Parc 2 lh Mon Dec 19 22:50:48 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 SynthN lh ../surf/lh.sphere.reg /usr/local/freesurfer/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 1.786 2016/11/21 03:01:17 fischl Exp $ reading atlas from /usr/local/freesurfer/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... 66 labels changed using aseg relabeling using gibbs priors... 000: 11396 changed, 185351 examined... 001: 2674 changed, 44195 examined... 002: 846 changed, 13997 examined... 003: 318 changed, 4659 examined... 004: 166 changed, 1883 examined... 005: 99 changed, 977 examined... 006: 57 changed, 579 examined... 007: 22 changed, 315 examined... 008: 11 changed, 123 examined... 009: 5 changed, 59 examined... 010: 1 changed, 32 examined... 011: 3 changed, 8 examined... 012: 2 changed, 14 examined... 013: 3 changed, 10 examined... 014: 2 changed, 13 examined... 015: 2 changed, 16 examined... 016: 1 changed, 10 examined... 017: 1 changed, 7 examined... 018: 2 changed, 6 examined... 019: 2 changed, 10 examined... 020: 0 changed, 12 examined... 13 labels changed using aseg 000: 307 total segments, 222 labels (3453 vertices) changed 001: 105 total segments, 20 labels (45 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 50 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1520 vertices marked for relabeling... 1520 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 16 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Mon Dec 19 22:51:04 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 SynthN rh ../surf/rh.sphere.reg /usr/local/freesurfer/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 1.786 2016/11/21 03:01:17 fischl Exp $ reading atlas from /usr/local/freesurfer/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... 133 labels changed using aseg relabeling using gibbs priors... 000: 11859 changed, 182025 examined... 001: 2825 changed, 46497 examined... 002: 777 changed, 14673 examined... 003: 344 changed, 4419 examined... 004: 169 changed, 2000 examined... 005: 84 changed, 967 examined... 006: 56 changed, 492 examined... 007: 29 changed, 327 examined... 008: 19 changed, 155 examined... 009: 9 changed, 109 examined... 010: 6 changed, 55 examined... 011: 3 changed, 34 examined... 012: 2 changed, 19 examined... 013: 2 changed, 10 examined... 014: 1 changed, 10 examined... 015: 0 changed, 7 examined... 38 labels changed using aseg 000: 346 total segments, 255 labels (4172 vertices) changed 001: 111 total segments, 22 labels (117 vertices) changed 002: 89 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 67 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1456 vertices marked for relabeling... 1456 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 17 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Mon Dec 19 22:51:21 GMT 2016 /usr/local/freesurfer/subjects/SynthN/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 SynthN lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /usr/local/freesurfer/subjects/SynthN/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/SynthN/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthN/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 308895 Total vertex volume 305343 (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) = 1204641 mm^3 (det: 1.617166 ) lhCtxGM: 303353.998 302860.000 diff= 494.0 pctdiff= 0.163 rhCtxGM: 296110.746 296782.000 diff= -671.3 pctdiff=-0.227 lhCtxWM: 316500.382 317449.500 diff= -949.1 pctdiff=-0.300 rhCtxWM: 330165.226 332241.500 diff=-2076.3 pctdiff=-0.629 SubCortGMVol 71549.000 SupraTentVol 1343879.351 (1341199.000) diff=2680.351 pctdiff=0.199 SupraTentVolNotVent 1323563.351 (1320883.000) diff=2680.351 pctdiff=0.203 BrainSegVol 1492481.000 (1489239.000) diff=3242.000 pctdiff=0.217 BrainSegVolNotVent 1467905.000 (1464577.351) diff=3327.649 pctdiff=0.227 BrainSegVolNotVent 1467905.000 CerebellumVol 146897.000 VentChorVol 20316.000 3rd4th5thCSF 4260.000 CSFVol 1018.000, OptChiasmVol 125.000 MaskVol 1847800.000 1701 1137 2900 2.454 0.568 0.125 0.026 18 1.8 G&S_frontomargin 2220 1449 3965 2.417 0.606 0.129 0.031 26 2.8 G&S_occipital_inf 2409 1481 3597 2.014 0.597 0.103 0.022 20 2.5 G&S_paracentral 1951 1290 3780 2.524 0.669 0.147 0.041 35 3.6 G&S_subcentral 1059 706 2340 2.701 0.608 0.165 0.051 19 2.4 G&S_transv_frontopol 2364 1701 4840 2.730 0.551 0.125 0.025 25 2.3 G&S_cingul-Ant 1767 1207 3465 2.805 0.739 0.119 0.020 20 1.4 G&S_cingul-Mid-Ant 1906 1368 3431 2.526 0.708 0.151 0.037 28 3.3 G&S_cingul-Mid-Post 913 609 2538 3.192 0.649 0.166 0.043 17 1.6 G_cingul-Post-dorsal 498 285 933 2.881 0.929 0.119 0.032 7 0.5 G_cingul-Post-ventral 2123 1494 3617 2.080 0.589 0.164 0.034 34 3.1 G_cuneus 1582 1102 4108 2.745 0.612 0.127 0.023 23 1.5 G_front_inf-Opercular 441 319 1427 2.965 0.593 0.158 0.032 8 0.6 G_front_inf-Orbital 1183 823 3262 2.773 0.626 0.134 0.026 17 1.4 G_front_inf-Triangul 7102 4404 11658 2.237 0.651 0.140 0.037 95 12.6 G_front_middle 10678 6974 22923 2.687 0.748 0.132 0.037 135 17.5 G_front_sup 835 553 1646 2.868 0.912 0.127 0.091 13 4.8 G_Ins_lg&S_cent_ins 838 582 2459 3.302 0.707 0.130 0.037 12 1.4 G_insular_short 4049 2290 6576 2.394 0.640 0.125 0.032 44 5.5 G_occipital_middle 2043 1305 2827 1.970 0.719 0.146 0.038 30 3.5 G_occipital_sup 2031 1535 5174 2.667 0.588 0.155 0.035 38 3.0 G_oc-temp_lat-fusifor 3320 2280 6207 2.350 0.811 0.152 0.038 47 5.6 G_oc-temp_med-Lingual 1202 804 3136 2.853 0.905 0.079 0.018 6 0.7 G_oc-temp_med-Parahip 2959 2037 8445 3.159 0.678 0.147 0.034 54 4.0 G_orbital 3851 2249 6174 2.378 0.664 0.118 0.034 40 5.7 G_pariet_inf-Angular 3650 2421 7115 2.501 0.658 0.134 0.037 55 5.7 G_pariet_inf-Supramar 5448 3224 8722 2.221 0.660 0.109 0.027 49 6.0 G_parietal_sup 5300 3253 7791 2.035 0.707 0.112 0.026 47 6.2 G_postcentral 4203 2473 7731 2.548 0.798 0.107 0.035 42 6.0 G_precentral 3579 2428 7523 2.519 0.617 0.139 0.031 45 4.9 G_precuneus 944 677 2300 2.583 0.839 0.168 0.052 21 2.1 G_rectus 856 544 1406 2.491 1.013 0.092 0.039 7 0.9 G_subcallosal 971 646 2407 2.770 0.612 0.121 0.036 14 1.2 G_temp_sup-G_T_transv 3621 2389 8902 2.806 0.783 0.142 0.039 57 6.4 G_temp_sup-Lateral 1012 695 2806 3.285 0.644 0.086 0.015 5 0.6 G_temp_sup-Plan_polar 1382 951 2224 2.350 0.473 0.100 0.018 11 1.1 G_temp_sup-Plan_tempo 3680 2476 8055 2.670 0.822 0.139 0.037 57 5.7 G_temporal_inf 4474 2596 8444 2.578 0.862 0.140 0.062 87 13.5 G_temporal_middle 401 277 589 2.457 0.613 0.101 0.014 2 0.2 Lat_Fis-ant-Horizont 482 364 681 2.374 0.749 0.074 0.010 1 0.2 Lat_Fis-ant-Vertical 1374 953 1976 2.631 0.536 0.123 0.020 12 1.2 Lat_Fis-post 2479 1786 3691 1.832 0.568 0.160 0.037 37 4.4 Pole_occipital 2038 1393 6059 3.186 0.704 0.127 0.035 33 2.9 Pole_temporal 2317 1582 2881 2.125 0.562 0.118 0.025 24 2.3 S_calcarine 4175 2848 4689 1.796 0.589 0.087 0.014 18 2.3 S_central 1085 739 1468 2.303 0.476 0.091 0.014 4 0.7 S_cingul-Marginalis 762 504 1292 2.848 0.717 0.073 0.010 2 0.3 S_circular_insula_ant 1838 1198 2745 2.530 0.702 0.084 0.011 7 0.8 S_circular_insula_inf 1746 1177 2645 2.636 0.616 0.099 0.016 8 1.2 S_circular_insula_sup 1298 952 1769 1.990 0.580 0.118 0.020 14 1.3 S_collat_transv_ant 540 374 558 1.805 0.463 0.111 0.013 4 0.3 S_collat_transv_post 3087 2135 4368 2.037 0.526 0.107 0.016 24 2.0 S_front_inf 2272 1545 3157 2.211 0.530 0.119 0.022 19 1.9 S_front_middle 4300 2852 6550 2.357 0.544 0.099 0.018 27 3.1 S_front_sup 119 85 231 2.707 0.487 0.098 0.016 1 0.1 S_interm_prim-Jensen 4705 3265 5606 1.898 0.428 0.104 0.015 31 3.2 S_intrapariet&P_trans 1454 993 1589 1.907 0.497 0.110 0.019 12 1.1 S_oc_middle&Lunatus 1895 1265 2044 1.767 0.388 0.101 0.016 13 1.1 S_oc_sup&transversal 1007 687 1099 1.851 0.373 0.099 0.017 6 0.7 S_occipital_ant 1341 973 1970 2.274 0.463 0.127 0.023 14 1.2 S_oc-temp_lat 2542 1807 3803 2.205 0.568 0.110 0.018 19 2.0 S_oc-temp_med&Lingual 419 305 617 2.369 0.409 0.120 0.014 3 0.3 S_orbital_lateral 558 421 977 2.481 0.905 0.147 0.031 6 1.0 S_orbital_med-olfact 1635 1157 3121 2.797 0.624 0.129 0.030 20 1.9 S_orbital-H_Shaped 2508 1700 3436 2.269 0.533 0.116 0.020 22 2.0 S_parieto_occipital 1676 1001 1518 2.071 1.158 0.120 0.019 25 1.1 S_pericallosal 6750 4457 8566 2.045 0.571 0.115 0.024 59 7.1 S_postcentral 3084 2092 4178 2.172 0.478 0.104 0.015 21 1.9 S_precentral-inf-part 1969 1331 2368 2.024 0.483 0.092 0.013 10 1.2 S_precentral-sup-part 691 493 1090 2.616 0.667 0.125 0.015 5 0.5 S_suborbital 1792 1258 2675 2.298 0.532 0.116 0.021 13 1.5 S_subparietal 2477 1687 3383 2.307 0.485 0.097 0.014 14 1.5 S_temporal_inf 8619 5804 14295 2.468 0.734 0.102 0.018 62 6.1 S_temporal_sup 580 393 808 2.510 0.482 0.112 0.021 3 0.4 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Mon Dec 19 22:51:53 GMT 2016 /usr/local/freesurfer/subjects/SynthN/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 SynthN rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /usr/local/freesurfer/subjects/SynthN/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/SynthN/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthN/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 301678 Total vertex volume 298678 (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) = 1204641 mm^3 (det: 1.617166 ) lhCtxGM: 303353.998 302860.000 diff= 494.0 pctdiff= 0.163 rhCtxGM: 296110.746 296782.000 diff= -671.3 pctdiff=-0.227 lhCtxWM: 316500.382 317449.500 diff= -949.1 pctdiff=-0.300 rhCtxWM: 330165.226 332241.500 diff=-2076.3 pctdiff=-0.629 SubCortGMVol 71549.000 SupraTentVol 1343879.351 (1341199.000) diff=2680.351 pctdiff=0.199 SupraTentVolNotVent 1323563.351 (1320883.000) diff=2680.351 pctdiff=0.203 BrainSegVol 1492481.000 (1489239.000) diff=3242.000 pctdiff=0.217 BrainSegVolNotVent 1467905.000 (1464577.351) diff=3327.649 pctdiff=0.227 BrainSegVolNotVent 1467905.000 CerebellumVol 146897.000 VentChorVol 20316.000 3rd4th5thCSF 4260.000 CSFVol 1018.000, OptChiasmVol 125.000 MaskVol 1847800.000 1377 921 2693 2.466 0.689 0.138 0.032 17 2.1 G&S_frontomargin 1576 1074 2487 2.339 0.519 0.142 0.035 17 2.4 G&S_occipital_inf 1918 1155 2733 2.027 0.580 0.128 0.039 39 3.9 G&S_paracentral 1779 1186 3330 2.417 0.686 0.128 0.029 19 2.2 G&S_subcentral 1460 872 2758 2.722 0.645 0.134 0.036 24 2.4 G&S_transv_frontopol 3672 2630 7021 2.549 0.715 0.130 0.028 44 4.3 G&S_cingul-Ant 1538 1117 3425 2.874 0.520 0.116 0.021 14 1.4 G&S_cingul-Mid-Ant 1870 1305 3644 2.751 0.660 0.130 0.024 18 2.0 G&S_cingul-Mid-Post 629 409 1829 3.272 0.644 0.151 0.034 9 0.8 G_cingul-Post-dorsal 327 190 534 2.275 0.927 0.097 0.043 4 0.6 G_cingul-Post-ventral 2194 1558 3513 1.944 0.659 0.162 0.036 36 3.6 G_cuneus 1886 1253 4537 2.743 0.630 0.133 0.035 26 3.0 G_front_inf-Opercular 632 407 1619 3.034 0.586 0.155 0.048 12 1.2 G_front_inf-Orbital 1530 904 2821 2.501 0.596 0.122 0.036 20 2.0 G_front_inf-Triangul 6836 4300 12716 2.410 0.620 0.132 0.036 83 10.9 G_front_middle 10942 6612 21050 2.616 0.925 0.131 0.038 224 20.0 G_front_sup 697 497 1535 2.926 0.961 0.163 0.062 13 2.3 G_Ins_lg&S_cent_ins 1192 778 2878 3.107 1.231 0.133 0.049 18 2.4 G_insular_short 4027 2501 7822 2.519 0.592 0.143 0.037 59 6.5 G_occipital_middle 2282 1485 3512 2.059 0.534 0.140 0.030 29 2.7 G_occipital_sup 2146 1468 4414 2.616 0.576 0.135 0.030 30 2.8 G_oc-temp_lat-fusifor 3103 2133 5250 2.057 0.700 0.148 0.041 46 5.6 G_oc-temp_med-Lingual 1152 811 3549 3.232 0.864 0.134 0.043 22 2.2 G_oc-temp_med-Parahip 3562 2356 8953 2.875 0.788 0.148 0.045 63 6.5 G_orbital 5102 3061 9822 2.466 0.757 0.122 0.034 70 7.0 G_pariet_inf-Angular 4124 2808 7528 2.349 0.611 0.152 0.046 68 8.8 G_pariet_inf-Supramar 4299 2493 6746 2.190 0.622 0.109 0.025 43 4.5 G_parietal_sup 2627 1644 3403 1.745 0.479 0.118 0.033 35 4.2 G_postcentral 4067 2517 7021 2.294 0.865 0.125 0.040 68 7.4 G_precentral 4034 2630 7952 2.461 0.626 0.138 0.027 54 4.3 G_precuneus 741 550 1966 2.492 0.785 0.161 0.051 19 1.6 G_rectus 546 382 1076 2.798 0.994 0.135 0.052 9 1.0 G_subcallosal 474 295 1023 2.749 0.819 0.134 0.037 8 0.8 G_temp_sup-G_T_transv 2410 1416 5959 3.108 0.798 0.122 0.036 28 3.7 G_temp_sup-Lateral 1126 762 2827 3.315 0.746 0.086 0.019 5 0.8 G_temp_sup-Plan_polar 1068 748 2343 2.869 0.590 0.109 0.024 9 0.8 G_temp_sup-Plan_tempo 5575 3659 8957 2.364 0.906 0.147 0.059 88 16.1 G_temporal_inf 4339 2878 8955 2.744 0.898 0.143 0.039 62 8.0 G_temporal_middle 387 277 584 2.376 0.538 0.115 0.016 2 0.3 Lat_Fis-ant-Horizont 338 244 485 2.513 0.463 0.120 0.023 2 0.4 Lat_Fis-ant-Vertical 1511 1044 1983 2.286 0.676 0.109 0.017 10 1.2 Lat_Fis-post 3814 2517 5450 2.013 0.494 0.142 0.033 44 5.1 Pole_occipital 2083 1527 6628 3.286 0.789 0.157 0.050 34 5.0 Pole_temporal 2127 1511 2587 2.010 0.605 0.113 0.021 18 1.7 S_calcarine 4090 2770 4390 1.774 0.547 0.083 0.012 16 2.1 S_central 1615 1129 2507 2.319 0.723 0.090 0.013 7 0.9 S_cingul-Marginalis 687 485 1103 2.870 0.548 0.102 0.022 3 0.7 S_circular_insula_ant 1322 851 1865 2.562 0.606 0.085 0.013 7 0.9 S_circular_insula_inf 1379 947 2039 2.416 0.579 0.094 0.016 5 1.0 S_circular_insula_sup 1195 902 2287 2.725 0.811 0.121 0.027 10 1.3 S_collat_transv_ant 628 425 1055 2.475 0.616 0.122 0.023 5 0.6 S_collat_transv_post 2991 2033 4115 2.225 0.508 0.123 0.023 29 2.7 S_front_inf 4183 2744 6432 2.271 0.636 0.119 0.026 39 4.6 S_front_middle 4396 2943 6334 2.276 0.517 0.106 0.021 29 3.8 S_front_sup 771 509 951 2.214 0.520 0.101 0.019 4 0.6 S_interm_prim-Jensen 4965 3319 5512 1.814 0.424 0.108 0.018 41 3.7 S_intrapariet&P_trans 1651 1132 2202 2.258 0.525 0.120 0.024 13 1.5 S_oc_middle&Lunatus 1868 1300 2125 1.759 0.449 0.103 0.019 11 1.4 S_oc_sup&transversal 790 548 1327 2.428 0.662 0.118 0.027 6 0.9 S_occipital_ant 1338 950 2550 2.760 0.662 0.129 0.037 12 1.9 S_oc-temp_lat 2667 1847 3785 2.386 0.526 0.136 0.032 31 4.0 S_oc-temp_med&Lingual 572 424 956 2.516 0.429 0.102 0.014 3 0.4 S_orbital_lateral 631 452 1076 2.147 0.777 0.122 0.027 7 0.8 S_orbital_med-olfact 1649 1161 2905 2.446 0.593 0.137 0.025 20 2.0 S_orbital-H_Shaped 2898 1968 3991 2.311 0.536 0.104 0.015 20 1.9 S_parieto_occipital 1308 796 1181 2.148 0.740 0.141 0.024 24 1.0 S_pericallosal 3476 2321 3671 1.762 0.471 0.106 0.016 28 2.0 S_postcentral 2369 1685 3405 2.168 0.519 0.106 0.017 16 1.7 S_precentral-inf-part 2319 1568 2683 2.007 0.567 0.105 0.019 14 2.2 S_precentral-sup-part 267 207 444 2.580 0.687 0.135 0.021 2 0.2 S_suborbital 1617 1165 2375 2.302 0.486 0.118 0.019 11 1.3 S_subparietal 1721 1423 2650 2.263 0.665 0.160 0.053 24 4.4 S_temporal_inf 9467 6503 14228 2.357 0.672 0.098 0.016 57 6.4 S_temporal_sup 371 243 612 2.742 0.748 0.128 0.015 4 0.3 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Mon Dec 19 22:52:24 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 SynthN lh ../surf/lh.sphere.reg /usr/local/freesurfer/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 1.786 2016/11/21 03:01:17 fischl Exp $ reading atlas from /usr/local/freesurfer/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... 1479 labels changed using aseg relabeling using gibbs priors... 000: 2439 changed, 185351 examined... 001: 548 changed, 11235 examined... 002: 152 changed, 3174 examined... 003: 66 changed, 893 examined... 004: 34 changed, 411 examined... 005: 21 changed, 199 examined... 006: 9 changed, 110 examined... 007: 5 changed, 59 examined... 008: 5 changed, 29 examined... 009: 2 changed, 36 examined... 010: 5 changed, 14 examined... 011: 1 changed, 21 examined... 012: 0 changed, 7 examined... 176 labels changed using aseg 000: 60 total segments, 27 labels (323 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 9 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 874 vertices marked for relabeling... 874 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 16 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Mon Dec 19 22:52:40 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 SynthN rh ../surf/rh.sphere.reg /usr/local/freesurfer/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 1.786 2016/11/21 03:01:17 fischl Exp $ reading atlas from /usr/local/freesurfer/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... 1709 labels changed using aseg relabeling using gibbs priors... 000: 2479 changed, 182025 examined... 001: 602 changed, 11419 examined... 002: 198 changed, 3345 examined... 003: 92 changed, 1149 examined... 004: 45 changed, 522 examined... 005: 29 changed, 236 examined... 006: 19 changed, 157 examined... 007: 16 changed, 102 examined... 008: 14 changed, 91 examined... 009: 12 changed, 71 examined... 010: 10 changed, 58 examined... 011: 7 changed, 51 examined... 012: 6 changed, 45 examined... 013: 5 changed, 32 examined... 014: 4 changed, 25 examined... 015: 6 changed, 27 examined... 016: 5 changed, 27 examined... 017: 5 changed, 24 examined... 018: 6 changed, 29 examined... 019: 2 changed, 24 examined... 020: 2 changed, 17 examined... 021: 0 changed, 10 examined... 401 labels changed using aseg 000: 57 total segments, 24 labels (559 vertices) changed 001: 34 total segments, 1 labels (6 vertices) changed 002: 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... 857 vertices marked for relabeling... 857 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 16 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Mon Dec 19 22:52:56 GMT 2016 /usr/local/freesurfer/subjects/SynthN/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 SynthN lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /usr/local/freesurfer/subjects/SynthN/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/SynthN/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthN/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 308895 Total vertex volume 305343 (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) = 1204641 mm^3 (det: 1.617166 ) lhCtxGM: 303353.998 302860.000 diff= 494.0 pctdiff= 0.163 rhCtxGM: 296110.746 296782.000 diff= -671.3 pctdiff=-0.227 lhCtxWM: 316500.382 317449.500 diff= -949.1 pctdiff=-0.300 rhCtxWM: 330165.226 332241.500 diff=-2076.3 pctdiff=-0.629 SubCortGMVol 71549.000 SupraTentVol 1343879.351 (1341199.000) diff=2680.351 pctdiff=0.199 SupraTentVolNotVent 1323563.351 (1320883.000) diff=2680.351 pctdiff=0.203 BrainSegVol 1492481.000 (1489239.000) diff=3242.000 pctdiff=0.217 BrainSegVolNotVent 1467905.000 (1464577.351) diff=3327.649 pctdiff=0.227 BrainSegVolNotVent 1467905.000 CerebellumVol 146897.000 VentChorVol 20316.000 3rd4th5thCSF 4260.000 CSFVol 1018.000, OptChiasmVol 125.000 MaskVol 1847800.000 2113 1380 4300 3.028 0.701 0.128 0.023 29 1.8 caudalanteriorcingulate 6117 4047 8649 2.091 0.544 0.120 0.028 65 8.1 caudalmiddlefrontal 3292 2270 5063 2.143 0.598 0.148 0.031 43 4.2 cuneus 560 427 1671 2.785 1.004 0.087 0.019 2 0.4 entorhinal 4902 3650 9208 2.280 0.631 0.138 0.027 71 5.8 fusiform 10760 6693 15684 2.271 0.642 0.113 0.026 93 12.5 inferiorparietal 6873 4677 13609 2.567 0.750 0.126 0.031 92 9.0 inferiortemporal 2016 1284 3763 2.679 0.886 0.123 0.028 26 2.1 isthmuscingulate 10344 6757 15012 2.057 0.639 0.134 0.030 124 13.8 lateraloccipital 5114 3534 11586 2.910 0.760 0.139 0.034 77 7.3 lateralorbitofrontal 5010 3474 8712 2.336 0.736 0.137 0.032 58 6.9 lingual 2470 1766 4976 2.485 0.795 0.139 0.036 39 3.6 medialorbitofrontal 9764 6175 17780 2.590 0.785 0.118 0.038 121 17.1 middletemporal 1021 641 1998 2.601 0.867 0.077 0.015 5 0.4 parahippocampal 3399 2260 5995 2.308 0.661 0.102 0.017 21 2.5 paracentral 2616 1811 5050 2.504 0.679 0.112 0.018 25 1.9 parsopercularis 1147 816 2858 2.859 0.637 0.126 0.025 13 1.1 parsorbitalis 2575 1805 5014 2.375 0.670 0.112 0.019 24 2.1 parstriangularis 1568 1060 1772 1.839 0.430 0.123 0.024 17 1.6 pericalcarine 13296 8511 18256 1.979 0.653 0.112 0.024 120 14.2 postcentral 2524 1730 4477 2.393 0.956 0.152 0.037 43 4.2 posteriorcingulate 10494 6721 17335 2.400 0.704 0.104 0.025 89 11.2 precentral 7419 5043 12627 2.372 0.589 0.125 0.025 78 7.7 precuneus 1827 1272 3542 2.729 0.755 0.135 0.027 24 1.9 rostralanteriorcingulate 9208 5943 15363 2.308 0.638 0.124 0.026 97 10.3 rostralmiddlefrontal 16027 10545 30514 2.586 0.709 0.126 0.033 175 22.7 superiorfrontal 11428 7244 15882 2.041 0.582 0.105 0.021 84 9.8 superiorparietal 11302 7630 24102 2.716 0.782 0.118 0.027 127 12.9 superiortemporal 6817 4589 11796 2.483 0.632 0.127 0.032 83 9.6 supramarginal 979 666 2186 2.758 0.593 0.121 0.027 11 1.1 transversetemporal 3178 2185 6562 2.914 0.726 0.104 0.035 28 6.3 insula #----------------------------------------- #@# Parcellation Stats 3 rh Mon Dec 19 22:53:29 GMT 2016 /usr/local/freesurfer/subjects/SynthN/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 SynthN rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /usr/local/freesurfer/subjects/SynthN/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/SynthN/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthN/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 301678 Total vertex volume 298678 (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) = 1204641 mm^3 (det: 1.617166 ) lhCtxGM: 303353.998 302860.000 diff= 494.0 pctdiff= 0.163 rhCtxGM: 296110.746 296782.000 diff= -671.3 pctdiff=-0.227 lhCtxWM: 316500.382 317449.500 diff= -949.1 pctdiff=-0.300 rhCtxWM: 330165.226 332241.500 diff=-2076.3 pctdiff=-0.629 SubCortGMVol 71549.000 SupraTentVol 1343879.351 (1341199.000) diff=2680.351 pctdiff=0.199 SupraTentVolNotVent 1323563.351 (1320883.000) diff=2680.351 pctdiff=0.203 BrainSegVol 1492481.000 (1489239.000) diff=3242.000 pctdiff=0.217 BrainSegVolNotVent 1467905.000 (1464577.351) diff=3327.649 pctdiff=0.227 BrainSegVolNotVent 1467905.000 CerebellumVol 146897.000 VentChorVol 20316.000 3rd4th5thCSF 4260.000 CSFVol 1018.000, OptChiasmVol 125.000 MaskVol 1847800.000 1311 893 2823 2.718 0.651 0.133 0.022 18 1.2 caudalanteriorcingulate 5572 3700 8199 2.170 0.509 0.119 0.027 48 6.7 caudalmiddlefrontal 3146 2163 4783 2.023 0.617 0.139 0.025 39 3.3 cuneus 479 347 2092 3.730 0.788 0.123 0.032 7 0.7 entorhinal 4733 3296 8933 2.635 0.545 0.128 0.026 54 5.1 fusiform 13436 8726 22355 2.262 0.697 0.112 0.025 135 13.9 inferiorparietal 9123 6249 15745 2.454 0.874 0.147 0.054 132 23.4 inferiortemporal 1205 804 2111 2.552 0.896 0.124 0.035 17 1.4 isthmuscingulate 9854 6464 14944 2.217 0.547 0.137 0.032 108 12.8 lateraloccipital 5130 3509 10431 2.548 0.798 0.143 0.041 82 9.1 lateralorbitofrontal 4800 3370 7871 2.153 0.684 0.143 0.035 62 7.4 lingual 2215 1637 4863 2.489 0.866 0.151 0.046 44 4.0 medialorbitofrontal 8297 5826 16010 2.715 0.801 0.133 0.035 97 13.6 middletemporal 1145 806 2052 2.510 0.716 0.159 0.057 24 3.3 parahippocampal 3114 2053 5210 2.342 0.605 0.104 0.016 21 2.1 paracentral 2739 1856 5172 2.528 0.602 0.126 0.031 31 3.7 parsopercularis 1374 915 3357 3.027 0.823 0.140 0.038 19 2.1 parsorbitalis 3375 2141 5694 2.511 0.611 0.119 0.029 34 3.9 parstriangularis 1828 1260 1931 1.663 0.380 0.113 0.027 17 2.1 pericalcarine 8627 5598 10504 1.764 0.567 0.106 0.026 97 10.7 postcentral 1977 1361 4259 2.892 0.765 0.146 0.030 27 2.5 posteriorcingulate 9987 6523 15892 2.248 0.713 0.109 0.026 102 11.5 precentral 8577 5783 14432 2.384 0.602 0.124 0.022 88 7.9 precuneus 1136 827 2148 2.510 0.650 0.143 0.029 19 1.4 rostralanteriorcingulate 9991 6544 17305 2.399 0.633 0.128 0.029 110 12.4 rostralmiddlefrontal 20651 13025 36767 2.554 0.825 0.125 0.033 316 31.2 superiorfrontal 10283 6486 13742 1.965 0.556 0.111 0.022 95 9.1 superiorparietal 8919 5795 19359 2.935 0.799 0.112 0.028 80 10.1 superiortemporal 7422 5027 11901 2.248 0.617 0.135 0.033 97 10.8 supramarginal 573 373 1105 2.608 0.752 0.138 0.036 9 0.9 transversetemporal 3301 2277 6690 2.876 0.815 0.116 0.028 30 4.5 insula #----------------------------------------- #@# WM/GM Contrast lh Mon Dec 19 22:54:03 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts pctsurfcon --s SynthN --lh-only Log file is /usr/local/freesurfer/subjects/SynthN/scripts/pctsurfcon.log Mon Dec 19 22:54:03 GMT 2016 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/SynthN/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux stefano-Q170M-C 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /usr/local/freesurfer/subjects/SynthN/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /usr/local/freesurfer/subjects/SynthN/surf/tmp.pctsurfcon.10467/lh.wm.mgh --regheader SynthN --cortex srcvol = /usr/local/freesurfer/subjects/SynthN/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /usr/local/freesurfer/subjects/SynthN/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 /usr/local/freesurfer/subjects/SynthN/label/lh.cortex.label Reading surface /usr/local/freesurfer/subjects/SynthN/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 = 102787 Masking with /usr/local/freesurfer/subjects/SynthN/label/lh.cortex.label Writing to /usr/local/freesurfer/subjects/SynthN/surf/tmp.pctsurfcon.10467/lh.wm.mgh Dim: 185351 1 1 mri_vol2surf --mov /usr/local/freesurfer/subjects/SynthN/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /usr/local/freesurfer/subjects/SynthN/surf/tmp.pctsurfcon.10467/lh.gm.mgh --projfrac 0.3 --regheader SynthN --cortex srcvol = /usr/local/freesurfer/subjects/SynthN/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /usr/local/freesurfer/subjects/SynthN/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 /usr/local/freesurfer/subjects/SynthN/label/lh.cortex.label Reading surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/SynthN/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 = 121117 Masking with /usr/local/freesurfer/subjects/SynthN/label/lh.cortex.label Writing to /usr/local/freesurfer/subjects/SynthN/surf/tmp.pctsurfcon.10467/lh.gm.mgh Dim: 185351 1 1 mri_concat /usr/local/freesurfer/subjects/SynthN/surf/tmp.pctsurfcon.10467/lh.wm.mgh /usr/local/freesurfer/subjects/SynthN/surf/tmp.pctsurfcon.10467/lh.gm.mgh --paired-diff-norm --mul 100 --o /usr/local/freesurfer/subjects/SynthN/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 /usr/local/freesurfer/subjects/SynthN/surf/lh.w-g.pct.mgh mri_segstats --in /usr/local/freesurfer/subjects/SynthN/surf/lh.w-g.pct.mgh --annot SynthN lh aparc --sum /usr/local/freesurfer/subjects/SynthN/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 /usr/local/freesurfer/subjects/SynthN/surf/lh.w-g.pct.mgh --annot SynthN lh aparc --sum /usr/local/freesurfer/subjects/SynthN/stats/lh.w-g.pct.stats --snr sysname Linux hostname stefano-Q170M-C machine x86_64 user stefano UseRobust 0 Constructing seg from annotation Reading annotation /usr/local/freesurfer/subjects/SynthN/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 /usr/local/freesurfer/subjects/SynthN/surf/lh.w-g.pct.mgh Vertex Area is 0.660716 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 Mon Dec 19 22:54:08 GMT 2016 /usr/local/freesurfer/subjects/SynthN/scripts pctsurfcon --s SynthN --rh-only Log file is /usr/local/freesurfer/subjects/SynthN/scripts/pctsurfcon.log Mon Dec 19 22:54:08 GMT 2016 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/SynthN/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux stefano-Q170M-C 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /usr/local/freesurfer/subjects/SynthN/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /usr/local/freesurfer/subjects/SynthN/surf/tmp.pctsurfcon.10542/rh.wm.mgh --regheader SynthN --cortex srcvol = /usr/local/freesurfer/subjects/SynthN/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /usr/local/freesurfer/subjects/SynthN/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 /usr/local/freesurfer/subjects/SynthN/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/SynthN/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 = 100827 Masking with /usr/local/freesurfer/subjects/SynthN/label/rh.cortex.label Writing to /usr/local/freesurfer/subjects/SynthN/surf/tmp.pctsurfcon.10542/rh.wm.mgh Dim: 182025 1 1 mri_vol2surf --mov /usr/local/freesurfer/subjects/SynthN/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /usr/local/freesurfer/subjects/SynthN/surf/tmp.pctsurfcon.10542/rh.gm.mgh --projfrac 0.3 --regheader SynthN --cortex srcvol = /usr/local/freesurfer/subjects/SynthN/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /usr/local/freesurfer/subjects/SynthN/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 /usr/local/freesurfer/subjects/SynthN/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/SynthN/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 = 118117 Masking with /usr/local/freesurfer/subjects/SynthN/label/rh.cortex.label Writing to /usr/local/freesurfer/subjects/SynthN/surf/tmp.pctsurfcon.10542/rh.gm.mgh Dim: 182025 1 1 mri_concat /usr/local/freesurfer/subjects/SynthN/surf/tmp.pctsurfcon.10542/rh.wm.mgh /usr/local/freesurfer/subjects/SynthN/surf/tmp.pctsurfcon.10542/rh.gm.mgh --paired-diff-norm --mul 100 --o /usr/local/freesurfer/subjects/SynthN/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 /usr/local/freesurfer/subjects/SynthN/surf/rh.w-g.pct.mgh mri_segstats --in /usr/local/freesurfer/subjects/SynthN/surf/rh.w-g.pct.mgh --annot SynthN rh aparc --sum /usr/local/freesurfer/subjects/SynthN/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 /usr/local/freesurfer/subjects/SynthN/surf/rh.w-g.pct.mgh --annot SynthN rh aparc --sum /usr/local/freesurfer/subjects/SynthN/stats/rh.w-g.pct.stats --snr sysname Linux hostname stefano-Q170M-C machine x86_64 user stefano UseRobust 0 Constructing seg from annotation Reading annotation /usr/local/freesurfer/subjects/SynthN/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 /usr/local/freesurfer/subjects/SynthN/surf/rh.w-g.pct.mgh Vertex Area is 0.663648 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 Mon Dec 19 22:54:14 GMT 2016 /usr/local/freesurfer/subjects/SynthN/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 1969 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 26722 voxels changed to hypointensity... 23671 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Mon Dec 19 22:54:33 GMT 2016 /usr/local/freesurfer/subjects/SynthN mri_aparc2aseg --s SynthN --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/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/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /usr/local/freesurfer/subjects subject SynthN outvol /usr/local/freesurfer/subjects/SynthN/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/SynthN/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/SynthN/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 /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/SynthN/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/SynthN/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 /usr/local/freesurfer/subjects/SynthN/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 /usr/local/freesurfer/subjects/SynthN/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 8.78 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 103 rescaling Left_Cerebral_Cortex from 61 --> 60 rescaling Left_Lateral_Ventricle from 13 --> 11 rescaling Left_Inf_Lat_Vent from 34 --> 31 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 67 rescaling Left_Thalamus from 94 --> 100 rescaling Left_Thalamus_Proper from 84 --> 94 rescaling Left_Caudate from 75 --> 79 rescaling Left_Putamen from 80 --> 84 rescaling Left_Pallidum from 98 --> 95 rescaling Third_Ventricle from 25 --> 12 rescaling Fourth_Ventricle from 22 --> 7 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 55 rescaling Left_Amygdala from 56 --> 67 rescaling CSF from 32 --> 17 rescaling Left_Accumbens_area from 62 --> 63 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 99 rescaling Right_Cerebral_Cortex from 58 --> 80 rescaling Right_Lateral_Ventricle from 13 --> 4 rescaling Right_Inf_Lat_Vent from 25 --> 22 rescaling Right_Cerebellum_White_Matter from 87 --> 85 rescaling Right_Cerebellum_Cortex from 59 --> 80 rescaling Right_Thalamus_Proper from 85 --> 89 rescaling Right_Caudate from 62 --> 66 rescaling Right_Putamen from 80 --> 74 rescaling Right_Pallidum from 97 --> 98 rescaling Right_Hippocampus from 53 --> 55 rescaling Right_Amygdala from 55 --> 62 rescaling Right_Accumbens_area from 65 --> 67 rescaling Right_VentralDC from 86 --> 104 rescaling Fifth_Ventricle from 40 --> 15 rescaling WM_hypointensities from 78 --> 74 rescaling non_WM_hypointensities from 40 --> 42 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 = 599387 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 168 changed. pass 2: 16 changed. pass 3: 1 changed. pass 4: 0 changed. Writing output aseg to /usr/local/freesurfer/subjects/SynthN/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Mon Dec 19 22:58:21 GMT 2016 /usr/local/freesurfer/subjects/SynthN mri_aparc2aseg --s SynthN --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/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/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /usr/local/freesurfer/subjects subject SynthN outvol /usr/local/freesurfer/subjects/SynthN/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/SynthN/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/SynthN/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/SynthN/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/SynthN/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 /usr/local/freesurfer/subjects/SynthN/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 /usr/local/freesurfer/subjects/SynthN/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 8.78 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 103 rescaling Left_Cerebral_Cortex from 61 --> 60 rescaling Left_Lateral_Ventricle from 13 --> 11 rescaling Left_Inf_Lat_Vent from 34 --> 31 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 67 rescaling Left_Thalamus from 94 --> 100 rescaling Left_Thalamus_Proper from 84 --> 94 rescaling Left_Caudate from 75 --> 79 rescaling Left_Putamen from 80 --> 84 rescaling Left_Pallidum from 98 --> 95 rescaling Third_Ventricle from 25 --> 12 rescaling Fourth_Ventricle from 22 --> 7 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 55 rescaling Left_Amygdala from 56 --> 67 rescaling CSF from 32 --> 17 rescaling Left_Accumbens_area from 62 --> 63 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 99 rescaling Right_Cerebral_Cortex from 58 --> 80 rescaling Right_Lateral_Ventricle from 13 --> 4 rescaling Right_Inf_Lat_Vent from 25 --> 22 rescaling Right_Cerebellum_White_Matter from 87 --> 85 rescaling Right_Cerebellum_Cortex from 59 --> 80 rescaling Right_Thalamus_Proper from 85 --> 89 rescaling Right_Caudate from 62 --> 66 rescaling Right_Putamen from 80 --> 74 rescaling Right_Pallidum from 97 --> 98 rescaling Right_Hippocampus from 53 --> 55 rescaling Right_Amygdala from 55 --> 62 rescaling Right_Accumbens_area from 65 --> 67 rescaling Right_VentralDC from 86 --> 104 rescaling Fifth_Ventricle from 40 --> 15 rescaling WM_hypointensities from 78 --> 74 rescaling non_WM_hypointensities from 40 --> 42 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 = 599433 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 168 changed. pass 2: 16 changed. pass 3: 1 changed. pass 4: 0 changed. Writing output aseg to /usr/local/freesurfer/subjects/SynthN/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Mon Dec 19 23:02:06 GMT 2016 /usr/local/freesurfer/subjects/SynthN mri_aparc2aseg --s SynthN --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/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/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /usr/local/freesurfer/subjects subject SynthN outvol /usr/local/freesurfer/subjects/SynthN/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/SynthN/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/SynthN/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/SynthN/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/SynthN/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 /usr/local/freesurfer/subjects/SynthN/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 /usr/local/freesurfer/subjects/SynthN/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 8.78 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 103 rescaling Left_Cerebral_Cortex from 61 --> 60 rescaling Left_Lateral_Ventricle from 13 --> 11 rescaling Left_Inf_Lat_Vent from 34 --> 31 rescaling Left_Cerebellum_White_Matter from 86 --> 86 rescaling Left_Cerebellum_Cortex from 60 --> 67 rescaling Left_Thalamus from 94 --> 100 rescaling Left_Thalamus_Proper from 84 --> 94 rescaling Left_Caudate from 75 --> 79 rescaling Left_Putamen from 80 --> 84 rescaling Left_Pallidum from 98 --> 95 rescaling Third_Ventricle from 25 --> 12 rescaling Fourth_Ventricle from 22 --> 7 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 55 rescaling Left_Amygdala from 56 --> 67 rescaling CSF from 32 --> 17 rescaling Left_Accumbens_area from 62 --> 63 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 99 rescaling Right_Cerebral_Cortex from 58 --> 80 rescaling Right_Lateral_Ventricle from 13 --> 4 rescaling Right_Inf_Lat_Vent from 25 --> 22 rescaling Right_Cerebellum_White_Matter from 87 --> 85 rescaling Right_Cerebellum_Cortex from 59 --> 80 rescaling Right_Thalamus_Proper from 85 --> 89 rescaling Right_Caudate from 62 --> 66 rescaling Right_Putamen from 80 --> 74 rescaling Right_Pallidum from 97 --> 98 rescaling Right_Hippocampus from 53 --> 55 rescaling Right_Amygdala from 55 --> 62 rescaling Right_Accumbens_area from 65 --> 67 rescaling Right_VentralDC from 86 --> 104 rescaling Fifth_Ventricle from 40 --> 15 rescaling WM_hypointensities from 78 --> 74 rescaling non_WM_hypointensities from 40 --> 42 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 = 599433 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 168 changed. pass 2: 16 changed. pass 3: 1 changed. pass 4: 0 changed. Writing output aseg to /usr/local/freesurfer/subjects/SynthN/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Mon Dec 19 23:06:13 GMT 2016 /usr/local/freesurfer/subjects/SynthN/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Mon Dec 19 23:06:13 GMT 2016 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/SynthN/mri /usr/local/freesurfer/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-dev-20161130-24fa2c9 $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux stefano-Q170M-C 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 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 /usr/local/freesurfer/subjects/SynthN/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 stefano-Q170M-C machine x86_64 user stefano 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 Mon Dec 19 23:06:13 GMT 2016 Ended at Mon Dec 19 23:06:17 GMT 2016 Apas2aseg-Run-Time-Sec 4 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Mon Dec 19 23:06:17 GMT 2016 /usr/local/freesurfer/subjects/SynthN 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/ASegStatsLUT.txt --subject SynthN $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/ASegStatsLUT.txt --subject SynthN sysname Linux hostname stefano-Q170M-C machine x86_64 user stefano UseRobust 0 atlas_icv (eTIV) = 1204641 mm^3 (det: 1.617166 ) Computing euler number orig.nofix lheno = -80, rheno = -152 orig.nofix lhholes = 41, rhholes = 77 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 303353.998 302860.000 diff= 494.0 pctdiff= 0.163 rhCtxGM: 296110.746 296782.000 diff= -671.3 pctdiff=-0.227 lhCtxWM: 316500.382 317449.500 diff= -949.1 pctdiff=-0.300 rhCtxWM: 330165.226 332241.500 diff=-2076.3 pctdiff=-0.629 SubCortGMVol 71549.000 SupraTentVol 1343879.351 (1341199.000) diff=2680.351 pctdiff=0.199 SupraTentVolNotVent 1323563.351 (1320883.000) diff=2680.351 pctdiff=0.203 BrainSegVol 1492481.000 (1489239.000) diff=3242.000 pctdiff=0.217 BrainSegVolNotVent 1467905.000 (1464577.351) diff=3327.649 pctdiff=0.227 BrainSegVolNotVent 1467905.000 CerebellumVol 146897.000 VentChorVol 20316.000 3rd4th5thCSF 4260.000 CSFVol 1018.000, OptChiasmVol 125.000 MaskVol 1847800.000 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 Mon Dec 19 23:09:00 GMT 2016 /usr/local/freesurfer/subjects/SynthN mri_aparc2aseg --s SynthN --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /usr/local/freesurfer/subjects subject SynthN outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /usr/local/freesurfer/subjects/SynthN/mri/aparc+aseg.mgz Reading lh white surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/SynthN/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/SynthN/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 /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/SynthN/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/SynthN/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 /usr/local/freesurfer/subjects/SynthN/mri/ribbon.mgz Loading filled from /usr/local/freesurfer/subjects/SynthN/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 9217 vertices from left hemi Ripped 7731 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 /usr/local/freesurfer/subjects/SynthN/mri/aseg.mgz Loading Ctx Seg File /usr/local/freesurfer/subjects/SynthN/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 = 1244419 Used brute-force search on 917 voxels Fixing Parahip LH WM Found 9 clusters 0 k 2.000000 1 k 1.000000 2 k 2.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 2.000000 7 k 3.000000 8 k 1325.000000 Fixing Parahip RH WM Found 17 clusters 0 k 5.000000 1 k 1.000000 2 k 1.000000 3 k 3.000000 4 k 1572.000000 5 k 1.000000 6 k 2.000000 7 k 1.000000 8 k 1.000000 9 k 1.000000 10 k 3.000000 11 k 1.000000 12 k 2.000000 13 k 1.000000 14 k 1.000000 15 k 1.000000 16 k 1.000000 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 SynthN --surf-wm-vol --ctab /usr/local/freesurfer/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 SynthN --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname stefano-Q170M-C machine x86_64 user stefano UseRobust 0 atlas_icv (eTIV) = 1204641 mm^3 (det: 1.617166 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 303353.998 302860.000 diff= 494.0 pctdiff= 0.163 rhCtxGM: 296110.746 296782.000 diff= -671.3 pctdiff=-0.227 lhCtxWM: 316500.382 317449.500 diff= -949.1 pctdiff=-0.300 rhCtxWM: 330165.226 332241.500 diff=-2076.3 pctdiff=-0.629 SubCortGMVol 71549.000 SupraTentVol 1343879.351 (1341199.000) diff=2680.351 pctdiff=0.199 SupraTentVolNotVent 1323563.351 (1320883.000) diff=2680.351 pctdiff=0.203 BrainSegVol 1492481.000 (1489239.000) diff=3242.000 pctdiff=0.217 BrainSegVolNotVent 1467905.000 (1464577.351) diff=3327.649 pctdiff=0.227 BrainSegVolNotVent 1467905.000 CerebellumVol 146897.000 VentChorVol 20316.000 3rd4th5thCSF 4260.000 CSFVol 1018.000, OptChiasmVol 125.000 MaskVol 1847800.000 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 /usr/local/freesurfer/subjects/SynthN/label #-------------------------------------------- #@# BA_exvivo Labels lh Mon Dec 19 23:17:26 GMT 2016 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject SynthN --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 2309 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 6438 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.label --trgsubject SynthN --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 4847 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 12756 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.label --trgsubject SynthN --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 489 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4566 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.label --trgsubject SynthN --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 1579 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 7562 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.label --trgsubject SynthN --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 1240 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 7024 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.label --trgsubject SynthN --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 463 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4533 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.label --trgsubject SynthN --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 4670 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 18259 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.label --trgsubject SynthN --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 1027 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 5208 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.label --trgsubject SynthN --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 991 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4413 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.label --trgsubject SynthN --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 1062 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5703 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.label --trgsubject SynthN --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 3775 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 11889 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.label --trgsubject SynthN --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 1150 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 3168 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject SynthN --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 60 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1350 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject SynthN --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 61 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1260 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject SynthN --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 697 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1711 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject SynthN --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 2062 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 4154 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject SynthN --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 199 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1703 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject SynthN --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 474 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2470 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject SynthN --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 319 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2638 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject SynthN --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 125 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1674 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject SynthN --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 2558 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 9593 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject SynthN --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 346 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2258 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject SynthN --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 294 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1445 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject SynthN --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 606 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4011 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject SynthN --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 1555 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4889 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject SynthN --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 227 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 740 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject SynthN --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 24 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 494 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject SynthN --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 185351 Number of reverse mapping hits = 24 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 474 mri_label2label: Done mris_label2annot --s SynthN --hemi lh --ctab /usr/local/freesurfer/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/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 /usr/local/freesurfer/subjects/SynthN/label cmdline mris_label2annot --s SynthN --hemi lh --ctab /usr/local/freesurfer/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 stefano-Q170M-C machine x86_64 user stefano subject SynthN hemi lh SUBJECTS_DIR /usr/local/freesurfer/subjects ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /usr/local/freesurfer/subjects/SynthN/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 126895 unhit vertices Writing annot to /usr/local/freesurfer/subjects/SynthN/label/lh.BA_exvivo.annot mris_label2annot --s SynthN --hemi lh --ctab /usr/local/freesurfer/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/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 /usr/local/freesurfer/subjects/SynthN/label cmdline mris_label2annot --s SynthN --hemi lh --ctab /usr/local/freesurfer/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 stefano-Q170M-C machine x86_64 user stefano subject SynthN hemi lh SUBJECTS_DIR /usr/local/freesurfer/subjects ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /usr/local/freesurfer/subjects/SynthN/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 151996 unhit vertices Writing annot to /usr/local/freesurfer/subjects/SynthN/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 SynthN lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /usr/local/freesurfer/subjects/SynthN/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/SynthN/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 308895 Total vertex volume 305343 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/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) = 1204641 mm^3 (det: 1.617166 ) lhCtxGM: 303353.998 302860.000 diff= 494.0 pctdiff= 0.163 rhCtxGM: 296110.746 296782.000 diff= -671.3 pctdiff=-0.227 lhCtxWM: 316500.382 317449.500 diff= -949.1 pctdiff=-0.300 rhCtxWM: 330165.226 332241.500 diff=-2076.3 pctdiff=-0.629 SubCortGMVol 71549.000 SupraTentVol 1343879.351 (1341199.000) diff=2680.351 pctdiff=0.199 SupraTentVolNotVent 1323563.351 (1320883.000) diff=2680.351 pctdiff=0.203 BrainSegVol 1492481.000 (1489239.000) diff=3242.000 pctdiff=0.217 BrainSegVolNotVent 1467905.000 (1464577.351) diff=3327.649 pctdiff=0.227 BrainSegVolNotVent 1467905.000 CerebellumVol 146897.000 VentChorVol 20316.000 3rd4th5thCSF 4260.000 CSFVol 1018.000, OptChiasmVol 125.000 MaskVol 1847800.000 2406 1375 3925 2.229 0.813 0.109 0.036 25 4.3 BA1_exvivo 9097 5919 12449 2.055 0.589 0.116 0.025 83 9.9 BA2_exvivo 1479 945 1326 1.646 0.461 0.106 0.018 9 1.0 BA3a_exvivo 3489 2351 4527 1.724 0.532 0.112 0.022 32 3.1 BA3b_exvivo 2016 1351 3552 2.317 0.621 0.110 0.029 18 3.0 BA4a_exvivo 1555 1039 2512 2.457 0.560 0.077 0.014 6 0.7 BA4p_exvivo 14845 9592 25080 2.330 0.704 0.114 0.030 150 19.8 BA6_exvivo 3241 2254 6117 2.436 0.587 0.110 0.018 31 2.5 BA44_exvivo 3458 2393 6900 2.431 0.706 0.114 0.020 35 2.8 BA45_exvivo 3005 2135 4040 1.798 0.461 0.130 0.027 35 3.5 V1_exvivo 9665 6563 14561 2.111 0.658 0.152 0.037 137 15.4 V2_exvivo 2990 1894 4067 2.202 0.605 0.118 0.024 27 3.2 MT_exvivo 551 410 1747 3.235 0.888 0.115 0.027 5 0.7 perirhinal_exvivo 659 468 1392 2.519 0.891 0.078 0.014 4 0.3 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab SynthN lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /usr/local/freesurfer/subjects/SynthN/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/SynthN/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthN/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 308895 Total vertex volume 305343 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/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) = 1204641 mm^3 (det: 1.617166 ) lhCtxGM: 303353.998 302860.000 diff= 494.0 pctdiff= 0.163 rhCtxGM: 296110.746 296782.000 diff= -671.3 pctdiff=-0.227 lhCtxWM: 316500.382 317449.500 diff= -949.1 pctdiff=-0.300 rhCtxWM: 330165.226 332241.500 diff=-2076.3 pctdiff=-0.629 SubCortGMVol 71549.000 SupraTentVol 1343879.351 (1341199.000) diff=2680.351 pctdiff=0.199 SupraTentVolNotVent 1323563.351 (1320883.000) diff=2680.351 pctdiff=0.203 BrainSegVol 1492481.000 (1489239.000) diff=3242.000 pctdiff=0.217 BrainSegVolNotVent 1467905.000 (1464577.351) diff=3327.649 pctdiff=0.227 BrainSegVolNotVent 1467905.000 CerebellumVol 146897.000 VentChorVol 20316.000 3rd4th5thCSF 4260.000 CSFVol 1018.000, OptChiasmVol 125.000 MaskVol 1847800.000 1675 998 2645 2.155 0.705 0.112 0.032 15 2.5 BA1_exvivo 4121 2632 5852 2.045 0.656 0.116 0.025 37 4.2 BA2_exvivo 1328 855 1102 1.585 0.400 0.110 0.018 8 1.0 BA3a_exvivo 2203 1478 2332 1.504 0.349 0.093 0.016 13 1.4 BA3b_exvivo 1954 1305 3426 2.395 0.644 0.097 0.024 14 2.3 BA4a_exvivo 1227 838 1835 2.268 0.516 0.078 0.012 4 0.5 BA4p_exvivo 8535 5506 13858 2.279 0.643 0.112 0.029 77 10.9 BA6_exvivo 1903 1361 3678 2.403 0.606 0.114 0.018 20 1.5 BA44_exvivo 1288 918 3351 2.702 0.702 0.122 0.024 16 1.4 BA45_exvivo 3253 2315 4450 1.780 0.498 0.130 0.027 38 3.7 V1_exvivo 4525 3227 6480 2.025 0.572 0.171 0.045 77 9.1 V2_exvivo 710 450 965 2.070 0.516 0.102 0.023 5 0.6 MT_exvivo 274 210 1104 3.620 0.693 0.075 0.009 1 0.1 perirhinal_exvivo 359 237 747 2.522 0.790 0.045 0.007 1 0.1 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Mon Dec 19 23:21:40 GMT 2016 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.label --trgsubject SynthN --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 182025 Number of reverse mapping hits = 792 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4754 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.label --trgsubject SynthN --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 182025 Number of reverse mapping hits = 1017 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7704 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.label --trgsubject SynthN --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 182025 Number of reverse mapping hits = 436 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4416 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.label --trgsubject SynthN --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 182025 Number of reverse mapping hits = 685 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 5207 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.label --trgsubject SynthN --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 182025 Number of reverse mapping hits = 1486 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 7233 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.label --trgsubject SynthN --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 182025 Number of reverse mapping hits = 477 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4950 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.label --trgsubject SynthN --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 182025 Number of reverse mapping hits = 4244 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 16500 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.label --trgsubject SynthN --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 182025 Number of reverse mapping hits = 1793 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 8705 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.label --trgsubject SynthN --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 182025 Number of reverse mapping hits = 2559 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 7914 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.label --trgsubject SynthN --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 182025 Number of reverse mapping hits = 1205 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5932 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.label --trgsubject SynthN --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 182025 Number of reverse mapping hits = 3636 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 11652 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.label --trgsubject SynthN --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = SynthN 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 /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/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 182025 Number of reverse mapping hits = 1216 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 3148 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject SynthN --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = SynthN trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 182025 Number of reverse mapping hits = 25 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1063 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject SynthN --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = SynthN trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 182025 Number of reverse mapping hits = 17 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 769 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject SynthN --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 182025 Number of reverse mapping hits = 172 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 1048 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject SynthN --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 182025 Number of reverse mapping hits = 240 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2928 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject SynthN --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 182025 Number of reverse mapping hits = 187 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1885 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject SynthN --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 182025 Number of reverse mapping hits = 337 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2520 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject SynthN --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 182025 Number of reverse mapping hits = 194 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1582 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject SynthN --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 182025 Number of reverse mapping hits = 169 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1658 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject SynthN --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 182025 Number of reverse mapping hits = 2682 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 9641 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject SynthN --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 182025 Number of reverse mapping hits = 284 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1296 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject SynthN --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 182025 Number of reverse mapping hits = 647 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1825 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject SynthN --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 182025 Number of reverse mapping hits = 650 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 3882 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject SynthN --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 182025 Number of reverse mapping hits = 1523 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4960 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject SynthN --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 182025 Number of reverse mapping hits = 138 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 406 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject SynthN --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 182025 Number of reverse mapping hits = 18 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 712 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject SynthN --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = SynthN trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthN/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 182025 Number of reverse mapping hits = 3 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 294 mri_label2label: Done mris_label2annot --s SynthN --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/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 /usr/local/freesurfer/subjects/SynthN/label cmdline mris_label2annot --s SynthN --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname stefano-Q170M-C machine x86_64 user stefano subject SynthN hemi rh SUBJECTS_DIR /usr/local/freesurfer/subjects ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /usr/local/freesurfer/subjects/SynthN/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 128385 unhit vertices Writing annot to /usr/local/freesurfer/subjects/SynthN/label/rh.BA_exvivo.annot mris_label2annot --s SynthN --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/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 /usr/local/freesurfer/subjects/SynthN/label cmdline mris_label2annot --s SynthN --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname stefano-Q170M-C machine x86_64 user stefano subject SynthN hemi rh SUBJECTS_DIR /usr/local/freesurfer/subjects ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /usr/local/freesurfer/subjects/SynthN/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 152925 unhit vertices Writing annot to /usr/local/freesurfer/subjects/SynthN/label/rh.BA_exvivo.thresh.annot mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab SynthN rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /usr/local/freesurfer/subjects/SynthN/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/SynthN/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 301678 Total vertex volume 298678 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/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) = 1204641 mm^3 (det: 1.617166 ) lhCtxGM: 303353.998 302860.000 diff= 494.0 pctdiff= 0.163 rhCtxGM: 296110.746 296782.000 diff= -671.3 pctdiff=-0.227 lhCtxWM: 316500.382 317449.500 diff= -949.1 pctdiff=-0.300 rhCtxWM: 330165.226 332241.500 diff=-2076.3 pctdiff=-0.629 SubCortGMVol 71549.000 SupraTentVol 1343879.351 (1341199.000) diff=2680.351 pctdiff=0.199 SupraTentVolNotVent 1323563.351 (1320883.000) diff=2680.351 pctdiff=0.203 BrainSegVol 1492481.000 (1489239.000) diff=3242.000 pctdiff=0.217 BrainSegVolNotVent 1467905.000 (1464577.351) diff=3327.649 pctdiff=0.227 BrainSegVolNotVent 1467905.000 CerebellumVol 146897.000 VentChorVol 20316.000 3rd4th5thCSF 4260.000 CSFVol 1018.000, OptChiasmVol 125.000 MaskVol 1847800.000 1362 751 1800 1.869 0.532 0.150 0.066 44 5.0 BA1_exvivo 4100 2723 4683 1.754 0.466 0.095 0.016 30 2.5 BA2_exvivo 1466 974 1334 1.723 0.521 0.117 0.019 10 1.1 BA3a_exvivo 2475 1678 2779 1.539 0.466 0.095 0.018 16 2.0 BA3b_exvivo 1968 1255 3299 2.373 0.601 0.083 0.016 9 1.1 BA4a_exvivo 1576 1031 2357 2.294 0.466 0.074 0.010 6 0.6 BA4p_exvivo 13255 8453 20624 2.235 0.810 0.125 0.035 223 22.2 BA6_exvivo 4614 3163 8959 2.507 0.656 0.117 0.023 47 4.3 BA44_exvivo 6234 3959 11919 2.631 0.711 0.133 0.036 78 9.7 BA45_exvivo 3417 2326 4555 1.813 0.484 0.123 0.027 35 3.7 V1_exvivo 9408 6367 14318 2.105 0.619 0.145 0.033 121 13.4 V2_exvivo 3047 1982 5252 2.512 0.600 0.123 0.030 34 3.7 MT_exvivo 446 330 2012 3.788 0.760 0.104 0.018 3 0.3 perirhinal_exvivo 272 195 717 2.951 0.671 0.081 0.018 2 0.3 entorhinal_exvivo mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab SynthN rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /usr/local/freesurfer/subjects/SynthN/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/SynthN/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthN/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 301678 Total vertex volume 298678 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/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) = 1204641 mm^3 (det: 1.617166 ) lhCtxGM: 303353.998 302860.000 diff= 494.0 pctdiff= 0.163 rhCtxGM: 296110.746 296782.000 diff= -671.3 pctdiff=-0.227 lhCtxWM: 316500.382 317449.500 diff= -949.1 pctdiff=-0.300 rhCtxWM: 330165.226 332241.500 diff=-2076.3 pctdiff=-0.629 SubCortGMVol 71549.000 SupraTentVol 1343879.351 (1341199.000) diff=2680.351 pctdiff=0.199 SupraTentVolNotVent 1323563.351 (1320883.000) diff=2680.351 pctdiff=0.203 BrainSegVol 1492481.000 (1489239.000) diff=3242.000 pctdiff=0.217 BrainSegVolNotVent 1467905.000 (1464577.351) diff=3327.649 pctdiff=0.227 BrainSegVolNotVent 1467905.000 CerebellumVol 146897.000 VentChorVol 20316.000 3rd4th5thCSF 4260.000 CSFVol 1018.000, OptChiasmVol 125.000 MaskVol 1847800.000 801 483 1140 1.852 0.502 0.136 0.037 11 1.4 BA1_exvivo 2119 1424 2395 1.682 0.424 0.090 0.013 13 1.2 BA2_exvivo 1333 871 1126 1.663 0.405 0.118 0.019 9 1.0 BA3a_exvivo 1976 1341 1973 1.468 0.444 0.076 0.011 8 1.0 BA3b_exvivo 1234 751 2189 2.432 0.610 0.086 0.017 6 0.8 BA4a_exvivo 1320 873 1931 2.280 0.451 0.064 0.007 3 0.4 BA4p_exvivo 8706 5566 12489 2.163 0.760 0.127 0.037 136 15.2 BA6_exvivo 1155 790 2710 2.750 0.639 0.105 0.022 10 1.1 BA44_exvivo 1744 1035 2929 2.456 0.596 0.141 0.045 28 3.5 BA45_exvivo 3211 2187 4193 1.806 0.473 0.121 0.028 32 3.9 V1_exvivo 4653 3207 6483 1.927 0.522 0.151 0.034 65 6.9 V2_exvivo 392 250 756 2.501 0.599 0.135 0.028 5 0.5 MT_exvivo 273 182 1139 3.833 0.731 0.093 0.016 2 0.2 perirhinal_exvivo 183 136 577 3.128 0.556 0.083 0.017 1 0.1 entorhinal_exvivo Started at Mon Dec 19 10:27:44 GMT 2016 Ended at Mon Dec 19 23:25:47 GMT 2016 #@#%# recon-all-run-time-hours 12.967 recon-all -s SynthN finished without error at Mon Dec 19 23:25:47 GMT 2016