Mon Dec 19 10:28:32 GMT 2016 /usr/local/freesurfer/subjects/SynthF /usr/local/freesurfer/bin/recon-all -subjid SynthF -i MniNick.nii -all subjid SynthF 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 7360868 7596468 225532 17840488 24733408 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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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: 2016/12/19-10:28:32-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/SynthF mri_convert /mnt/8E74B1C874B1B377/Desktop/Synth_Nick/MniNick.nii /usr/local/freesurfer/subjects/SynthF/mri/orig/001.mgz mri_convert.bin /mnt/8E74B1C874B1B377/Desktop/Synth_Nick/MniNick.nii /usr/local/freesurfer/subjects/SynthF/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/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/SynthF/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon Dec 19 10:28:33 GMT 2016 Found 1 runs /usr/local/freesurfer/subjects/SynthF/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/SynthF/mri/orig/001.mgz /usr/local/freesurfer/subjects/SynthF/mri/rawavg.mgz /usr/local/freesurfer/subjects/SynthF mri_convert /usr/local/freesurfer/subjects/SynthF/mri/rawavg.mgz /usr/local/freesurfer/subjects/SynthF/mri/orig.mgz --conform mri_convert.bin /usr/local/freesurfer/subjects/SynthF/mri/rawavg.mgz /usr/local/freesurfer/subjects/SynthF/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/SynthF/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/SynthF/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/SynthF/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/SynthF/mri/orig.mgz /usr/local/freesurfer/subjects/SynthF/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Dec 19 10:28:41 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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/SynthF/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 10:28:41 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.2999 /usr/local/freesurfer/subjects/SynthF/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2999/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.2999/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.2999/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Dec 19 10:28:43 GMT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.2999/nu0.mnc ./tmp.mri_nu_correct.mni.2999/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.2999/0/ -iterations 1000 -distance 50 [stefano@stefano-Q170M-C:/usr/local/freesurfer/subjects/SynthF/mri/] [2016-12-19 10:28:43] 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.2999/0/ ./tmp.mri_nu_correct.mni.2999/nu0.mnc ./tmp.mri_nu_correct.mni.2999/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 Number of iterations: 17 CV of field change: 0.00099674 mri_convert ./tmp.mri_nu_correct.mni.2999/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.2999/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.2999/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 10:29:21 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 10:29:21 GMT 2016 Ended at Mon Dec 19 10:29:50 GMT 2016 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Dec 19 10:29:52 GMT 2016 /usr/local/freesurfer/subjects/SynthF/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6662, pval=0.3663 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/SynthF/mri/transforms/talairach_avi.log tal_QC_AZS /usr/local/freesurfer/subjects/SynthF/mri/transforms/talairach_avi.log TalAviQA: 0.95857 z-score: -4 #-------------------------------------------- #@# Nu Intensity Correction Mon Dec 19 10:29:52 GMT 2016 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /usr/local/freesurfer/subjects/SynthF/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 10:29:52 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.4263 /usr/local/freesurfer/subjects/SynthF/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4263/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.4263/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.4263/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Dec 19 10:29:54 GMT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.4263/nu0.mnc ./tmp.mri_nu_correct.mni.4263/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.4263/0/ [stefano@stefano-Q170M-C:/usr/local/freesurfer/subjects/SynthF/mri/] [2016-12-19 10:29:54] 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.4263/0/ ./tmp.mri_nu_correct.mni.4263/nu0.mnc ./tmp.mri_nu_correct.mni.4263/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: 0.000877168 -------------------------------------------------------- Iteration 2 Mon Dec 19 10:30:23 GMT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.4263/nu1.mnc ./tmp.mri_nu_correct.mni.4263/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.4263/1/ [stefano@stefano-Q170M-C:/usr/local/freesurfer/subjects/SynthF/mri/] [2016-12-19 10:30:23] 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.4263/1/ ./tmp.mri_nu_correct.mni.4263/nu1.mnc ./tmp.mri_nu_correct.mni.4263/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 6 CV of field change: 0.000859773 mri_binarize --i ./tmp.mri_nu_correct.mni.4263/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.4263/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /usr/local/freesurfer/subjects/SynthF/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.4263/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.4263/ones.mgz sysname Linux hostname stefano-Q170M-C machine x86_64 user stefano input ./tmp.mri_nu_correct.mni.4263/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.4263/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.4263/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.4263/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4263/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.4263/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.4263/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4263/input.mean.dat sysname Linux hostname stefano-Q170M-C machine x86_64 user stefano UseRobust 0 Loading ./tmp.mri_nu_correct.mni.4263/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.4263/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4263/ones.mgz --i ./tmp.mri_nu_correct.mni.4263/nu2.mnc --sum ./tmp.mri_nu_correct.mni.4263/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4263/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.4263/ones.mgz --i ./tmp.mri_nu_correct.mni.4263/nu2.mnc --sum ./tmp.mri_nu_correct.mni.4263/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4263/output.mean.dat sysname Linux hostname stefano-Q170M-C machine x86_64 user stefano UseRobust 0 Loading ./tmp.mri_nu_correct.mni.4263/ones.mgz Loading ./tmp.mri_nu_correct.mni.4263/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.4263/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.4263/nu2.mnc ./tmp.mri_nu_correct.mni.4263/nu2.mnc mul 1.00556367455351685355 Saving result to './tmp.mri_nu_correct.mni.4263/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.4263/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.4263/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.4263/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 (41, 167) to ( 3, 110) Mon Dec 19 10:31:20 GMT 2016 mri_nu_correct.mni done mri_add_xform_to_header -c /usr/local/freesurfer/subjects/SynthF/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Mon Dec 19 10:31:21 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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 1.08173 0.01620 0.02377 -0.97022; 0.00629 1.22575 -0.03492 5.95348; 0.04626 -0.23827 1.25289 -10.12711; 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 = 22 Starting OpenSpline(): npoints = 22 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 63 (63), valley at 0 (-1) csf peak at 31, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 13 seconds. #-------------------------------------------- #@# Skull Stripping Mon Dec 19 10:33:35 GMT 2016 /usr/local/freesurfer/subjects/SynthF/mri mri_em_register -rusage /usr/local/freesurfer/subjects/SynthF/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=25.9 skull bounding box = (54, 64, 43) --> (196, 193, 217) using (101, 107, 130) as brain centroid... mean wm in atlas = 108, using box (84,91,109) --> (118, 122,151) to find MRI wm before smoothing, mri peak at 94 robust fit to distribution - 94 +- 7.0 after smoothing, mri peak at 94, scaling input intensities by 1.149 scaling channel 0 by 1.14894 initial log_p = -4.784 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.713004 @ (-9.091, -9.091, -9.091) max log p = -4.498116 @ (4.545, -4.545, -4.545) max log p = -4.498116 @ (0.000, 0.000, 0.000) max log p = -4.498116 @ (0.000, 0.000, 0.000) max log p = -4.489663 @ (3.977, -1.705, -2.841) max log p = -4.489663 @ (0.000, 0.000, 0.000) Found translation: (-0.6, -15.3, -16.5): log p = -4.490 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.422, old_max_log_p =-4.490 (thresh=-4.5) 1.07500 0.00000 0.00000 -9.97645; 0.00000 1.15000 0.00000 -38.96817; 0.00000 0.00000 1.07500 -26.03231; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.416, old_max_log_p =-4.422 (thresh=-4.4) 1.15563 0.00000 0.00000 -20.09034; 0.00000 1.22567 -0.15084 -24.17093; 0.00000 0.16136 1.14574 -67.96156; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.398, old_max_log_p =-4.416 (thresh=-4.4) 1.23167 0.17198 -0.02117 -52.97039; -0.16215 1.30633 -0.16077 -14.77602; 0.00000 0.16136 1.14574 -60.46156; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.394, old_max_log_p =-4.398 (thresh=-4.4) 1.14896 -0.00119 -0.01822 -16.73615; 0.00138 1.32740 -0.01252 -57.49441; 0.02117 -0.01053 1.15692 -38.50924; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.394, old_max_log_p =-4.394 (thresh=-4.4) 1.14896 -0.00119 -0.01822 -16.73615; 0.00138 1.32740 -0.01252 -57.49441; 0.02117 -0.01053 1.15692 -38.50924; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.362, old_max_log_p =-4.394 (thresh=-4.4) 1.14659 0.08563 -0.01900 -29.49190; -0.07797 1.40008 -0.01194 -58.62499; 0.02196 -0.01092 1.20031 -44.11295; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.362, old_max_log_p =-4.362 (thresh=-4.4) 1.14659 0.08563 -0.01900 -29.49190; -0.07797 1.40008 -0.01194 -58.62499; 0.02196 -0.01092 1.20031 -44.11295; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.360, old_max_log_p =-4.362 (thresh=-4.4) 1.14659 0.08563 -0.01900 -29.49190; -0.07797 1.40008 -0.01194 -58.62499; 0.02198 -0.01093 1.20171 -44.29463; 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 1.14659 0.08563 -0.01900 -29.49190; -0.07797 1.40008 -0.01194 -58.62499; 0.02198 -0.01093 1.20171 -44.29463; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.14659 0.08563 -0.01900 -29.49190; -0.07797 1.40008 -0.01194 -58.62499; 0.02198 -0.01093 1.20171 -44.29463; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.14659 0.08563 -0.01900 -29.49190; -0.07797 1.40008 -0.01194 -58.62499; 0.02198 -0.01093 1.20171 -44.29463; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.360 (old=-4.784) transform before final EM align: 1.14659 0.08563 -0.01900 -29.49190; -0.07797 1.40008 -0.01194 -58.62499; 0.02198 -0.01093 1.20171 -44.29463; 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 1.14659 0.08563 -0.01900 -29.49190; -0.07797 1.40008 -0.01194 -58.62499; 0.02198 -0.01093 1.20171 -44.29463; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.14659 0.08563 -0.01900 -29.49190; -0.07797 1.40008 -0.01194 -58.62499; 0.02198 -0.01093 1.20171 -44.29463; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.8 tol 0.000000 final transform: 1.14659 0.08563 -0.01900 -29.49190; -0.07797 1.40008 -0.01194 -58.62499; 0.02198 -0.01093 1.20171 -44.29463; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 981.440000 mri_em_register stimesec 2.252000 mri_em_register ru_maxrss 613940 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 156665 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 18 mri_em_register ru_nivcsw 13588 registration took 16 minutes and 25 seconds. mri_watershed -rusage /usr/local/freesurfer/subjects/SynthF/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=129 r=61 first estimation of the main basin volume: 967014 voxels Looking for seedpoints 2 found in the cerebellum 12 found in the rest of the brain global maximum in x=103, y=118, z=101, 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=584019151 voxels, voxel volume =1.000 = 584019151 mmm3 = 584019.136 cm3 done. PostAnalyze...Basin Prior 160 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 = 44900 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1037205109 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1043668449 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1065535252 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1073447460 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1076376864 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 3, 3, 7, 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, 43, 90 after analyzing : 3, 29, 43, 44 RIGHT_BRAIN before analyzing : 3, 3, 9, 90 after analyzing : 3, 17, 25, 35 LEFT_BRAIN before analyzing : 3, 4, 28, 50 after analyzing : 3, 20, 28, 27 OTHER before analyzing : 3, 4, 57, 91 after analyzing : 3, 39, 57, 52 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...73 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.011 curvature mean = 74.699, std = 8.297 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.98, sigma = 7.91 after rotation: sse = 4.98, sigma = 7.91 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 5.86, its var is 10.18 before Erosion-Dilatation 2.99% of inacurate vertices after Erosion-Dilatation 5.94% 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...36 iterations mri_strip_skull: done peeling brain Brain Size = 2006569 voxels, voxel volume = 1.000 mm3 = 2006569 mmm3 = 2006.569 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 18.648000 mri_watershed stimesec 0.192000 mri_watershed ru_maxrss 822068 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 207574 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 2888 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 1 mri_watershed ru_nivcsw 567 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Mon Dec 19 10:50:20 GMT 2016 /usr/local/freesurfer/subjects/SynthF/mri mri_em_register -rusage /usr/local/freesurfer/subjects/SynthF/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=26.9 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 94 robust fit to distribution - 94 +- 5.8 after smoothing, mri peak at 94, scaling input intensities by 1.138 scaling channel 0 by 1.1383 initial log_p = -4.521 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.340415 @ (-9.091, -9.091, -9.091) max log p = -4.120872 @ (4.545, -4.545, -4.545) max log p = -3.987556 @ (2.273, -6.818, -6.818) max log p = -3.966741 @ (-1.136, 1.136, 3.409) max log p = -3.966741 @ (0.000, 0.000, 0.000) max log p = -3.966741 @ (0.000, 0.000, 0.000) Found translation: (-3.4, -19.3, -17.0): log p = -3.967 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.967, old_max_log_p =-3.967 (thresh=-4.0) 1.00000 0.00000 0.00000 -3.40909; 0.00000 1.00000 0.00000 -19.31818; 0.00000 0.00000 1.00000 -17.04546; 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=-3.940, old_max_log_p =-3.967 (thresh=-4.0) 0.99732 0.06076 -0.03547 -4.90366; -0.06537 0.95852 -0.06076 3.98727; 0.03272 0.06292 0.95992 -27.22582; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.929, old_max_log_p =-3.940 (thresh=-3.9) 0.99893 0.02937 -0.03347 -1.06058; -0.03270 0.95999 -0.06189 -2.13316; 0.03211 0.06174 0.94193 -24.73826; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.929, old_max_log_p =-3.929 (thresh=-3.9) 0.99893 0.02937 -0.03347 -1.06058; -0.03270 0.95999 -0.06189 -2.13316; 0.03211 0.06174 0.94193 -24.73826; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.906, old_max_log_p =-3.929 (thresh=-3.9) 0.99849 0.04557 -0.02677 -4.09087; -0.04898 0.95826 -0.06126 0.11391; 0.02397 0.06144 0.94328 -23.82356; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.902, old_max_log_p =-3.906 (thresh=-3.9) 0.99849 0.04557 -0.02677 -4.09087; -0.04898 0.95826 -0.06126 0.11391; 0.02402 0.06158 0.94549 -24.12654; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.902, old_max_log_p =-3.902 (thresh=-3.9) 0.99849 0.04557 -0.02677 -4.09087; -0.04898 0.95826 -0.06126 0.11391; 0.02402 0.06158 0.94549 -24.12654; 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 0.99849 0.04557 -0.02677 -4.09087; -0.04898 0.95826 -0.06126 0.11391; 0.02402 0.06158 0.94549 -24.12654; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.99849 0.04557 -0.02677 -4.09087; -0.04898 0.95826 -0.06126 0.11391; 0.02402 0.06158 0.94549 -24.12654; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.99849 0.04557 -0.02677 -4.09087; -0.04898 0.95826 -0.06126 0.11391; 0.02402 0.06158 0.94549 -24.12654; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.902 (old=-4.521) transform before final EM align: 0.99849 0.04557 -0.02677 -4.09087; -0.04898 0.95826 -0.06126 0.11391; 0.02402 0.06158 0.94549 -24.12654; 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 0.99849 0.04557 -0.02677 -4.09087; -0.04898 0.95826 -0.06126 0.11391; 0.02402 0.06158 0.94549 -24.12654; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.99849 0.04557 -0.02677 -4.09087; -0.04898 0.95826 -0.06126 0.11391; 0.02402 0.06158 0.94549 -24.12654; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.3 tol 0.000000 final transform: 0.99849 0.04557 -0.02677 -4.09087; -0.04898 0.95826 -0.06126 0.11391; 0.02402 0.06158 0.94549 -24.12654; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 746.652000 mri_em_register stimesec 1.312000 mri_em_register ru_maxrss 603268 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 158430 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 22 mri_em_register ru_nivcsw 10610 registration took 12 minutes and 29 seconds. #-------------------------------------- #@# CA Normalize Mon Dec 19 11:02:49 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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=26.9 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 94 robust fit to distribution - 94 +- 5.8 after smoothing, mri peak at 94, scaling input intensities by 1.138 scaling channel 0 by 1.1383 using 246344 sample points... INFO: compute sample coordinates transform 0.99849 0.04557 -0.02677 -4.09087; -0.04898 0.95826 -0.06126 0.11391; 0.02402 0.06158 0.94549 -24.12654; 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 (124, 68, 39) --> (194, 197, 218) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 2 of 3678 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (62, 67, 41) --> (131, 194, 219) Right_Cerebral_White_Matter: limiting intensities to 104.0 --> 128.0 643 of 3994 (16.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (126, 156, 61) --> (174, 202, 118) Left_Cerebellum_White_Matter: limiting intensities to 103.0 --> 132.0 0 of 18 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (80, 156, 59) --> (126, 199, 121) Right_Cerebellum_White_Matter: limiting intensities to 108.0 --> 132.0 0 of 42 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (109, 149, 95) --> (144, 222, 132) Brain_Stem: limiting intensities to 104.0 --> 132.0 0 of 39 (0.0%) samples deleted using 7771 total control points for intensity normalization... bias field = 0.960 +- 0.060 43 of 7126 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (124, 68, 39) --> (194, 197, 218) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 185 of 4366 (4.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (62, 67, 41) --> (131, 194, 219) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 116.0 47 of 4718 (1.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (126, 156, 61) --> (174, 202, 118) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 9 of 78 (11.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (80, 156, 59) --> (126, 199, 121) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 6 of 84 (7.1%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (109, 149, 95) --> (144, 222, 132) Brain_Stem: limiting intensities to 88.0 --> 132.0 5 of 109 (4.6%) samples deleted using 9355 total control points for intensity normalization... bias field = 1.085 +- 0.073 33 of 9028 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (124, 68, 39) --> (194, 197, 218) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 119.0 109 of 4579 (2.4%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (62, 67, 41) --> (131, 194, 219) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 24 of 5170 (0.5%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (126, 156, 61) --> (174, 202, 118) Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0 119 of 134 (88.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (80, 156, 59) --> (126, 199, 121) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 95 of 148 (64.2%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (109, 149, 95) --> (144, 222, 132) Brain_Stem: limiting intensities to 88.0 --> 132.0 66 of 165 (40.0%) samples deleted using 10196 total control points for intensity normalization... bias field = 1.085 +- 0.070 24 of 9683 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 8 seconds. #-------------------------------------- #@# CA Reg Mon Dec 19 11:03:57 GMT 2016 /usr/local/freesurfer/subjects/SynthF/mri mri_ca_register -rusage /usr/local/freesurfer/subjects/SynthF/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=1.050, neg=0, invalid=4512 0001: dt=316.241283, rms=0.943 (10.133%), neg=0, invalid=4512 0002: dt=279.553544, rms=0.913 (3.264%), neg=0, invalid=4512 0003: dt=237.953003, rms=0.899 (1.490%), neg=0, invalid=4512 0004: dt=295.936000, rms=0.889 (1.120%), neg=0, invalid=4512 0005: dt=221.952000, rms=0.882 (0.794%), neg=0, invalid=4512 0006: dt=295.936000, rms=0.876 (0.698%), neg=0, invalid=4512 0007: dt=129.472000, rms=0.873 (0.340%), neg=0, invalid=4512 0008: dt=1775.616000, rms=0.861 (1.341%), neg=0, invalid=4512 0009: dt=443.904000, rms=0.858 (0.350%), neg=0, invalid=4512 0010: dt=295.936000, rms=0.856 (0.197%), neg=0, invalid=4512 0011: dt=295.936000, rms=0.855 (0.163%), neg=0, invalid=4512 0012: dt=295.936000, rms=0.853 (0.243%), neg=0, invalid=4512 0013: dt=295.936000, rms=0.850 (0.311%), neg=0, invalid=4512 0014: dt=295.936000, rms=0.848 (0.272%), neg=0, invalid=4512 0015: dt=295.936000, rms=0.845 (0.318%), neg=0, invalid=4512 0016: dt=295.936000, rms=0.842 (0.380%), neg=0, invalid=4512 0017: dt=295.936000, rms=0.839 (0.323%), neg=0, invalid=4512 0018: dt=295.936000, rms=0.837 (0.241%), neg=0, invalid=4512 0019: dt=295.936000, rms=0.836 (0.177%), neg=0, invalid=4512 0020: dt=295.936000, rms=0.834 (0.162%), neg=0, invalid=4512 0021: dt=295.936000, rms=0.833 (0.156%), neg=0, invalid=4512 0022: dt=295.936000, rms=0.832 (0.156%), neg=0, invalid=4512 0023: dt=295.936000, rms=0.830 (0.192%), neg=0, invalid=4512 0024: dt=295.936000, rms=0.828 (0.207%), neg=0, invalid=4512 0025: dt=295.936000, rms=0.827 (0.200%), neg=0, invalid=4512 0026: dt=295.936000, rms=0.825 (0.176%), neg=0, invalid=4512 0027: dt=295.936000, rms=0.824 (0.135%), neg=0, invalid=4512 0028: dt=295.936000, rms=0.823 (0.151%), neg=0, invalid=4512 0029: dt=295.936000, rms=0.821 (0.185%), neg=0, invalid=4512 0030: dt=295.936000, rms=0.820 (0.134%), neg=0, invalid=4512 0031: dt=295.936000, rms=0.820 (0.088%), neg=0, invalid=4512 0032: dt=295.936000, rms=0.819 (0.065%), neg=0, invalid=4512 0033: dt=517.888000, rms=0.819 (0.047%), neg=0, invalid=4512 0034: dt=517.888000, rms=0.819 (-0.147%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.820, neg=0, invalid=4512 0035: dt=92.480000, rms=0.818 (0.156%), neg=0, invalid=4512 0036: dt=32.368000, rms=0.818 (0.003%), neg=0, invalid=4512 0037: dt=32.368000, rms=0.818 (0.003%), neg=0, invalid=4512 0038: dt=32.368000, rms=0.818 (-0.011%), neg=0, invalid=4512 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.829, neg=0, invalid=4512 0039: dt=226.691589, rms=0.818 (1.299%), neg=0, invalid=4512 0040: dt=129.516074, rms=0.809 (1.142%), neg=0, invalid=4512 0041: dt=86.036630, rms=0.805 (0.505%), neg=0, invalid=4512 0042: dt=248.832000, rms=0.799 (0.721%), neg=0, invalid=4512 0043: dt=65.841727, rms=0.794 (0.557%), neg=0, invalid=4512 0044: dt=580.608000, rms=0.785 (1.177%), neg=0, invalid=4512 0045: dt=36.288000, rms=0.782 (0.346%), neg=0, invalid=4512 0046: dt=82.944000, rms=0.781 (0.147%), neg=0, invalid=4512 0047: dt=82.944000, rms=0.780 (0.157%), neg=0, invalid=4512 0048: dt=82.944000, rms=0.778 (0.208%), neg=0, invalid=4512 0049: dt=82.944000, rms=0.776 (0.287%), neg=0, invalid=4512 0050: dt=82.944000, rms=0.774 (0.317%), neg=0, invalid=4512 0051: dt=82.944000, rms=0.770 (0.432%), neg=0, invalid=4512 0052: dt=82.944000, rms=0.767 (0.400%), neg=0, invalid=4512 0053: dt=82.944000, rms=0.767 (0.012%), neg=0, invalid=4512 0054: dt=41.472000, rms=0.767 (0.068%), neg=0, invalid=4512 0055: dt=10.368000, rms=0.767 (0.007%), neg=0, invalid=4512 0056: dt=2.268000, rms=0.767 (0.001%), neg=0, invalid=4512 0057: dt=2.268000, rms=0.767 (0.003%), neg=0, invalid=4512 0058: dt=0.283500, rms=0.767 (0.000%), neg=0, invalid=4512 0059: dt=0.035437, rms=0.767 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.767, neg=0, invalid=4512 0060: dt=0.030375, rms=0.767 (0.126%), neg=0, invalid=4512 0061: dt=0.001898, rms=0.767 (0.000%), neg=0, invalid=4512 0062: dt=0.000059, rms=0.767 (0.000%), neg=0, invalid=4512 0063: dt=0.000007, rms=0.767 (0.000%), neg=0, invalid=4512 0064: dt=0.000002, rms=0.767 (-0.000%), neg=0, invalid=4512 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.797, neg=0, invalid=4512 0065: dt=23.567568, rms=0.792 (0.524%), neg=0, invalid=4512 0066: dt=44.800000, rms=0.788 (0.554%), neg=0, invalid=4512 0067: dt=58.616822, rms=0.783 (0.635%), neg=0, invalid=4512 0068: dt=22.293333, rms=0.779 (0.527%), neg=0, invalid=4512 0069: dt=44.800000, rms=0.777 (0.300%), neg=0, invalid=4512 0070: dt=32.000000, rms=0.775 (0.192%), neg=0, invalid=4512 0071: dt=32.000000, rms=0.774 (0.178%), neg=0, invalid=4512 0072: dt=32.000000, rms=0.771 (0.303%), neg=0, invalid=4512 0073: dt=32.000000, rms=0.769 (0.315%), neg=0, invalid=4512 0074: dt=32.000000, rms=0.765 (0.461%), neg=0, invalid=4512 0075: dt=32.000000, rms=0.763 (0.341%), neg=0, invalid=4512 0076: dt=32.000000, rms=0.761 (0.260%), neg=0, invalid=4512 0077: dt=32.000000, rms=0.760 (0.160%), neg=0, invalid=4512 0078: dt=32.000000, rms=0.758 (0.239%), neg=0, invalid=4512 0079: dt=32.000000, rms=0.757 (0.082%), neg=0, invalid=4512 0080: dt=32.000000, rms=0.757 (0.074%), neg=0, invalid=4512 0081: dt=25.600000, rms=0.756 (0.090%), neg=0, invalid=4512 0082: dt=2.800000, rms=0.756 (0.003%), neg=0, invalid=4512 0083: dt=2.800000, rms=0.756 (-0.001%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.757, neg=0, invalid=4512 0084: dt=0.000000, rms=0.756 (0.098%), neg=0, invalid=4512 0085: dt=0.000000, rms=0.756 (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=0.807, neg=0, invalid=4512 0086: dt=0.000000, rms=0.806 (0.086%), neg=0, invalid=4512 0087: dt=0.000000, rms=0.806 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.807, neg=0, invalid=4512 0088: dt=0.000000, rms=0.806 (0.086%), neg=0, invalid=4512 0089: dt=0.000000, rms=0.806 (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=0.905, neg=0, invalid=4512 0090: dt=1.184591, rms=0.890 (1.633%), neg=0, invalid=4512 0091: dt=0.448000, rms=0.888 (0.183%), neg=0, invalid=4512 0092: dt=0.448000, rms=0.888 (0.060%), neg=0, invalid=4512 0093: dt=0.448000, rms=0.888 (-0.150%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.889, neg=0, invalid=4512 0094: dt=0.448000, rms=0.887 (0.129%), neg=0, invalid=4512 0095: dt=0.112000, rms=0.887 (0.006%), neg=0, invalid=4512 0096: dt=0.112000, rms=0.887 (0.003%), neg=0, invalid=4512 0097: dt=0.112000, rms=0.887 (-0.006%), 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=0.797, neg=0, invalid=4512 0098: dt=1.091686, rms=0.763 (4.278%), neg=0, invalid=4512 0099: dt=0.096000, rms=0.762 (0.170%), neg=0, invalid=4512 0100: dt=0.096000, rms=0.762 (-0.104%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.762, neg=0, invalid=4512 0101: dt=0.028000, rms=0.762 (0.118%), neg=0, invalid=4512 0102: dt=0.004000, rms=0.762 (-0.000%), neg=0, invalid=4512 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.17907 (13) Left_Lateral_Ventricle (4): linear fit = 0.60 x + 0.0 (1451 voxels, overlap=0.020) Left_Lateral_Ventricle (4): linear fit = 0.60 x + 0.0 (1451 voxels, peak = 12), gca=11.9 gca peak = 0.15565 (16) mri peak = 0.13357 (13) Right_Lateral_Ventricle (43): linear fit = 0.74 x + 0.0 (1567 voxels, overlap=0.595) Right_Lateral_Ventricle (43): linear fit = 0.74 x + 0.0 (1567 voxels, peak = 12), gca=11.8 gca peak = 0.26829 (96) mri peak = 0.06124 (98) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (1358 voxels, overlap=0.990) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (1358 voxels, peak = 97), gca=97.4 gca peak = 0.20183 (93) mri peak = 0.06346 (98) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (1119 voxels, overlap=0.854) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (1119 voxels, peak = 97), gca=97.2 gca peak = 0.21683 (55) mri peak = 0.06745 (59) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (1256 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (1256 voxels, peak = 56), gca=56.4 gca peak = 0.30730 (58) mri peak = 0.06143 (50) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (681 voxels, overlap=0.997) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (681 voxels, peak = 54), gca=54.2 gca peak = 0.11430 (101) mri peak = 0.07385 (98) Right_Cerebral_White_Matter (41): linear fit = 0.99 x + 0.0 (84041 voxels, overlap=0.951) Right_Cerebral_White_Matter (41): linear fit = 0.99 x + 0.0 (84041 voxels, peak = 99), gca=99.5 gca peak = 0.12076 (102) mri peak = 0.07835 (97) Left_Cerebral_White_Matter (2): linear fit = 0.98 x + 0.0 (84378 voxels, overlap=0.964) Left_Cerebral_White_Matter (2): linear fit = 0.98 x + 0.0 (84378 voxels, peak = 99), gca=99.5 gca peak = 0.14995 (59) mri peak = 0.02870 (62) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (25528 voxels, overlap=0.668) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (25528 voxels, peak = 60), gca=60.5 gca peak = 0.15082 (58) mri peak = 0.02335 (63) Right_Cerebral_Cortex (42): linear fit = 1.48 x + 0.0 (34707 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.48 x + 0.0 (34707 voxels, peak = 86), gca=85.6 gca peak = 0.14161 (67) mri peak = 0.09112 (70) Right_Caudate (50): linear fit = 1.00 x + 0.0 (796 voxels, overlap=0.974) Right_Caudate (50): linear fit = 1.00 x + 0.0 (796 voxels, peak = 67), gca=67.0 gca peak = 0.15243 (71) mri peak = 0.05765 (75) Left_Caudate (11): linear fit = 1.03 x + 0.0 (1531 voxels, overlap=0.922) Left_Caudate (11): linear fit = 1.03 x + 0.0 (1531 voxels, peak = 73), gca=73.5 gca peak = 0.13336 (57) mri peak = 0.03146 (61) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (21832 voxels, overlap=0.513) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (21832 voxels, peak = 64), gca=63.6 gca peak = 0.13252 (56) mri peak = 0.03437 (83) Right_Cerebellum_Cortex (47): linear fit = 1.46 x + 0.0 (30630 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.46 x + 0.0 (30630 voxels, peak = 81), gca=81.5 gca peak = 0.18181 (84) mri peak = 0.04680 (80) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (13178 voxels, overlap=0.977) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (13178 voxels, peak = 83), gca=82.7 gca peak = 0.20573 (83) mri peak = 0.06116 (83) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (11127 voxels, overlap=0.945) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (11127 voxels, peak = 85), gca=85.1 gca peak = 0.21969 (57) mri peak = 0.07109 (61) Left_Amygdala (18): linear fit = 1.08 x + 0.0 (596 voxels, overlap=0.995) Left_Amygdala (18): linear fit = 1.08 x + 0.0 (596 voxels, peak = 61), gca=61.3 gca peak = 0.39313 (56) mri peak = 0.08684 (57) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (770 voxels, overlap=0.992) Right_Amygdala (54): linear fit = 1.04 x + 0.0 (770 voxels, peak = 59), gca=58.5 gca peak = 0.14181 (85) mri peak = 0.06078 (94) Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (7781 voxels, overlap=0.487) Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (7781 voxels, peak = 93), gca=93.1 gca peak = 0.11978 (83) mri peak = 0.07420 (95) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5324 voxels, overlap=0.481) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5324 voxels, peak = 93), gca=92.5 gca peak = 0.13399 (79) mri peak = 0.05107 (83) Left_Putamen (12): linear fit = 1.11 x + 0.0 (3214 voxels, overlap=0.775) Left_Putamen (12): linear fit = 1.11 x + 0.0 (3214 voxels, peak = 87), gca=87.3 gca peak = 0.14159 (79) mri peak = 0.05667 (79) Right_Putamen (51): linear fit = 1.04 x + 0.0 (3455 voxels, overlap=0.999) Right_Putamen (51): linear fit = 1.04 x + 0.0 (3455 voxels, peak = 83), gca=82.6 gca peak = 0.10025 (80) mri peak = 0.06641 (85) Brain_Stem (16): linear fit = 1.10 x + 0.0 (13554 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (13554 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.06553 (104) Right_VentralDC (60): linear fit = 1.17 x + 0.0 (1546 voxels, overlap=0.307) Right_VentralDC (60): linear fit = 1.17 x + 0.0 (1546 voxels, peak = 101), gca=101.0 gca peak = 0.12801 (89) mri peak = 0.06805 (95) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1840 voxels, overlap=0.403) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1840 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15061 (21) mri peak = 0.15756 ( 5) Fourth_Ventricle (15): linear fit = 0.23 x + 0.0 (124 voxels, overlap=0.018) Fourth_Ventricle (15): linear fit = 0.23 x + 0.0 (124 voxels, peak = 5), gca=4.9 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 1.10 x + 0.0 estimating mean wm scale to be 0.98 x + 0.0 estimating mean csf scale to be 0.67 x + 0.0 Left_Pallidum too bright - rescaling by 0.993 (from 1.045) to 96.5 (was 97.2) Right_Pallidum too bright - rescaling by 0.990 (from 1.015) to 96.5 (was 97.4) 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=0.768, neg=0, invalid=4512 0103: dt=99.103926, rms=0.749 (2.492%), neg=0, invalid=4512 0104: dt=145.822785, rms=0.745 (0.495%), neg=0, invalid=4512 0105: dt=369.920000, rms=0.742 (0.437%), neg=0, invalid=4512 0106: dt=221.952000, rms=0.740 (0.162%), neg=0, invalid=4512 0107: dt=129.472000, rms=0.739 (0.123%), neg=0, invalid=4512 0108: dt=221.952000, rms=0.739 (0.073%), neg=0, invalid=4512 0109: dt=129.472000, rms=0.738 (0.072%), neg=0, invalid=4512 0110: dt=295.936000, rms=0.738 (0.045%), neg=0, invalid=4512 0111: dt=295.936000, rms=0.738 (-0.029%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.739, neg=0, invalid=4512 0112: dt=129.472000, rms=0.736 (0.333%), neg=0, invalid=4512 0113: dt=443.904000, rms=0.734 (0.290%), neg=0, invalid=4512 0114: dt=73.984000, rms=0.734 (0.074%), neg=0, invalid=4512 0115: dt=129.472000, rms=0.733 (0.016%), neg=0, invalid=4512 0116: dt=129.472000, rms=0.733 (0.033%), neg=0, invalid=4512 0117: dt=129.472000, rms=0.733 (0.049%), neg=0, invalid=4512 0118: dt=129.472000, rms=0.732 (0.059%), neg=0, invalid=4512 0119: dt=129.472000, rms=0.732 (0.066%), neg=0, invalid=4512 0120: dt=129.472000, rms=0.731 (0.077%), neg=0, invalid=4512 0121: dt=129.472000, rms=0.731 (0.078%), neg=0, invalid=4512 0122: dt=129.472000, rms=0.730 (0.073%), neg=0, invalid=4512 0123: dt=129.472000, rms=0.730 (0.065%), neg=0, invalid=4512 0124: dt=129.472000, rms=0.729 (0.056%), neg=0, invalid=4512 0125: dt=129.472000, rms=0.729 (0.061%), neg=0, invalid=4512 0126: dt=129.472000, rms=0.729 (0.064%), neg=0, invalid=4512 0127: dt=129.472000, rms=0.728 (0.069%), neg=0, invalid=4512 0128: dt=129.472000, rms=0.728 (0.062%), neg=0, invalid=4512 0129: dt=129.472000, rms=0.727 (0.058%), neg=0, invalid=4512 0130: dt=129.472000, rms=0.727 (0.052%), neg=0, invalid=4512 0131: dt=129.472000, rms=0.726 (0.051%), neg=0, invalid=4512 0132: dt=129.472000, rms=0.726 (0.053%), neg=0, invalid=4512 0133: dt=129.472000, rms=0.726 (0.050%), neg=0, invalid=4512 0134: dt=129.472000, rms=0.725 (0.050%), neg=0, invalid=4512 0135: dt=129.472000, rms=0.725 (0.044%), neg=0, invalid=4512 0136: dt=129.472000, rms=0.725 (0.037%), neg=0, invalid=4512 0137: dt=129.472000, rms=0.724 (0.044%), neg=0, invalid=4512 0138: dt=129.472000, rms=0.724 (0.048%), neg=0, invalid=4512 0139: dt=129.472000, rms=0.724 (0.046%), neg=0, invalid=4512 0140: dt=129.472000, rms=0.723 (0.047%), neg=0, invalid=4512 0141: dt=129.472000, rms=0.723 (0.041%), neg=0, invalid=4512 0142: dt=129.472000, rms=0.723 (0.034%), neg=0, invalid=4512 0143: dt=129.472000, rms=0.723 (0.029%), neg=0, invalid=4512 0144: dt=129.472000, rms=0.722 (0.026%), neg=0, invalid=4512 0145: dt=129.472000, rms=0.722 (0.027%), neg=0, invalid=4512 0146: dt=129.472000, rms=0.722 (0.032%), neg=0, invalid=4512 0147: dt=129.472000, rms=0.722 (0.036%), neg=0, invalid=4512 0148: dt=129.472000, rms=0.722 (0.033%), neg=0, invalid=4512 0149: dt=129.472000, rms=0.721 (0.026%), neg=0, invalid=4512 0150: dt=129.472000, rms=0.721 (0.016%), neg=0, invalid=4512 0151: dt=129.472000, rms=0.721 (0.014%), neg=0, invalid=4512 0152: dt=517.888000, rms=0.721 (0.025%), neg=0, invalid=4512 0153: dt=73.984000, rms=0.721 (0.012%), neg=0, invalid=4512 0154: dt=73.984000, rms=0.721 (-0.006%), neg=0, invalid=4512 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.722, neg=0, invalid=4512 0155: dt=36.288000, rms=0.720 (0.307%), neg=0, invalid=4512 0156: dt=124.416000, rms=0.717 (0.383%), neg=0, invalid=4512 0157: dt=9.072000, rms=0.716 (0.074%), neg=0, invalid=4512 0158: dt=9.072000, rms=0.716 (0.069%), neg=0, invalid=4512 0159: dt=7.776000, rms=0.716 (0.056%), neg=0, invalid=4512 0160: dt=0.141750, rms=0.716 (0.001%), neg=0, invalid=4512 0161: dt=0.141750, rms=0.716 (0.001%), neg=0, invalid=4512 0162: dt=0.008859, rms=0.716 (0.000%), neg=0, invalid=4512 0163: dt=0.000004, rms=0.716 (-0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.716, neg=0, invalid=4512 0164: dt=112.290909, rms=0.710 (0.839%), neg=0, invalid=4512 0165: dt=90.803419, rms=0.707 (0.420%), neg=0, invalid=4512 0166: dt=69.071698, rms=0.706 (0.249%), neg=0, invalid=4512 0167: dt=124.416000, rms=0.703 (0.316%), neg=0, invalid=4512 0168: dt=36.288000, rms=0.702 (0.201%), neg=0, invalid=4512 0169: dt=580.608000, rms=0.695 (1.039%), neg=0, invalid=4512 0170: dt=36.288000, rms=0.693 (0.302%), neg=0, invalid=4512 0171: dt=145.152000, rms=0.691 (0.170%), neg=0, invalid=4512 0172: dt=82.944000, rms=0.690 (0.145%), neg=0, invalid=4512 0173: dt=82.944000, rms=0.690 (0.106%), neg=0, invalid=4512 0174: dt=62.208000, rms=0.689 (0.088%), neg=0, invalid=4512 0175: dt=103.680000, rms=0.688 (0.127%), neg=0, invalid=4512 0176: dt=36.288000, rms=0.688 (0.072%), neg=0, invalid=4512 0177: dt=145.152000, rms=0.686 (0.167%), neg=0, invalid=4512 0178: dt=145.152000, rms=0.685 (0.144%), neg=0, invalid=4512 0179: dt=36.288000, rms=0.685 (0.051%), neg=0, invalid=4512 0180: dt=36.288000, rms=0.685 (0.038%), neg=0, invalid=4512 0181: dt=18.144000, rms=0.685 (0.017%), neg=0, invalid=4512 0182: dt=2.268000, rms=0.685 (0.002%), neg=0, invalid=4512 0183: dt=0.567000, rms=0.685 (0.001%), neg=0, invalid=4512 0184: dt=0.141750, rms=0.685 (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=0.688, neg=0, invalid=4512 0185: dt=0.002734, rms=0.688 (0.095%), neg=0, invalid=4512 0186: dt=0.000684, rms=0.688 (0.000%), neg=0, invalid=4512 0187: dt=0.000342, rms=0.688 (0.000%), neg=0, invalid=4512 0188: dt=0.000043, rms=0.688 (0.000%), neg=0, invalid=4512 0189: dt=0.000011, rms=0.688 (0.000%), neg=0, invalid=4512 0190: dt=0.000000, rms=0.688 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.688, neg=0, invalid=4512 0191: dt=0.000000, rms=0.688 (0.095%), neg=0, invalid=4512 0192: dt=0.000000, rms=0.688 (0.000%), neg=0, invalid=4512 0193: dt=0.000008, rms=0.688 (0.000%), neg=0, invalid=4512 0194: dt=0.000004, rms=0.688 (0.000%), neg=0, invalid=4512 0195: dt=0.000001, rms=0.688 (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=0.698, neg=0, invalid=4512 0196: dt=0.000000, rms=0.697 (0.093%), neg=0, invalid=4512 0197: dt=0.000000, rms=0.697 (0.000%), neg=0, invalid=4512 0198: dt=0.000000, rms=0.697 (0.000%), neg=0, invalid=4512 0199: dt=0.000000, rms=0.697 (-0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.698, neg=0, invalid=4512 0200: dt=16.128000, rms=0.655 (6.058%), neg=0, invalid=4512 0201: dt=16.128000, rms=0.645 (1.577%), neg=0, invalid=4512 0202: dt=4.032000, rms=0.643 (0.318%), neg=0, invalid=4512 0203: dt=16.128000, rms=0.638 (0.816%), neg=0, invalid=4512 0204: dt=4.032000, rms=0.637 (0.157%), neg=0, invalid=4512 0205: dt=11.520000, rms=0.635 (0.320%), neg=0, invalid=4512 0206: dt=16.128000, rms=0.632 (0.348%), neg=0, invalid=4512 0207: dt=4.032000, rms=0.632 (0.087%), neg=0, invalid=4512 0208: dt=13.824000, rms=0.630 (0.237%), neg=0, invalid=4512 0209: dt=16.128000, rms=0.629 (0.200%), neg=0, invalid=4512 0210: dt=4.032000, rms=0.629 (0.057%), neg=0, invalid=4512 0211: dt=16.128000, rms=0.628 (0.192%), neg=0, invalid=4512 0212: dt=16.128000, rms=0.627 (0.129%), neg=0, invalid=4512 0213: dt=11.520000, rms=0.626 (0.115%), neg=0, invalid=4512 0214: dt=16.128000, rms=0.625 (0.087%), neg=0, invalid=4512 0215: dt=4.032000, rms=0.625 (0.063%), neg=0, invalid=4512 0216: dt=16.128000, rms=0.624 (0.113%), neg=0, invalid=4512 0217: dt=10.033898, rms=0.624 (0.049%), neg=0, invalid=4512 0218: dt=10.033898, rms=0.624 (0.079%), neg=0, invalid=4512 0219: dt=10.033898, rms=0.623 (0.113%), neg=0, invalid=4512 0220: dt=10.033898, rms=0.622 (0.138%), neg=0, invalid=4512 0221: dt=10.033898, rms=0.621 (0.172%), neg=0, invalid=4512 0222: dt=10.033898, rms=0.621 (0.033%), neg=0, invalid=4512 0223: dt=10.033898, rms=0.621 (0.035%), neg=0, invalid=4512 0224: dt=2.508475, rms=0.620 (0.013%), neg=0, invalid=4512 0225: dt=0.078390, rms=0.620 (-0.000%), neg=0, invalid=4512 0226: dt=0.063000, rms=0.620 (0.000%), neg=0, invalid=4512 0227: dt=0.015750, rms=0.620 (0.000%), neg=0, invalid=4512 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.636, neg=0, invalid=4512 0228: dt=0.000000, rms=0.635 (0.109%), neg=0, invalid=4512 0229: dt=0.000000, rms=0.635 (0.000%), neg=0, invalid=4512 0230: dt=0.100000, rms=0.635 (-0.135%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.636, neg=0, invalid=4512 0231: dt=0.000000, rms=0.635 (0.109%), neg=0, invalid=4512 0232: dt=0.000000, rms=0.635 (0.000%), neg=0, invalid=4512 0233: dt=0.100000, rms=0.635 (-0.123%), 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=0.611, neg=0, invalid=4512 0234: dt=0.384000, rms=0.593 (2.981%), neg=0, invalid=4512 0235: dt=0.384000, rms=0.586 (1.064%), neg=0, invalid=4512 0236: dt=0.384000, rms=0.584 (0.465%), neg=0, invalid=4512 0237: dt=0.384000, rms=0.582 (0.260%), neg=0, invalid=4512 0238: dt=0.384000, rms=0.581 (0.159%), neg=0, invalid=4512 0239: dt=0.384000, rms=0.581 (0.124%), neg=0, invalid=4512 0240: dt=0.384000, rms=0.580 (0.077%), neg=0, invalid=4512 0241: dt=0.384000, rms=0.580 (0.074%), neg=0, invalid=4512 0242: dt=0.384000, rms=0.579 (0.051%), neg=0, invalid=4512 0243: dt=0.384000, rms=0.579 (0.052%), neg=0, invalid=4512 0244: dt=0.384000, rms=0.579 (0.035%), neg=0, invalid=4512 0245: dt=0.384000, rms=0.579 (0.036%), neg=0, invalid=4512 0246: dt=0.384000, rms=0.578 (0.062%), neg=0, invalid=4512 0247: dt=0.384000, rms=0.578 (0.069%), neg=0, invalid=4512 0248: dt=0.384000, rms=0.577 (0.078%), neg=0, invalid=4512 0249: dt=0.384000, rms=0.577 (0.014%), neg=0, invalid=4512 0250: dt=0.384000, rms=0.577 (0.007%), neg=0, invalid=4512 0251: dt=0.320000, rms=0.577 (0.008%), neg=0, invalid=4512 0252: dt=0.256000, rms=0.577 (0.008%), neg=0, invalid=4512 0253: dt=0.256000, rms=0.577 (0.006%), neg=0, invalid=4512 0254: dt=0.256000, rms=0.577 (0.020%), neg=0, invalid=4512 0255: dt=0.256000, rms=0.577 (0.011%), neg=0, invalid=4512 0256: dt=0.256000, rms=0.577 (0.007%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.578, neg=0, invalid=4512 0257: dt=0.384000, rms=0.571 (1.149%), neg=0, invalid=4512 0258: dt=0.384000, rms=0.569 (0.291%), neg=0, invalid=4512 0259: dt=0.384000, rms=0.569 (0.117%), neg=0, invalid=4512 0260: dt=0.384000, rms=0.569 (0.045%), neg=0, invalid=4512 0261: dt=0.384000, rms=0.568 (0.028%), neg=0, invalid=4512 0262: dt=0.384000, rms=0.568 (0.037%), neg=0, invalid=4512 0263: dt=0.192000, rms=0.568 (-0.003%), neg=0, invalid=4512 0264: dt=0.080000, rms=0.568 (0.001%), neg=0, invalid=4512 0265: dt=0.112000, rms=0.568 (0.003%), neg=0, invalid=4512 0266: dt=0.384000, rms=0.568 (0.006%), neg=0, invalid=4512 0267: dt=0.000000, rms=0.568 (-0.002%), 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=0.566, neg=0, invalid=4512 0268: dt=0.000000, rms=0.566 (0.136%), neg=0, invalid=4512 0269: dt=0.000000, rms=0.566 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.566, neg=0, invalid=4512 0270: dt=0.000000, rms=0.566 (0.136%), neg=0, invalid=4512 0271: dt=0.000000, rms=0.566 (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=0.566, neg=0, invalid=4512 0272: dt=7.776000, rms=0.566 (0.143%), neg=0, invalid=4512 0273: dt=4.571429, rms=0.566 (0.003%), neg=0, invalid=4512 0274: dt=4.571429, rms=0.566 (0.002%), neg=0, invalid=4512 0275: dt=4.571429, rms=0.566 (-0.006%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.566, neg=0, invalid=4512 0276: dt=36.288000, rms=0.565 (0.259%), neg=0, invalid=4512 0277: dt=124.416000, rms=0.564 (0.193%), neg=0, invalid=4512 0278: dt=124.416000, rms=0.564 (-0.790%), neg=0, invalid=4512 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.565, neg=0, invalid=4512 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0279: dt=22.068966, rms=0.561 (0.671%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0280: dt=32.000000, rms=0.559 (0.358%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0281: dt=20.700565, rms=0.558 (0.217%), neg=0, invalid=4512 0282: dt=20.700565, rms=0.557 (0.072%), neg=0, invalid=4512 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0283: dt=20.700565, rms=0.557 (0.081%), neg=0, invalid=4512 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0284: dt=20.700565, rms=0.557 (0.062%), neg=0, invalid=4512 iter 0, gcam->neg = 15 after 3 iterations, nbhd size=0, neg = 0 0285: dt=20.700565, rms=0.557 (-0.089%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.557, neg=0, invalid=4512 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0286: dt=42.407477, rms=0.550 (1.341%), neg=0, invalid=4512 0287: dt=22.030769, rms=0.548 (0.352%), neg=0, invalid=4512 0288: dt=32.000000, rms=0.547 (0.195%), neg=0, invalid=4512 0289: dt=32.000000, rms=0.547 (0.042%), neg=0, invalid=4512 0290: dt=32.000000, rms=0.545 (0.285%), neg=0, invalid=4512 0291: dt=32.000000, rms=0.545 (0.081%), neg=0, invalid=4512 0292: dt=32.000000, rms=0.543 (0.226%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0293: dt=32.000000, rms=0.543 (0.154%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0294: dt=32.000000, rms=0.541 (0.258%), neg=0, invalid=4512 0295: dt=32.000000, rms=0.540 (0.164%), neg=0, invalid=4512 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0296: dt=32.000000, rms=0.539 (0.201%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0297: dt=32.000000, rms=0.538 (0.226%), neg=0, invalid=4512 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0298: dt=32.000000, rms=0.537 (0.142%), neg=0, invalid=4512 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0299: dt=32.000000, rms=0.537 (0.119%), neg=0, invalid=4512 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 0300: dt=32.000000, rms=0.536 (0.145%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0301: dt=32.000000, rms=0.535 (0.131%), neg=0, invalid=4512 iter 0, gcam->neg = 3 after 4 iterations, nbhd size=0, neg = 0 0302: dt=32.000000, rms=0.535 (-0.025%), neg=0, invalid=4512 0303: dt=11.200000, rms=0.535 (0.043%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0304: dt=25.600000, rms=0.535 (0.037%), neg=0, invalid=4512 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.541, neg=0, invalid=4512 0305: dt=2.880000, rms=0.540 (0.201%), neg=0, invalid=4512 0306: dt=1.008000, rms=0.540 (0.007%), neg=0, invalid=4512 0307: dt=1.008000, rms=0.540 (0.001%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0308: dt=1.008000, rms=0.540 (-0.008%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.541, neg=0, invalid=4512 0309: dt=2.880000, rms=0.540 (0.173%), neg=0, invalid=4512 0310: dt=3.333333, rms=0.540 (0.019%), neg=0, invalid=4512 0311: dt=3.333333, rms=0.540 (0.013%), neg=0, invalid=4512 0312: dt=3.333333, rms=0.540 (-0.009%), neg=0, invalid=4512 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.548, neg=0, invalid=4512 0313: dt=0.112000, rms=0.547 (0.145%), neg=0, invalid=4512 0314: dt=0.096000, rms=0.547 (0.005%), neg=0, invalid=4512 0315: dt=0.096000, rms=0.547 (0.000%), neg=0, invalid=4512 0316: dt=0.096000, rms=0.547 (-0.004%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.548, neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0317: dt=1.536000, rms=0.546 (0.281%), neg=0, invalid=4512 0318: dt=1.792000, rms=0.546 (0.146%), neg=0, invalid=4512 0319: dt=1.792000, rms=0.545 (0.055%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0320: dt=1.792000, rms=0.545 (0.050%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 4 iterations, nbhd size=0, neg = 0 0321: dt=1.792000, rms=0.545 (0.005%), neg=0, invalid=4512 iter 0, gcam->neg = 80 after 12 iterations, nbhd size=1, neg = 0 0322: dt=7.781818, rms=0.543 (0.387%), neg=0, invalid=4512 0323: dt=1.792000, rms=0.542 (0.100%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0324: dt=1.792000, rms=0.542 (0.036%), neg=0, invalid=4512 0325: dt=1.792000, rms=0.542 (0.049%), neg=0, invalid=4512 iter 0, gcam->neg = 5 after 9 iterations, nbhd size=1, neg = 0 0326: dt=1.792000, rms=0.542 (0.027%), neg=0, invalid=4512 0327: dt=1.792000, rms=0.541 (0.074%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0328: dt=1.792000, rms=0.541 (0.110%), neg=0, invalid=4512 0329: dt=1.792000, rms=0.540 (0.144%), neg=0, invalid=4512 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 0330: dt=1.792000, rms=0.539 (0.131%), neg=0, invalid=4512 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0331: dt=1.792000, rms=0.539 (0.092%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0332: dt=1.792000, rms=0.539 (0.043%), neg=0, invalid=4512 0333: dt=1.024000, rms=0.539 (0.005%), neg=0, invalid=4512 0334: dt=1.024000, rms=0.539 (0.006%), neg=0, invalid=4512 0335: dt=1.024000, rms=0.539 (-0.007%), 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=0.535, neg=0, invalid=4512 iter 0, gcam->neg = 1312 after 14 iterations, nbhd size=1, neg = 0 0336: dt=2.334370, rms=0.496 (7.332%), neg=0, invalid=4512 0337: dt=0.112000, rms=0.495 (0.147%), neg=0, invalid=4512 0338: dt=0.112000, rms=0.495 (-0.064%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.496, neg=0, invalid=4512 0339: dt=0.096000, rms=0.495 (0.273%), neg=0, invalid=4512 0340: dt=0.016000, rms=0.495 (0.003%), neg=0, invalid=4512 0341: dt=0.016000, rms=0.495 (0.000%), neg=0, invalid=4512 0342: dt=0.016000, rms=0.495 (-0.009%), 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 0343: 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 0344: dt=32.368000, rms=0.477 (0.006%), neg=0, invalid=4512 0345: dt=8.092000, rms=0.477 (0.000%), neg=0, invalid=4512 0346: dt=8.092000, rms=0.477 (0.000%), neg=0, invalid=4512 0347: dt=8.092000, 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 0348: dt=3.888000, rms=0.477 (0.004%), neg=0, invalid=4512 0349: dt=0.567000, rms=0.477 (0.000%), neg=0, invalid=4512 0350: dt=0.567000, rms=0.477 (0.000%), neg=0, invalid=4512 0351: dt=0.567000, 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 0352: dt=36.288000, rms=0.476 (0.062%), neg=0, invalid=4512 0353: dt=103.680000, rms=0.476 (0.072%), neg=0, invalid=4512 0354: dt=145.152000, rms=0.476 (0.088%), neg=0, invalid=4512 0355: dt=36.288000, rms=0.475 (0.045%), neg=0, invalid=4512 0356: dt=36.288000, rms=0.475 (0.009%), neg=0, invalid=4512 0357: dt=36.288000, rms=0.475 (0.016%), neg=0, invalid=4512 0358: dt=36.288000, rms=0.475 (0.035%), neg=0, invalid=4512 0359: dt=36.288000, rms=0.475 (0.042%), neg=0, invalid=4512 0360: dt=36.288000, rms=0.475 (0.042%), neg=0, invalid=4512 0361: dt=36.288000, rms=0.475 (0.031%), neg=0, invalid=4512 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.476, neg=0, invalid=4512 0362: dt=6.400000, rms=0.475 (0.050%), neg=0, invalid=4512 0363: dt=2.800000, rms=0.475 (0.006%), neg=0, invalid=4512 0364: dt=2.800000, rms=0.475 (0.001%), neg=0, invalid=4512 0365: dt=2.800000, rms=0.475 (-0.016%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.475, neg=0, invalid=4512 0366: dt=44.800000, rms=0.473 (0.501%), neg=0, invalid=4512 0367: dt=11.200000, rms=0.472 (0.155%), neg=0, invalid=4512 0368: dt=11.200000, rms=0.472 (0.064%), neg=0, invalid=4512 0369: dt=11.200000, rms=0.471 (0.093%), neg=0, invalid=4512 0370: dt=11.200000, rms=0.471 (0.112%), neg=0, invalid=4512 0371: dt=11.200000, rms=0.470 (0.136%), neg=0, invalid=4512 0372: dt=11.200000, rms=0.470 (0.143%), neg=0, invalid=4512 0373: dt=11.200000, rms=0.469 (0.128%), neg=0, invalid=4512 0374: dt=11.200000, rms=0.468 (0.110%), neg=0, invalid=4512 0375: dt=11.200000, rms=0.468 (0.094%), neg=0, invalid=4512 0376: dt=38.400000, rms=0.468 (0.025%), neg=0, invalid=4512 0377: dt=38.400000, rms=0.468 (0.051%), neg=0, invalid=4512 0378: dt=38.400000, rms=0.468 (0.035%), neg=0, invalid=4512 0379: dt=38.400000, rms=0.467 (0.067%), neg=0, invalid=4512 0380: dt=38.400000, rms=0.467 (0.043%), neg=0, invalid=4512 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.471, neg=0, invalid=4512 0381: dt=2.304000, rms=0.471 (0.035%), neg=0, invalid=4512 0382: dt=0.108000, rms=0.471 (0.000%), neg=0, invalid=4512 0383: dt=0.108000, rms=0.471 (-0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.471, neg=0, invalid=4512 0384: dt=5.090909, rms=0.471 (0.047%), neg=0, invalid=4512 0385: dt=8.754717, rms=0.471 (0.051%), neg=0, invalid=4512 0386: dt=24.000000, rms=0.470 (0.108%), neg=0, invalid=4512 iter 0, gcam->neg = 7 after 4 iterations, nbhd size=0, neg = 0 0387: dt=27.648000, rms=0.469 (0.209%), neg=0, invalid=4512 0388: dt=4.923077, rms=0.469 (0.054%), neg=0, invalid=4512 0389: dt=4.923077, rms=0.469 (0.047%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0390: dt=4.923077, rms=0.469 (0.036%), neg=0, invalid=4512 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0391: dt=4.923077, rms=0.469 (0.036%), neg=0, invalid=4512 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 0392: dt=4.923077, rms=0.468 (0.031%), neg=0, invalid=4512 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.475, neg=0, invalid=4512 0393: dt=0.000050, rms=0.475 (0.000%), neg=0, invalid=4512 0394: dt=0.000000, rms=0.475 (0.000%), neg=0, invalid=4512 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.475, neg=0, invalid=4512 0395: dt=0.000000, rms=0.475 (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=0.464, neg=0, invalid=4512 iter 0, gcam->neg = 708 after 13 iterations, nbhd size=1, neg = 0 0396: dt=1.426929, rms=0.450 (3.021%), neg=0, invalid=4512 0397: dt=0.000013, rms=0.450 (0.000%), neg=0, invalid=4512 0398: dt=0.000013, rms=0.450 (0.000%), neg=0, invalid=4512 0399: dt=0.000013, 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 0400: dt=0.112000, rms=0.449 (0.106%), neg=0, invalid=4512 0401: dt=0.064000, rms=0.449 (0.023%), neg=0, invalid=4512 0402: dt=0.064000, rms=0.449 (0.007%), neg=0, invalid=4512 0403: dt=0.064000, rms=0.449 (-0.045%), neg=0, invalid=4512 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 4 minutes and 59 seconds. mri_ca_register utimesec 7447.988000 mri_ca_register stimesec 10.092000 mri_ca_register ru_maxrss 1350264 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 4821414 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 62976 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 15 mri_ca_register ru_nivcsw 307365 FSRUNTIME@ mri_ca_register 2.0829 hours 1 threads #-------------------------------------- #@# SubCort Seg Mon Dec 19 13:08:56 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/SynthF/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 = 0.14102 (13) Left_Lateral_Ventricle (4): linear fit = 0.60 x + 0.0 (1613 voxels, overlap=0.136) Left_Lateral_Ventricle (4): linear fit = 0.60 x + 0.0 (1613 voxels, peak = 12), gca=11.9 gca peak = 0.17677 (13) mri peak = 0.08407 (13) Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (2538 voxels, overlap=0.631) Right_Lateral_Ventricle (43): linear fit = 0.51 x + 0.0 (2538 voxels, peak = 7), gca=6.7 gca peak = 0.28129 (95) mri peak = 0.08564 (97) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (1222 voxels, overlap=1.016) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (1222 voxels, peak = 96), gca=96.4 gca peak = 0.16930 (96) mri peak = 0.10576 (98) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (1164 voxels, overlap=1.009) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (1164 voxels, peak = 98), gca=98.4 gca peak = 0.24553 (55) mri peak = 0.08738 (59) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1058 voxels, overlap=1.008) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1058 voxels, peak = 54), gca=54.2 gca peak = 0.30264 (59) mri peak = 0.07320 (62) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (1022 voxels, overlap=1.013) Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (1022 voxels, peak = 56), gca=55.8 gca peak = 0.07580 (103) mri peak = 0.07494 (98) Right_Cerebral_White_Matter (41): linear fit = 0.96 x + 0.0 (57311 voxels, overlap=0.696) Right_Cerebral_White_Matter (41): linear fit = 0.96 x + 0.0 (57311 voxels, peak = 99), gca=99.4 gca peak = 0.07714 (104) mri peak = 0.07155 (97) Left_Cerebral_White_Matter (2): linear fit = 0.95 x + 0.0 (73228 voxels, overlap=0.817) Left_Cerebral_White_Matter (2): linear fit = 0.95 x + 0.0 (73228 voxels, peak = 99), gca=99.3 gca peak = 0.09712 (58) mri peak = 0.02767 (60) Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (29839 voxels, overlap=0.764) Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (29839 voxels, peak = 61), gca=60.6 gca peak = 0.11620 (58) mri peak = 0.02444 (84) Right_Cerebral_Cortex (42): linear fit = 1.46 x + 0.0 (34462 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.46 x + 0.0 (34462 voxels, peak = 84), gca=84.4 gca peak = 0.30970 (66) mri peak = 0.11877 (70) Right_Caudate (50): linear fit = 1.03 x + 0.0 (1987 voxels, overlap=1.008) Right_Caudate (50): linear fit = 1.03 x + 0.0 (1987 voxels, peak = 68), gca=68.3 gca peak = 0.15280 (69) mri peak = 0.08308 (75) Left_Caudate (11): linear fit = 0.99 x + 0.0 (1649 voxels, overlap=0.940) Left_Caudate (11): linear fit = 0.99 x + 0.0 (1649 voxels, peak = 68), gca=68.0 gca peak = 0.13902 (56) mri peak = 0.03007 (66) Left_Cerebellum_Cortex (8): linear fit = 1.30 x + 0.0 (25619 voxels, overlap=0.220) Left_Cerebellum_Cortex (8): linear fit = 1.30 x + 0.0 (25619 voxels, peak = 73), gca=73.1 gca peak = 0.14777 (55) mri peak = 0.03924 (83) Right_Cerebellum_Cortex (47): linear fit = 1.42 x + 0.0 (26045 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.42 x + 0.0 (26045 voxels, peak = 78), gca=78.4 gca peak = 0.16765 (84) mri peak = 0.06381 (84) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (8179 voxels, overlap=0.947) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (8179 voxels, peak = 85), gca=85.3 gca peak = 0.18739 (84) mri peak = 0.08340 (83) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (4865 voxels, overlap=0.944) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (4865 voxels, peak = 85), gca=85.3 gca peak = 0.29869 (57) mri peak = 0.10079 (68) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (504 voxels, overlap=0.352) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (504 voxels, peak = 66), gca=66.4 gca peak = 0.33601 (57) mri peak = 0.08590 (62) Right_Amygdala (54): linear fit = 1.10 x + 0.0 (466 voxels, overlap=1.026) Right_Amygdala (54): linear fit = 1.10 x + 0.0 (466 voxels, peak = 62), gca=62.4 gca peak = 0.11131 (90) mri peak = 0.07169 (94) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5993 voxels, overlap=0.911) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5993 voxels, peak = 95), gca=94.9 gca peak = 0.11793 (83) mri peak = 0.08227 (95) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5204 voxels, overlap=0.426) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (5204 voxels, peak = 93), gca=92.5 gca peak = 0.08324 (81) mri peak = 0.08854 (80) Left_Putamen (12): linear fit = 1.04 x + 0.0 (2910 voxels, overlap=0.706) Left_Putamen (12): linear fit = 1.04 x + 0.0 (2910 voxels, peak = 85), gca=84.6 gca peak = 0.10360 (77) mri peak = 0.06686 (75) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2763 voxels, overlap=0.940) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2763 voxels, peak = 78), gca=78.2 gca peak = 0.08424 (78) mri peak = 0.06419 (85) Brain_Stem (16): linear fit = 1.12 x + 0.0 (12734 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.12 x + 0.0 (12734 voxels, peak = 88), gca=87.8 gca peak = 0.12631 (89) mri peak = 0.06930 (104) Right_VentralDC (60): linear fit = 1.17 x + 0.0 (2117 voxels, overlap=0.215) Right_VentralDC (60): linear fit = 1.17 x + 0.0 (2117 voxels, peak = 105), gca=104.6 gca peak = 0.14500 (87) mri peak = 0.06263 (98) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (2195 voxels, overlap=0.482) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (2195 voxels, peak = 99), gca=98.7 gca peak = 0.14975 (24) mri peak = 0.13686 (17) Third_Ventricle (14): linear fit = 0.58 x + 0.0 (87 voxels, overlap=0.039) Third_Ventricle (14): linear fit = 0.58 x + 0.0 (87 voxels, peak = 14), gca=14.0 gca peak = 0.19357 (14) mri peak = 0.14496 ( 3) Fourth_Ventricle (15): linear fit = 0.12 x + 0.0 (117 voxels, overlap=0.018) Fourth_Ventricle (15): linear fit = 0.12 x + 0.0 (117 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 1.12 x + 0.0 estimating mean wm scale to be 0.96 x + 0.0 estimating mean csf scale to be 0.56 x + 0.0 Left_Pallidum too bright - rescaling by 0.979 (from 1.025) to 96.4 (was 98.4) Right_Pallidum too bright - rescaling by 0.999 (from 1.015) to 96.4 (was 96.4) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.26695 (12) mri peak = 0.14102 (13) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (1613 voxels, overlap=0.959) Left_Lateral_Ventricle (4): linear fit = 1.03 x + 0.0 (1613 voxels, peak = 12), gca=12.4 gca peak = 0.29918 ( 7) mri peak = 0.08407 (13) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (2538 voxels, overlap=0.995) Right_Lateral_Ventricle (43): linear fit = 1.08 x + 0.0 (2538 voxels, peak = 8), gca=7.5 gca peak = 0.28940 (97) mri peak = 0.08564 (97) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (1222 voxels, overlap=1.011) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (1222 voxels, peak = 96), gca=95.5 gca peak = 0.18489 (97) mri peak = 0.10576 (98) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (1164 voxels, overlap=1.004) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (1164 voxels, peak = 99), gca=99.4 gca peak = 0.28829 (55) mri peak = 0.08738 (59) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1058 voxels, overlap=0.977) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1058 voxels, peak = 55), gca=55.0 gca peak = 0.29509 (53) mri peak = 0.07320 (62) Left_Hippocampus (17): linear fit = 1.07 x + 0.0 (1022 voxels, overlap=1.004) Left_Hippocampus (17): linear fit = 1.07 x + 0.0 (1022 voxels, peak = 56), gca=56.4 gca peak = 0.08019 (99) mri peak = 0.07494 (98) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (57311 voxels, overlap=0.804) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (57311 voxels, peak = 99), gca=99.5 gca peak = 0.08250 (100) mri peak = 0.07155 (97) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (73228 voxels, overlap=0.828) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (73228 voxels, peak = 102), gca=101.5 gca peak = 0.09152 (61) mri peak = 0.02767 (60) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (29839 voxels, overlap=0.644) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (29839 voxels, peak = 63), gca=62.5 gca peak = 0.07967 (86) mri peak = 0.02444 (84) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (34462 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (34462 voxels, peak = 84), gca=83.8 gca peak = 0.26235 (69) mri peak = 0.11877 (70) Right_Caudate (50): linear fit = 0.99 x + 0.0 (1987 voxels, overlap=1.008) Right_Caudate (50): linear fit = 0.99 x + 0.0 (1987 voxels, peak = 68), gca=68.0 gca peak = 0.16321 (68) mri peak = 0.08308 (75) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1649 voxels, overlap=1.002) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1649 voxels, peak = 68), gca=68.0 gca peak = 0.10586 (72) mri peak = 0.03007 (66) Left_Cerebellum_Cortex (8): linear fit = 1.03 x + 0.0 (25619 voxels, overlap=0.890) Left_Cerebellum_Cortex (8): linear fit = 1.03 x + 0.0 (25619 voxels, peak = 75), gca=74.5 gca peak = 0.10713 (78) mri peak = 0.03924 (83) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (26045 voxels, overlap=0.940) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (26045 voxels, peak = 78), gca=78.0 gca peak = 0.16360 (86) mri peak = 0.06381 (84) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (8179 voxels, overlap=0.967) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (8179 voxels, peak = 85), gca=84.7 gca peak = 0.15873 (86) mri peak = 0.08340 (83) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4865 voxels, overlap=0.991) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4865 voxels, peak = 85), gca=84.7 gca peak = 0.26591 (66) mri peak = 0.10079 (68) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (504 voxels, overlap=1.014) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (504 voxels, peak = 65), gca=65.0 gca peak = 0.28006 (62) mri peak = 0.08590 (62) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (466 voxels, overlap=0.803) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (466 voxels, peak = 61), gca=61.1 gca peak = 0.11498 (95) mri peak = 0.07169 (94) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5993 voxels, overlap=0.988) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5993 voxels, peak = 95), gca=94.5 gca peak = 0.11011 (90) mri peak = 0.08227 (95) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (5204 voxels, overlap=0.907) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (5204 voxels, peak = 89), gca=88.7 gca peak = 0.07357 (79) mri peak = 0.08854 (80) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2910 voxels, overlap=0.852) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2910 voxels, peak = 79), gca=78.6 gca peak = 0.08539 (78) mri peak = 0.06686 (75) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2763 voxels, overlap=0.943) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2763 voxels, peak = 76), gca=76.1 gca peak = 0.07728 (88) mri peak = 0.06419 (85) Brain_Stem (16): linear fit = 0.99 x + 0.0 (12734 voxels, overlap=0.858) Brain_Stem (16): linear fit = 0.99 x + 0.0 (12734 voxels, peak = 87), gca=86.7 gca peak = 0.14087 (103) mri peak = 0.06930 (104) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (2117 voxels, overlap=0.869) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (2117 voxels, peak = 104), gca=103.5 gca peak = 0.17578 (97) mri peak = 0.06263 (98) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (2195 voxels, overlap=0.955) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (2195 voxels, peak = 97), gca=97.5 gca peak = 0.25308 (14) mri peak = 0.13686 (17) Third_Ventricle (14): linear fit = 1.03 x + 0.0 (87 voxels, overlap=0.999) Third_Ventricle (14): linear fit = 1.03 x + 0.0 (87 voxels, peak = 14), gca=14.5 gca peak = 0.34244 ( 8) mri peak = 0.14496 ( 3) Fourth_Ventricle (15): linear fit = 0.25 x + 0.0 (117 voxels, overlap=0.058) Fourth_Ventricle (15): linear fit = 0.25 x + 0.0 (117 voxels, peak = 2), gca=2.0 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.19706 (30) gca peak Left_Thalamus = 0.36646 (97) gca peak Fourth_Ventricle = 0.34244 ( 8) gca peak CSF = 0.38039 (20) gca peak Left_Accumbens_area = 0.64419 (61) 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 = 0.26283 (23) gca peak Right_Accumbens_area = 0.33360 (69) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65358 (18) gca peak WM_hypointensities = 0.07973 (73) gca peak non_WM_hypointensities = 0.07897 (42) gca peak Optic_Chiasm = 0.61068 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.05 x + 0.0 Left_Pallidum too bright - rescaling by 0.980 (from 1.025) to 97.5 (was 99.4) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 111944 voxels changed in iteration 0 of unlikely voxel relabeling 645 voxels changed in iteration 1 of unlikely voxel relabeling 20 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 115579 gm and wm labels changed (%23 to gray, %77 to white out of all changed labels) 537 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 107253 changed. image ll: -2.300, PF=0.500 pass 2: 32462 changed. image ll: -2.299, PF=0.500 pass 3: 10914 changed. pass 4: 4183 changed. 115927 voxels changed in iteration 0 of unlikely voxel relabeling 1278 voxels changed in iteration 1 of unlikely voxel relabeling 60 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 14727 voxels changed in iteration 0 of unlikely voxel relabeling 306 voxels changed in iteration 1 of unlikely voxel relabeling 76 voxels changed in iteration 2 of unlikely voxel relabeling 39 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 11273 voxels changed in iteration 0 of unlikely voxel relabeling 227 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 10139 voxels changed in iteration 0 of unlikely voxel relabeling 83 voxels changed in iteration 1 of unlikely voxel relabeling 1 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 4396.972000 mri_ca_label stimesec 2.168000 mri_ca_label ru_maxrss 2131080 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 600021 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 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 40 mri_ca_label ru_nivcsw 250994 auto-labeling took 73 minutes and 30 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /usr/local/freesurfer/subjects/SynthF/mri/transforms/cc_up.lta SynthF 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/SynthF/mri/transforms/cc_up.lta reading aseg from /usr/local/freesurfer/subjects/SynthF/mri/aseg.auto_noCCseg.mgz reading norm from /usr/local/freesurfer/subjects/SynthF/mri/norm.mgz 41630 voxels in left wm, 62487 in right wm, xrange [120, 131] searching rotation angles z=[-7 7], y=[-9 5] searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.8 global minimum found at slice 126.0, rotations (-1.88, 0.04) final transformation (x=126.0, yr=-1.880, zr=0.039): 0.99946 -0.00068 -0.03280 6.21674; 0.00068 1.00000 -0.00002 7.91732; 0.03280 -0.00000 0.99946 -0.06633; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 120 124 eigenvectors: 0.00012 -0.00361 0.99999; 0.15865 -0.98733 -0.00358; 0.98734 0.15865 0.00045; writing aseg with callosum to /usr/local/freesurfer/subjects/SynthF/mri/aseg.auto.mgz... corpus callosum segmentation took 0.8 minutes #-------------------------------------- #@# Merge ASeg Mon Dec 19 14:23:17 GMT 2016 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Mon Dec 19 14:23:17 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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... 2061 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 12 (12) csf peak at 33, 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 63 (63), valley at 11 (11) csf peak at 32, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 2 seconds. #-------------------------------------------- #@# Mask BFS Mon Dec 19 14:26:21 GMT 2016 /usr/local/freesurfer/subjects/SynthF/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1836253 voxels in mask (pct= 10.94) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Dec 19 14:26:24 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 (105.0): 105.4 +- 5.0 [79.0 --> 125.0] GM (69.0) : 67.5 +- 10.3 [30.0 --> 95.0] setting bottom of white matter range to 77.9 setting top of gray matter range to 88.2 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... 7093 sparsely connected voxels removed... thickening thin strands.... 20 segments, 2576 filled 5426 bright non-wm voxels segmented. 3572 diagonally connected voxels added... white matter segmentation took 1.7 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 0.55 minutes reading wm segmentation from wm.seg.mgz... 475 voxels added to wm to prevent paths from MTL structures to cortex 6480 additional wm voxels added 0 additional wm voxels added SEG EDIT: 64493 voxels turned on, 65089 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+): 40 found - 40 modified | TOTAL: 40 pass 2 (xy+): 0 found - 40 modified | TOTAL: 40 pass 1 (xy-): 57 found - 57 modified | TOTAL: 97 pass 2 (xy-): 0 found - 57 modified | TOTAL: 97 pass 1 (yz+): 43 found - 43 modified | TOTAL: 140 pass 2 (yz+): 0 found - 43 modified | TOTAL: 140 pass 1 (yz-): 40 found - 40 modified | TOTAL: 180 pass 2 (yz-): 0 found - 40 modified | TOTAL: 180 pass 1 (xz+): 39 found - 39 modified | TOTAL: 219 pass 2 (xz+): 0 found - 39 modified | TOTAL: 219 pass 1 (xz-): 40 found - 40 modified | TOTAL: 259 pass 2 (xz-): 0 found - 40 modified | TOTAL: 259 Iteration Number : 1 pass 1 (+++): 46 found - 46 modified | TOTAL: 46 pass 2 (+++): 0 found - 46 modified | TOTAL: 46 pass 1 (+++): 87 found - 87 modified | TOTAL: 133 pass 2 (+++): 0 found - 87 modified | TOTAL: 133 pass 1 (+++): 57 found - 57 modified | TOTAL: 190 pass 2 (+++): 0 found - 57 modified | TOTAL: 190 pass 1 (+++): 46 found - 46 modified | TOTAL: 236 pass 2 (+++): 0 found - 46 modified | TOTAL: 236 Iteration Number : 1 pass 1 (++): 72 found - 72 modified | TOTAL: 72 pass 2 (++): 0 found - 72 modified | TOTAL: 72 pass 1 (+-): 225 found - 225 modified | TOTAL: 297 pass 2 (+-): 0 found - 225 modified | TOTAL: 297 pass 1 (--): 85 found - 85 modified | TOTAL: 382 pass 2 (--): 0 found - 85 modified | TOTAL: 382 pass 1 (-+): 110 found - 110 modified | TOTAL: 492 pass 2 (-+): 0 found - 110 modified | TOTAL: 492 Iteration Number : 2 pass 1 (xy+): 10 found - 10 modified | TOTAL: 10 pass 2 (xy+): 0 found - 10 modified | TOTAL: 10 pass 1 (xy-): 14 found - 14 modified | TOTAL: 24 pass 2 (xy-): 0 found - 14 modified | TOTAL: 24 pass 1 (yz+): 18 found - 18 modified | TOTAL: 42 pass 2 (yz+): 0 found - 18 modified | TOTAL: 42 pass 1 (yz-): 13 found - 13 modified | TOTAL: 55 pass 2 (yz-): 0 found - 13 modified | TOTAL: 55 pass 1 (xz+): 9 found - 9 modified | TOTAL: 64 pass 2 (xz+): 0 found - 9 modified | TOTAL: 64 pass 1 (xz-): 15 found - 15 modified | TOTAL: 79 pass 2 (xz-): 0 found - 15 modified | TOTAL: 79 Iteration Number : 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 18 found - 18 modified | TOTAL: 22 pass 2 (+++): 0 found - 18 modified | TOTAL: 22 pass 1 (+++): 2 found - 2 modified | TOTAL: 24 pass 2 (+++): 0 found - 2 modified | TOTAL: 24 pass 1 (+++): 4 found - 4 modified | TOTAL: 28 pass 2 (+++): 0 found - 4 modified | TOTAL: 28 Iteration Number : 2 pass 1 (++): 5 found - 5 modified | TOTAL: 5 pass 2 (++): 0 found - 5 modified | TOTAL: 5 pass 1 (+-): 9 found - 9 modified | TOTAL: 14 pass 2 (+-): 1 found - 10 modified | TOTAL: 15 pass 3 (+-): 0 found - 10 modified | TOTAL: 15 pass 1 (--): 5 found - 5 modified | TOTAL: 20 pass 2 (--): 0 found - 5 modified | TOTAL: 20 pass 1 (-+): 9 found - 9 modified | TOTAL: 29 pass 2 (-+): 0 found - 9 modified | TOTAL: 29 Iteration Number : 3 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+): 2 found - 2 modified | TOTAL: 4 pass 2 (yz+): 0 found - 2 modified | TOTAL: 4 pass 1 (yz-): 0 found - 0 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 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 : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 1129 (out of 765452: 0.147495) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Mon Dec 19 14:28:42 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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 0.99849 0.04557 -0.02677 -4.09088; -0.04898 0.95826 -0.06126 0.11391; 0.02402 0.06158 0.94549 -24.12654; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 0.99849 0.04557 -0.02677 -4.09088; -0.04898 0.95826 -0.06126 0.11391; 0.02402 0.06158 0.94549 -24.12654; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1190 (min = 350, max = 1400), aspect = 0.53 (min = 0.10, max = 0.75) no need to search using seed (125, 105, 106), TAL = (3.0, -22.0, 23.0) talairach voxel to voxel transform 0.99850 -0.04910 0.02509 4.69563; 0.04921 1.03681 0.06857 1.73763; -0.02857 -0.06628 1.05255 25.28498; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 105, 106) --> (3.0, -22.0, 23.0) done. writing output to filled.mgz... filling took 0.6 minutes talairach cc position changed to (3.00, -22.00, 23.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, -22.00, 23.00) SRC: (109.04, 123.14, 126.84) search lh wm seed point around talairach space (-15.00, -22.00, 23.00), SRC: (144.99, 124.91, 125.81) 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 14:29:19 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 6 found - 6 modified | TOTAL: 8 pass 2 (xy-): 0 found - 6 modified | TOTAL: 8 pass 1 (yz+): 0 found - 0 modified | TOTAL: 8 pass 1 (yz-): 3 found - 3 modified | TOTAL: 11 pass 2 (yz-): 0 found - 3 modified | TOTAL: 11 pass 1 (xz+): 3 found - 3 modified | TOTAL: 14 pass 2 (xz+): 0 found - 3 modified | TOTAL: 14 pass 1 (xz-): 1 found - 1 modified | TOTAL: 15 pass 2 (xz-): 0 found - 1 modified | TOTAL: 15 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 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 (+++): 4 found - 4 modified | TOTAL: 6 pass 2 (+++): 0 found - 4 modified | TOTAL: 6 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 2 found - 2 modified | TOTAL: 3 pass 2 (+-): 0 found - 2 modified | TOTAL: 3 pass 1 (--): 0 found - 0 modified | TOTAL: 3 pass 1 (-+): 0 found - 0 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 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 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 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 363084: 0.007987) 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: 2623 vertices, 2795 faces slice 60: 10662 vertices, 10995 faces slice 70: 22462 vertices, 22902 faces slice 80: 36201 vertices, 36675 faces slice 90: 50527 vertices, 50957 faces slice 100: 64418 vertices, 64855 faces slice 110: 80244 vertices, 80789 faces slice 120: 95161 vertices, 95685 faces slice 130: 109674 vertices, 110222 faces slice 140: 124679 vertices, 125172 faces slice 150: 139255 vertices, 139795 faces slice 160: 152490 vertices, 152931 faces slice 170: 163754 vertices, 164222 faces slice 180: 173357 vertices, 173729 faces slice 190: 182341 vertices, 182724 faces slice 200: 189345 vertices, 189699 faces slice 210: 194029 vertices, 194266 faces slice 220: 194718 vertices, 194838 faces slice 230: 194718 vertices, 194838 faces slice 240: 194718 vertices, 194838 faces slice 250: 194718 vertices, 194838 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... 194718 voxel in cpt #1: X=-120 [v=194718,e=584514,f=389676] located at (-29.279049, -5.988635, -2.240681) For the whole surface: X=-120 [v=194718,e=584514,f=389676] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Mon Dec 19 14:29:25 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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-): 3 found - 3 modified | TOTAL: 3 pass 2 (xy-): 0 found - 3 modified | TOTAL: 3 pass 1 (yz+): 4 found - 4 modified | TOTAL: 7 pass 2 (yz+): 0 found - 4 modified | TOTAL: 7 pass 1 (yz-): 3 found - 3 modified | TOTAL: 10 pass 2 (yz-): 0 found - 3 modified | TOTAL: 10 pass 1 (xz+): 2 found - 2 modified | TOTAL: 12 pass 2 (xz+): 0 found - 2 modified | TOTAL: 12 pass 1 (xz-): 2 found - 2 modified | TOTAL: 14 pass 2 (xz-): 0 found - 2 modified | TOTAL: 14 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 (+-): 3 found - 3 modified | TOTAL: 3 pass 2 (+-): 0 found - 3 modified | TOTAL: 3 pass 1 (--): 1 found - 1 modified | TOTAL: 4 pass 2 (--): 0 found - 1 modified | TOTAL: 4 pass 1 (-+): 0 found - 0 modified | TOTAL: 4 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 = 18 (out of 381841: 0.004714) 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: 1131 vertices, 1236 faces slice 60: 6493 vertices, 6714 faces slice 70: 15222 vertices, 15576 faces slice 80: 26819 vertices, 27235 faces slice 90: 39918 vertices, 40355 faces slice 100: 54732 vertices, 55186 faces slice 110: 69256 vertices, 69806 faces slice 120: 85180 vertices, 85766 faces slice 130: 101692 vertices, 102323 faces slice 140: 118044 vertices, 118647 faces slice 150: 133150 vertices, 133753 faces slice 160: 146560 vertices, 147114 faces slice 170: 158956 vertices, 159501 faces slice 180: 170014 vertices, 170519 faces slice 190: 179480 vertices, 179971 faces slice 200: 187667 vertices, 188121 faces slice 210: 193443 vertices, 193792 faces slice 220: 195136 vertices, 195324 faces slice 230: 195136 vertices, 195324 faces slice 240: 195136 vertices, 195324 faces slice 250: 195136 vertices, 195324 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... 195136 voxel in cpt #1: X=-188 [v=195136,e=585972,f=390648] located at (32.790955, -0.542165, -1.817994) For the whole surface: X=-188 [v=195136,e=585972,f=390648] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Mon Dec 19 14:29:32 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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 14:29:38 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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 14:29:45 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 51.4 mm, total surface area = 104121 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.8 minutes step 000: RMS=0.155 (target=0.015) step 005: RMS=0.120 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.082 (target=0.015) step 020: RMS=0.072 (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=0.053 (target=0.015) step 050: RMS=0.052 (target=0.015) step 055: RMS=0.051 (target=0.015) step 060: RMS=0.051 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 46.604000 mris_inflate stimesec 0.092000 mris_inflate ru_maxrss 252820 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 30937 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 13704 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 3293 #-------------------------------------------- #@# Inflation1 rh Mon Dec 19 14:30:32 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 50.9 mm, total surface area = 103378 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.8 minutes step 000: RMS=0.160 (target=0.015) step 005: RMS=0.124 (target=0.015) step 010: RMS=0.099 (target=0.015) step 015: RMS=0.089 (target=0.015) step 020: RMS=0.080 (target=0.015) step 025: RMS=0.075 (target=0.015) step 030: RMS=0.070 (target=0.015) step 035: RMS=0.067 (target=0.015) step 040: RMS=0.064 (target=0.015) step 045: RMS=0.062 (target=0.015) step 050: RMS=0.062 (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 46.520000 mris_inflate stimesec 0.120000 mris_inflate ru_maxrss 253412 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 31108 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 13736 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 3155 #-------------------------------------------- #@# QSphere lh Mon Dec 19 14:31:19 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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 0.82 +- 0.52 (0.00-->7.20) (max @ vno 136014 --> 136048) face area 0.02 +- 0.03 (-0.23-->0.68) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.277... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.844, avgs=0 005/300: dt: 0.9000, rms radial error=175.586, avgs=0 010/300: dt: 0.9000, rms radial error=175.031, avgs=0 015/300: dt: 0.9000, rms radial error=174.303, avgs=0 020/300: dt: 0.9000, rms radial error=173.476, avgs=0 025/300: dt: 0.9000, rms radial error=172.591, avgs=0 030/300: dt: 0.9000, rms radial error=171.676, avgs=0 035/300: dt: 0.9000, rms radial error=170.745, avgs=0 040/300: dt: 0.9000, rms radial error=169.806, avgs=0 045/300: dt: 0.9000, rms radial error=168.865, avgs=0 050/300: dt: 0.9000, rms radial error=167.925, avgs=0 055/300: dt: 0.9000, rms radial error=166.988, avgs=0 060/300: dt: 0.9000, rms radial error=166.055, avgs=0 065/300: dt: 0.9000, rms radial error=165.125, avgs=0 070/300: dt: 0.9000, rms radial error=164.201, avgs=0 075/300: dt: 0.9000, rms radial error=163.281, avgs=0 080/300: dt: 0.9000, rms radial error=162.367, avgs=0 085/300: dt: 0.9000, rms radial error=161.458, avgs=0 090/300: dt: 0.9000, rms radial error=160.554, avgs=0 095/300: dt: 0.9000, rms radial error=159.655, avgs=0 100/300: dt: 0.9000, rms radial error=158.760, avgs=0 105/300: dt: 0.9000, rms radial error=157.871, avgs=0 110/300: dt: 0.9000, rms radial error=156.986, avgs=0 115/300: dt: 0.9000, rms radial error=156.105, avgs=0 120/300: dt: 0.9000, rms radial error=155.230, avgs=0 125/300: dt: 0.9000, rms radial error=154.359, avgs=0 130/300: dt: 0.9000, rms radial error=153.493, avgs=0 135/300: dt: 0.9000, rms radial error=152.631, avgs=0 140/300: dt: 0.9000, rms radial error=151.774, avgs=0 145/300: dt: 0.9000, rms radial error=150.922, avgs=0 150/300: dt: 0.9000, rms radial error=150.074, avgs=0 155/300: dt: 0.9000, rms radial error=149.230, avgs=0 160/300: dt: 0.9000, rms radial error=148.391, avgs=0 165/300: dt: 0.9000, rms radial error=147.557, avgs=0 170/300: dt: 0.9000, rms radial error=146.727, avgs=0 175/300: dt: 0.9000, rms radial error=145.902, avgs=0 180/300: dt: 0.9000, rms radial error=145.081, avgs=0 185/300: dt: 0.9000, rms radial error=144.264, avgs=0 190/300: dt: 0.9000, rms radial error=143.452, avgs=0 195/300: dt: 0.9000, rms radial error=142.644, avgs=0 200/300: dt: 0.9000, rms radial error=141.841, avgs=0 205/300: dt: 0.9000, rms radial error=141.041, avgs=0 210/300: dt: 0.9000, rms radial error=140.247, avgs=0 215/300: dt: 0.9000, rms radial error=139.456, avgs=0 220/300: dt: 0.9000, rms radial error=138.670, avgs=0 225/300: dt: 0.9000, rms radial error=137.888, avgs=0 230/300: dt: 0.9000, rms radial error=137.111, avgs=0 235/300: dt: 0.9000, rms radial error=136.337, avgs=0 240/300: dt: 0.9000, rms radial error=135.568, avgs=0 245/300: dt: 0.9000, rms radial error=134.803, avgs=0 250/300: dt: 0.9000, rms radial error=134.042, avgs=0 255/300: dt: 0.9000, rms radial error=133.285, avgs=0 260/300: dt: 0.9000, rms radial error=132.530, avgs=0 265/300: dt: 0.9000, rms radial error=131.779, avgs=0 270/300: dt: 0.9000, rms radial error=131.032, avgs=0 275/300: dt: 0.9000, rms radial error=130.290, avgs=0 280/300: dt: 0.9000, rms radial error=129.551, avgs=0 285/300: dt: 0.9000, rms radial error=128.817, avgs=0 290/300: dt: 0.9000, rms radial error=128.090, avgs=0 295/300: dt: 0.9000, rms radial error=127.368, avgs=0 300/300: dt: 0.9000, rms radial error=126.651, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 23602.62 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 2 (K=40.0), pass 1, starting sse = 4296.46 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 3 (K=160.0), pass 1, starting sse = 509.15 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00577 epoch 4 (K=640.0), pass 1, starting sse = 37.88 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00536 final distance error %27.30 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 257.252000 mris_sphere stimesec 0.592000 mris_sphere ru_maxrss 252824 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 30442 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 13704 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 4 mris_sphere ru_nivcsw 15651 FSRUNTIME@ mris_sphere 0.0720 hours 1 threads #-------------------------------------------- #@# QSphere rh Mon Dec 19 14:35:38 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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-->9.15) (max @ vno 70471 --> 70472) face area 0.02 +- 0.03 (-0.26-->0.91) == 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=176.216, avgs=0 005/300: dt: 0.9000, rms radial error=175.955, avgs=0 010/300: dt: 0.9000, rms radial error=175.395, avgs=0 015/300: dt: 0.9000, rms radial error=174.662, avgs=0 020/300: dt: 0.9000, rms radial error=173.827, avgs=0 025/300: dt: 0.9000, rms radial error=172.934, avgs=0 030/300: dt: 0.9000, rms radial error=172.008, avgs=0 035/300: dt: 0.9000, rms radial error=171.066, avgs=0 040/300: dt: 0.9000, rms radial error=170.115, avgs=0 045/300: dt: 0.9000, rms radial error=169.162, avgs=0 050/300: dt: 0.9000, rms radial error=168.210, avgs=0 055/300: dt: 0.9000, rms radial error=167.260, avgs=0 060/300: dt: 0.9000, rms radial error=166.323, avgs=0 065/300: dt: 0.9000, rms radial error=165.393, avgs=0 070/300: dt: 0.9000, rms radial error=164.468, avgs=0 075/300: dt: 0.9000, rms radial error=163.546, avgs=0 080/300: dt: 0.9000, rms radial error=162.630, avgs=0 085/300: dt: 0.9000, rms radial error=161.718, avgs=0 090/300: dt: 0.9000, rms radial error=160.811, avgs=0 095/300: dt: 0.9000, rms radial error=159.908, avgs=0 100/300: dt: 0.9000, rms radial error=159.010, avgs=0 105/300: dt: 0.9000, rms radial error=158.115, avgs=0 110/300: dt: 0.9000, rms radial error=157.225, avgs=0 115/300: dt: 0.9000, rms radial error=156.341, avgs=0 120/300: dt: 0.9000, rms radial error=155.462, avgs=0 125/300: dt: 0.9000, rms radial error=154.587, avgs=0 130/300: dt: 0.9000, rms radial error=153.717, avgs=0 135/300: dt: 0.9000, rms radial error=152.852, avgs=0 140/300: dt: 0.9000, rms radial error=151.991, avgs=0 145/300: dt: 0.9000, rms radial error=151.136, avgs=0 150/300: dt: 0.9000, rms radial error=150.284, avgs=0 155/300: dt: 0.9000, rms radial error=149.437, avgs=0 160/300: dt: 0.9000, rms radial error=148.595, avgs=0 165/300: dt: 0.9000, rms radial error=147.758, avgs=0 170/300: dt: 0.9000, rms radial error=146.925, avgs=0 175/300: dt: 0.9000, rms radial error=146.097, avgs=0 180/300: dt: 0.9000, rms radial error=145.274, avgs=0 185/300: dt: 0.9000, rms radial error=144.456, avgs=0 190/300: dt: 0.9000, rms radial error=143.642, avgs=0 195/300: dt: 0.9000, rms radial error=142.833, avgs=0 200/300: dt: 0.9000, rms radial error=142.028, avgs=0 205/300: dt: 0.9000, rms radial error=141.227, avgs=0 210/300: dt: 0.9000, rms radial error=140.431, avgs=0 215/300: dt: 0.9000, rms radial error=139.640, avgs=0 220/300: dt: 0.9000, rms radial error=138.853, avgs=0 225/300: dt: 0.9000, rms radial error=138.070, avgs=0 230/300: dt: 0.9000, rms radial error=137.292, avgs=0 235/300: dt: 0.9000, rms radial error=136.518, avgs=0 240/300: dt: 0.9000, rms radial error=135.748, avgs=0 245/300: dt: 0.9000, rms radial error=134.982, avgs=0 250/300: dt: 0.9000, rms radial error=134.221, avgs=0 255/300: dt: 0.9000, rms radial error=133.464, avgs=0 260/300: dt: 0.9000, rms radial error=132.711, avgs=0 265/300: dt: 0.9000, rms radial error=131.962, avgs=0 270/300: dt: 0.9000, rms radial error=131.218, avgs=0 275/300: dt: 0.9000, rms radial error=130.478, avgs=0 280/300: dt: 0.9000, rms radial error=129.742, avgs=0 285/300: dt: 0.9000, rms radial error=129.010, avgs=0 290/300: dt: 0.9000, rms radial error=128.282, avgs=0 295/300: dt: 0.9000, rms radial error=127.558, avgs=0 300/300: dt: 0.9000, rms radial error=126.838, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 23620.36 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 = 4291.67 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00002 epoch 3 (K=160.0), pass 1, starting sse = 522.66 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/10 = 0.00222 epoch 4 (K=640.0), pass 1, starting sse = 54.19 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00545 final distance error %27.86 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 248.124000 mris_sphere stimesec 0.120000 mris_sphere ru_maxrss 253660 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 30611 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 13736 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 1 mris_sphere ru_nivcsw 10317 FSRUNTIME@ mris_sphere 0.0692 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Mon Dec 19 14:39:48 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Mon Dec 19 14:39:48 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Mon Dec 19 14:39:48 GMT 2016 mris_fix_topology -rusage /usr/local/freesurfer/subjects/SynthF/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 SynthF 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=-120 (nv=194718, nf=389676, ne=584514, g=61) 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... 14876 ambiguous faces found in tessellation segmenting defects... 62 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 14 into 9 -merging segment 23 into 22 -merging segment 40 into 36 -merging segment 58 into 56 58 defects to be corrected 0 vertices coincident reading input surface /usr/local/freesurfer/subjects/SynthF/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.6722 (-4.8361) -vertex loglikelihood: -6.4274 (-3.2137) -normal dot loglikelihood: -3.6413 (-3.6413) -quad curv loglikelihood: -6.0320 (-3.0160) Total Loglikelihood : -25.7729 CORRECTING DEFECT 0 (vertices=69, convex hull=58, v0=465) After retessellation of defect 0 (v0=465), euler #=-59 (186120,555959,369780) : difference with theory (-55) = 4 CORRECTING DEFECT 1 (vertices=105, convex hull=138, v0=17575) After retessellation of defect 1 (v0=17575), euler #=-58 (186129,556052,369865) : difference with theory (-54) = 4 CORRECTING DEFECT 2 (vertices=475, convex hull=252, v0=23685) After retessellation of defect 2 (v0=23685), euler #=-57 (186235,556487,370195) : difference with theory (-53) = 4 CORRECTING DEFECT 3 (vertices=126, convex hull=153, v0=28098) After retessellation of defect 3 (v0=28098), euler #=-56 (186299,556756,370401) : difference with theory (-52) = 4 CORRECTING DEFECT 4 (vertices=256, convex hull=146, v0=31636) After retessellation of defect 4 (v0=31636), euler #=-55 (186357,556995,370583) : difference with theory (-51) = 4 CORRECTING DEFECT 5 (vertices=14, convex hull=36, v0=33022) After retessellation of defect 5 (v0=33022), euler #=-54 (186358,557010,370598) : difference with theory (-50) = 4 CORRECTING DEFECT 6 (vertices=186, convex hull=93, v0=45870) After retessellation of defect 6 (v0=45870), euler #=-53 (186388,557142,370701) : difference with theory (-49) = 4 CORRECTING DEFECT 7 (vertices=36, convex hull=76, v0=50981) After retessellation of defect 7 (v0=50981), euler #=-52 (186407,557230,370771) : difference with theory (-48) = 4 CORRECTING DEFECT 8 (vertices=149, convex hull=35, v0=59275) After retessellation of defect 8 (v0=59275), euler #=-51 (186415,557265,370799) : difference with theory (-47) = 4 CORRECTING DEFECT 9 (vertices=324, convex hull=256, v0=61811) After retessellation of defect 9 (v0=61811), euler #=-49 (186455,557522,371018) : difference with theory (-46) = 3 CORRECTING DEFECT 10 (vertices=33, convex hull=69, v0=62554) After retessellation of defect 10 (v0=62554), euler #=-48 (186470,557594,371076) : difference with theory (-45) = 3 CORRECTING DEFECT 11 (vertices=8, convex hull=31, v0=64085) After retessellation of defect 11 (v0=64085), euler #=-47 (186473,557614,371094) : difference with theory (-44) = 3 CORRECTING DEFECT 12 (vertices=35, convex hull=34, v0=65852) After retessellation of defect 12 (v0=65852), euler #=-46 (186476,557636,371114) : difference with theory (-43) = 3 CORRECTING DEFECT 13 (vertices=209, convex hull=100, v0=68286) After retessellation of defect 13 (v0=68286), euler #=-45 (186512,557790,371233) : difference with theory (-42) = 3 CORRECTING DEFECT 14 (vertices=260, convex hull=104, v0=79029) After retessellation of defect 14 (v0=79029), euler #=-44 (186526,557878,371308) : difference with theory (-41) = 3 CORRECTING DEFECT 15 (vertices=65, convex hull=92, v0=79823) After retessellation of defect 15 (v0=79823), euler #=-43 (186549,557989,371397) : difference with theory (-40) = 3 CORRECTING DEFECT 16 (vertices=36, convex hull=21, v0=85678) After retessellation of defect 16 (v0=85678), euler #=-42 (186552,558003,371409) : difference with theory (-39) = 3 CORRECTING DEFECT 17 (vertices=85, convex hull=45, v0=96129) After retessellation of defect 17 (v0=96129), euler #=-41 (186561,558047,371445) : difference with theory (-38) = 3 CORRECTING DEFECT 18 (vertices=6, convex hull=31, v0=97284) After retessellation of defect 18 (v0=97284), euler #=-40 (186564,558065,371461) : difference with theory (-37) = 3 CORRECTING DEFECT 19 (vertices=118, convex hull=142, v0=99767) After retessellation of defect 19 (v0=99767), euler #=-39 (186625,558315,371651) : difference with theory (-36) = 3 CORRECTING DEFECT 20 (vertices=449, convex hull=179, v0=104847) After retessellation of defect 20 (v0=104847), euler #=-38 (186722,558696,371936) : difference with theory (-35) = 3 CORRECTING DEFECT 21 (vertices=70, convex hull=71, v0=105997) After retessellation of defect 21 (v0=105997), euler #=-36 (186734,558763,371993) : difference with theory (-34) = 2 CORRECTING DEFECT 22 (vertices=78, convex hull=31, v0=107484) After retessellation of defect 22 (v0=107484), euler #=-35 (186753,558827,372039) : difference with theory (-33) = 2 CORRECTING DEFECT 23 (vertices=59, convex hull=27, v0=109648) After retessellation of defect 23 (v0=109648), euler #=-34 (186760,558857,372063) : difference with theory (-32) = 2 CORRECTING DEFECT 24 (vertices=13, convex hull=33, v0=109670) After retessellation of defect 24 (v0=109670), euler #=-33 (186762,558873,372078) : difference with theory (-31) = 2 CORRECTING DEFECT 25 (vertices=27, convex hull=33, v0=112262) After retessellation of defect 25 (v0=112262), euler #=-32 (186767,558897,372098) : difference with theory (-30) = 2 CORRECTING DEFECT 26 (vertices=809, convex hull=545, v0=115535) L defect detected... After retessellation of defect 26 (v0=115535), euler #=-31 (187028,559958,372899) : difference with theory (-29) = 2 CORRECTING DEFECT 27 (vertices=42, convex hull=79, v0=118370) After retessellation of defect 27 (v0=118370), euler #=-30 (187051,560063,372982) : difference with theory (-28) = 2 CORRECTING DEFECT 28 (vertices=26, convex hull=28, v0=118410) After retessellation of defect 28 (v0=118410), euler #=-29 (187058,560095,373008) : difference with theory (-27) = 2 CORRECTING DEFECT 29 (vertices=452, convex hull=178, v0=120247) After retessellation of defect 29 (v0=120247), euler #=-28 (187111,560340,373201) : difference with theory (-26) = 2 CORRECTING DEFECT 30 (vertices=77, convex hull=68, v0=122641) After retessellation of defect 30 (v0=122641), euler #=-27 (187139,560452,373286) : difference with theory (-25) = 2 CORRECTING DEFECT 31 (vertices=88, convex hull=82, v0=123261) After retessellation of defect 31 (v0=123261), euler #=-26 (187172,560587,373389) : difference with theory (-24) = 2 CORRECTING DEFECT 32 (vertices=397, convex hull=131, v0=123284) After retessellation of defect 32 (v0=123284), euler #=-25 (187198,560736,373513) : difference with theory (-23) = 2 CORRECTING DEFECT 33 (vertices=28, convex hull=32, v0=124326) After retessellation of defect 33 (v0=124326), euler #=-24 (187204,560767,373539) : difference with theory (-22) = 2 CORRECTING DEFECT 34 (vertices=197, convex hull=168, v0=128694) After retessellation of defect 34 (v0=128694), euler #=-22 (187288,561105,373795) : difference with theory (-21) = 1 CORRECTING DEFECT 35 (vertices=34, convex hull=33, v0=128730) After retessellation of defect 35 (v0=128730), euler #=-21 (187290,561120,373809) : difference with theory (-20) = 1 CORRECTING DEFECT 36 (vertices=336, convex hull=326, v0=129385) After retessellation of defect 36 (v0=129385), euler #=-20 (187445,561736,374271) : difference with theory (-19) = 1 CORRECTING DEFECT 37 (vertices=100, convex hull=68, v0=129878) After retessellation of defect 37 (v0=129878), euler #=-19 (187463,561814,374332) : difference with theory (-18) = 1 CORRECTING DEFECT 38 (vertices=26, convex hull=22, v0=131814) After retessellation of defect 38 (v0=131814), euler #=-18 (187470,561843,374355) : difference with theory (-17) = 1 CORRECTING DEFECT 39 (vertices=29, convex hull=23, v0=134425) After retessellation of defect 39 (v0=134425), euler #=-17 (187475,561868,374376) : difference with theory (-16) = 1 CORRECTING DEFECT 40 (vertices=10, convex hull=42, v0=134547) After retessellation of defect 40 (v0=134547), euler #=-16 (187479,561892,374397) : difference with theory (-15) = 1 CORRECTING DEFECT 41 (vertices=114, convex hull=80, v0=138882) After retessellation of defect 41 (v0=138882), euler #=-15 (187494,561972,374463) : difference with theory (-14) = 1 CORRECTING DEFECT 42 (vertices=46, convex hull=74, v0=139232) After retessellation of defect 42 (v0=139232), euler #=-14 (187509,562046,374523) : difference with theory (-13) = 1 CORRECTING DEFECT 43 (vertices=114, convex hull=59, v0=140299) After retessellation of defect 43 (v0=140299), euler #=-13 (187521,562107,374573) : difference with theory (-12) = 1 CORRECTING DEFECT 44 (vertices=63, convex hull=96, v0=142507) After retessellation of defect 44 (v0=142507), euler #=-12 (187534,562189,374643) : difference with theory (-11) = 1 CORRECTING DEFECT 45 (vertices=22, convex hull=25, v0=144643) After retessellation of defect 45 (v0=144643), euler #=-11 (187539,562211,374661) : difference with theory (-10) = 1 CORRECTING DEFECT 46 (vertices=1158, convex hull=204, v0=149939) After retessellation of defect 46 (v0=149939), euler #=-10 (187557,562359,374792) : difference with theory (-9) = 1 CORRECTING DEFECT 47 (vertices=639, convex hull=153, v0=153510) After retessellation of defect 47 (v0=153510), euler #=-9 (187624,562636,375003) : difference with theory (-8) = 1 CORRECTING DEFECT 48 (vertices=98, convex hull=125, v0=153797) After retessellation of defect 48 (v0=153797), euler #=-8 (187675,562844,375161) : difference with theory (-7) = 1 CORRECTING DEFECT 49 (vertices=15, convex hull=27, v0=154001) After retessellation of defect 49 (v0=154001), euler #=-7 (187680,562868,375181) : difference with theory (-6) = 1 CORRECTING DEFECT 50 (vertices=21, convex hull=64, v0=154525) After retessellation of defect 50 (v0=154525), euler #=-6 (187689,562921,375226) : difference with theory (-5) = 1 CORRECTING DEFECT 51 (vertices=99, convex hull=28, v0=154539) After retessellation of defect 51 (v0=154539), euler #=-5 (187696,562950,375249) : difference with theory (-4) = 1 CORRECTING DEFECT 52 (vertices=85, convex hull=41, v0=155606) After retessellation of defect 52 (v0=155606), euler #=-4 (187705,562993,375284) : difference with theory (-3) = 1 CORRECTING DEFECT 53 (vertices=67, convex hull=88, v0=157612) After retessellation of defect 53 (v0=157612), euler #=-2 (187715,563065,375348) : difference with theory (-2) = 0 CORRECTING DEFECT 54 (vertices=27, convex hull=35, v0=158552) After retessellation of defect 54 (v0=158552), euler #=-1 (187721,563093,375371) : difference with theory (-1) = 0 CORRECTING DEFECT 55 (vertices=34, convex hull=65, v0=163575) After retessellation of defect 55 (v0=163575), euler #=0 (187744,563188,375444) : difference with theory (0) = 0 CORRECTING DEFECT 56 (vertices=22, convex hull=38, v0=164942) After retessellation of defect 56 (v0=164942), euler #=1 (187755,563234,375480) : difference with theory (1) = 0 CORRECTING DEFECT 57 (vertices=30, convex hull=67, v0=187101) After retessellation of defect 57 (v0=187101), euler #=2 (187767,563295,375530) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.05-->9.49) (max @ vno 122489 --> 132944) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.05-->9.49) (max @ vno 122489 --> 132944) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 225 mutations (34.7%), 423 crossovers (65.3%), 483 vertices were eliminated building final representation... 6951 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=187767, nf=375530, ne=563295, g=0) writing corrected surface to /usr/local/freesurfer/subjects/SynthF/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 52.9 minutes 0 defective edges removing intersecting faces 000: 523 intersecting 001: 18 intersecting 002: 2 intersecting mris_fix_topology utimesec 3152.380000 mris_fix_topology stimesec 4.032000 mris_fix_topology ru_maxrss 600848 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 66159 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 17792 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 3 mris_fix_topology ru_nivcsw 173458 FSRUNTIME@ mris_fix_topology lh 0.8808 hours 1 threads #@# Fix Topology rh Mon Dec 19 15:32:39 GMT 2016 mris_fix_topology -rusage /usr/local/freesurfer/subjects/SynthF/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 SynthF 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=-188 (nv=195136, nf=390648, ne=585972, g=95) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 7 iterations marking ambiguous vertices... 28905 ambiguous faces found in tessellation segmenting defects... 72 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 21 into 10 -merging segment 49 into 31 -merging segment 57 into 31 -merging segment 56 into 31 -merging segment 46 into 44 -merging segment 62 into 55 -merging segment 65 into 55 -merging segment 67 into 55 64 defects to be corrected 0 vertices coincident reading input surface /usr/local/freesurfer/subjects/SynthF/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5493 (-4.7747) -vertex loglikelihood: -6.4307 (-3.2154) -normal dot loglikelihood: -3.5663 (-3.5663) -quad curv loglikelihood: -5.8068 (-2.9034) Total Loglikelihood : -25.3531 CORRECTING DEFECT 0 (vertices=14, convex hull=28, v0=25107) After retessellation of defect 0 (v0=25107), euler #=-65 (178544,531141,352532) : difference with theory (-61) = 4 CORRECTING DEFECT 1 (vertices=78, convex hull=49, v0=34286) After retessellation of defect 1 (v0=34286), euler #=-64 (178553,531186,352569) : difference with theory (-60) = 4 CORRECTING DEFECT 2 (vertices=798, convex hull=369, v0=37070) After retessellation of defect 2 (v0=37070), euler #=-63 (178798,532107,353246) : difference with theory (-59) = 4 CORRECTING DEFECT 3 (vertices=41, convex hull=81, v0=37849) After retessellation of defect 3 (v0=37849), euler #=-62 (178822,532216,353332) : difference with theory (-58) = 4 CORRECTING DEFECT 4 (vertices=258, convex hull=128, v0=39847) After retessellation of defect 4 (v0=39847), euler #=-61 (178871,532425,353493) : difference with theory (-57) = 4 CORRECTING DEFECT 5 (vertices=515, convex hull=112, v0=40823) After retessellation of defect 5 (v0=40823), euler #=-60 (178908,532581,353613) : difference with theory (-56) = 4 CORRECTING DEFECT 6 (vertices=64, convex hull=47, v0=43393) After retessellation of defect 6 (v0=43393), euler #=-59 (178913,532612,353640) : difference with theory (-55) = 4 CORRECTING DEFECT 7 (vertices=206, convex hull=204, v0=49762) After retessellation of defect 7 (v0=49762), euler #=-58 (178974,532887,353855) : difference with theory (-54) = 4 CORRECTING DEFECT 8 (vertices=419, convex hull=175, v0=51837) After retessellation of defect 8 (v0=51837), euler #=-57 (179005,533071,354009) : difference with theory (-53) = 4 CORRECTING DEFECT 9 (vertices=129, convex hull=160, v0=58787) After retessellation of defect 9 (v0=58787), euler #=-56 (179056,533300,354188) : difference with theory (-52) = 4 CORRECTING DEFECT 10 (vertices=589, convex hull=402, v0=59503) After retessellation of defect 10 (v0=59503), euler #=-54 (179188,533899,354657) : difference with theory (-51) = 3 CORRECTING DEFECT 11 (vertices=50, convex hull=22, v0=60536) After retessellation of defect 11 (v0=60536), euler #=-53 (179189,533910,354668) : difference with theory (-50) = 3 CORRECTING DEFECT 12 (vertices=120, convex hull=27, v0=60564) After retessellation of defect 12 (v0=60564), euler #=-52 (179197,533942,354693) : difference with theory (-49) = 3 CORRECTING DEFECT 13 (vertices=39, convex hull=37, v0=61667) After retessellation of defect 13 (v0=61667), euler #=-51 (179211,533999,354737) : difference with theory (-48) = 3 CORRECTING DEFECT 14 (vertices=19, convex hull=37, v0=63401) After retessellation of defect 14 (v0=63401), euler #=-50 (179214,534022,354758) : difference with theory (-47) = 3 CORRECTING DEFECT 15 (vertices=1350, convex hull=393, v0=64712) After retessellation of defect 15 (v0=64712), euler #=-49 (179409,534793,355335) : difference with theory (-46) = 3 CORRECTING DEFECT 16 (vertices=54, convex hull=36, v0=66136) After retessellation of defect 16 (v0=66136), euler #=-48 (179416,534825,355361) : difference with theory (-45) = 3 CORRECTING DEFECT 17 (vertices=189, convex hull=240, v0=68608) After retessellation of defect 17 (v0=68608), euler #=-47 (179521,535260,355692) : difference with theory (-44) = 3 CORRECTING DEFECT 18 (vertices=23, convex hull=56, v0=73161) After retessellation of defect 18 (v0=73161), euler #=-46 (179530,535309,355733) : difference with theory (-43) = 3 CORRECTING DEFECT 19 (vertices=785, convex hull=324, v0=73635) After retessellation of defect 19 (v0=73635), euler #=-45 (179741,536117,356331) : difference with theory (-42) = 3 CORRECTING DEFECT 20 (vertices=772, convex hull=309, v0=82063) After retessellation of defect 20 (v0=82063), euler #=-44 (179897,536742,356801) : difference with theory (-41) = 3 CORRECTING DEFECT 21 (vertices=26, convex hull=29, v0=83388) After retessellation of defect 21 (v0=83388), euler #=-43 (179901,536761,356817) : difference with theory (-40) = 3 CORRECTING DEFECT 22 (vertices=864, convex hull=465, v0=83619) L defect detected... After retessellation of defect 22 (v0=83619), euler #=-42 (180149,537757,357566) : difference with theory (-39) = 3 CORRECTING DEFECT 23 (vertices=182, convex hull=130, v0=84906) After retessellation of defect 23 (v0=84906), euler #=-41 (180223,538045,357781) : difference with theory (-38) = 3 CORRECTING DEFECT 24 (vertices=36, convex hull=29, v0=86297) After retessellation of defect 24 (v0=86297), euler #=-40 (180229,538071,357802) : difference with theory (-37) = 3 CORRECTING DEFECT 25 (vertices=25, convex hull=20, v0=88585) After retessellation of defect 25 (v0=88585), euler #=-39 (180232,538087,357816) : difference with theory (-36) = 3 CORRECTING DEFECT 26 (vertices=339, convex hull=152, v0=91397) After retessellation of defect 26 (v0=91397), euler #=-38 (180282,538305,357985) : difference with theory (-35) = 3 CORRECTING DEFECT 27 (vertices=28, convex hull=28, v0=91407) After retessellation of defect 27 (v0=91407), euler #=-37 (180290,538338,358011) : difference with theory (-34) = 3 CORRECTING DEFECT 28 (vertices=22, convex hull=14, v0=95058) After retessellation of defect 28 (v0=95058), euler #=-36 (180292,538345,358017) : difference with theory (-33) = 3 CORRECTING DEFECT 29 (vertices=115, convex hull=55, v0=97524) After retessellation of defect 29 (v0=97524), euler #=-35 (180301,538394,358058) : difference with theory (-32) = 3 CORRECTING DEFECT 30 (vertices=2555, convex hull=1563, v0=98961) XL defect detected... After retessellation of defect 30 (v0=98961), euler #=-33 (180736,540520,359751) : difference with theory (-31) = 2 CORRECTING DEFECT 31 (vertices=157, convex hull=63, v0=100172) After retessellation of defect 31 (v0=100172), euler #=-32 (180759,540611,359820) : difference with theory (-30) = 2 CORRECTING DEFECT 32 (vertices=74, convex hull=48, v0=101150) After retessellation of defect 32 (v0=101150), euler #=-31 (180766,540647,359850) : difference with theory (-29) = 2 CORRECTING DEFECT 33 (vertices=78, convex hull=67, v0=101683) After retessellation of defect 33 (v0=101683), euler #=-30 (180791,540747,359926) : difference with theory (-28) = 2 CORRECTING DEFECT 34 (vertices=265, convex hull=359, v0=102931) After retessellation of defect 34 (v0=102931), euler #=-29 (180948,541391,360414) : difference with theory (-27) = 2 CORRECTING DEFECT 35 (vertices=7, convex hull=19, v0=104490) After retessellation of defect 35 (v0=104490), euler #=-28 (180949,541398,360421) : difference with theory (-26) = 2 CORRECTING DEFECT 36 (vertices=35, convex hull=36, v0=106084) After retessellation of defect 36 (v0=106084), euler #=-27 (180958,541437,360452) : difference with theory (-25) = 2 CORRECTING DEFECT 37 (vertices=135, convex hull=70, v0=106364) After retessellation of defect 37 (v0=106364), euler #=-26 (180993,541574,360555) : difference with theory (-24) = 2 CORRECTING DEFECT 38 (vertices=64, convex hull=34, v0=107264) After retessellation of defect 38 (v0=107264), euler #=-25 (181003,541618,360590) : difference with theory (-23) = 2 CORRECTING DEFECT 39 (vertices=6, convex hull=18, v0=111157) After retessellation of defect 39 (v0=111157), euler #=-24 (181005,541628,360599) : difference with theory (-22) = 2 CORRECTING DEFECT 40 (vertices=16, convex hull=36, v0=111554) After retessellation of defect 40 (v0=111554), euler #=-23 (181009,541652,360620) : difference with theory (-21) = 2 CORRECTING DEFECT 41 (vertices=114, convex hull=87, v0=116235) After retessellation of defect 41 (v0=116235), euler #=-24 (181030,541757,360703) : difference with theory (-20) = 4 CORRECTING DEFECT 42 (vertices=353, convex hull=81, v0=116256) After retessellation of defect 42 (v0=116256), euler #=-23 (181068,541908,360817) : difference with theory (-19) = 4 CORRECTING DEFECT 43 (vertices=151, convex hull=139, v0=119235) After retessellation of defect 43 (v0=119235), euler #=-21 (181088,542039,360930) : difference with theory (-18) = 3 CORRECTING DEFECT 44 (vertices=76, convex hull=106, v0=122750) After retessellation of defect 44 (v0=122750), euler #=-20 (181117,542171,361034) : difference with theory (-17) = 3 CORRECTING DEFECT 45 (vertices=124, convex hull=44, v0=126156) After retessellation of defect 45 (v0=126156), euler #=-19 (181127,542222,361076) : difference with theory (-16) = 3 CORRECTING DEFECT 46 (vertices=515, convex hull=233, v0=126987) After retessellation of defect 46 (v0=126987), euler #=-18 (181284,542804,361502) : difference with theory (-15) = 3 CORRECTING DEFECT 47 (vertices=29, convex hull=53, v0=129315) After retessellation of defect 47 (v0=129315), euler #=-17 (181294,542857,361546) : difference with theory (-14) = 3 CORRECTING DEFECT 48 (vertices=20, convex hull=54, v0=132609) After retessellation of defect 48 (v0=132609), euler #=-16 (181303,542902,361583) : difference with theory (-13) = 3 CORRECTING DEFECT 49 (vertices=23, convex hull=20, v0=133109) After retessellation of defect 49 (v0=133109), euler #=-15 (181306,542916,361595) : difference with theory (-12) = 3 CORRECTING DEFECT 50 (vertices=325, convex hull=247, v0=134624) After retessellation of defect 50 (v0=134624), euler #=-14 (181387,543270,361869) : difference with theory (-11) = 3 CORRECTING DEFECT 51 (vertices=13, convex hull=28, v0=138385) After retessellation of defect 51 (v0=138385), euler #=-13 (181388,543283,361882) : difference with theory (-10) = 3 CORRECTING DEFECT 52 (vertices=1237, convex hull=767, v0=141787) XL defect detected... After retessellation of defect 52 (v0=141787), euler #=-9 (181728,544698,362961) : difference with theory (-9) = 0 CORRECTING DEFECT 53 (vertices=1307, convex hull=360, v0=146560) After retessellation of defect 53 (v0=146560), euler #=-8 (181873,545307,363426) : difference with theory (-8) = 0 CORRECTING DEFECT 54 (vertices=19, convex hull=51, v0=147624) After retessellation of defect 54 (v0=147624), euler #=-7 (181886,545364,363471) : difference with theory (-7) = 0 CORRECTING DEFECT 55 (vertices=87, convex hull=60, v0=152920) After retessellation of defect 55 (v0=152920), euler #=-6 (181895,545419,363518) : difference with theory (-6) = 0 CORRECTING DEFECT 56 (vertices=380, convex hull=160, v0=153803) After retessellation of defect 56 (v0=153803), euler #=-5 (181971,545726,363750) : difference with theory (-5) = 0 CORRECTING DEFECT 57 (vertices=67, convex hull=84, v0=157467) After retessellation of defect 57 (v0=157467), euler #=-4 (181998,545844,363842) : difference with theory (-4) = 0 CORRECTING DEFECT 58 (vertices=26, convex hull=62, v0=158605) After retessellation of defect 58 (v0=158605), euler #=-3 (182012,545911,363896) : difference with theory (-3) = 0 CORRECTING DEFECT 59 (vertices=67, convex hull=82, v0=174729) After retessellation of defect 59 (v0=174729), euler #=-2 (182023,545987,363962) : difference with theory (-2) = 0 CORRECTING DEFECT 60 (vertices=6, convex hull=15, v0=181172) After retessellation of defect 60 (v0=181172), euler #=-1 (182023,545991,363967) : difference with theory (-1) = 0 CORRECTING DEFECT 61 (vertices=17, convex hull=55, v0=184197) After retessellation of defect 61 (v0=184197), euler #=0 (182032,546038,364006) : difference with theory (0) = 0 CORRECTING DEFECT 62 (vertices=36, convex hull=70, v0=185420) After retessellation of defect 62 (v0=185420), euler #=1 (182040,546089,364050) : difference with theory (1) = 0 CORRECTING DEFECT 63 (vertices=48, convex hull=69, v0=194588) After retessellation of defect 63 (v0=194588), euler #=2 (182051,546147,364098) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.90 +- 0.28 (0.09-->19.94) (max @ vno 141646 --> 152755) 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 (0.09-->19.94) (max @ vno 141646 --> 152755) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 213 mutations (33.2%), 429 crossovers (66.8%), 1473 vertices were eliminated building final representation... 13085 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=182051, nf=364098, ne=546147, g=0) writing corrected surface to /usr/local/freesurfer/subjects/SynthF/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 105.1 minutes 0 defective edges removing intersecting faces 000: 1117 intersecting 001: 35 intersecting mris_fix_topology utimesec 6284.388000 mris_fix_topology stimesec 3.188000 mris_fix_topology ru_maxrss 679084 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 79251 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 17392 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 8 mris_fix_topology ru_nivcsw 332858 FSRUNTIME@ mris_fix_topology rh 1.7520 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 187767 - 563295 + 375530 = 2 --> 0 holes F =2V-4: 375530 = 375534-4 (0) 2E=3F: 1126590 = 1126590 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 182051 - 546147 + 364098 = 2 --> 0 holes F =2V-4: 364098 = 364102-4 (0) 2E=3F: 1092294 = 1092294 (0) total defect index = 0 /usr/local/freesurfer/subjects/SynthF/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 97 intersecting 001: 3 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /usr/local/freesurfer/subjects/SynthF/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 259 intersecting 001: 30 intersecting 002: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Mon Dec 19 17:17:59 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs SynthF 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/SynthF/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/SynthF/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/SynthF/mri/../mri/aseg.presurf.mgz... reading volume /usr/local/freesurfer/subjects/SynthF/mri/wm.mgz... 20390 bright wm thresholded. 5551 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/SynthF/surf/lh.orig... computing class statistics... border white: 368268 voxels (2.20%) border gray 422696 voxels (2.52%) WM (96.0): 96.9 +- 8.9 [70.0 --> 110.0] GM (69.0) : 67.9 +- 11.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.2 (was 70) setting MAX_BORDER_WHITE to 111.9 (was 105) setting MIN_BORDER_WHITE to 61.0 (was 85) setting MAX_CSF to 37.5 (was 40) setting MAX_GRAY to 94.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 49.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 25.7 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.22 (0.02-->4.55) (max @ vno 128013 --> 187004) face area 0.28 +- 0.12 (0.00-->3.66) mean absolute distance = 0.67 +- 0.87 5898 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+-5.2, GM=61+-10.4 mean inside = 92.4, mean outside = 71.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=76.4, 89 (89) missing vertices, mean dist 0.3 [0.6 (%32.1)->0.7 (%67.9))] %68 local maxima, %27 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-->4.72) (max @ vno 128013 --> 187004) face area 0.28 +- 0.13 (0.00-->3.06) mean absolute distance = 0.40 +- 0.76 8651 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5398776.0, rms=11.301 001: dt: 0.5000, sse=3007033.2, rms=7.880 (30.266%) 002: dt: 0.5000, sse=2023863.9, rms=5.893 (25.217%) 003: dt: 0.5000, sse=1578090.8, rms=4.762 (19.200%) 004: dt: 0.5000, sse=1381757.0, rms=4.149 (12.862%) 005: dt: 0.5000, sse=1312828.8, rms=3.889 (6.272%) 006: dt: 0.5000, sse=1267031.8, rms=3.737 (3.905%) 007: dt: 0.5000, sse=1253379.6, rms=3.683 (1.452%) 008: dt: 0.5000, sse=1245480.2, rms=3.632 (1.384%) rms = 3.63, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=1241004.0, rms=3.628 (0.110%) 010: dt: 0.2500, sse=942300.5, rms=2.102 (42.068%) 011: dt: 0.2500, sse=910950.9, rms=1.673 (20.397%) 012: dt: 0.2500, sse=872105.8, rms=1.557 (6.917%) 013: dt: 0.2500, sse=865033.1, rms=1.493 (4.146%) rms = 1.46, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=861168.9, rms=1.459 (2.289%) 015: dt: 0.1250, sse=855489.1, rms=1.390 (4.675%) rms = 1.38, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=852277.1, rms=1.377 (0.950%) positioning took 2.1 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=79.7, 134 (18) missing vertices, mean dist -0.3 [0.5 (%71.7)->0.2 (%28.3))] %75 local maxima, %21 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 0.90 +- 0.25 (0.08-->4.79) (max @ vno 128013 --> 187004) face area 0.35 +- 0.16 (0.00-->3.92) mean absolute distance = 0.34 +- 0.54 7828 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1956464.0, rms=5.258 017: dt: 0.5000, sse=1423179.8, rms=3.577 (31.968%) rms = 3.56, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=1414507.8, rms=3.560 (0.474%) 019: dt: 0.2500, sse=1119555.4, rms=2.085 (41.421%) 020: dt: 0.2500, sse=1069938.5, rms=1.744 (16.368%) 021: dt: 0.2500, sse=1051741.6, rms=1.581 (9.365%) 022: dt: 0.2500, sse=1037862.7, rms=1.470 (6.993%) 023: dt: 0.2500, sse=1031235.6, rms=1.414 (3.855%) 024: dt: 0.2500, sse=1030101.4, rms=1.344 (4.888%) rms = 1.31, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=1023208.6, rms=1.308 (2.676%) 026: dt: 0.1250, sse=1013518.9, rms=1.240 (5.250%) rms = 1.23, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=1013843.6, rms=1.228 (0.950%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=82.5, 132 (8) missing vertices, mean dist -0.2 [0.4 (%72.5)->0.3 (%27.5))] %84 local maxima, %12 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 0.89 +- 0.25 (0.06-->4.98) (max @ vno 128013 --> 187004) face area 0.34 +- 0.16 (0.00-->4.22) mean absolute distance = 0.27 +- 0.44 6915 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1568314.9, rms=4.212 028: dt: 0.5000, sse=1289460.9, rms=3.125 (25.819%) rms = 3.28, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=1100097.8, rms=2.164 (30.758%) 030: dt: 0.2500, sse=1020853.4, rms=1.549 (28.423%) 031: dt: 0.2500, sse=995150.1, rms=1.306 (15.643%) 032: dt: 0.2500, sse=989306.2, rms=1.237 (5.320%) rms = 1.20, time step reduction 2 of 3 to 0.125... 033: dt: 0.2500, sse=987190.6, rms=1.200 (2.973%) 034: dt: 0.1250, sse=978184.9, rms=1.123 (6.399%) rms = 1.11, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=973769.8, rms=1.106 (1.497%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=83.6, 197 (8) missing vertices, mean dist -0.1 [0.3 (%60.4)->0.2 (%39.6))] %88 local maxima, % 8 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/SynthF/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=1079420.6, rms=2.172 036: dt: 0.5000, sse=1080792.4, rms=2.101 (3.259%) rms = 2.66, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=975344.6, rms=1.311 (37.620%) 038: dt: 0.2500, sse=960882.2, rms=1.108 (15.485%) 039: dt: 0.2500, sse=948288.5, rms=1.007 (9.138%) rms = 1.04, time step reduction 2 of 3 to 0.125... 040: dt: 0.1250, sse=941284.3, rms=0.951 (5.554%) 041: dt: 0.1250, sse=939090.1, rms=0.891 (6.238%) rms = 0.86, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=941206.5, rms=0.863 (3.189%) positioning took 0.8 minutes generating cortex label... 15 non-cortical segments detected only using segment with 8709 vertices erasing segment 0 (vno[0] = 37771) erasing segment 1 (vno[0] = 43351) erasing segment 3 (vno[0] = 114434) erasing segment 4 (vno[0] = 120233) erasing segment 5 (vno[0] = 129964) erasing segment 6 (vno[0] = 130770) erasing segment 7 (vno[0] = 132484) erasing segment 8 (vno[0] = 132535) erasing segment 9 (vno[0] = 133786) erasing segment 10 (vno[0] = 134610) erasing segment 11 (vno[0] = 138722) erasing segment 12 (vno[0] = 139030) erasing segment 13 (vno[0] = 151703) erasing segment 14 (vno[0] = 157910) writing cortex label to /usr/local/freesurfer/subjects/SynthF/label/lh.cortex.label... writing curvature file /usr/local/freesurfer/subjects/SynthF/surf/lh.curv writing smoothed area to lh.area writing curvature file /usr/local/freesurfer/subjects/SynthF/surf/lh.area vertex spacing 0.89 +- 0.25 (0.02-->5.18) (max @ vno 128013 --> 187004) face area 0.33 +- 0.16 (0.00-->4.99) refinement took 6.9 minutes #-------------------------------------------- #@# Make White Surf rh Mon Dec 19 17:24:51 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs SynthF 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/SynthF/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/SynthF/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/SynthF/mri/../mri/aseg.presurf.mgz... reading volume /usr/local/freesurfer/subjects/SynthF/mri/wm.mgz... 20390 bright wm thresholded. 5551 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/SynthF/surf/rh.orig... computing class statistics... border white: 368268 voxels (2.20%) border gray 422696 voxels (2.52%) WM (96.0): 96.9 +- 8.9 [70.0 --> 110.0] GM (69.0) : 67.9 +- 11.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 50.2 (was 70) setting MAX_BORDER_WHITE to 111.9 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 38.5 (was 40) setting MAX_GRAY to 94.1 (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 +- 0.23 (0.02-->7.30) (max @ vno 141664 --> 143535) face area 0.29 +- 0.14 (0.00-->16.51) mean absolute distance = 0.73 +- 0.99 5441 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+-13.0 mean inside = 92.1, mean outside = 72.8 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=77.9, 275 (275) missing vertices, mean dist 0.2 [0.7 (%36.3)->0.7 (%63.7))] %69 local maxima, %27 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-->7.42) (max @ vno 141664 --> 143535) face area 0.29 +- 0.15 (0.00-->13.84) mean absolute distance = 0.43 +- 0.79 8048 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4800009.0, rms=10.700 001: dt: 0.5000, sse=2782229.0, rms=7.602 (28.952%) 002: dt: 0.5000, sse=1917753.9, rms=5.781 (23.954%) 003: dt: 0.5000, sse=1525197.9, rms=4.710 (18.529%) 004: dt: 0.5000, sse=1348873.5, rms=4.149 (11.906%) 005: dt: 0.5000, sse=1279682.8, rms=3.881 (6.462%) 006: dt: 0.5000, sse=1237593.1, rms=3.730 (3.893%) 007: dt: 0.5000, sse=1227092.0, rms=3.672 (1.538%) 008: dt: 0.5000, sse=1208253.8, rms=3.609 (1.734%) rms = 3.59, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=1217848.1, rms=3.591 (0.504%) 010: dt: 0.2500, sse=946176.8, rms=2.261 (37.036%) 011: dt: 0.2500, sse=899918.1, rms=1.921 (15.021%) 012: dt: 0.2500, sse=886219.3, rms=1.822 (5.175%) 013: dt: 0.2500, sse=877625.2, rms=1.759 (3.429%) rms = 1.73, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=876982.2, rms=1.731 (1.598%) 015: dt: 0.1250, sse=866079.9, rms=1.663 (3.943%) rms = 1.64, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=863715.8, rms=1.642 (1.229%) positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=80.7, 240 (75) missing vertices, mean dist -0.3 [0.5 (%69.0)->0.3 (%31.0))] %74 local maxima, %22 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 (0.04-->7.20) (max @ vno 141664 --> 143535) face area 0.35 +- 0.18 (0.00-->16.66) mean absolute distance = 0.37 +- 0.59 7678 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1818856.5, rms=4.989 017: dt: 0.5000, sse=1401654.6, rms=3.460 (30.645%) 018: dt: 0.5000, sse=1347490.0, rms=3.405 (1.596%) 019: dt: 0.5000, sse=1327236.0, rms=3.339 (1.935%) rms = 3.44, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=1132261.5, rms=2.332 (30.159%) 021: dt: 0.2500, sse=1064204.1, rms=1.839 (21.121%) 022: dt: 0.2500, sse=1041401.8, rms=1.648 (10.418%) 023: dt: 0.2500, sse=1032962.8, rms=1.569 (4.795%) 024: dt: 0.2500, sse=1026875.5, rms=1.506 (3.988%) rms = 1.48, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=1026931.0, rms=1.479 (1.803%) rms = 1.43, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=1017253.6, rms=1.432 (3.202%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=83.4, 209 (43) missing vertices, mean dist -0.2 [0.4 (%71.1)->0.3 (%28.9))] %83 local maxima, %12 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 (0.08-->7.09) (max @ vno 141664 --> 143535) face area 0.34 +- 0.18 (0.00-->15.66) mean absolute distance = 0.30 +- 0.49 6138 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1516392.6, rms=4.139 027: dt: 0.5000, sse=1240600.1, rms=2.984 (27.899%) rms = 3.11, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=1088923.6, rms=2.189 (26.643%) 029: dt: 0.2500, sse=1022495.9, rms=1.682 (23.146%) 030: dt: 0.2500, sse=1004085.0, rms=1.485 (11.750%) rms = 1.46, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=1019987.3, rms=1.455 (1.976%) 032: dt: 0.1250, sse=994424.3, rms=1.370 (5.870%) rms = 1.35, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=991838.4, rms=1.353 (1.216%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 1 vertex label from ripped group mean border=84.4, 273 (31) missing vertices, mean dist -0.1 [0.3 (%60.3)->0.3 (%39.7))] %87 local maxima, % 8 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/SynthF/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=1094982.9, rms=2.329 034: dt: 0.5000, sse=1067337.8, rms=2.098 (9.919%) rms = 2.53, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=979807.3, rms=1.459 (30.472%) 036: dt: 0.2500, sse=961097.9, rms=1.300 (10.907%) 037: dt: 0.2500, sse=952918.4, rms=1.199 (7.714%) rms = 1.20, time step reduction 2 of 3 to 0.125... rms = 1.16, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=943752.4, rms=1.156 (3.662%) positioning took 0.6 minutes generating cortex label... 22 non-cortical segments detected only using segment with 7404 vertices erasing segment 0 (vno[0] = 41939) erasing segment 2 (vno[0] = 58496) erasing segment 3 (vno[0] = 62093) erasing segment 4 (vno[0] = 86618) erasing segment 5 (vno[0] = 89484) erasing segment 6 (vno[0] = 95282) erasing segment 7 (vno[0] = 95930) erasing segment 8 (vno[0] = 100872) erasing segment 9 (vno[0] = 117594) erasing segment 10 (vno[0] = 120376) erasing segment 11 (vno[0] = 120807) erasing segment 12 (vno[0] = 122050) erasing segment 13 (vno[0] = 126689) erasing segment 14 (vno[0] = 127110) erasing segment 15 (vno[0] = 128427) erasing segment 16 (vno[0] = 134242) erasing segment 17 (vno[0] = 136520) erasing segment 18 (vno[0] = 138895) erasing segment 19 (vno[0] = 143802) erasing segment 20 (vno[0] = 143816) erasing segment 21 (vno[0] = 179235) writing cortex label to /usr/local/freesurfer/subjects/SynthF/label/rh.cortex.label... writing curvature file /usr/local/freesurfer/subjects/SynthF/surf/rh.curv writing smoothed area to rh.area writing curvature file /usr/local/freesurfer/subjects/SynthF/surf/rh.area vertex spacing 0.89 +- 0.27 (0.02-->6.92) (max @ vno 141664 --> 143535) face area 0.34 +- 0.18 (0.00-->14.56) refinement took 6.4 minutes #-------------------------------------------- #@# Smooth2 lh Mon Dec 19 17:31:17 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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 17:31:23 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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 17:31:29 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts mris_inflate -rusage /usr/local/freesurfer/subjects/SynthF/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 51.2 mm, total surface area = 113311 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.169 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.093 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.065 (target=0.015) step 025: RMS=0.055 (target=0.015) step 030: RMS=0.046 (target=0.015) step 035: RMS=0.039 (target=0.015) step 040: RMS=0.034 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. inflation took 0.7 minutes mris_inflate utimesec 42.644000 mris_inflate stimesec 0.044000 mris_inflate ru_maxrss 243908 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 29790 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 14680 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 1286 #-------------------------------------------- #@# Inflation2 rh Mon Dec 19 17:32:11 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts mris_inflate -rusage /usr/local/freesurfer/subjects/SynthF/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 51.2 mm, total surface area = 110144 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.174 (target=0.015) step 005: RMS=0.125 (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=0.049 (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=0.029 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. inflation took 0.7 minutes mris_inflate utimesec 43.852000 mris_inflate stimesec 0.072000 mris_inflate ru_maxrss 237496 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 29115 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 1087 #-------------------------------------------- #@# Curv .H and .K lh Mon Dec 19 17:32:55 GMT 2016 /usr/local/freesurfer/subjects/SynthF/surf mris_curvature -w lh.white.preaparc total integrated curvature = 26.774*4pi (336.451) --> -26 handles ICI = 224.4, FI = 2091.7, variation=33436.276 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 249 vertices thresholded to be in k1 ~ [-0.27 0.58], k2 ~ [-0.15 0.06] total integrated curvature = 0.321*4pi (4.036) --> 1 handles ICI = 1.8, FI = 12.3, variation=212.536 203 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 197 vertices thresholded to be in [-0.15 0.21] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.024 done. #-------------------------------------------- #@# Curv .H and .K rh Mon Dec 19 17:34:18 GMT 2016 /usr/local/freesurfer/subjects/SynthF/surf mris_curvature -w rh.white.preaparc total integrated curvature = 40.741*4pi (511.965) --> -40 handles ICI = 246.2, FI = 2227.7, variation=35648.078 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 240 vertices thresholded to be in k1 ~ [-0.24 0.38], k2 ~ [-0.11 0.07] total integrated curvature = 0.277*4pi (3.479) --> 1 handles ICI = 1.7, FI = 11.0, variation=192.666 169 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 179 vertices thresholded to be in [-0.14 0.16] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.023 done. #----------------------------------------- #@# Curvature Stats lh Mon Dec 19 17:35:38 GMT 2016 /usr/local/freesurfer/subjects/SynthF/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm SynthF 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 [ SynthF/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 [ 342 ] Gb_filter = 0 WARN: S lookup min: -0.811247 WARN: S explicit min: 0.000000 vertex = 246 #----------------------------------------- #@# Curvature Stats rh Mon Dec 19 17:35:41 GMT 2016 /usr/local/freesurfer/subjects/SynthF/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm SynthF 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 [ SynthF/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 [ 345 ] Gb_filter = 0 WARN: S lookup min: -0.947419 WARN: S explicit min: 0.000000 vertex = 154 #-------------------------------------------- #@# Sphere lh Mon Dec 19 17:35:45 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts mris_sphere -rusage /usr/local/freesurfer/subjects/SynthF/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 0.262... 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 %20.68 pass 1: epoch 2 of 3 starting distance error %20.66 unfolding complete - removing small folds... starting distance error %20.58 removing remaining folds... final distance error %20.60 MRISunfold() return, current seed 1234 -01: dt=0.0000, 169 negative triangles 195: dt=0.9900, 169 negative triangles 196: dt=0.9900, 103 negative triangles 197: dt=0.9900, 88 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, 62 negative triangles 202: dt=0.9900, 58 negative triangles 203: dt=0.9900, 54 negative triangles 204: dt=0.9900, 55 negative triangles 205: dt=0.9900, 52 negative triangles 206: dt=0.9900, 54 negative triangles 207: dt=0.9900, 50 negative triangles 208: dt=0.9900, 52 negative triangles 209: dt=0.9900, 51 negative triangles 210: dt=0.9900, 48 negative triangles 211: dt=0.9900, 54 negative triangles 212: dt=0.9900, 51 negative triangles 213: dt=0.9900, 55 negative triangles 214: dt=0.9900, 51 negative triangles 215: dt=0.9900, 48 negative triangles 216: dt=0.9900, 48 negative triangles 217: dt=0.9900, 51 negative triangles 218: dt=0.9900, 49 negative triangles 219: dt=0.9900, 48 negative triangles 220: dt=0.9405, 50 negative triangles 221: dt=0.9405, 52 negative triangles 222: dt=0.9405, 56 negative triangles 223: dt=0.9405, 52 negative triangles 224: dt=0.9405, 51 negative triangles 225: dt=0.9405, 49 negative triangles 226: dt=0.9405, 51 negative triangles 227: dt=0.9405, 51 negative triangles 228: dt=0.9405, 53 negative triangles 229: dt=0.9405, 52 negative triangles 230: dt=0.8935, 52 negative triangles 231: dt=0.8935, 59 negative triangles 232: dt=0.8935, 48 negative triangles 233: dt=0.8935, 49 negative triangles 234: dt=0.8935, 52 negative triangles 235: dt=0.8935, 50 negative triangles 236: dt=0.8935, 50 negative triangles 237: dt=0.8935, 47 negative triangles 238: dt=0.8935, 55 negative triangles 239: dt=0.8935, 50 negative triangles 240: dt=0.8935, 47 negative triangles 241: dt=0.8935, 44 negative triangles 242: dt=0.8935, 47 negative triangles 243: dt=0.8935, 49 negative triangles 244: dt=0.8935, 50 negative triangles 245: dt=0.8935, 48 negative triangles 246: dt=0.8935, 44 negative triangles 247: dt=0.8935, 44 negative triangles 248: dt=0.8935, 49 negative triangles 249: dt=0.8935, 44 negative triangles 250: dt=0.8935, 44 negative triangles 251: dt=0.8488, 47 negative triangles 252: dt=0.8488, 49 negative triangles 253: dt=0.8488, 43 negative triangles 254: dt=0.8488, 44 negative triangles 255: dt=0.8488, 40 negative triangles 256: dt=0.8488, 48 negative triangles 257: dt=0.8488, 46 negative triangles 258: dt=0.8488, 48 negative triangles 259: dt=0.8488, 45 negative triangles 260: dt=0.8488, 45 negative triangles 261: dt=0.8488, 47 negative triangles 262: dt=0.8488, 47 negative triangles 263: dt=0.8488, 42 negative triangles 264: dt=0.8488, 43 negative triangles 265: dt=0.8064, 40 negative triangles 266: dt=0.8064, 38 negative triangles 267: dt=0.8064, 35 negative triangles 268: dt=0.8064, 40 negative triangles 269: dt=0.8064, 39 negative triangles 270: dt=0.8064, 37 negative triangles 271: dt=0.8064, 36 negative triangles 272: dt=0.8064, 35 negative triangles 273: dt=0.8064, 41 negative triangles 274: dt=0.8064, 43 negative triangles 275: dt=0.8064, 39 negative triangles 276: dt=0.8064, 41 negative triangles 277: dt=0.7660, 40 negative triangles 278: dt=0.7660, 37 negative triangles 279: dt=0.7660, 39 negative triangles 280: dt=0.7660, 42 negative triangles 281: dt=0.7660, 38 negative triangles 282: dt=0.7660, 35 negative triangles 283: dt=0.7660, 36 negative triangles 284: dt=0.7660, 35 negative triangles 285: dt=0.7660, 39 negative triangles 286: dt=0.7660, 42 negative triangles 287: dt=0.7277, 42 negative triangles 288: dt=0.7277, 33 negative triangles 289: dt=0.7277, 36 negative triangles 290: dt=0.7277, 34 negative triangles 291: dt=0.7277, 35 negative triangles 292: dt=0.7277, 31 negative triangles 293: dt=0.7277, 37 negative triangles 294: dt=0.7277, 36 negative triangles 295: dt=0.7277, 34 negative triangles 296: dt=0.7277, 30 negative triangles 297: dt=0.7277, 32 negative triangles 298: dt=0.7277, 34 negative triangles 299: dt=0.7277, 31 negative triangles 300: dt=0.7277, 30 negative triangles 301: dt=0.7277, 29 negative triangles 302: dt=0.7277, 29 negative triangles 303: dt=0.7277, 28 negative triangles 304: dt=0.7277, 28 negative triangles 305: dt=0.7277, 29 negative triangles 306: dt=0.7277, 31 negative triangles 307: dt=0.7277, 26 negative triangles 308: dt=0.7277, 25 negative triangles 309: dt=0.7277, 26 negative triangles 310: dt=0.7277, 26 negative triangles 311: dt=0.7277, 23 negative triangles 312: dt=0.7277, 30 negative triangles 313: dt=0.7277, 26 negative triangles 314: dt=0.7277, 25 negative triangles 315: dt=0.7277, 21 negative triangles 316: dt=0.7277, 22 negative triangles 317: dt=0.7277, 23 negative triangles 318: dt=0.7277, 24 negative triangles 319: dt=0.7277, 23 negative triangles 320: dt=0.7277, 25 negative triangles 321: dt=0.7277, 25 negative triangles 322: dt=0.7277, 24 negative triangles 323: dt=0.7277, 24 negative triangles 324: dt=0.7277, 17 negative triangles 325: dt=0.7277, 17 negative triangles 326: dt=0.7277, 15 negative triangles 327: dt=0.7277, 14 negative triangles 328: dt=0.7277, 14 negative triangles 329: dt=0.7277, 17 negative triangles 330: dt=0.7277, 15 negative triangles 331: dt=0.7277, 11 negative triangles 332: dt=0.7277, 14 negative triangles 333: dt=0.7277, 11 negative triangles 334: dt=0.7277, 15 negative triangles 335: dt=0.7277, 13 negative triangles 336: dt=0.7277, 10 negative triangles 337: dt=0.7277, 8 negative triangles 338: dt=0.7277, 8 negative triangles 339: dt=0.7277, 9 negative triangles 340: dt=0.7277, 9 negative triangles 341: dt=0.7277, 7 negative triangles 342: dt=0.7277, 6 negative triangles 343: dt=0.7277, 4 negative triangles 344: dt=0.7277, 8 negative triangles 345: dt=0.7277, 2 negative triangles 346: dt=0.7277, 5 negative triangles 347: dt=0.7277, 2 negative triangles 348: dt=0.7277, 2 negative triangles 349: dt=0.7277, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.92 hours mris_sphere utimesec 3310.624000 mris_sphere stimesec 1.676000 mris_sphere ru_maxrss 334808 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 52356 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 13208 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 5 mris_sphere ru_nivcsw 83422 FSRUNTIME@ mris_sphere 0.9212 hours 1 threads #-------------------------------------------- #@# Sphere rh Mon Dec 19 18:31:01 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts mris_sphere -rusage /usr/local/freesurfer/subjects/SynthF/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 %21.19 pass 1: epoch 2 of 3 starting distance error %21.17 unfolding complete - removing small folds... starting distance error %21.06 removing remaining folds... final distance error %21.09 MRISunfold() return, current seed 1234 -01: dt=0.0000, 362 negative triangles 221: dt=0.9900, 362 negative triangles 222: dt=0.9900, 188 negative triangles 223: dt=0.9900, 159 negative triangles 224: dt=0.9900, 145 negative triangles 225: dt=0.9900, 130 negative triangles 226: dt=0.9900, 120 negative triangles 227: dt=0.9900, 100 negative triangles 228: dt=0.9900, 114 negative triangles 229: dt=0.9900, 108 negative triangles 230: dt=0.9900, 86 negative triangles 231: dt=0.9900, 102 negative triangles 232: dt=0.9900, 79 negative triangles 233: dt=0.9900, 80 negative triangles 234: dt=0.9900, 82 negative triangles 235: dt=0.9900, 81 negative triangles 236: dt=0.9900, 66 negative triangles 237: dt=0.9900, 67 negative triangles 238: dt=0.9900, 58 negative triangles 239: dt=0.9900, 63 negative triangles 240: dt=0.9900, 55 negative triangles 241: dt=0.9900, 62 negative triangles 242: dt=0.9900, 53 negative triangles 243: dt=0.9900, 56 negative triangles 244: dt=0.9900, 55 negative triangles 245: dt=0.9900, 45 negative triangles 246: dt=0.9900, 44 negative triangles 247: dt=0.9900, 46 negative triangles 248: dt=0.9900, 41 negative triangles 249: dt=0.9900, 47 negative triangles 250: dt=0.9900, 42 negative triangles 251: dt=0.9900, 38 negative triangles 252: dt=0.9900, 37 negative triangles 253: dt=0.9900, 36 negative triangles 254: dt=0.9900, 37 negative triangles 255: dt=0.9900, 33 negative triangles 256: dt=0.9900, 27 negative triangles 257: dt=0.9900, 28 negative triangles 258: dt=0.9900, 31 negative triangles 259: dt=0.9900, 25 negative triangles 260: dt=0.9900, 25 negative triangles 261: dt=0.9900, 27 negative triangles 262: dt=0.9900, 21 negative triangles 263: dt=0.9900, 28 negative triangles 264: dt=0.9900, 23 negative triangles 265: dt=0.9900, 23 negative triangles 266: dt=0.9900, 30 negative triangles 267: dt=0.9900, 27 negative triangles 268: dt=0.9900, 22 negative triangles 269: dt=0.9900, 31 negative triangles 270: dt=0.9900, 24 negative triangles 271: dt=0.9900, 21 negative triangles 272: dt=0.9900, 20 negative triangles 273: dt=0.9900, 24 negative triangles 274: dt=0.9900, 16 negative triangles 275: dt=0.9900, 19 negative triangles 276: dt=0.9900, 15 negative triangles 277: dt=0.9900, 23 negative triangles 278: dt=0.9900, 16 negative triangles 279: dt=0.9900, 20 negative triangles 280: dt=0.9900, 16 negative triangles 281: dt=0.9900, 24 negative triangles 282: dt=0.9900, 21 negative triangles 283: dt=0.9900, 19 negative triangles 284: dt=0.9900, 18 negative triangles 285: dt=0.9900, 18 negative triangles 286: dt=0.9405, 18 negative triangles 287: dt=0.9405, 15 negative triangles 288: dt=0.9405, 19 negative triangles 289: dt=0.9405, 12 negative triangles 290: dt=0.9405, 16 negative triangles 291: dt=0.9405, 12 negative triangles 292: dt=0.9405, 20 negative triangles 293: dt=0.9405, 12 negative triangles 294: dt=0.9405, 14 negative triangles 295: dt=0.9405, 11 negative triangles 296: dt=0.9405, 13 negative triangles 297: dt=0.9405, 8 negative triangles 298: dt=0.9405, 5 negative triangles 299: dt=0.9405, 6 negative triangles 300: dt=0.9405, 6 negative triangles 301: dt=0.9405, 4 negative triangles 302: dt=0.9405, 6 negative triangles 303: dt=0.9405, 4 negative triangles 304: dt=0.9405, 4 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.82 hours mris_sphere utimesec 2939.300000 mris_sphere stimesec 0.836000 mris_sphere ru_maxrss 325064 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 50986 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 6 mris_sphere ru_nivcsw 49661 FSRUNTIME@ mris_sphere 0.8175 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Mon Dec 19 19:20:05 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts mris_register -curv -rusage /usr/local/freesurfer/subjects/SynthF/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/SynthF/scripts cmdline mris_register -curv -rusage /usr/local/freesurfer/subjects/SynthF/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 = 5.891 curvature mean = 0.025, std = 0.817 curvature mean = 0.019, std = 0.832 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 496365.6, tmin=1.2629 d=32.00 min @ (8.00, 8.00, 8.00) sse = 448952.5, tmin=2.5422 d=16.00 min @ (0.00, -4.00, -4.00) sse = 424858.4, tmin=3.8700 d=4.00 min @ (-1.00, 0.00, 0.00) sse = 424530.5, tmin=6.4690 d=2.00 min @ (0.00, 0.00, 0.50) sse = 424362.8, tmin=7.8012 d=1.00 min @ (0.25, 0.25, -0.25) sse = 424269.1, tmin=9.1254 d=0.50 min @ (0.00, -0.12, 0.00) sse = 424251.9, tmin=10.4498 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 10.45 min curvature mean = -0.018, std = 0.809 curvature mean = 0.008, std = 0.922 curvature mean = -0.035, std = 0.811 curvature mean = 0.003, std = 0.964 curvature mean = -0.039, std = 0.811 curvature mean = 0.001, std = 0.983 2 Reading smoothwm curvature mean = -0.028, std = 0.265 curvature mean = 0.030, std = 0.243 curvature mean = 0.064, std = 0.350 curvature mean = 0.029, std = 0.298 curvature mean = 0.041, std = 0.538 curvature mean = 0.029, std = 0.323 curvature mean = 0.024, std = 0.685 curvature mean = 0.029, std = 0.333 curvature mean = 0.009, std = 0.801 MRISregister() return, current seed 0 -01: dt=0.0000, 111 negative triangles 151: dt=0.9900, 111 negative triangles 152: dt=0.9900, 85 negative triangles 153: dt=0.9900, 92 negative triangles 154: dt=0.9900, 75 negative triangles 155: dt=0.9900, 75 negative triangles 156: dt=0.9900, 64 negative triangles 157: dt=0.9900, 65 negative triangles 158: dt=0.9900, 52 negative triangles 159: dt=0.9900, 51 negative triangles 160: dt=0.9900, 50 negative triangles 161: dt=0.9900, 54 negative triangles 162: dt=0.9900, 49 negative triangles 163: dt=0.9900, 52 negative triangles 164: dt=0.9900, 46 negative triangles 165: dt=0.9900, 41 negative triangles 166: dt=0.9900, 42 negative triangles 167: dt=0.9900, 39 negative triangles 168: dt=0.9900, 37 negative triangles 169: dt=0.9900, 40 negative triangles 170: dt=0.9900, 40 negative triangles 171: dt=0.9900, 34 negative triangles 172: dt=0.9900, 33 negative triangles 173: dt=0.9900, 29 negative triangles 174: dt=0.9900, 31 negative triangles 175: dt=0.9900, 24 negative triangles 176: dt=0.9900, 31 negative triangles 177: dt=0.9900, 31 negative triangles 178: dt=0.9900, 30 negative triangles 179: dt=0.9900, 28 negative triangles 180: dt=0.9900, 26 negative triangles 181: dt=0.9900, 32 negative triangles 182: dt=0.9900, 24 negative triangles 183: dt=0.9900, 22 negative triangles 184: dt=0.9900, 29 negative triangles 185: dt=0.9900, 29 negative triangles 186: dt=0.9900, 26 negative triangles 187: dt=0.9900, 25 negative triangles 188: dt=0.9900, 27 negative triangles 189: dt=0.9900, 21 negative triangles 190: dt=0.9900, 25 negative triangles 191: dt=0.9900, 27 negative triangles 192: dt=0.9900, 24 negative triangles 193: dt=0.9900, 23 negative triangles 194: dt=0.9900, 24 negative triangles 195: dt=0.9900, 22 negative triangles 196: dt=0.9900, 18 negative triangles 197: dt=0.9900, 23 negative triangles 198: dt=0.9900, 22 negative triangles 199: dt=0.9900, 17 negative triangles 200: dt=0.9900, 18 negative triangles 201: dt=0.9900, 20 negative triangles 202: dt=0.9900, 20 negative triangles 203: dt=0.9900, 17 negative triangles 204: dt=0.9900, 20 negative triangles 205: dt=0.9900, 15 negative triangles 206: dt=0.9900, 14 negative triangles 207: dt=0.9900, 16 negative triangles 208: dt=0.9900, 10 negative triangles 209: dt=0.9900, 13 negative triangles 210: dt=0.9900, 16 negative triangles 211: dt=0.9900, 13 negative triangles 212: dt=0.9900, 8 negative triangles 213: dt=0.9900, 13 negative triangles 214: dt=0.9900, 8 negative triangles 215: dt=0.9900, 9 negative triangles 216: dt=0.9900, 5 negative triangles 217: dt=0.9900, 4 negative triangles 218: dt=0.9900, 3 negative triangles 219: dt=0.9900, 2 negative triangles 220: dt=0.9900, 2 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.25 hours mris_register utimesec 4483.400000 mris_register stimesec 1.104000 mris_register ru_maxrss 298004 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 34945 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 13216 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 2 mris_register ru_nivcsw 66355 FSRUNTIME@ mris_register 1.2470 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Mon Dec 19 20:34:54 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts mris_register -curv -rusage /usr/local/freesurfer/subjects/SynthF/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/SynthF/scripts cmdline mris_register -curv -rusage /usr/local/freesurfer/subjects/SynthF/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 = 5.845 curvature mean = 0.011, std = 0.801 curvature mean = 0.021, std = 0.834 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 16.00) sse = 428305.2, tmin=1.0925 d=32.00 min @ (-8.00, 0.00, 0.00) sse = 399435.8, tmin=2.2004 d=16.00 min @ (0.00, -4.00, -4.00) sse = 377000.8, tmin=3.3159 d=8.00 min @ (2.00, 2.00, 2.00) sse = 367815.0, tmin=4.4536 d=4.00 min @ (-1.00, -1.00, 0.00) sse = 367581.3, tmin=5.5952 d=2.00 min @ (0.50, 0.50, -0.50) sse = 366861.6, tmin=6.7849 d=1.00 min @ (-0.25, 0.00, 0.00) sse = 366809.3, tmin=8.0710 d=0.50 min @ (0.00, 0.00, 0.12) sse = 366803.1, tmin=9.3654 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 9.37 min curvature mean = -0.029, std = 0.795 curvature mean = 0.012, std = 0.929 curvature mean = -0.040, std = 0.796 curvature mean = 0.005, std = 0.967 curvature mean = -0.043, std = 0.796 curvature mean = 0.002, std = 0.985 2 Reading smoothwm curvature mean = -0.025, std = 0.342 curvature mean = 0.025, std = 0.231 curvature mean = 0.052, std = 0.264 curvature mean = 0.023, std = 0.286 curvature mean = 0.029, std = 0.409 curvature mean = 0.023, std = 0.310 curvature mean = 0.015, std = 0.528 curvature mean = 0.023, std = 0.321 curvature mean = 0.005, std = 0.624 MRISregister() return, current seed 0 -01: dt=0.0000, 280 negative triangles 163: dt=0.9900, 280 negative triangles 164: dt=0.9900, 250 negative triangles 165: dt=0.9900, 235 negative triangles 166: dt=0.9900, 233 negative triangles 167: dt=0.9900, 215 negative triangles 168: dt=0.9900, 194 negative triangles 169: dt=0.9900, 193 negative triangles 170: dt=0.9900, 185 negative triangles 171: dt=0.9900, 164 negative triangles 172: dt=0.9900, 167 negative triangles 173: dt=0.9900, 146 negative triangles 174: dt=0.9900, 168 negative triangles 175: dt=0.9900, 133 negative triangles 176: dt=0.9900, 144 negative triangles 177: dt=0.9900, 126 negative triangles 178: dt=0.9900, 120 negative triangles 179: dt=0.9900, 111 negative triangles 180: dt=0.9900, 118 negative triangles 181: dt=0.9900, 97 negative triangles 182: dt=0.9900, 101 negative triangles 183: dt=0.9900, 94 negative triangles 184: dt=0.9900, 92 negative triangles 185: dt=0.9900, 81 negative triangles 186: dt=0.9900, 82 negative triangles 187: dt=0.9900, 76 negative triangles 188: dt=0.9900, 71 negative triangles 189: dt=0.9900, 60 negative triangles 190: dt=0.9900, 50 negative triangles 191: dt=0.9900, 49 negative triangles 192: dt=0.9900, 48 negative triangles 193: dt=0.9900, 47 negative triangles 194: dt=0.9900, 46 negative triangles 195: dt=0.9900, 32 negative triangles 196: dt=0.9900, 41 negative triangles 197: dt=0.9900, 34 negative triangles 198: dt=0.9900, 32 negative triangles 199: dt=0.9900, 24 negative triangles 200: dt=0.9900, 24 negative triangles 201: dt=0.9900, 21 negative triangles 202: dt=0.9900, 15 negative triangles 203: dt=0.9900, 25 negative triangles 204: dt=0.9900, 18 negative triangles 205: dt=0.9900, 16 negative triangles 206: dt=0.9900, 16 negative triangles 207: dt=0.9900, 7 negative triangles 208: dt=0.9900, 11 negative triangles 209: dt=0.9900, 11 negative triangles 210: dt=0.9900, 6 negative triangles 211: dt=0.9900, 9 negative triangles 212: dt=0.9900, 10 negative triangles 213: dt=0.9900, 10 negative triangles 214: dt=0.9900, 6 negative triangles 215: dt=0.9900, 8 negative triangles 216: dt=0.9900, 10 negative triangles 217: dt=0.9900, 3 negative triangles 218: dt=0.9900, 3 negative triangles 219: dt=0.9900, 1 negative triangles 220: dt=0.9900, 4 negative triangles 221: dt=0.9900, 2 negative triangles 222: dt=0.9900, 1 negative triangles 223: dt=0.9900, 1 negative triangles 224: dt=0.9900, 3 negative triangles 225: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.35 hours mris_register utimesec 4842.700000 mris_register stimesec 1.260000 mris_register ru_maxrss 290856 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 34652 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 2 mris_register ru_nivcsw 68286 FSRUNTIME@ mris_register 1.3469 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Mon Dec 19 21:55:42 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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 21:55:45 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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 21:55:47 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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 21:55:48 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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 21:55:50 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 SynthF 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... 2106 labels changed using aseg relabeling using gibbs priors... 000: 3866 changed, 187767 examined... 001: 904 changed, 15964 examined... 002: 243 changed, 4967 examined... 003: 69 changed, 1438 examined... 004: 36 changed, 445 examined... 005: 17 changed, 236 examined... 006: 11 changed, 103 examined... 007: 7 changed, 58 examined... 008: 9 changed, 41 examined... 009: 4 changed, 46 examined... 010: 4 changed, 21 examined... 011: 5 changed, 20 examined... 012: 2 changed, 25 examined... 013: 0 changed, 11 examined... 328 labels changed using aseg 000: 152 total segments, 110 labels (578 vertices) changed 001: 44 total segments, 2 labels (10 vertices) changed 002: 42 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... 2322 vertices marked for relabeling... 2322 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 14 seconds. #----------------------------------------- #@# Cortical Parc rh Mon Dec 19 21:56:04 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 SynthF 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... 1358 labels changed using aseg relabeling using gibbs priors... 000: 3458 changed, 182051 examined... 001: 811 changed, 14663 examined... 002: 214 changed, 4598 examined... 003: 74 changed, 1232 examined... 004: 27 changed, 428 examined... 005: 8 changed, 154 examined... 006: 8 changed, 46 examined... 007: 5 changed, 52 examined... 008: 5 changed, 33 examined... 009: 3 changed, 26 examined... 010: 2 changed, 19 examined... 011: 0 changed, 9 examined... 173 labels changed using aseg 000: 96 total segments, 56 labels (276 vertices) changed 001: 41 total segments, 1 labels (1 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... 2132 vertices marked for relabeling... 2132 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 21:56:17 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs SynthF 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/SynthF/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/SynthF/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/SynthF/mri/../mri/aseg.presurf.mgz... reading volume /usr/local/freesurfer/subjects/SynthF/mri/wm.mgz... 20390 bright wm thresholded. 5551 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/SynthF/surf/lh.orig... computing class statistics... border white: 368268 voxels (2.20%) border gray 422696 voxels (2.52%) WM (96.0): 96.9 +- 8.9 [70.0 --> 110.0] GM (69.0) : 67.9 +- 11.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 49.2 (was 70) setting MAX_BORDER_WHITE to 111.9 (was 105) setting MIN_BORDER_WHITE to 61.0 (was 85) setting MAX_CSF to 37.5 (was 40) setting MAX_GRAY to 94.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 49.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 25.7 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103+-5.2, GM=61+-10.4 mean inside = 92.4, mean outside = 71.7 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.02-->5.18) (max @ vno 128013 --> 187004) face area 0.33 +- 0.16 (0.00-->4.93) mean absolute distance = 0.65 +- 0.90 6262 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown deleting segment 1 with 16 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 123 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 136 points - only 0.00% unknown deleting segment 8 with 160 points - only 0.00% unknown deleting segment 9 with 15 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 deleting segment 12 with 13 points - only 0.00% unknown deleting segment 13 with 77 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown deleting segment 15 with 6 points - only 0.00% unknown deleting segment 16 with 189 points - only 0.00% unknown deleting segment 17 with 16 points - only 0.00% unknown deleting segment 18 with 8 points - only 0.00% unknown deleting segment 19 with 38 points - only 0.00% unknown deleting segment 20 with 32 points - only 0.00% unknown deleting segment 21 with 18 points - only 0.00% unknown mean border=76.1, 188 (184) missing vertices, mean dist 0.4 [0.9 (%13.3)->0.6 (%86.7))] %67 local maxima, %29 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-->4.57) (max @ vno 128013 --> 187004) face area 0.33 +- 0.16 (0.00-->3.85) mean absolute distance = 0.41 +- 0.77 8881 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4224734.5, rms=9.580 001: dt: 0.5000, sse=2283003.0, rms=6.183 (35.466%) 002: dt: 0.5000, sse=1710493.1, rms=4.758 (23.040%) 003: dt: 0.5000, sse=1547464.8, rms=4.257 (10.536%) 004: dt: 0.5000, sse=1431265.4, rms=3.870 (9.096%) 005: dt: 0.5000, sse=1419418.0, rms=3.813 (1.458%) 006: dt: 0.5000, sse=1358355.9, rms=3.599 (5.605%) rms = 3.64, time step reduction 1 of 3 to 0.250... 007: dt: 0.2500, sse=1123157.4, rms=2.491 (30.791%) 008: dt: 0.2500, sse=1036723.8, rms=1.908 (23.420%) 009: dt: 0.2500, sse=1010561.7, rms=1.710 (10.390%) 010: dt: 0.2500, sse=998115.9, rms=1.604 (6.177%) rms = 1.56, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=992685.2, rms=1.556 (2.972%) 012: dt: 0.1250, sse=989364.5, rms=1.486 (4.538%) rms = 1.46, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=982587.9, rms=1.462 (1.571%) positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 1 with 30 points - only 0.00% unknown deleting segment 2 with 125 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 130 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown deleting segment 7 with 8 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 84 points - only 0.00% unknown deleting segment 11 with 13 points - only 0.00% unknown deleting segment 12 with 67 points - only 0.00% unknown deleting segment 13 with 7 points - only 0.00% unknown deleting segment 14 with 170 points - only 0.00% unknown deleting segment 15 with 12 points - only 0.00% unknown deleting segment 16 with 12 points - only 0.00% unknown deleting segment 17 with 35 points - only 0.00% unknown deleting segment 18 with 29 points - only 0.00% unknown deleting segment 19 with 10 points - only 0.00% unknown mean border=79.6, 128 (31) missing vertices, mean dist -0.3 [0.5 (%72.4)->0.2 (%27.6))] %75 local maxima, %21 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 0.90 +- 0.25 (0.05-->4.55) (max @ vno 128013 --> 187004) face area 0.36 +- 0.17 (0.00-->4.45) mean absolute distance = 0.34 +- 0.55 8137 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2014895.9, rms=5.354 014: dt: 0.5000, sse=1464744.0, rms=3.668 (31.485%) 015: dt: 0.5000, sse=1442308.9, rms=3.589 (2.167%) 016: dt: 0.5000, sse=1424025.6, rms=3.525 (1.774%) rms = 3.60, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=1182531.2, rms=2.398 (31.985%) 018: dt: 0.2500, sse=1101989.6, rms=1.819 (24.115%) 019: dt: 0.2500, sse=1078649.8, rms=1.599 (12.099%) 020: dt: 0.2500, sse=1062577.8, rms=1.492 (6.735%) 021: dt: 0.2500, sse=1050042.0, rms=1.404 (5.876%) 022: dt: 0.2500, sse=1048152.1, rms=1.342 (4.396%) rms = 1.30, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=1045165.8, rms=1.300 (3.134%) 024: dt: 0.1250, sse=1030623.9, rms=1.237 (4.877%) rms = 1.21, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=1029163.8, rms=1.210 (2.155%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 21 points - only 0.00% unknown deleting segment 1 with 121 points - only 0.00% unknown deleting segment 2 with 13 points - only 0.00% unknown deleting segment 3 with 128 points - only 0.00% unknown deleting segment 4 with 110 points - only 0.00% unknown deleting segment 5 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 16 points - only 0.00% unknown deleting segment 8 with 105 points - only 0.00% unknown deleting segment 9 with 7 points - only 0.00% unknown deleting segment 10 with 179 points - only 0.00% unknown deleting segment 11 with 14 points - only 0.00% unknown deleting segment 12 with 8 points - only 0.00% unknown deleting segment 13 with 35 points - only 0.00% unknown deleting segment 14 with 29 points - only 0.00% unknown deleting segment 15 with 11 points - only 0.00% unknown mean border=82.5, 146 (13) missing vertices, mean dist -0.2 [0.4 (%73.1)->0.3 (%26.9))] %84 local maxima, %12 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 0.89 +- 0.25 (0.05-->4.79) (max @ vno 128013 --> 187004) face area 0.34 +- 0.17 (0.00-->4.57) mean absolute distance = 0.27 +- 0.44 5898 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1592975.9, rms=4.258 026: dt: 0.5000, sse=1304556.6, rms=3.146 (26.121%) rms = 3.26, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=1115450.0, rms=2.186 (30.518%) 028: dt: 0.2500, sse=1030607.2, rms=1.544 (29.352%) 029: dt: 0.2500, sse=1009508.0, rms=1.286 (16.727%) 030: dt: 0.2500, sse=996100.1, rms=1.211 (5.797%) 031: dt: 0.2500, sse=990337.2, rms=1.161 (4.194%) rms = 1.14, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=990726.9, rms=1.138 (1.898%) 033: dt: 0.1250, sse=981033.9, rms=1.063 (6.606%) rms = 1.05, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=980475.3, rms=1.046 (1.586%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 21 points - only 0.00% unknown deleting segment 1 with 124 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown deleting segment 3 with 115 points - only 0.00% unknown deleting segment 4 with 117 points - only 0.00% unknown deleting segment 5 with 10 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 19 points - only 0.00% unknown deleting segment 9 with 112 points - only 0.00% unknown deleting segment 10 with 8 points - only 0.00% unknown deleting segment 11 with 190 points - only 0.00% unknown deleting segment 12 with 14 points - only 0.00% unknown deleting segment 13 with 8 points - only 0.00% unknown deleting segment 14 with 35 points - only 0.00% unknown deleting segment 15 with 29 points - only 0.00% unknown deleting segment 16 with 11 points - only 0.00% unknown mean border=83.6, 172 (6) missing vertices, mean dist -0.1 [0.3 (%60.7)->0.2 (%39.3))] %88 local maxima, % 8 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/SynthF/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=1090167.2, rms=2.176 035: dt: 0.5000, sse=1091147.0, rms=2.114 (2.883%) rms = 2.65, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=984196.1, rms=1.298 (38.580%) 037: dt: 0.2500, sse=969340.9, rms=1.078 (16.954%) 038: dt: 0.2500, sse=954784.9, rms=0.969 (10.109%) rms = 1.00, time step reduction 2 of 3 to 0.125... 039: dt: 0.1250, sse=947787.8, rms=0.910 (6.146%) 040: dt: 0.1250, sse=944105.9, rms=0.832 (8.508%) rms = 0.81, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=942975.2, rms=0.814 (2.173%) positioning took 0.8 minutes generating cortex label... 22 non-cortical segments detected only using segment with 8686 vertices erasing segment 0 (vno[0] = 37771) erasing segment 1 (vno[0] = 64063) erasing segment 3 (vno[0] = 66874) erasing segment 4 (vno[0] = 68338) erasing segment 5 (vno[0] = 77819) erasing segment 6 (vno[0] = 114434) erasing segment 7 (vno[0] = 118865) erasing segment 8 (vno[0] = 119270) erasing segment 9 (vno[0] = 120223) erasing segment 10 (vno[0] = 126190) erasing segment 11 (vno[0] = 128248) erasing segment 12 (vno[0] = 131254) erasing segment 13 (vno[0] = 132484) erasing segment 14 (vno[0] = 132536) erasing segment 15 (vno[0] = 133786) erasing segment 16 (vno[0] = 134610) erasing segment 17 (vno[0] = 138722) erasing segment 18 (vno[0] = 139030) erasing segment 19 (vno[0] = 140026) erasing segment 20 (vno[0] = 151703) erasing segment 21 (vno[0] = 157910) writing cortex label to /usr/local/freesurfer/subjects/SynthF/label/lh.cortex.label... writing curvature file /usr/local/freesurfer/subjects/SynthF/surf/lh.curv writing smoothed area to lh.area writing curvature file /usr/local/freesurfer/subjects/SynthF/surf/lh.area vertex spacing 0.89 +- 0.26 (0.02-->5.07) (max @ vno 128013 --> 187004) face area 0.33 +- 0.16 (0.00-->5.03) 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 10 points - only 0.00% unknown deleting segment 1 with 43 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 12 points - only 0.00% unknown deleting segment 9 with 25 points - only 0.00% unknown deleting segment 10 with 23 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=47.9, 236 (236) missing vertices, mean dist 1.4 [1.1 (%0.1)->2.5 (%99.9))] % 6 local maxima, %46 large gradients and %43 min vals, 745 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=49317760.0, rms=36.643 001: dt: 0.0500, sse=43967152.0, rms=34.559 (5.686%) 002: dt: 0.0500, sse=40165408.0, rms=32.998 (4.515%) 003: dt: 0.0500, sse=37247484.0, rms=31.749 (3.787%) 004: dt: 0.0500, sse=34871812.0, rms=30.693 (3.324%) 005: dt: 0.0500, sse=32853338.0, rms=29.767 (3.017%) 006: dt: 0.0500, sse=31089262.0, rms=28.934 (2.800%) 007: dt: 0.0500, sse=29511736.0, rms=28.168 (2.649%) 008: dt: 0.0500, sse=28081142.0, rms=27.454 (2.533%) 009: dt: 0.0500, sse=26767830.0, rms=26.782 (2.447%) 010: dt: 0.0500, sse=25552172.0, rms=26.145 (2.379%) positioning took 1.1 minutes mean border=47.5, 194 (124) missing vertices, mean dist 1.1 [0.7 (%0.1)->2.0 (%99.9))] % 7 local maxima, %47 large gradients and %42 min vals, 746 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=27250472.0, rms=27.025 011: dt: 0.0500, sse=26095470.0, rms=26.425 (2.217%) 012: dt: 0.0500, sse=25014950.0, rms=25.852 (2.169%) 013: dt: 0.0500, sse=24000512.0, rms=25.302 (2.128%) 014: dt: 0.0500, sse=23046068.0, rms=24.774 (2.090%) 015: dt: 0.0500, sse=22147424.0, rms=24.265 (2.052%) 016: dt: 0.0500, sse=21300084.0, rms=23.776 (2.017%) 017: dt: 0.0500, sse=20500572.0, rms=23.305 (1.982%) 018: dt: 0.0500, sse=19746318.0, rms=22.851 (1.946%) 019: dt: 0.0500, sse=19033802.0, rms=22.414 (1.912%) 020: dt: 0.0500, sse=18361536.0, rms=21.994 (1.875%) positioning took 1.1 minutes mean border=47.3, 183 (86) missing vertices, mean dist 0.9 [0.2 (%0.7)->1.7 (%99.3))] % 7 local maxima, %47 large gradients and %42 min vals, 704 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=18532266.0, rms=22.103 021: dt: 0.0500, sse=17874742.0, rms=21.686 (1.886%) 022: dt: 0.0500, sse=17255236.0, rms=21.286 (1.846%) 023: dt: 0.0500, sse=16668749.0, rms=20.900 (1.814%) 024: dt: 0.0500, sse=16115899.0, rms=20.529 (1.773%) 025: dt: 0.0500, sse=15595292.0, rms=20.174 (1.731%) 026: dt: 0.0500, sse=15104610.0, rms=19.833 (1.689%) 027: dt: 0.0500, sse=14638500.0, rms=19.503 (1.661%) 028: dt: 0.0500, sse=14192516.0, rms=19.183 (1.643%) 029: dt: 0.0500, sse=13764603.0, rms=18.870 (1.630%) 030: dt: 0.0500, sse=13354260.0, rms=18.565 (1.616%) positioning took 1.1 minutes mean border=47.2, 198 (69) missing vertices, mean dist 0.8 [0.1 (%10.8)->1.5 (%89.2))] % 7 local maxima, %48 large gradients and %41 min vals, 675 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=13490185.0, rms=18.665 031: dt: 0.5000, sse=10634108.0, rms=16.402 (12.125%) 032: dt: 0.5000, sse=8594502.0, rms=14.567 (11.191%) 033: dt: 0.5000, sse=6969081.5, rms=12.921 (11.296%) 034: dt: 0.5000, sse=5726715.5, rms=11.500 (11.000%) 035: dt: 0.5000, sse=4749192.5, rms=10.248 (10.887%) 036: dt: 0.5000, sse=3997136.8, rms=9.163 (10.584%) 037: dt: 0.5000, sse=3445640.5, rms=8.283 (9.605%) 038: dt: 0.5000, sse=3086761.8, rms=7.650 (7.643%) 039: dt: 0.5000, sse=2834606.5, rms=7.178 (6.167%) 040: dt: 0.5000, sse=2687437.0, rms=6.881 (4.135%) 041: dt: 0.5000, sse=2580123.2, rms=6.663 (3.173%) 042: dt: 0.5000, sse=2523666.8, rms=6.541 (1.840%) 043: dt: 0.5000, sse=2477253.8, rms=6.443 (1.493%) rms = 6.40, time step reduction 1 of 3 to 0.250... 044: dt: 0.5000, sse=2460877.5, rms=6.404 (0.611%) 045: dt: 0.2500, sse=2231871.8, rms=5.846 (8.707%) 046: dt: 0.2500, sse=2168574.2, rms=5.692 (2.628%) rms = 5.70, time step reduction 2 of 3 to 0.125... 047: dt: 0.1250, sse=2134550.5, rms=5.605 (1.530%) 048: dt: 0.1250, sse=2087622.0, rms=5.482 (2.195%) rms = 5.45, time step reduction 3 of 3 to 0.062... 049: dt: 0.1250, sse=2075638.4, rms=5.450 (0.579%) positioning took 2.2 minutes mean border=46.7, 4936 (26) missing vertices, mean dist 0.1 [0.2 (%58.7)->0.6 (%41.3))] %12 local maxima, %43 large gradients and %39 min vals, 289 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=2364965.2, rms=5.654 rms = 5.73, time step reduction 1 of 3 to 0.250... 050: dt: 0.2500, sse=2185066.2, rms=5.177 (8.421%) 051: dt: 0.2500, sse=2117270.8, rms=4.982 (3.773%) rms = 5.02, time step reduction 2 of 3 to 0.125... 052: dt: 0.1250, sse=2079399.8, rms=4.871 (2.231%) 053: dt: 0.1250, sse=2026825.6, rms=4.713 (3.241%) rms = 4.67, time step reduction 3 of 3 to 0.062... 054: dt: 0.1250, sse=2010925.0, rms=4.666 (0.999%) positioning took 0.7 minutes mean border=45.8, 5222 (19) missing vertices, mean dist 0.1 [0.1 (%56.6)->0.6 (%43.4))] %23 local maxima, %32 large gradients and %38 min vals, 319 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=2101812.2, rms=4.960 rms = 5.56, time step reduction 1 of 3 to 0.250... 055: dt: 0.2500, sse=2027727.8, rms=4.747 (4.298%) rms = 4.77, time step reduction 2 of 3 to 0.125... rms = 4.72, time step reduction 3 of 3 to 0.062... 056: dt: 0.1250, sse=2018102.2, rms=4.718 (0.612%) positioning took 0.4 minutes mean border=45.1, 9025 (19) missing vertices, mean dist 0.1 [0.1 (%50.0)->0.5 (%50.0))] %30 local maxima, %25 large gradients and %37 min vals, 368 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/SynthF/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=2104710.2, rms=4.961 rms = 5.16, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=2014411.8, rms=4.702 (5.220%) 058: dt: 0.2500, sse=1941304.9, rms=4.496 (4.396%) rms = 4.46, time step reduction 2 of 3 to 0.125... 059: dt: 0.2500, sse=1928107.4, rms=4.465 (0.685%) 060: dt: 0.1250, sse=1853015.0, rms=4.219 (5.508%) 061: dt: 0.1250, sse=1825553.2, rms=4.131 (2.081%) rms = 4.10, time step reduction 3 of 3 to 0.062... 062: dt: 0.1250, sse=1814140.5, rms=4.095 (0.863%) positioning took 0.7 minutes writing curvature file /usr/local/freesurfer/subjects/SynthF/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /usr/local/freesurfer/subjects/SynthF/surf/lh.area.pial vertex spacing 1.00 +- 0.42 (0.09-->6.68) (max @ vno 123238 --> 121961) face area 0.39 +- 0.29 (0.00-->5.73) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 187767 vertices processed 25000 of 187767 vertices processed 50000 of 187767 vertices processed 75000 of 187767 vertices processed 100000 of 187767 vertices processed 125000 of 187767 vertices processed 150000 of 187767 vertices processed 175000 of 187767 vertices processed 0 of 187767 vertices processed 25000 of 187767 vertices processed 50000 of 187767 vertices processed 75000 of 187767 vertices processed 100000 of 187767 vertices processed 125000 of 187767 vertices processed 150000 of 187767 vertices processed 175000 of 187767 vertices processed thickness calculation complete, 184:1031 truncations. 61804 vertices at 0 distance 147094 vertices at 1 distance 95905 vertices at 2 distance 36902 vertices at 3 distance 12791 vertices at 4 distance 4268 vertices at 5 distance 1322 vertices at 6 distance 462 vertices at 7 distance 166 vertices at 8 distance 72 vertices at 9 distance 41 vertices at 10 distance 43 vertices at 11 distance 32 vertices at 12 distance 24 vertices at 13 distance 27 vertices at 14 distance 27 vertices at 15 distance 26 vertices at 16 distance 23 vertices at 17 distance 15 vertices at 18 distance 8 vertices at 19 distance 8 vertices at 20 distance writing curvature file /usr/local/freesurfer/subjects/SynthF/surf/lh.thickness positioning took 16.3 minutes #-------------------------------------------- #@# Make Pial Surf rh Mon Dec 19 22:12:37 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs SynthF 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/SynthF/mri/filled.mgz... reading volume /usr/local/freesurfer/subjects/SynthF/mri/brain.finalsurfs.mgz... reading volume /usr/local/freesurfer/subjects/SynthF/mri/../mri/aseg.presurf.mgz... reading volume /usr/local/freesurfer/subjects/SynthF/mri/wm.mgz... 20390 bright wm thresholded. 5551 bright non-wm voxels segmented. reading original surface position from /usr/local/freesurfer/subjects/SynthF/surf/rh.orig... computing class statistics... border white: 368268 voxels (2.20%) border gray 422696 voxels (2.52%) WM (96.0): 96.9 +- 8.9 [70.0 --> 110.0] GM (69.0) : 67.9 +- 11.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 50.2 (was 70) setting MAX_BORDER_WHITE to 111.9 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 38.5 (was 40) setting MAX_GRAY to 94.1 (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+-13.0 mean inside = 92.1, mean outside = 72.8 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.27 (0.02-->6.92) (max @ vno 141664 --> 143535) face area 0.33 +- 0.18 (0.00-->14.37) mean absolute distance = 0.68 +- 0.97 5008 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 30 points - only 0.00% unknown deleting segment 1 with 23 points - only 0.00% unknown deleting segment 2 with 32 points - only 0.00% unknown deleting segment 4 with 20 points - only 0.00% unknown deleting segment 5 with 18 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 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 deleting segment 10 with 37 points - only 0.00% unknown deleting segment 11 with 51 points - only 0.00% unknown deleting segment 12 with 11 points - only 0.00% unknown deleting segment 13 with 30 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 15 with 1 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 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 18 with 1 points - only 0.00% unknown deleting segment 19 with 211 points - only 0.00% unknown deleting segment 20 with 65 points - only 0.00% unknown deleting segment 21 with 59 points - only 0.00% unknown deleting segment 22 with 46 points - only 0.00% unknown deleting segment 23 with 28 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 24 with 1 points - only 0.00% unknown mean border=77.6, 428 (418) missing vertices, mean dist 0.4 [1.0 (%15.6)->0.6 (%84.4))] %67 local maxima, %29 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 0.93 +- 0.27 (0.09-->7.04) (max @ vno 132696 --> 180597) face area 0.33 +- 0.18 (0.00-->14.43) mean absolute distance = 0.44 +- 0.81 7809 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3788122.2, rms=9.092 001: dt: 0.5000, sse=2169592.0, rms=6.049 (33.465%) 002: dt: 0.5000, sse=1639392.4, rms=4.651 (23.110%) 003: dt: 0.5000, sse=1479349.0, rms=4.104 (11.762%) 004: dt: 0.5000, sse=1356958.0, rms=3.669 (10.617%) 005: dt: 0.5000, sse=1332331.1, rms=3.600 (1.866%) 006: dt: 0.5000, sse=1277242.2, rms=3.379 (6.152%) rms = 3.44, time step reduction 1 of 3 to 0.250... 007: dt: 0.2500, sse=1079830.2, rms=2.360 (30.143%) 008: dt: 0.2500, sse=1011522.1, rms=1.848 (21.693%) 009: dt: 0.2500, sse=992193.8, rms=1.681 (9.052%) 010: dt: 0.2500, sse=984497.5, rms=1.614 (3.974%) rms = 1.59, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=979483.4, rms=1.590 (1.500%) 012: dt: 0.1250, sse=973591.2, rms=1.531 (3.699%) rms = 1.52, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=973432.8, rms=1.515 (1.042%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 28 points - only 0.00% unknown deleting segment 1 with 25 points - only 0.00% unknown deleting segment 2 with 30 points - only 0.00% unknown deleting segment 3 with 14 points - only 0.00% unknown deleting segment 4 with 13 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 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 35 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown deleting segment 10 with 29 points - only 0.00% unknown deleting segment 11 with 8 points - only 0.00% unknown deleting segment 12 with 213 points - only 0.00% unknown deleting segment 13 with 25 points - only 0.00% unknown deleting segment 14 with 60 points - only 0.00% unknown deleting segment 15 with 59 points - only 0.00% unknown deleting segment 16 with 39 points - only 0.00% unknown deleting segment 17 with 23 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 18 with 1 points - only 0.00% unknown mean border=80.6, 240 (73) missing vertices, mean dist -0.3 [0.5 (%69.7)->0.3 (%30.3))] %74 local maxima, %22 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 (0.04-->6.94) (max @ vno 132696 --> 180597) face area 0.36 +- 0.19 (0.00-->15.30) mean absolute distance = 0.37 +- 0.59 7981 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1824873.8, rms=4.950 014: dt: 0.5000, sse=1380263.1, rms=3.418 (30.957%) 015: dt: 0.5000, sse=1351169.0, rms=3.334 (2.464%) 016: dt: 0.5000, sse=1331434.4, rms=3.274 (1.789%) rms = 3.35, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=1139383.6, rms=2.276 (30.488%) 018: dt: 0.2500, sse=1074189.4, rms=1.753 (22.987%) 019: dt: 0.2500, sse=1049099.8, rms=1.551 (11.481%) 020: dt: 0.2500, sse=1037552.7, rms=1.463 (5.686%) 021: dt: 0.2500, sse=1034256.4, rms=1.399 (4.363%) rms = 1.38, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=1030752.9, rms=1.376 (1.707%) rms = 1.33, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=1023220.4, rms=1.333 (3.067%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 27 points - only 0.00% unknown deleting segment 1 with 26 points - only 0.00% unknown deleting segment 2 with 30 points - only 0.00% unknown deleting segment 3 with 15 points - only 0.00% unknown deleting segment 4 with 11 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 38 points - only 0.00% unknown deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 11 points - only 0.00% unknown deleting segment 10 with 30 points - only 0.00% unknown deleting segment 11 with 8 points - only 0.00% unknown deleting segment 12 with 199 points - only 0.00% unknown deleting segment 13 with 56 points - only 0.00% unknown deleting segment 14 with 56 points - only 0.00% unknown deleting segment 15 with 39 points - only 0.00% unknown deleting segment 16 with 22 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 17 with 1 points - only 0.00% unknown mean border=83.3, 203 (33) missing vertices, mean dist -0.2 [0.4 (%71.5)->0.3 (%28.5))] %84 local maxima, %12 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-->7.18) (max @ vno 179299 --> 179298) face area 0.35 +- 0.19 (0.00-->14.26) mean absolute distance = 0.30 +- 0.48 6181 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1529656.9, rms=4.150 024: dt: 0.5000, sse=1248906.1, rms=2.961 (28.654%) rms = 3.06, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=1097175.8, rms=2.164 (26.929%) 026: dt: 0.2500, sse=1035761.0, rms=1.622 (25.052%) 027: dt: 0.2500, sse=1008430.8, rms=1.413 (12.863%) 028: dt: 0.2500, sse=998221.8, rms=1.344 (4.912%) rms = 1.31, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=993027.6, rms=1.309 (2.594%) 030: dt: 0.1250, sse=984267.8, rms=1.241 (5.144%) rms = 1.23, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=981948.8, rms=1.228 (1.047%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 27 points - only 0.00% unknown deleting segment 1 with 22 points - only 0.00% unknown deleting segment 2 with 31 points - only 0.00% unknown deleting segment 3 with 15 points - only 0.00% unknown deleting segment 4 with 12 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 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 37 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown deleting segment 12 with 15 points - only 0.00% unknown deleting segment 13 with 20 points - only 0.00% unknown deleting segment 14 with 30 points - only 0.00% unknown deleting segment 15 with 9 points - only 0.00% unknown deleting segment 16 with 8 points - only 0.00% unknown deleting segment 17 with 196 points - only 0.00% unknown deleting segment 18 with 55 points - only 0.00% unknown deleting segment 19 with 55 points - only 0.00% unknown deleting segment 20 with 40 points - only 0.00% unknown deleting segment 21 with 17 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 22 with 1 points - only 0.00% unknown mean border=84.4, 257 (28) missing vertices, mean dist -0.1 [0.3 (%60.8)->0.3 (%39.2))] %88 local maxima, % 8 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/SynthF/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=1088506.9, rms=2.290 032: dt: 0.5000, sse=1064143.0, rms=2.030 (11.371%) rms = 2.48, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=977946.6, rms=1.377 (32.171%) 034: dt: 0.2500, sse=964492.7, rms=1.219 (11.474%) 035: dt: 0.2500, sse=956472.3, rms=1.114 (8.632%) rms = 1.14, time step reduction 2 of 3 to 0.125... rms = 1.07, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=947103.6, rms=1.069 (3.989%) positioning took 0.6 minutes generating cortex label... 25 non-cortical segments detected only using segment with 7380 vertices erasing segment 0 (vno[0] = 43237) erasing segment 2 (vno[0] = 58512) erasing segment 3 (vno[0] = 62094) erasing segment 4 (vno[0] = 67362) erasing segment 5 (vno[0] = 71507) erasing segment 6 (vno[0] = 74184) erasing segment 7 (vno[0] = 75856) erasing segment 8 (vno[0] = 77050) erasing segment 9 (vno[0] = 85158) erasing segment 10 (vno[0] = 93870) erasing segment 11 (vno[0] = 95931) erasing segment 12 (vno[0] = 100872) erasing segment 13 (vno[0] = 116368) erasing segment 14 (vno[0] = 120376) erasing segment 15 (vno[0] = 120807) erasing segment 16 (vno[0] = 120818) erasing segment 17 (vno[0] = 126689) erasing segment 18 (vno[0] = 127110) erasing segment 19 (vno[0] = 128427) erasing segment 20 (vno[0] = 134242) erasing segment 21 (vno[0] = 136520) erasing segment 22 (vno[0] = 138895) erasing segment 23 (vno[0] = 143807) erasing segment 24 (vno[0] = 143816) writing cortex label to /usr/local/freesurfer/subjects/SynthF/label/rh.cortex.label... writing curvature file /usr/local/freesurfer/subjects/SynthF/surf/rh.curv writing smoothed area to rh.area writing curvature file /usr/local/freesurfer/subjects/SynthF/surf/rh.area vertex spacing 0.89 +- 0.28 (0.02-->7.00) (max @ vno 179298 --> 179299) face area 0.34 +- 0.19 (0.00-->13.30) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown deleting segment 1 with 7 points - only 0.00% unknown deleting segment 2 with 26 points - only 0.00% unknown deleting segment 3 with 78 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 9 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 11 with 4 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 10 points - only 0.00% unknown deleting segment 14 with 41 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown deleting segment 16 with 19 points - only 0.00% unknown deleting segment 17 with 84 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=49.9, 444 (444) missing vertices, mean dist 1.4 [1.5 (%0.0)->2.6 (%100.0))] % 8 local maxima, %42 large gradients and %46 min vals, 783 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=45157304.0, rms=35.568 001: dt: 0.0500, sse=40450496.0, rms=33.624 (5.465%) 002: dt: 0.0500, sse=37098144.0, rms=32.168 (4.331%) 003: dt: 0.0500, sse=34518796.0, rms=31.001 (3.628%) 004: dt: 0.0500, sse=32413434.0, rms=30.015 (3.181%) 005: dt: 0.0500, sse=30625234.0, rms=29.151 (2.878%) 006: dt: 0.0500, sse=29060148.0, rms=28.373 (2.668%) 007: dt: 0.0500, sse=27657788.0, rms=27.658 (2.522%) 008: dt: 0.0500, sse=26382980.0, rms=26.991 (2.411%) 009: dt: 0.0500, sse=25210282.0, rms=26.363 (2.328%) 010: dt: 0.0500, sse=24121472.0, rms=25.765 (2.266%) positioning took 1.1 minutes mean border=49.5, 283 (185) missing vertices, mean dist 1.1 [0.9 (%0.1)->2.1 (%99.9))] % 8 local maxima, %43 large gradients and %44 min vals, 805 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=25926722.0, rms=26.732 011: dt: 0.0500, sse=24885606.0, rms=26.170 (2.102%) 012: dt: 0.0500, sse=23907956.0, rms=25.631 (2.060%) 013: dt: 0.0500, sse=22988030.0, rms=25.113 (2.020%) 014: dt: 0.0500, sse=22119208.0, rms=24.614 (1.987%) 015: dt: 0.0500, sse=21298256.0, rms=24.133 (1.955%) 016: dt: 0.0500, sse=20521880.0, rms=23.669 (1.923%) 017: dt: 0.0500, sse=19786574.0, rms=23.221 (1.893%) 018: dt: 0.0500, sse=19090302.0, rms=22.788 (1.863%) 019: dt: 0.0500, sse=18430598.0, rms=22.371 (1.832%) 020: dt: 0.0500, sse=17805352.0, rms=21.968 (1.802%) positioning took 1.1 minutes mean border=49.3, 300 (119) missing vertices, mean dist 0.9 [0.1 (%0.8)->1.8 (%99.2))] % 9 local maxima, %43 large gradients and %44 min vals, 766 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=17959052.0, rms=22.068 021: dt: 0.0500, sse=17346538.0, rms=21.668 (1.814%) 022: dt: 0.0500, sse=16767762.0, rms=21.283 (1.778%) 023: dt: 0.0500, sse=16219073.0, rms=20.911 (1.747%) 024: dt: 0.0500, sse=15701332.0, rms=20.554 (1.707%) 025: dt: 0.0500, sse=15212793.0, rms=20.211 (1.668%) 026: dt: 0.0500, sse=14750947.0, rms=19.882 (1.630%) 027: dt: 0.0500, sse=14311371.0, rms=19.563 (1.604%) 028: dt: 0.0500, sse=13888774.0, rms=19.251 (1.593%) 029: dt: 0.0500, sse=13481824.0, rms=18.946 (1.584%) 030: dt: 0.0500, sse=13090790.0, rms=18.649 (1.572%) positioning took 1.1 minutes mean border=49.2, 347 (95) missing vertices, mean dist 0.8 [0.1 (%11.4)->1.6 (%88.6))] % 9 local maxima, %44 large gradients and %44 min vals, 741 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=13268158.0, rms=18.783 031: dt: 0.5000, sse=10508218.0, rms=16.549 (11.896%) 032: dt: 0.5000, sse=8494541.0, rms=14.700 (11.171%) 033: dt: 0.5000, sse=6872164.0, rms=13.024 (11.401%) 034: dt: 0.5000, sse=5640659.0, rms=11.585 (11.046%) 035: dt: 0.5000, sse=4674602.5, rms=10.321 (10.912%) 036: dt: 0.5000, sse=3959989.2, rms=9.272 (10.168%) 037: dt: 0.5000, sse=3454159.8, rms=8.454 (8.823%) 038: dt: 0.5000, sse=3118206.2, rms=7.860 (7.026%) 039: dt: 0.5000, sse=2897531.8, rms=7.447 (5.247%) 040: dt: 0.5000, sse=2767209.5, rms=7.188 (3.482%) 041: dt: 0.5000, sse=2668962.5, rms=6.990 (2.751%) 042: dt: 0.5000, sse=2609251.8, rms=6.863 (1.827%) 043: dt: 0.5000, sse=2555241.0, rms=6.751 (1.629%) rms = 6.70, time step reduction 1 of 3 to 0.250... 044: dt: 0.5000, sse=2535301.0, rms=6.704 (0.697%) 045: dt: 0.2500, sse=2325134.0, rms=6.202 (7.483%) 046: dt: 0.2500, sse=2265800.8, rms=6.062 (2.253%) rms = 6.07, time step reduction 2 of 3 to 0.125... 047: dt: 0.1250, sse=2234475.0, rms=5.985 (1.282%) 048: dt: 0.1250, sse=2191020.8, rms=5.874 (1.847%) rms = 5.85, time step reduction 3 of 3 to 0.062... 049: dt: 0.1250, sse=2180481.0, rms=5.847 (0.466%) positioning took 2.2 minutes mean border=48.8, 5572 (36) missing vertices, mean dist 0.1 [0.2 (%57.2)->0.7 (%42.8))] %12 local maxima, %40 large gradients and %41 min vals, 228 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=2405889.2, rms=5.918 rms = 5.94, time step reduction 1 of 3 to 0.250... 050: dt: 0.2500, sse=2233503.2, rms=5.472 (7.537%) 051: dt: 0.2500, sse=2163070.2, rms=5.276 (3.574%) rms = 5.31, time step reduction 2 of 3 to 0.125... 052: dt: 0.1250, sse=2128328.8, rms=5.177 (1.884%) 053: dt: 0.1250, sse=2082324.1, rms=5.042 (2.603%) rms = 4.99, time step reduction 3 of 3 to 0.062... 054: dt: 0.1250, sse=2065298.4, rms=4.993 (0.966%) positioning took 0.7 minutes mean border=48.1, 5975 (30) missing vertices, mean dist 0.1 [0.1 (%55.7)->0.6 (%44.3))] %21 local maxima, %31 large gradients and %40 min vals, 300 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=2144537.2, rms=5.251 rms = 5.73, time step reduction 1 of 3 to 0.250... 055: dt: 0.2500, sse=2078707.1, rms=5.069 (3.476%) rms = 5.07, time step reduction 2 of 3 to 0.125... rms = 5.04, time step reduction 3 of 3 to 0.062... 056: dt: 0.1250, sse=2068933.0, rms=5.040 (0.557%) positioning took 0.4 minutes mean border=47.5, 9881 (29) missing vertices, mean dist 0.1 [0.1 (%50.3)->0.5 (%49.7))] %27 local maxima, %25 large gradients and %39 min vals, 331 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/SynthF/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=2139300.2, rms=5.232 rms = 5.36, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=2052602.2, rms=4.992 (4.595%) 058: dt: 0.2500, sse=1970879.2, rms=4.768 (4.478%) rms = 4.72, time step reduction 2 of 3 to 0.125... 059: dt: 0.2500, sse=1952260.5, rms=4.722 (0.962%) 060: dt: 0.1250, sse=1874424.6, rms=4.474 (5.253%) 061: dt: 0.1250, sse=1848751.4, rms=4.395 (1.771%) rms = 4.35, time step reduction 3 of 3 to 0.062... 062: dt: 0.1250, sse=1834336.0, rms=4.351 (1.006%) positioning took 0.7 minutes writing curvature file /usr/local/freesurfer/subjects/SynthF/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /usr/local/freesurfer/subjects/SynthF/surf/rh.area.pial vertex spacing 0.99 +- 0.43 (0.09-->8.45) (max @ vno 179346 --> 84169) face area 0.39 +- 0.30 (0.00-->18.94) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 182051 vertices processed 25000 of 182051 vertices processed 50000 of 182051 vertices processed 75000 of 182051 vertices processed 100000 of 182051 vertices processed 125000 of 182051 vertices processed 150000 of 182051 vertices processed 175000 of 182051 vertices processed 0 of 182051 vertices processed 25000 of 182051 vertices processed 50000 of 182051 vertices processed 75000 of 182051 vertices processed 100000 of 182051 vertices processed 125000 of 182051 vertices processed 150000 of 182051 vertices processed 175000 of 182051 vertices processed thickness calculation complete, 475:1229 truncations. 58580 vertices at 0 distance 138840 vertices at 1 distance 94821 vertices at 2 distance 37660 vertices at 3 distance 13460 vertices at 4 distance 4578 vertices at 5 distance 1553 vertices at 6 distance 555 vertices at 7 distance 251 vertices at 8 distance 123 vertices at 9 distance 90 vertices at 10 distance 58 vertices at 11 distance 49 vertices at 12 distance 32 vertices at 13 distance 24 vertices at 14 distance 16 vertices at 15 distance 27 vertices at 16 distance 19 vertices at 17 distance 20 vertices at 18 distance 8 vertices at 19 distance 24 vertices at 20 distance writing curvature file /usr/local/freesurfer/subjects/SynthF/surf/rh.thickness positioning took 15.5 minutes #-------------------------------------------- #@# Surf Volume lh Mon Dec 19 22:28:08 GMT 2016 /usr/local/freesurfer/subjects/SynthF/surf /usr/local/freesurfer/subjects/SynthF/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 SynthF lh /usr/local/freesurfer/subjects/SynthF/surf/lh.volume masking with /usr/local/freesurfer/subjects/SynthF/label/lh.cortex.label Total face volume 321558 Total vertex volume 318104 (mask=0) #@# SynthF lh 318104 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Mon Dec 19 22:28:11 GMT 2016 /usr/local/freesurfer/subjects/SynthF/surf /usr/local/freesurfer/subjects/SynthF/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 SynthF rh /usr/local/freesurfer/subjects/SynthF/surf/rh.volume masking with /usr/local/freesurfer/subjects/SynthF/label/rh.cortex.label Total face volume 309486 Total vertex volume 306722 (mask=0) #@# SynthF rh 306722 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Mon Dec 19 22:28:13 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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 SynthF 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 = 51 writing volume /usr/local/freesurfer/subjects/SynthF/mri/ribbon.mgz mris_volmask took 13.38 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Mon Dec 19 22:41:36 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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 SynthF lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /usr/local/freesurfer/subjects/SynthF/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthF/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/SynthF/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthF/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 321558 Total vertex volume 318104 (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) = 1180158 mm^3 (det: 1.650715 ) lhCtxGM: 316058.717 315676.000 diff= 382.7 pctdiff= 0.121 rhCtxGM: 304031.649 304306.000 diff= -274.4 pctdiff=-0.090 lhCtxWM: 312652.444 313883.000 diff=-1230.6 pctdiff=-0.394 rhCtxWM: 327003.381 328754.000 diff=-1750.6 pctdiff=-0.535 SubCortGMVol 71273.000 SupraTentVol 1357578.191 (1354505.000) diff=3073.191 pctdiff=0.226 SupraTentVolNotVent 1336967.191 (1333894.000) diff=3073.191 pctdiff=0.230 BrainSegVol 1502470.000 (1499154.000) diff=3316.000 pctdiff=0.221 BrainSegVolNotVent 1477416.000 (1474442.191) diff=2973.809 pctdiff=0.201 BrainSegVolNotVent 1477416.000 CerebellumVol 143421.000 VentChorVol 20611.000 3rd4th5thCSF 4443.000 CSFVol 1127.000, OptChiasmVol 101.000 MaskVol 1849883.000 1469 1008 2182 2.147 0.488 0.082 0.011 5 0.6 bankssts 1277 825 2839 3.172 0.620 0.154 0.032 25 1.7 caudalanteriorcingulate 5340 3547 7978 2.171 0.595 0.118 0.030 56 7.5 caudalmiddlefrontal 2360 1610 3358 2.075 0.478 0.169 0.039 40 4.1 cuneus 627 466 1941 3.048 0.888 0.080 0.017 3 0.4 entorhinal 5760 4188 11244 2.388 0.653 0.138 0.029 81 8.0 fusiform 10814 6760 16348 2.340 0.625 0.113 0.028 111 12.9 inferiorparietal 7020 4764 13714 2.582 0.762 0.127 0.033 87 10.3 inferiortemporal 2119 1347 3983 2.626 0.885 0.120 0.024 27 1.9 isthmuscingulate 10350 6515 14634 2.108 0.643 0.128 0.028 127 12.0 lateraloccipital 4533 3242 10721 2.922 0.692 0.138 0.033 64 6.0 lateralorbitofrontal 5408 3700 9273 2.276 0.712 0.144 0.034 69 7.9 lingual 3310 2333 6478 2.545 0.772 0.139 0.043 58 5.3 medialorbitofrontal 7608 4929 15255 2.702 0.795 0.131 0.038 92 12.8 middletemporal 1014 635 2014 2.724 0.801 0.082 0.019 7 0.7 parahippocampal 2612 1714 4322 2.267 0.565 0.103 0.017 17 1.8 paracentral 2902 1988 5517 2.526 0.632 0.111 0.017 31 2.0 parsopercularis 1286 869 3549 3.069 0.580 0.143 0.031 21 1.6 parsorbitalis 2294 1573 4734 2.502 0.656 0.108 0.017 22 1.6 parstriangularis 1698 1151 1940 1.791 0.413 0.126 0.024 18 1.6 pericalcarine 11414 7224 16528 2.037 0.686 0.108 0.023 100 10.9 postcentral 2400 1621 4370 2.514 0.888 0.143 0.030 40 3.0 posteriorcingulate 10743 6913 18384 2.441 0.681 0.103 0.023 83 10.9 precentral 7360 5060 12927 2.428 0.542 0.126 0.025 81 7.6 precuneus 1262 865 2686 2.872 0.611 0.140 0.032 19 1.5 rostralanteriorcingulate 12804 8291 22016 2.383 0.609 0.125 0.027 139 14.5 rostralmiddlefrontal 15487 10125 30159 2.678 0.671 0.119 0.030 162 19.4 superiorfrontal 14061 8829 20554 2.146 0.594 0.110 0.022 120 13.1 superiorparietal 9139 6136 20052 2.803 0.700 0.116 0.024 104 9.4 superiortemporal 7723 5236 13877 2.510 0.674 0.128 0.030 91 10.3 supramarginal 545 384 1446 2.966 0.614 0.187 0.065 12 1.7 frontalpole 759 555 2833 3.689 0.599 0.116 0.022 8 0.7 temporalpole 1059 704 2101 2.634 0.538 0.119 0.028 12 1.1 transversetemporal 4052 2766 8083 2.950 0.750 0.114 0.028 37 4.6 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 SynthF lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /usr/local/freesurfer/subjects/SynthF/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthF/surf/lh.pial... reading input pial surface /usr/local/freesurfer/subjects/SynthF/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthF/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 321558 Total vertex volume 318104 (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) = 1180158 mm^3 (det: 1.650715 ) lhCtxGM: 316058.717 315676.000 diff= 382.7 pctdiff= 0.121 rhCtxGM: 304031.649 304306.000 diff= -274.4 pctdiff=-0.090 lhCtxWM: 312652.444 313883.000 diff=-1230.6 pctdiff=-0.394 rhCtxWM: 327003.381 328754.000 diff=-1750.6 pctdiff=-0.535 SubCortGMVol 71273.000 SupraTentVol 1357578.191 (1354505.000) diff=3073.191 pctdiff=0.226 SupraTentVolNotVent 1336967.191 (1333894.000) diff=3073.191 pctdiff=0.230 BrainSegVol 1502470.000 (1499154.000) diff=3316.000 pctdiff=0.221 BrainSegVolNotVent 1477416.000 (1474442.191) diff=2973.809 pctdiff=0.201 BrainSegVolNotVent 1477416.000 CerebellumVol 143421.000 VentChorVol 20611.000 3rd4th5thCSF 4443.000 CSFVol 1127.000, OptChiasmVol 101.000 MaskVol 1849883.000 1469 967 2182 2.147 0.488 0.095 0.018 9 1.1 bankssts 1277 1027 2839 3.172 0.620 0.179 0.066 69 4.2 caudalanteriorcingulate 5340 3846 7978 2.171 0.595 0.110 0.025 49 6.1 caudalmiddlefrontal 2360 1778 3358 2.075 0.478 0.157 0.036 48 4.2 cuneus 627 788 1941 3.048 0.888 0.161 0.030 4 0.9 entorhinal 5760 5139 11244 2.388 0.653 0.170 0.040 100 11.3 fusiform 10814 7485 16348 2.340 0.625 0.109 0.023 109 11.0 inferiorparietal 7020 5692 13714 2.582 0.762 0.138 0.034 116 11.0 inferiortemporal 2119 1658 3983 2.626 0.885 0.152 0.042 46 3.7 isthmuscingulate 10350 7788 14634 2.108 0.643 0.127 0.030 130 14.3 lateraloccipital 4533 4106 10721 2.922 0.692 0.166 0.044 98 10.0 lateralorbitofrontal 5408 4577 9273 2.276 0.712 0.158 0.045 84 11.8 lingual 3310 2770 6478 2.545 0.772 0.171 0.050 66 7.5 medialorbitofrontal 7608 6158 15255 2.702 0.795 0.124 0.025 145 8.8 middletemporal 1014 900 2014 2.724 0.801 0.188 0.054 17 2.8 parahippocampal 2612 2083 4322 2.267 0.565 0.123 0.024 25 2.6 paracentral 2902 2384 5517 2.526 0.632 0.147 0.035 38 4.6 parsopercularis 1286 1369 3549 3.069 0.580 0.180 0.037 21 2.2 parsorbitalis 2294 2062 4734 2.502 0.656 0.160 0.038 32 4.0 parstriangularis 1698 1062 1940 1.791 0.413 0.115 0.028 27 1.9 pericalcarine 11414 9004 16528 2.037 0.686 0.123 0.026 121 13.3 postcentral 2400 1967 4370 2.514 0.888 0.173 0.050 74 5.7 posteriorcingulate 10743 7994 18384 2.441 0.681 0.112 0.024 103 11.6 precentral 7360 5459 12927 2.428 0.542 0.133 0.032 126 10.4 precuneus 1262 1116 2686 2.872 0.611 0.176 0.045 21 2.8 rostralanteriorcingulate 12804 10035 22016 2.383 0.609 0.132 0.029 149 17.5 rostralmiddlefrontal 15487 12372 30159 2.678 0.671 0.139 0.034 193 24.7 superiorfrontal 14061 10354 20554 2.146 0.594 0.118 0.024 147 15.4 superiorparietal 9139 7897 20052 2.803 0.700 0.152 0.038 142 16.7 superiortemporal 7723 5918 13877 2.510 0.674 0.128 0.033 104 11.6 supramarginal 545 584 1446 2.966 0.614 0.184 0.037 7 1.1 frontalpole 759 1001 2833 3.689 0.599 0.178 0.032 8 1.1 temporalpole 1059 1000 2101 2.634 0.538 0.176 0.047 15 2.3 transversetemporal 4052 2846 8083 2.950 0.750 0.168 0.052 75 10.0 insula #----------------------------------------- #@# Parcellation Stats rh Mon Dec 19 22:42:41 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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 SynthF rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /usr/local/freesurfer/subjects/SynthF/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthF/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/SynthF/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthF/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 309486 Total vertex volume 306722 (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) = 1180158 mm^3 (det: 1.650715 ) lhCtxGM: 316058.717 315676.000 diff= 382.7 pctdiff= 0.121 rhCtxGM: 304031.649 304306.000 diff= -274.4 pctdiff=-0.090 lhCtxWM: 312652.444 313883.000 diff=-1230.6 pctdiff=-0.394 rhCtxWM: 327003.381 328754.000 diff=-1750.6 pctdiff=-0.535 SubCortGMVol 71273.000 SupraTentVol 1357578.191 (1354505.000) diff=3073.191 pctdiff=0.226 SupraTentVolNotVent 1336967.191 (1333894.000) diff=3073.191 pctdiff=0.230 BrainSegVol 1502470.000 (1499154.000) diff=3316.000 pctdiff=0.221 BrainSegVolNotVent 1477416.000 (1474442.191) diff=2973.809 pctdiff=0.201 BrainSegVolNotVent 1477416.000 CerebellumVol 143421.000 VentChorVol 20611.000 3rd4th5thCSF 4443.000 CSFVol 1127.000, OptChiasmVol 101.000 MaskVol 1849883.000 1780 1238 2907 2.494 0.630 0.115 0.021 15 1.4 bankssts 1264 858 2604 2.631 0.603 0.135 0.020 19 1.1 caudalanteriorcingulate 5216 3655 8302 2.213 0.552 0.127 0.033 56 7.8 caudalmiddlefrontal 2367 1649 3495 1.941 0.605 0.152 0.030 34 2.9 cuneus 474 350 2115 3.893 0.851 0.108 0.028 4 0.5 entorhinal 5069 3520 10060 2.663 0.575 0.128 0.029 65 5.9 fusiform 13591 8908 23534 2.339 0.646 0.114 0.024 145 13.2 inferiorparietal 8635 5884 14815 2.468 0.863 0.146 0.053 127 21.2 inferiortemporal 1219 759 2144 2.444 0.802 0.119 0.039 18 2.0 isthmuscingulate 9047 5928 13891 2.231 0.552 0.141 0.033 107 12.7 lateraloccipital 5248 3656 10046 2.511 0.753 0.149 0.048 97 10.7 lateralorbitofrontal 4897 3381 7938 2.126 0.702 0.142 0.036 65 7.6 lingual 2753 2057 5499 2.353 0.699 0.143 0.032 53 4.0 medialorbitofrontal 7167 5019 13704 2.697 0.832 0.139 0.038 83 12.0 middletemporal 997 642 1815 2.476 0.691 0.096 0.028 9 1.2 parahippocampal 2792 1850 5014 2.474 0.587 0.104 0.016 19 1.9 paracentral 2580 1709 5025 2.592 0.629 0.116 0.026 27 2.7 parsopercularis 1754 1167 4439 3.134 0.738 0.139 0.036 28 2.2 parsorbitalis 3287 2098 6023 2.575 0.602 0.128 0.032 40 4.4 parstriangularis 1818 1248 1935 1.712 0.381 0.109 0.022 16 1.7 pericalcarine 7556 5002 10031 1.853 0.583 0.103 0.020 60 6.2 postcentral 2065 1399 4152 2.773 0.707 0.144 0.031 30 2.7 posteriorcingulate 10368 6774 17650 2.403 0.641 0.108 0.024 100 11.3 precentral 8609 5714 14920 2.461 0.556 0.122 0.022 95 7.8 precuneus 1022 716 1914 2.598 0.668 0.143 0.029 17 1.3 rostralanteriorcingulate 14033 9251 24405 2.416 0.604 0.129 0.031 462 18.8 rostralmiddlefrontal 15726 9987 30608 2.759 0.726 0.123 0.035 217 25.8 superiorfrontal 11899 7491 16595 2.054 0.548 0.111 0.021 108 10.4 superiorparietal 7324 4693 14873 2.870 0.722 0.111 0.028 79 8.9 superiortemporal 8019 5393 13051 2.236 0.629 0.133 0.033 103 11.2 supramarginal 575 362 1660 3.250 0.668 0.154 0.040 12 0.9 frontalpole 770 560 2927 3.869 0.763 0.140 0.037 11 1.5 temporalpole 554 364 1055 2.480 0.671 0.144 0.042 11 0.9 transversetemporal 3672 2495 7552 2.929 0.789 0.116 0.033 44 5.3 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 SynthF rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /usr/local/freesurfer/subjects/SynthF/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthF/surf/rh.pial... reading input pial surface /usr/local/freesurfer/subjects/SynthF/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthF/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 309486 Total vertex volume 306722 (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) = 1180158 mm^3 (det: 1.650715 ) lhCtxGM: 316058.717 315676.000 diff= 382.7 pctdiff= 0.121 rhCtxGM: 304031.649 304306.000 diff= -274.4 pctdiff=-0.090 lhCtxWM: 312652.444 313883.000 diff=-1230.6 pctdiff=-0.394 rhCtxWM: 327003.381 328754.000 diff=-1750.6 pctdiff=-0.535 SubCortGMVol 71273.000 SupraTentVol 1357578.191 (1354505.000) diff=3073.191 pctdiff=0.226 SupraTentVolNotVent 1336967.191 (1333894.000) diff=3073.191 pctdiff=0.230 BrainSegVol 1502470.000 (1499154.000) diff=3316.000 pctdiff=0.221 BrainSegVolNotVent 1477416.000 (1474442.191) diff=2973.809 pctdiff=0.201 BrainSegVolNotVent 1477416.000 CerebellumVol 143421.000 VentChorVol 20611.000 3rd4th5thCSF 4443.000 CSFVol 1127.000, OptChiasmVol 101.000 MaskVol 1849883.000 1780 1105 2907 2.494 0.630 0.131 0.036 25 3.1 bankssts 1264 1131 2604 2.631 0.603 0.195 0.055 48 3.4 caudalanteriorcingulate 5216 3979 8302 2.213 0.552 0.120 0.050 399 9.2 caudalmiddlefrontal 2367 1997 3495 1.941 0.605 0.158 0.035 32 3.8 cuneus 474 705 2115 3.893 0.851 0.185 0.035 3 0.8 entorhinal 5069 3995 10060 2.663 0.575 0.157 0.039 101 9.5 fusiform 13591 10895 23534 2.339 0.646 0.132 0.026 135 16.8 inferiorparietal 8635 6321 14815 2.468 0.863 0.114 0.037 193 15.4 inferiortemporal 1219 956 2144 2.444 0.802 0.150 0.055 39 3.5 isthmuscingulate 9047 6736 13891 2.231 0.552 0.130 0.032 135 13.1 lateraloccipital 5248 4500 10046 2.511 0.753 0.181 0.053 114 13.0 lateralorbitofrontal 4897 4196 7938 2.126 0.702 0.158 0.041 87 10.2 lingual 2753 2720 5499 2.353 0.699 0.187 0.045 45 6.0 medialorbitofrontal 7167 5560 13704 2.697 0.832 0.121 0.032 133 9.8 middletemporal 997 835 1815 2.476 0.691 0.179 0.049 18 2.4 parahippocampal 2792 2190 5014 2.474 0.587 0.127 0.026 31 3.3 paracentral 2580 2120 5025 2.592 0.629 0.159 0.041 44 5.3 parsopercularis 1754 1673 4439 3.134 0.738 0.176 0.037 42 3.2 parsorbitalis 3287 2600 6023 2.575 0.602 0.141 0.036 42 5.6 parstriangularis 1818 1121 1935 1.712 0.381 0.114 0.032 37 2.2 pericalcarine 7556 5955 10031 1.853 0.583 0.120 0.024 65 8.4 postcentral 2065 1582 4152 2.773 0.707 0.156 0.044 51 4.2 posteriorcingulate 10368 7783 17650 2.403 0.641 0.114 0.024 114 11.5 precentral 8609 6412 14920 2.461 0.556 0.136 0.030 145 11.8 precuneus 1022 818 1914 2.598 0.668 0.170 0.046 19 2.3 rostralanteriorcingulate 14033 11292 24405 2.416 0.604 0.142 0.033 213 22.0 rostralmiddlefrontal 15726 12030 30608 2.759 0.726 0.134 0.036 240 25.6 superiorfrontal 11899 8775 16595 2.054 0.548 0.118 0.022 113 11.5 superiorparietal 7324 5801 14873 2.870 0.722 0.145 0.036 103 12.6 superiortemporal 8019 6368 13051 2.236 0.629 0.148 0.039 131 15.0 supramarginal 575 632 1660 3.250 0.668 0.192 0.038 8 1.2 frontalpole 770 951 2927 3.869 0.763 0.183 0.037 12 1.4 temporalpole 554 507 1055 2.480 0.671 0.190 0.059 8 1.5 transversetemporal 3672 2555 7552 2.929 0.789 0.162 0.054 87 9.3 insula #----------------------------------------- #@# Cortical Parc 2 lh Mon Dec 19 22:43:41 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 SynthF 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... 45 labels changed using aseg relabeling using gibbs priors... 000: 11490 changed, 187767 examined... 001: 2767 changed, 44678 examined... 002: 817 changed, 14309 examined... 003: 378 changed, 4689 examined... 004: 180 changed, 2124 examined... 005: 77 changed, 1037 examined... 006: 52 changed, 443 examined... 007: 20 changed, 302 examined... 008: 10 changed, 115 examined... 009: 9 changed, 68 examined... 010: 7 changed, 50 examined... 011: 3 changed, 39 examined... 012: 2 changed, 15 examined... 013: 1 changed, 14 examined... 014: 0 changed, 7 examined... 2 labels changed using aseg 000: 309 total segments, 222 labels (3110 vertices) changed 001: 103 total segments, 17 labels (85 vertices) changed 002: 87 total segments, 1 labels (3 vertices) changed 003: 86 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 55 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1649 vertices marked for relabeling... 1649 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 19 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Mon Dec 19 22:44:00 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 SynthF 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... 60 labels changed using aseg relabeling using gibbs priors... 000: 12037 changed, 182051 examined... 001: 2760 changed, 46992 examined... 002: 795 changed, 14494 examined... 003: 335 changed, 4464 examined... 004: 172 changed, 1920 examined... 005: 96 changed, 941 examined... 006: 53 changed, 531 examined... 007: 28 changed, 302 examined... 008: 13 changed, 150 examined... 009: 8 changed, 72 examined... 010: 4 changed, 36 examined... 011: 4 changed, 28 examined... 012: 5 changed, 28 examined... 013: 5 changed, 22 examined... 014: 2 changed, 25 examined... 015: 1 changed, 14 examined... 016: 0 changed, 8 examined... 24 labels changed using aseg 000: 342 total segments, 248 labels (4644 vertices) changed 001: 113 total segments, 21 labels (132 vertices) changed 002: 92 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 51 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1691 vertices marked for relabeling... 1691 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 18 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Mon Dec 19 22:44:18 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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 SynthF lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /usr/local/freesurfer/subjects/SynthF/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthF/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/SynthF/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthF/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 321558 Total vertex volume 318104 (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) = 1180158 mm^3 (det: 1.650715 ) lhCtxGM: 316058.717 315676.000 diff= 382.7 pctdiff= 0.121 rhCtxGM: 304031.649 304306.000 diff= -274.4 pctdiff=-0.090 lhCtxWM: 312652.444 313883.000 diff=-1230.6 pctdiff=-0.394 rhCtxWM: 327003.381 328754.000 diff=-1750.6 pctdiff=-0.535 SubCortGMVol 71273.000 SupraTentVol 1357578.191 (1354505.000) diff=3073.191 pctdiff=0.226 SupraTentVolNotVent 1336967.191 (1333894.000) diff=3073.191 pctdiff=0.230 BrainSegVol 1502470.000 (1499154.000) diff=3316.000 pctdiff=0.221 BrainSegVolNotVent 1477416.000 (1474442.191) diff=2973.809 pctdiff=0.201 BrainSegVolNotVent 1477416.000 CerebellumVol 143421.000 VentChorVol 20611.000 3rd4th5thCSF 4443.000 CSFVol 1127.000, OptChiasmVol 101.000 MaskVol 1849883.000 1851 1234 3052 2.446 0.519 0.119 0.024 18 1.8 G&S_frontomargin 2456 1559 4438 2.493 0.665 0.129 0.029 32 3.1 G&S_occipital_inf 2510 1541 3826 2.079 0.554 0.098 0.017 16 1.9 G&S_paracentral 1848 1223 3654 2.530 0.640 0.141 0.034 29 2.4 G&S_subcentral 1179 757 2580 2.738 0.602 0.160 0.053 21 2.9 G&S_transv_frontopol 2674 1876 5397 2.741 0.556 0.121 0.025 26 2.7 G&S_cingul-Ant 1802 1213 3604 2.856 0.676 0.120 0.022 23 1.5 G&S_cingul-Mid-Ant 1995 1382 3639 2.600 0.648 0.133 0.029 23 2.4 G&S_cingul-Mid-Post 951 628 2665 3.270 0.650 0.165 0.040 21 1.5 G_cingul-Post-dorsal 444 276 836 2.635 0.932 0.123 0.043 7 0.7 G_cingul-Post-ventral 2297 1578 3820 2.106 0.623 0.172 0.040 40 4.1 G_cuneus 1669 1152 4288 2.797 0.586 0.128 0.022 26 1.6 G_front_inf-Opercular 499 329 1556 3.053 0.457 0.154 0.030 10 0.6 G_front_inf-Orbital 1129 785 3232 2.847 0.632 0.130 0.022 18 1.1 G_front_inf-Triangul 7939 4915 14447 2.401 0.698 0.139 0.039 109 14.3 G_front_middle 10799 6976 23444 2.758 0.714 0.131 0.036 145 16.9 G_front_sup 753 497 1617 2.975 0.827 0.135 0.036 10 1.1 G_Ins_lg&S_cent_ins 817 562 2341 3.248 0.709 0.131 0.036 13 1.3 G_insular_short 4058 2267 6726 2.449 0.618 0.124 0.032 54 5.2 G_occipital_middle 1919 1178 2708 1.942 0.666 0.141 0.039 30 3.3 G_occipital_sup 2402 1757 5669 2.660 0.594 0.151 0.034 42 3.8 G_oc-temp_lat-fusifor 3764 2542 6878 2.266 0.767 0.159 0.040 59 6.6 G_oc-temp_med-Lingual 1317 903 3480 3.010 0.800 0.088 0.019 7 1.0 G_oc-temp_med-Parahip 3089 2120 8841 3.146 0.619 0.153 0.038 60 4.7 G_orbital 3913 2352 6534 2.434 0.680 0.132 0.039 53 7.2 G_pariet_inf-Angular 3748 2490 7795 2.623 0.681 0.135 0.039 60 6.4 G_pariet_inf-Supramar 5431 3131 9061 2.325 0.653 0.109 0.027 51 5.9 G_parietal_sup 5028 3047 7751 2.150 0.720 0.112 0.027 48 5.8 G_postcentral 4335 2522 8451 2.649 0.760 0.104 0.032 37 6.1 G_precentral 3676 2443 7844 2.571 0.564 0.138 0.032 50 4.8 G_precuneus 955 685 2313 2.589 0.826 0.171 0.056 24 2.4 G_rectus 1002 631 1741 2.719 0.972 0.102 0.049 11 1.2 G_subcallosal 964 635 2187 2.681 0.569 0.126 0.032 17 1.2 G_temp_sup-G_T_transv 3393 2209 8816 2.947 0.705 0.131 0.032 55 4.6 G_temp_sup-Lateral 1098 751 3171 3.402 0.588 0.085 0.015 5 0.7 G_temp_sup-Plan_polar 1377 958 2380 2.475 0.483 0.100 0.020 10 1.3 G_temp_sup-Plan_tempo 3577 2443 8301 2.741 0.824 0.145 0.044 60 7.3 G_temporal_inf 4231 2606 8374 2.563 0.844 0.146 0.052 65 10.1 G_temporal_middle 467 321 693 2.376 0.519 0.095 0.014 2 0.3 Lat_Fis-ant-Horizont 483 343 737 2.639 0.664 0.068 0.009 1 0.1 Lat_Fis-ant-Vertical 1508 1024 2205 2.656 0.539 0.123 0.020 15 1.3 Lat_Fis-post 2341 1512 2896 1.854 0.552 0.139 0.032 32 3.2 Pole_occipital 2055 1395 6211 3.251 0.714 0.127 0.038 27 3.2 Pole_temporal 2491 1706 3134 2.095 0.563 0.122 0.024 27 2.5 S_calcarine 4164 2856 4854 1.821 0.590 0.084 0.012 17 2.1 S_central 1090 741 1534 2.381 0.446 0.089 0.013 4 0.6 S_cingul-Marginalis 718 506 1327 2.966 0.888 0.077 0.011 2 0.3 S_circular_insula_ant 1860 1247 2942 2.607 0.730 0.087 0.013 7 1.0 S_circular_insula_inf 1791 1208 2664 2.658 0.567 0.104 0.017 9 1.3 S_circular_insula_sup 1375 991 1954 2.012 0.597 0.117 0.023 15 1.7 S_collat_transv_ant 696 458 652 1.685 0.358 0.115 0.013 6 0.4 S_collat_transv_post 3102 2154 4625 2.122 0.569 0.102 0.015 22 1.8 S_front_inf 2011 1402 2766 2.159 0.452 0.112 0.019 16 1.2 S_front_middle 4332 2915 6637 2.375 0.484 0.098 0.019 27 3.0 S_front_sup 142 82 237 2.696 0.387 0.080 0.015 0 0.1 S_interm_prim-Jensen 4766 3305 6059 2.020 0.432 0.104 0.014 32 2.7 S_intrapariet&P_trans 1415 927 1591 2.038 0.513 0.111 0.022 12 1.2 S_oc_middle&Lunatus 1966 1301 2239 1.877 0.397 0.102 0.015 14 1.1 S_oc_sup&transversal 1007 688 1181 1.955 0.402 0.095 0.016 5 0.6 S_occipital_ant 1384 968 2156 2.377 0.504 0.124 0.021 12 1.3 S_oc-temp_lat 2546 1840 3854 2.225 0.575 0.111 0.019 19 1.9 S_oc-temp_med&Lingual 438 318 612 2.262 0.410 0.119 0.015 3 0.3 S_orbital_lateral 556 453 1155 2.768 0.812 0.147 0.027 6 0.6 S_orbital_med-olfact 1652 1182 3080 2.681 0.559 0.133 0.031 19 1.9 S_orbital-H_Shaped 2650 1786 3679 2.287 0.525 0.119 0.020 24 2.2 S_parieto_occipital 1654 1010 1567 2.062 0.959 0.123 0.016 26 1.0 S_pericallosal 6437 4304 8485 2.080 0.584 0.114 0.021 51 5.8 S_postcentral 2904 1971 3870 2.198 0.426 0.105 0.015 22 1.7 S_precentral-inf-part 1757 1216 2256 2.110 0.463 0.092 0.012 9 1.0 S_precentral-sup-part 746 533 1191 2.541 0.580 0.121 0.020 6 0.7 S_suborbital 1687 1196 2647 2.376 0.515 0.121 0.022 13 1.5 S_subparietal 2432 1673 3332 2.304 0.470 0.101 0.014 14 1.3 S_temporal_inf 8477 5801 14754 2.526 0.709 0.105 0.019 61 6.5 S_temporal_sup 655 429 873 2.381 0.490 0.112 0.022 4 0.6 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Mon Dec 19 22:44:51 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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 SynthF rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /usr/local/freesurfer/subjects/SynthF/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthF/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/SynthF/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthF/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 309486 Total vertex volume 306722 (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) = 1180158 mm^3 (det: 1.650715 ) lhCtxGM: 316058.717 315676.000 diff= 382.7 pctdiff= 0.121 rhCtxGM: 304031.649 304306.000 diff= -274.4 pctdiff=-0.090 lhCtxWM: 312652.444 313883.000 diff=-1230.6 pctdiff=-0.394 rhCtxWM: 327003.381 328754.000 diff=-1750.6 pctdiff=-0.535 SubCortGMVol 71273.000 SupraTentVol 1357578.191 (1354505.000) diff=3073.191 pctdiff=0.226 SupraTentVolNotVent 1336967.191 (1333894.000) diff=3073.191 pctdiff=0.230 BrainSegVol 1502470.000 (1499154.000) diff=3316.000 pctdiff=0.221 BrainSegVolNotVent 1477416.000 (1474442.191) diff=2973.809 pctdiff=0.201 BrainSegVolNotVent 1477416.000 CerebellumVol 143421.000 VentChorVol 20611.000 3rd4th5thCSF 4443.000 CSFVol 1127.000, OptChiasmVol 101.000 MaskVol 1849883.000 1389 967 2747 2.472 0.712 0.142 0.031 19 2.1 G&S_frontomargin 1557 1067 2574 2.348 0.550 0.153 0.045 20 2.9 G&S_occipital_inf 1791 1097 2978 2.256 0.607 0.109 0.021 14 1.5 G&S_paracentral 1701 1152 3407 2.491 0.659 0.128 0.030 20 2.0 G&S_subcentral 1673 973 3101 2.699 0.653 0.135 0.046 33 3.7 G&S_transv_frontopol 3646 2592 6911 2.577 0.646 0.130 0.027 49 4.2 G&S_cingul-Ant 1674 1198 3540 2.802 0.452 0.116 0.022 17 1.5 G&S_cingul-Mid-Ant 1902 1334 3617 2.732 0.572 0.125 0.023 18 1.8 G&S_cingul-Mid-Post 564 380 1714 3.190 0.648 0.152 0.033 9 0.8 G_cingul-Post-dorsal 369 205 627 2.395 0.865 0.102 0.064 5 1.0 G_cingul-Post-ventral 2164 1507 3303 1.904 0.621 0.157 0.032 35 2.9 G_cuneus 1783 1172 4568 2.804 0.662 0.128 0.031 26 2.2 G_front_inf-Opercular 615 401 1651 3.033 0.604 0.158 0.043 13 1.0 G_front_inf-Orbital 1439 819 2797 2.637 0.596 0.128 0.041 22 2.5 G_front_inf-Triangul 7011 4590 13214 2.408 0.634 0.138 0.041 96 12.9 G_front_middle 10722 6529 23047 2.871 0.767 0.127 0.039 175 19.7 G_front_sup 856 581 1868 3.150 0.820 0.141 0.061 19 2.1 G_Ins_lg&S_cent_ins 1266 858 2996 3.114 1.034 0.165 0.074 37 4.4 G_insular_short 3894 2417 7889 2.623 0.538 0.141 0.037 59 5.8 G_occipital_middle 2415 1541 3860 2.135 0.549 0.141 0.029 32 2.9 G_occipital_sup 1805 1229 3914 2.638 0.620 0.130 0.033 28 2.5 G_oc-temp_lat-fusifor 3169 2151 5291 2.010 0.703 0.146 0.044 48 6.3 G_oc-temp_med-Lingual 1045 716 3367 3.196 0.999 0.112 0.030 11 1.2 G_oc-temp_med-Parahip 3663 2443 9114 2.833 0.799 0.148 0.045 63 6.7 G_orbital 5205 3188 10268 2.481 0.721 0.126 0.032 76 6.7 G_pariet_inf-Angular 4286 2892 7945 2.354 0.628 0.149 0.041 69 8.0 G_pariet_inf-Supramar 4426 2533 6912 2.227 0.583 0.112 0.024 45 4.6 G_parietal_sup 2599 1666 3795 1.877 0.509 0.117 0.027 26 2.9 G_postcentral 4187 2594 8183 2.544 0.737 0.122 0.037 61 7.1 G_precentral 4096 2616 8408 2.553 0.601 0.134 0.026 58 4.1 G_precuneus 707 545 1997 2.527 0.726 0.173 0.046 22 1.5 G_rectus 623 407 1014 2.300 0.981 0.142 0.063 15 1.4 G_subcallosal 501 316 996 2.561 0.708 0.146 0.042 10 0.9 G_temp_sup-G_T_transv 2520 1532 5803 2.840 0.849 0.143 0.049 50 5.7 G_temp_sup-Lateral 1130 779 3008 3.497 0.684 0.095 0.019 6 0.9 G_temp_sup-Plan_polar 1065 705 2181 2.795 0.696 0.102 0.020 9 0.7 G_temp_sup-Plan_tempo 5581 3651 9208 2.410 0.895 0.144 0.055 88 15.0 G_temporal_inf 4729 3188 9555 2.678 0.901 0.142 0.038 61 7.7 G_temporal_middle 368 275 598 2.464 0.503 0.122 0.016 2 0.3 Lat_Fis-ant-Horizont 565 389 749 2.370 0.478 0.133 0.030 5 0.8 Lat_Fis-ant-Vertical 1538 1055 1982 2.261 0.660 0.107 0.019 10 1.2 Lat_Fis-post 3450 2230 5031 2.049 0.538 0.139 0.032 41 4.4 Pole_occipital 2109 1515 6493 3.273 0.841 0.151 0.050 35 4.4 Pole_temporal 2048 1452 2488 2.026 0.579 0.116 0.023 21 1.9 S_calcarine 3740 2556 4166 1.852 0.579 0.083 0.012 15 1.8 S_central 1613 1133 2464 2.357 0.610 0.098 0.015 10 1.1 S_cingul-Marginalis 725 498 1151 2.887 0.473 0.092 0.016 3 0.5 S_circular_insula_ant 1373 906 2070 2.613 0.573 0.078 0.009 4 0.6 S_circular_insula_inf 1423 982 2257 2.471 0.577 0.096 0.017 5 1.0 S_circular_insula_sup 1174 849 2255 2.833 0.779 0.122 0.030 11 1.5 S_collat_transv_ant 609 404 933 2.373 0.629 0.121 0.024 4 0.6 S_collat_transv_post 2938 2103 4463 2.335 0.530 0.137 0.029 335 3.8 S_front_inf 4078 2770 6548 2.324 0.617 0.121 0.026 36 4.1 S_front_middle 4292 2884 6292 2.311 0.468 0.100 0.019 24 3.2 S_front_sup 889 593 1156 2.242 0.494 0.101 0.018 4 0.7 S_interm_prim-Jensen 4633 3132 5331 1.891 0.383 0.110 0.017 39 3.4 S_intrapariet&P_trans 1226 854 1640 2.209 0.485 0.126 0.024 10 1.2 S_oc_middle&Lunatus 1838 1288 2176 1.819 0.415 0.105 0.019 11 1.3 S_oc_sup&transversal 855 618 1448 2.435 0.533 0.145 0.031 9 1.1 S_occipital_ant 1501 1105 2866 2.682 0.595 0.141 0.034 16 2.0 S_oc-temp_lat 2562 1744 3741 2.402 0.522 0.116 0.020 24 2.0 S_oc-temp_med&Lingual 566 411 864 2.403 0.349 0.111 0.015 4 0.4 S_orbital_lateral 631 480 1113 2.049 0.827 0.125 0.026 7 0.7 S_orbital_med-olfact 1748 1240 3152 2.454 0.560 0.138 0.026 25 2.0 S_orbital-H_Shaped 2953 1970 4011 2.288 0.498 0.105 0.016 22 2.1 S_parieto_occipital 1405 823 1264 2.106 0.696 0.138 0.022 25 1.2 S_pericallosal 3316 2192 3509 1.799 0.449 0.099 0.015 23 2.0 S_postcentral 2447 1678 3446 2.235 0.466 0.100 0.015 15 1.5 S_precentral-inf-part 1890 1318 2491 2.266 0.462 0.104 0.015 10 1.6 S_precentral-sup-part 425 331 702 2.451 0.624 0.150 0.023 9 0.5 S_suborbital 1712 1237 2787 2.431 0.508 0.121 0.019 14 1.5 S_subparietal 1491 1130 2059 2.277 0.669 0.167 0.064 22 4.4 S_temporal_inf 9918 6888 15154 2.399 0.623 0.101 0.017 62 6.9 S_temporal_sup 346 227 504 2.523 0.708 0.115 0.011 3 0.2 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Mon Dec 19 22:45:23 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 SynthF 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... 1662 labels changed using aseg relabeling using gibbs priors... 000: 2447 changed, 187767 examined... 001: 547 changed, 11381 examined... 002: 140 changed, 3075 examined... 003: 58 changed, 849 examined... 004: 29 changed, 327 examined... 005: 19 changed, 163 examined... 006: 15 changed, 109 examined... 007: 6 changed, 83 examined... 008: 5 changed, 35 examined... 009: 5 changed, 33 examined... 010: 3 changed, 26 examined... 011: 3 changed, 18 examined... 012: 2 changed, 17 examined... 013: 2 changed, 15 examined... 014: 2 changed, 14 examined... 015: 2 changed, 14 examined... 016: 1 changed, 14 examined... 017: 1 changed, 7 examined... 018: 1 changed, 7 examined... 019: 1 changed, 6 examined... 020: 2 changed, 9 examined... 021: 3 changed, 11 examined... 022: 1 changed, 18 examined... 023: 1 changed, 7 examined... 024: 1 changed, 7 examined... 025: 1 changed, 6 examined... 026: 3 changed, 7 examined... 027: 1 changed, 12 examined... 028: 1 changed, 8 examined... 029: 0 changed, 7 examined... 216 labels changed using aseg 000: 58 total segments, 25 labels (277 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 4 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1175 vertices marked for relabeling... 1175 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 15 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Mon Dec 19 22:45:38 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 SynthF 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... 1818 labels changed using aseg relabeling using gibbs priors... 000: 2416 changed, 182051 examined... 001: 547 changed, 11197 examined... 002: 154 changed, 3067 examined... 003: 70 changed, 905 examined... 004: 42 changed, 396 examined... 005: 28 changed, 234 examined... 006: 22 changed, 147 examined... 007: 17 changed, 111 examined... 008: 15 changed, 79 examined... 009: 9 changed, 71 examined... 010: 10 changed, 45 examined... 011: 8 changed, 48 examined... 012: 5 changed, 38 examined... 013: 2 changed, 26 examined... 014: 2 changed, 18 examined... 015: 4 changed, 16 examined... 016: 4 changed, 17 examined... 017: 2 changed, 26 examined... 018: 1 changed, 13 examined... 019: 0 changed, 7 examined... 384 labels changed using aseg 000: 60 total segments, 27 labels (629 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1072 vertices marked for relabeling... 1072 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 14 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Mon Dec 19 22:45:53 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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 SynthF lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /usr/local/freesurfer/subjects/SynthF/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthF/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/SynthF/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthF/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 321558 Total vertex volume 318104 (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) = 1180158 mm^3 (det: 1.650715 ) lhCtxGM: 316058.717 315676.000 diff= 382.7 pctdiff= 0.121 rhCtxGM: 304031.649 304306.000 diff= -274.4 pctdiff=-0.090 lhCtxWM: 312652.444 313883.000 diff=-1230.6 pctdiff=-0.394 rhCtxWM: 327003.381 328754.000 diff=-1750.6 pctdiff=-0.535 SubCortGMVol 71273.000 SupraTentVol 1357578.191 (1354505.000) diff=3073.191 pctdiff=0.226 SupraTentVolNotVent 1336967.191 (1333894.000) diff=3073.191 pctdiff=0.230 BrainSegVol 1502470.000 (1499154.000) diff=3316.000 pctdiff=0.221 BrainSegVolNotVent 1477416.000 (1474442.191) diff=2973.809 pctdiff=0.201 BrainSegVolNotVent 1477416.000 CerebellumVol 143421.000 VentChorVol 20611.000 3rd4th5thCSF 4443.000 CSFVol 1127.000, OptChiasmVol 101.000 MaskVol 1849883.000 2217 1445 4442 2.983 0.594 0.132 0.026 33 2.2 caudalanteriorcingulate 5728 3767 8548 2.186 0.605 0.117 0.029 60 7.8 caudalmiddlefrontal 3383 2278 5168 2.169 0.594 0.153 0.035 48 5.2 cuneus 572 425 1763 2.989 0.939 0.078 0.015 2 0.3 entorhinal 5430 3942 9946 2.315 0.638 0.137 0.027 72 6.9 fusiform 10896 6774 16347 2.340 0.626 0.117 0.029 115 13.6 inferiorparietal 6925 4753 14356 2.621 0.754 0.130 0.036 93 11.1 inferiortemporal 2098 1330 3920 2.627 0.899 0.121 0.027 28 2.2 isthmuscingulate 10345 6467 14692 2.110 0.647 0.129 0.028 131 12.4 lateraloccipital 5286 3696 12242 2.913 0.705 0.144 0.037 82 8.0 lateralorbitofrontal 5460 3745 9398 2.279 0.708 0.143 0.033 70 7.9 lingual 2488 1800 5268 2.595 0.741 0.145 0.042 47 3.8 medialorbitofrontal 9465 6173 17868 2.614 0.780 0.121 0.033 98 13.6 middletemporal 1026 652 2082 2.733 0.796 0.079 0.013 6 0.3 parahippocampal 3274 2146 5783 2.354 0.611 0.100 0.016 20 2.2 paracentral 2784 1885 5165 2.530 0.642 0.112 0.018 29 2.0 parsopercularis 1247 869 3000 2.825 0.602 0.126 0.025 14 1.3 parsorbitalis 2695 1868 5591 2.473 0.664 0.113 0.018 27 2.0 parstriangularis 1726 1172 1972 1.788 0.411 0.128 0.024 19 1.6 pericalcarine 12824 8166 18284 2.038 0.663 0.110 0.023 114 12.1 postcentral 2565 1738 4643 2.513 0.876 0.140 0.031 40 3.2 posteriorcingulate 10462 6738 18121 2.470 0.680 0.103 0.023 81 10.6 precentral 7383 5034 13051 2.421 0.555 0.127 0.027 84 8.1 precuneus 2071 1396 3942 2.720 0.676 0.127 0.030 27 2.0 rostralanteriorcingulate 9424 6148 16470 2.363 0.618 0.124 0.027 102 10.5 rostralmiddlefrontal 16913 11026 32728 2.649 0.683 0.123 0.032 187 23.2 superiorfrontal 11322 7093 16463 2.142 0.579 0.105 0.020 88 9.6 superiorparietal 11183 7561 24930 2.817 0.743 0.115 0.024 123 11.4 superiortemporal 7138 4872 13056 2.540 0.674 0.129 0.031 86 9.7 supramarginal 1056 699 2093 2.629 0.543 0.120 0.027 12 1.1 transversetemporal 3258 2250 6768 2.939 0.765 0.107 0.023 28 3.1 insula #----------------------------------------- #@# Parcellation Stats 3 rh Mon Dec 19 22:46:23 GMT 2016 /usr/local/freesurfer/subjects/SynthF/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 SynthF rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /usr/local/freesurfer/subjects/SynthF/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthF/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/SynthF/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthF/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 309486 Total vertex volume 306722 (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) = 1180158 mm^3 (det: 1.650715 ) lhCtxGM: 316058.717 315676.000 diff= 382.7 pctdiff= 0.121 rhCtxGM: 304031.649 304306.000 diff= -274.4 pctdiff=-0.090 lhCtxWM: 312652.444 313883.000 diff=-1230.6 pctdiff=-0.394 rhCtxWM: 327003.381 328754.000 diff=-1750.6 pctdiff=-0.535 SubCortGMVol 71273.000 SupraTentVol 1357578.191 (1354505.000) diff=3073.191 pctdiff=0.226 SupraTentVolNotVent 1336967.191 (1333894.000) diff=3073.191 pctdiff=0.230 BrainSegVol 1502470.000 (1499154.000) diff=3316.000 pctdiff=0.221 BrainSegVolNotVent 1477416.000 (1474442.191) diff=2973.809 pctdiff=0.201 BrainSegVolNotVent 1477416.000 CerebellumVol 143421.000 VentChorVol 20611.000 3rd4th5thCSF 4443.000 CSFVol 1127.000, OptChiasmVol 101.000 MaskVol 1849883.000 1382 942 2799 2.627 0.594 0.134 0.020 20 1.2 caudalanteriorcingulate 5350 3771 8511 2.232 0.543 0.130 0.033 59 8.0 caudalmiddlefrontal 3172 2141 4685 2.016 0.596 0.141 0.026 42 3.5 cuneus 413 303 1906 3.940 0.845 0.114 0.030 4 0.5 entorhinal 4555 3167 8589 2.628 0.544 0.122 0.026 52 4.8 fusiform 13433 8826 23412 2.335 0.652 0.114 0.024 144 13.0 inferiorparietal 8998 6132 16051 2.510 0.865 0.146 0.053 135 22.0 inferiortemporal 1263 780 2190 2.451 0.805 0.116 0.039 18 2.0 isthmuscingulate 9261 6065 14272 2.228 0.557 0.141 0.034 111 13.0 lateraloccipital 5531 3836 11003 2.516 0.773 0.150 0.046 110 11.3 lateralorbitofrontal 4873 3354 7936 2.123 0.698 0.142 0.035 67 7.4 lingual 2319 1722 4882 2.389 0.807 0.155 0.045 58 4.5 medialorbitofrontal 8765 6135 16438 2.682 0.794 0.134 0.035 94 13.3 middletemporal 1043 680 1945 2.502 0.698 0.103 0.032 10 1.6 parahippocampal 3019 1990 5348 2.456 0.584 0.103 0.016 21 2.0 paracentral 2992 1955 5569 2.527 0.624 0.121 0.030 34 3.6 parsopercularis 1464 979 3582 2.977 0.792 0.136 0.036 20 2.4 parsorbitalis 3182 2048 5646 2.591 0.605 0.124 0.028 35 3.8 parstriangularis 1724 1196 1853 1.715 0.372 0.106 0.018 13 1.2 pericalcarine 8295 5487 11152 1.865 0.589 0.102 0.020 64 6.8 postcentral 2108 1436 4196 2.779 0.716 0.145 0.031 31 2.7 posteriorcingulate 9776 6385 16997 2.415 0.644 0.107 0.024 91 10.8 precentral 8634 5779 15016 2.440 0.582 0.124 0.023 97 8.3 precuneus 1402 980 2638 2.544 0.677 0.140 0.030 23 1.7 rostralanteriorcingulate 10337 6793 17878 2.433 0.624 0.127 0.031 415 13.6 rostralmiddlefrontal 20047 12821 38689 2.714 0.713 0.125 0.034 272 31.2 superiorfrontal 10151 6328 13929 2.044 0.530 0.109 0.021 93 8.7 superiorparietal 9335 6107 19764 2.870 0.809 0.117 0.030 105 12.3 superiortemporal 7521 5041 11959 2.240 0.622 0.132 0.032 97 10.3 supramarginal 551 361 1056 2.532 0.695 0.146 0.042 11 0.9 transversetemporal 3267 2257 6830 2.943 0.753 0.113 0.028 31 3.8 insula #----------------------------------------- #@# WM/GM Contrast lh Mon Dec 19 22:46:55 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts pctsurfcon --s SynthF --lh-only Log file is /usr/local/freesurfer/subjects/SynthF/scripts/pctsurfcon.log Mon Dec 19 22:46:55 GMT 2016 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/SynthF/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/SynthF/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /usr/local/freesurfer/subjects/SynthF/surf/tmp.pctsurfcon.8561/lh.wm.mgh --regheader SynthF --cortex srcvol = /usr/local/freesurfer/subjects/SynthF/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/SynthF/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/SynthF/label/lh.cortex.label Reading surface /usr/local/freesurfer/subjects/SynthF/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 = 102503 Masking with /usr/local/freesurfer/subjects/SynthF/label/lh.cortex.label Writing to /usr/local/freesurfer/subjects/SynthF/surf/tmp.pctsurfcon.8561/lh.wm.mgh Dim: 187767 1 1 mri_vol2surf --mov /usr/local/freesurfer/subjects/SynthF/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /usr/local/freesurfer/subjects/SynthF/surf/tmp.pctsurfcon.8561/lh.gm.mgh --projfrac 0.3 --regheader SynthF --cortex srcvol = /usr/local/freesurfer/subjects/SynthF/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/SynthF/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/SynthF/label/lh.cortex.label Reading surface /usr/local/freesurfer/subjects/SynthF/surf/lh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/SynthF/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 = 122741 Masking with /usr/local/freesurfer/subjects/SynthF/label/lh.cortex.label Writing to /usr/local/freesurfer/subjects/SynthF/surf/tmp.pctsurfcon.8561/lh.gm.mgh Dim: 187767 1 1 mri_concat /usr/local/freesurfer/subjects/SynthF/surf/tmp.pctsurfcon.8561/lh.wm.mgh /usr/local/freesurfer/subjects/SynthF/surf/tmp.pctsurfcon.8561/lh.gm.mgh --paired-diff-norm --mul 100 --o /usr/local/freesurfer/subjects/SynthF/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/SynthF/surf/lh.w-g.pct.mgh mri_segstats --in /usr/local/freesurfer/subjects/SynthF/surf/lh.w-g.pct.mgh --annot SynthF lh aparc --sum /usr/local/freesurfer/subjects/SynthF/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/SynthF/surf/lh.w-g.pct.mgh --annot SynthF lh aparc --sum /usr/local/freesurfer/subjects/SynthF/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/SynthF/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/SynthF/surf/lh.w-g.pct.mgh Vertex Area is 0.659341 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 22:47:00 GMT 2016 /usr/local/freesurfer/subjects/SynthF/scripts pctsurfcon --s SynthF --rh-only Log file is /usr/local/freesurfer/subjects/SynthF/scripts/pctsurfcon.log Mon Dec 19 22:47:00 GMT 2016 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/SynthF/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/SynthF/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /usr/local/freesurfer/subjects/SynthF/surf/tmp.pctsurfcon.8635/rh.wm.mgh --regheader SynthF --cortex srcvol = /usr/local/freesurfer/subjects/SynthF/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/SynthF/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/SynthF/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/SynthF/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 = 99751 Masking with /usr/local/freesurfer/subjects/SynthF/label/rh.cortex.label Writing to /usr/local/freesurfer/subjects/SynthF/surf/tmp.pctsurfcon.8635/rh.wm.mgh Dim: 182051 1 1 mri_vol2surf --mov /usr/local/freesurfer/subjects/SynthF/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /usr/local/freesurfer/subjects/SynthF/surf/tmp.pctsurfcon.8635/rh.gm.mgh --projfrac 0.3 --regheader SynthF --cortex srcvol = /usr/local/freesurfer/subjects/SynthF/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/SynthF/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/SynthF/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/SynthF/surf/rh.white Done reading source surface Reading thickness /usr/local/freesurfer/subjects/SynthF/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 = 118791 Masking with /usr/local/freesurfer/subjects/SynthF/label/rh.cortex.label Writing to /usr/local/freesurfer/subjects/SynthF/surf/tmp.pctsurfcon.8635/rh.gm.mgh Dim: 182051 1 1 mri_concat /usr/local/freesurfer/subjects/SynthF/surf/tmp.pctsurfcon.8635/rh.wm.mgh /usr/local/freesurfer/subjects/SynthF/surf/tmp.pctsurfcon.8635/rh.gm.mgh --paired-diff-norm --mul 100 --o /usr/local/freesurfer/subjects/SynthF/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/SynthF/surf/rh.w-g.pct.mgh mri_segstats --in /usr/local/freesurfer/subjects/SynthF/surf/rh.w-g.pct.mgh --annot SynthF rh aparc --sum /usr/local/freesurfer/subjects/SynthF/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/SynthF/surf/rh.w-g.pct.mgh --annot SynthF rh aparc --sum /usr/local/freesurfer/subjects/SynthF/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/SynthF/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/SynthF/surf/rh.w-g.pct.mgh Vertex Area is 0.664864 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 22:47:06 GMT 2016 /usr/local/freesurfer/subjects/SynthF/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 2144 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 23488 voxels changed to hypointensity... 21234 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Mon Dec 19 22:47:27 GMT 2016 /usr/local/freesurfer/subjects/SynthF mri_aparc2aseg --s SynthF --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 SynthF outvol /usr/local/freesurfer/subjects/SynthF/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /usr/local/freesurfer/subjects/SynthF/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/SynthF/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/SynthF/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/SynthF/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/SynthF/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/SynthF/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/SynthF/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/SynthF/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 --> 102 rescaling Left_Cerebral_Cortex from 61 --> 63 rescaling Left_Lateral_Ventricle from 13 --> 12 rescaling Left_Inf_Lat_Vent from 34 --> 32 rescaling Left_Cerebellum_White_Matter from 86 --> 85 rescaling Left_Cerebellum_Cortex from 60 --> 75 rescaling Left_Thalamus from 94 --> 98 rescaling Left_Thalamus_Proper from 84 --> 95 rescaling Left_Caudate from 75 --> 68 rescaling Left_Putamen from 80 --> 79 rescaling Left_Pallidum from 98 --> 97 rescaling Third_Ventricle from 25 --> 14 rescaling Fourth_Ventricle from 22 --> 8 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 56 rescaling Left_Amygdala from 56 --> 65 rescaling CSF from 32 --> 21 rescaling Left_Accumbens_area from 62 --> 61 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 99 rescaling Right_Cerebral_Cortex from 58 --> 84 rescaling Right_Lateral_Ventricle from 13 --> 8 rescaling Right_Inf_Lat_Vent from 25 --> 23 rescaling Right_Cerebellum_White_Matter from 87 --> 85 rescaling Right_Cerebellum_Cortex from 59 --> 78 rescaling Right_Thalamus_Proper from 85 --> 89 rescaling Right_Caudate from 62 --> 68 rescaling Right_Putamen from 80 --> 76 rescaling Right_Pallidum from 97 --> 96 rescaling Right_Hippocampus from 53 --> 55 rescaling Right_Amygdala from 55 --> 61 rescaling Right_Accumbens_area from 65 --> 68 rescaling Right_VentralDC from 86 --> 104 rescaling Fifth_Ventricle from 40 --> 19 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 = 619759 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 185 changed. pass 2: 15 changed. pass 3: 4 changed. pass 4: 2 changed. pass 5: 0 changed. Writing output aseg to /usr/local/freesurfer/subjects/SynthF/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Mon Dec 19 22:51:28 GMT 2016 /usr/local/freesurfer/subjects/SynthF mri_aparc2aseg --s SynthF --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 SynthF outvol /usr/local/freesurfer/subjects/SynthF/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /usr/local/freesurfer/subjects/SynthF/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/SynthF/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/SynthF/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/SynthF/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/SynthF/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/SynthF/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/SynthF/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/SynthF/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 --> 102 rescaling Left_Cerebral_Cortex from 61 --> 63 rescaling Left_Lateral_Ventricle from 13 --> 12 rescaling Left_Inf_Lat_Vent from 34 --> 32 rescaling Left_Cerebellum_White_Matter from 86 --> 85 rescaling Left_Cerebellum_Cortex from 60 --> 75 rescaling Left_Thalamus from 94 --> 98 rescaling Left_Thalamus_Proper from 84 --> 95 rescaling Left_Caudate from 75 --> 68 rescaling Left_Putamen from 80 --> 79 rescaling Left_Pallidum from 98 --> 97 rescaling Third_Ventricle from 25 --> 14 rescaling Fourth_Ventricle from 22 --> 8 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 56 rescaling Left_Amygdala from 56 --> 65 rescaling CSF from 32 --> 21 rescaling Left_Accumbens_area from 62 --> 61 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 99 rescaling Right_Cerebral_Cortex from 58 --> 84 rescaling Right_Lateral_Ventricle from 13 --> 8 rescaling Right_Inf_Lat_Vent from 25 --> 23 rescaling Right_Cerebellum_White_Matter from 87 --> 85 rescaling Right_Cerebellum_Cortex from 59 --> 78 rescaling Right_Thalamus_Proper from 85 --> 89 rescaling Right_Caudate from 62 --> 68 rescaling Right_Putamen from 80 --> 76 rescaling Right_Pallidum from 97 --> 96 rescaling Right_Hippocampus from 53 --> 55 rescaling Right_Amygdala from 55 --> 61 rescaling Right_Accumbens_area from 65 --> 68 rescaling Right_VentralDC from 86 --> 104 rescaling Fifth_Ventricle from 40 --> 19 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 = 619826 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 185 changed. pass 2: 15 changed. pass 3: 4 changed. pass 4: 2 changed. pass 5: 0 changed. Writing output aseg to /usr/local/freesurfer/subjects/SynthF/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Mon Dec 19 22:55:30 GMT 2016 /usr/local/freesurfer/subjects/SynthF mri_aparc2aseg --s SynthF --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 SynthF outvol /usr/local/freesurfer/subjects/SynthF/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /usr/local/freesurfer/subjects/SynthF/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/SynthF/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/SynthF/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/SynthF/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/SynthF/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/SynthF/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/SynthF/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/SynthF/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 --> 102 rescaling Left_Cerebral_Cortex from 61 --> 63 rescaling Left_Lateral_Ventricle from 13 --> 12 rescaling Left_Inf_Lat_Vent from 34 --> 32 rescaling Left_Cerebellum_White_Matter from 86 --> 85 rescaling Left_Cerebellum_Cortex from 60 --> 75 rescaling Left_Thalamus from 94 --> 98 rescaling Left_Thalamus_Proper from 84 --> 95 rescaling Left_Caudate from 75 --> 68 rescaling Left_Putamen from 80 --> 79 rescaling Left_Pallidum from 98 --> 97 rescaling Third_Ventricle from 25 --> 14 rescaling Fourth_Ventricle from 22 --> 8 rescaling Brain_Stem from 81 --> 87 rescaling Left_Hippocampus from 57 --> 56 rescaling Left_Amygdala from 56 --> 65 rescaling CSF from 32 --> 21 rescaling Left_Accumbens_area from 62 --> 61 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 99 rescaling Right_Cerebral_Cortex from 58 --> 84 rescaling Right_Lateral_Ventricle from 13 --> 8 rescaling Right_Inf_Lat_Vent from 25 --> 23 rescaling Right_Cerebellum_White_Matter from 87 --> 85 rescaling Right_Cerebellum_Cortex from 59 --> 78 rescaling Right_Thalamus_Proper from 85 --> 89 rescaling Right_Caudate from 62 --> 68 rescaling Right_Putamen from 80 --> 76 rescaling Right_Pallidum from 97 --> 96 rescaling Right_Hippocampus from 53 --> 55 rescaling Right_Amygdala from 55 --> 61 rescaling Right_Accumbens_area from 65 --> 68 rescaling Right_VentralDC from 86 --> 104 rescaling Fifth_Ventricle from 40 --> 19 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 = 619826 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 185 changed. pass 2: 15 changed. pass 3: 4 changed. pass 4: 2 changed. pass 5: 0 changed. Writing output aseg to /usr/local/freesurfer/subjects/SynthF/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Mon Dec 19 22:59:28 GMT 2016 /usr/local/freesurfer/subjects/SynthF/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Mon Dec 19 22:59:28 GMT 2016 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /usr/local/freesurfer/subjects/SynthF/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/SynthF/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 22:59:28 GMT 2016 Ended at Mon Dec 19 22:59:33 GMT 2016 Apas2aseg-Run-Time-Sec 5 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Mon Dec 19 22:59:33 GMT 2016 /usr/local/freesurfer/subjects/SynthF 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 SynthF $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 SynthF sysname Linux hostname stefano-Q170M-C machine x86_64 user stefano UseRobust 0 atlas_icv (eTIV) = 1180158 mm^3 (det: 1.650715 ) Computing euler number orig.nofix lheno = -120, rheno = -188 orig.nofix lhholes = 61, rhholes = 95 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 316058.717 315676.000 diff= 382.7 pctdiff= 0.121 rhCtxGM: 304031.649 304306.000 diff= -274.4 pctdiff=-0.090 lhCtxWM: 312652.444 313883.000 diff=-1230.6 pctdiff=-0.394 rhCtxWM: 327003.381 328754.000 diff=-1750.6 pctdiff=-0.535 SubCortGMVol 71273.000 SupraTentVol 1357578.191 (1354505.000) diff=3073.191 pctdiff=0.226 SupraTentVolNotVent 1336967.191 (1333894.000) diff=3073.191 pctdiff=0.230 BrainSegVol 1502470.000 (1499154.000) diff=3316.000 pctdiff=0.221 BrainSegVolNotVent 1477416.000 (1474442.191) diff=2973.809 pctdiff=0.201 BrainSegVolNotVent 1477416.000 CerebellumVol 143421.000 VentChorVol 20611.000 3rd4th5thCSF 4443.000 CSFVol 1127.000, OptChiasmVol 101.000 MaskVol 1849883.000 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 23:02:23 GMT 2016 /usr/local/freesurfer/subjects/SynthF mri_aparc2aseg --s SynthF --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /usr/local/freesurfer/subjects subject SynthF 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/SynthF/mri/aparc+aseg.mgz Reading lh white surface /usr/local/freesurfer/subjects/SynthF/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/SynthF/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/SynthF/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/SynthF/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/SynthF/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/SynthF/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/SynthF/mri/ribbon.mgz Loading filled from /usr/local/freesurfer/subjects/SynthF/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 9158 vertices from left hemi Ripped 7904 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/SynthF/mri/aseg.mgz Loading Ctx Seg File /usr/local/freesurfer/subjects/SynthF/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 = 1257578 Used brute-force search on 976 voxels Fixing Parahip LH WM Found 14 clusters 0 k 1.000000 1 k 2.000000 2 k 5.000000 3 k 4.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 1.000000 8 k 1.000000 9 k 1.000000 10 k 1357.000000 11 k 1.000000 12 k 1.000000 13 k 1.000000 Fixing Parahip RH WM Found 16 clusters 0 k 1.000000 1 k 1557.000000 2 k 2.000000 3 k 1.000000 4 k 1.000000 5 k 5.000000 6 k 3.000000 7 k 1.000000 8 k 24.000000 9 k 1.000000 10 k 3.000000 11 k 1.000000 12 k 3.000000 13 k 4.000000 14 k 7.000000 15 k 3.000000 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 SynthF --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 SynthF --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) = 1180158 mm^3 (det: 1.650715 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 316058.717 315676.000 diff= 382.7 pctdiff= 0.121 rhCtxGM: 304031.649 304306.000 diff= -274.4 pctdiff=-0.090 lhCtxWM: 312652.444 313883.000 diff=-1230.6 pctdiff=-0.394 rhCtxWM: 327003.381 328754.000 diff=-1750.6 pctdiff=-0.535 SubCortGMVol 71273.000 SupraTentVol 1357578.191 (1354505.000) diff=3073.191 pctdiff=0.226 SupraTentVolNotVent 1336967.191 (1333894.000) diff=3073.191 pctdiff=0.230 BrainSegVol 1502470.000 (1499154.000) diff=3316.000 pctdiff=0.221 BrainSegVolNotVent 1477416.000 (1474442.191) diff=2973.809 pctdiff=0.201 BrainSegVolNotVent 1477416.000 CerebellumVol 143421.000 VentChorVol 20611.000 3rd4th5thCSF 4443.000 CSFVol 1127.000, OptChiasmVol 101.000 MaskVol 1849883.000 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/SynthF/label #-------------------------------------------- #@# BA_exvivo Labels lh Mon Dec 19 23:11:21 GMT 2016 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject SynthF --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 2213 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 6342 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.label --trgsubject SynthF --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 4127 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 12036 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.label --trgsubject SynthF --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 552 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4629 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.label --trgsubject SynthF --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 1649 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 7632 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.label --trgsubject SynthF --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 1183 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6967 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.label --trgsubject SynthF --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 504 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4574 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.label --trgsubject SynthF --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 4274 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 17863 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.label --trgsubject SynthF --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 1000 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 5181 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.label --trgsubject SynthF --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 1078 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4500 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.label --trgsubject SynthF --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 1201 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5842 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.label --trgsubject SynthF --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 4034 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 12148 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.label --trgsubject SynthF --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 1236 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 3254 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject SynthF --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 117 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1407 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject SynthF --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 95 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1294 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 661 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1675 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 1669 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 3761 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 190 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1694 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 543 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2539 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 337 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2656 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 120 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1669 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 2159 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 9194 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 363 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2275 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 324 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1475 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 831 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4236 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 1717 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 5051 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 292 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 805 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 33 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 503 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/lh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 187767 Number of reverse mapping hits = 39 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 489 mri_label2label: Done mris_label2annot --s SynthF --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/SynthF/label cmdline mris_label2annot --s SynthF --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 SynthF 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/SynthF/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 129306 unhit vertices Writing annot to /usr/local/freesurfer/subjects/SynthF/label/lh.BA_exvivo.annot mris_label2annot --s SynthF --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/SynthF/label cmdline mris_label2annot --s SynthF --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 SynthF 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/SynthF/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 154315 unhit vertices Writing annot to /usr/local/freesurfer/subjects/SynthF/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 SynthF lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /usr/local/freesurfer/subjects/SynthF/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthF/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/SynthF/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthF/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 321558 Total vertex volume 318104 (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) = 1180158 mm^3 (det: 1.650715 ) lhCtxGM: 316058.717 315676.000 diff= 382.7 pctdiff= 0.121 rhCtxGM: 304031.649 304306.000 diff= -274.4 pctdiff=-0.090 lhCtxWM: 312652.444 313883.000 diff=-1230.6 pctdiff=-0.394 rhCtxWM: 327003.381 328754.000 diff=-1750.6 pctdiff=-0.535 SubCortGMVol 71273.000 SupraTentVol 1357578.191 (1354505.000) diff=3073.191 pctdiff=0.226 SupraTentVolNotVent 1336967.191 (1333894.000) diff=3073.191 pctdiff=0.230 BrainSegVol 1502470.000 (1499154.000) diff=3316.000 pctdiff=0.221 BrainSegVolNotVent 1477416.000 (1474442.191) diff=2973.809 pctdiff=0.201 BrainSegVolNotVent 1477416.000 CerebellumVol 143421.000 VentChorVol 20611.000 3rd4th5thCSF 4443.000 CSFVol 1127.000, OptChiasmVol 101.000 MaskVol 1849883.000 2330 1345 3767 2.266 0.780 0.107 0.030 22 3.1 BA1_exvivo 8391 5521 12209 2.133 0.602 0.117 0.023 75 8.2 BA2_exvivo 1448 942 1344 1.625 0.446 0.106 0.019 9 1.0 BA3a_exvivo 3638 2387 4864 1.800 0.609 0.105 0.019 30 2.7 BA3b_exvivo 2109 1379 3749 2.357 0.581 0.101 0.019 12 1.8 BA4a_exvivo 1607 1090 2797 2.491 0.562 0.084 0.019 9 1.2 BA4p_exvivo 14455 9269 25132 2.405 0.677 0.113 0.030 148 19.3 BA6_exvivo 3251 2257 6167 2.479 0.552 0.110 0.017 33 2.5 BA44_exvivo 3573 2437 7572 2.555 0.694 0.114 0.020 40 2.9 BA45_exvivo 3334 2292 4534 1.844 0.484 0.134 0.030 38 4.3 V1_exvivo 9901 6523 14139 2.074 0.641 0.151 0.036 149 15.6 V2_exvivo 3100 1880 4387 2.318 0.628 0.109 0.022 26 2.8 MT_exvivo 590 413 1724 3.260 0.800 0.118 0.032 7 0.8 perirhinal_exvivo 734 521 1524 2.554 0.829 0.079 0.015 4 0.5 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 SynthF lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /usr/local/freesurfer/subjects/SynthF/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthF/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/SynthF/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthF/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 321558 Total vertex volume 318104 (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) = 1180158 mm^3 (det: 1.650715 ) lhCtxGM: 316058.717 315676.000 diff= 382.7 pctdiff= 0.121 rhCtxGM: 304031.649 304306.000 diff= -274.4 pctdiff=-0.090 lhCtxWM: 312652.444 313883.000 diff=-1230.6 pctdiff=-0.394 rhCtxWM: 327003.381 328754.000 diff=-1750.6 pctdiff=-0.535 SubCortGMVol 71273.000 SupraTentVol 1357578.191 (1354505.000) diff=3073.191 pctdiff=0.226 SupraTentVolNotVent 1336967.191 (1333894.000) diff=3073.191 pctdiff=0.230 BrainSegVol 1502470.000 (1499154.000) diff=3316.000 pctdiff=0.221 BrainSegVolNotVent 1477416.000 (1474442.191) diff=2973.809 pctdiff=0.201 BrainSegVolNotVent 1477416.000 CerebellumVol 143421.000 VentChorVol 20611.000 3rd4th5thCSF 4443.000 CSFVol 1127.000, OptChiasmVol 101.000 MaskVol 1849883.000 1624 947 2384 2.145 0.696 0.108 0.032 16 2.5 BA1_exvivo 3721 2360 5823 2.188 0.705 0.116 0.025 37 3.5 BA2_exvivo 1267 834 1056 1.546 0.355 0.108 0.018 7 0.9 BA3a_exvivo 2280 1518 2544 1.550 0.367 0.091 0.015 13 1.3 BA3b_exvivo 1991 1322 3614 2.442 0.586 0.091 0.016 9 1.3 BA4a_exvivo 1234 859 1978 2.360 0.449 0.079 0.011 4 0.5 BA4p_exvivo 8224 5302 13964 2.368 0.629 0.111 0.031 73 11.5 BA6_exvivo 1946 1374 3768 2.463 0.577 0.113 0.017 22 1.6 BA44_exvivo 1335 929 3627 2.833 0.687 0.121 0.022 19 1.3 BA45_exvivo 3636 2471 5010 1.862 0.493 0.135 0.031 43 4.8 V1_exvivo 4715 3143 6072 1.967 0.583 0.162 0.041 79 8.6 V2_exvivo 780 469 1105 2.182 0.611 0.106 0.023 6 0.7 MT_exvivo 285 214 1129 3.713 0.528 0.073 0.010 1 0.1 perirhinal_exvivo 414 268 884 2.647 0.692 0.047 0.007 1 0.1 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Mon Dec 19 23:15:41 GMT 2016 mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.label --trgsubject SynthF --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 615 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4577 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.label --trgsubject SynthF --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 980 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7667 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.label --trgsubject SynthF --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 265 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4245 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.label --trgsubject SynthF --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 483 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 5005 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.label --trgsubject SynthF --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 1268 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 7015 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.label --trgsubject SynthF --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 398 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4871 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.label --trgsubject SynthF --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 3634 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 15890 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.label --trgsubject SynthF --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 2057 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 8969 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.label --trgsubject SynthF --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 2558 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 7913 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.label --trgsubject SynthF --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 1166 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5893 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.label --trgsubject SynthF --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 3380 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 11396 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.label --trgsubject SynthF --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 1137 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 3069 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject SynthF --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 34 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1072 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject SynthF --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /usr/local/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 37 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 789 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 200 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 1076 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 278 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2966 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 107 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1805 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 221 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2404 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 184 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1572 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 103 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1592 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 2244 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 9203 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 355 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1367 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 634 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1812 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 632 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 3864 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 1429 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4866 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 122 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 390 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 19 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 713 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject SynthF --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 = SynthF 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/SynthF/surf/rh.white Reading target registration /usr/local/freesurfer/subjects/SynthF/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 182051 Number of reverse mapping hits = 11 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 302 mri_label2label: Done mris_label2annot --s SynthF --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/SynthF/label cmdline mris_label2annot --s SynthF --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 SynthF 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/SynthF/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 129867 unhit vertices Writing annot to /usr/local/freesurfer/subjects/SynthF/label/rh.BA_exvivo.annot mris_label2annot --s SynthF --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/SynthF/label cmdline mris_label2annot --s SynthF --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 SynthF 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/SynthF/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 153941 unhit vertices Writing annot to /usr/local/freesurfer/subjects/SynthF/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 SynthF rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /usr/local/freesurfer/subjects/SynthF/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthF/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/SynthF/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthF/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 309486 Total vertex volume 306722 (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) = 1180158 mm^3 (det: 1.650715 ) lhCtxGM: 316058.717 315676.000 diff= 382.7 pctdiff= 0.121 rhCtxGM: 304031.649 304306.000 diff= -274.4 pctdiff=-0.090 lhCtxWM: 312652.444 313883.000 diff=-1230.6 pctdiff=-0.394 rhCtxWM: 327003.381 328754.000 diff=-1750.6 pctdiff=-0.535 SubCortGMVol 71273.000 SupraTentVol 1357578.191 (1354505.000) diff=3073.191 pctdiff=0.226 SupraTentVolNotVent 1336967.191 (1333894.000) diff=3073.191 pctdiff=0.230 BrainSegVol 1502470.000 (1499154.000) diff=3316.000 pctdiff=0.221 BrainSegVolNotVent 1477416.000 (1474442.191) diff=2973.809 pctdiff=0.201 BrainSegVolNotVent 1477416.000 CerebellumVol 143421.000 VentChorVol 20611.000 3rd4th5thCSF 4443.000 CSFVol 1127.000, OptChiasmVol 101.000 MaskVol 1849883.000 1216 748 2070 2.117 0.520 0.137 0.034 14 1.6 BA1_exvivo 4154 2729 5017 1.837 0.460 0.094 0.015 29 2.5 BA2_exvivo 1317 853 1157 1.787 0.560 0.119 0.022 10 1.2 BA3a_exvivo 2356 1593 2760 1.591 0.494 0.091 0.017 16 1.8 BA3b_exvivo 1982 1205 3588 2.611 0.490 0.078 0.013 9 1.0 BA4a_exvivo 1440 992 2380 2.396 0.424 0.077 0.010 6 0.5 BA4p_exvivo 12465 8039 22256 2.486 0.715 0.124 0.036 181 21.7 BA6_exvivo 4885 3298 9755 2.590 0.639 0.116 0.023 349 4.7 BA44_exvivo 6173 3989 11910 2.620 0.709 0.138 0.038 84 10.2 BA45_exvivo 3344 2263 4480 1.839 0.508 0.120 0.026 34 3.5 V1_exvivo 9117 6156 13809 2.072 0.614 0.147 0.033 124 13.1 V2_exvivo 2989 1987 5275 2.550 0.580 0.137 0.033 35 3.9 MT_exvivo 460 329 1998 3.834 0.778 0.099 0.020 3 0.3 perirhinal_exvivo 286 200 793 3.115 0.722 0.087 0.022 3 0.2 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 SynthF rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /usr/local/freesurfer/subjects/SynthF/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/SynthF/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/SynthF/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/SynthF/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 309486 Total vertex volume 306722 (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) = 1180158 mm^3 (det: 1.650715 ) lhCtxGM: 316058.717 315676.000 diff= 382.7 pctdiff= 0.121 rhCtxGM: 304031.649 304306.000 diff= -274.4 pctdiff=-0.090 lhCtxWM: 312652.444 313883.000 diff=-1230.6 pctdiff=-0.394 rhCtxWM: 327003.381 328754.000 diff=-1750.6 pctdiff=-0.535 SubCortGMVol 71273.000 SupraTentVol 1357578.191 (1354505.000) diff=3073.191 pctdiff=0.226 SupraTentVolNotVent 1336967.191 (1333894.000) diff=3073.191 pctdiff=0.230 BrainSegVol 1502470.000 (1499154.000) diff=3316.000 pctdiff=0.221 BrainSegVolNotVent 1477416.000 (1474442.191) diff=2973.809 pctdiff=0.201 BrainSegVolNotVent 1477416.000 CerebellumVol 143421.000 VentChorVol 20611.000 3rd4th5thCSF 4443.000 CSFVol 1127.000, OptChiasmVol 101.000 MaskVol 1849883.000 891 562 1414 1.963 0.530 0.132 0.028 9 1.0 BA1_exvivo 2163 1453 2716 1.790 0.432 0.086 0.014 11 1.1 BA2_exvivo 1182 761 950 1.724 0.454 0.119 0.022 8 1.0 BA3a_exvivo 1838 1258 1896 1.501 0.452 0.075 0.009 9 0.7 BA3b_exvivo 1186 696 2365 2.726 0.530 0.086 0.016 7 0.7 BA4a_exvivo 1190 823 1931 2.411 0.408 0.070 0.008 3 0.4 BA4p_exvivo 8171 5228 13442 2.405 0.681 0.125 0.038 127 15.7 BA6_exvivo 1265 838 3046 2.811 0.649 0.099 0.019 10 1.0 BA44_exvivo 1740 998 2886 2.461 0.643 0.143 0.047 30 3.6 BA45_exvivo 3145 2104 4088 1.824 0.494 0.115 0.026 29 3.2 V1_exvivo 4496 3112 6296 1.901 0.541 0.156 0.036 70 7.2 V2_exvivo 381 255 739 2.752 0.641 0.134 0.027 4 0.5 MT_exvivo 275 189 1140 3.871 0.746 0.083 0.014 1 0.2 perirhinal_exvivo 187 133 583 3.262 0.718 0.105 0.029 2 0.2 entorhinal_exvivo Started at Mon Dec 19 10:28:32 GMT 2016 Ended at Mon Dec 19 23:19:49 GMT 2016 #@#%# recon-all-run-time-hours 12.855 recon-all -s SynthF finished without error at Mon Dec 19 23:19:49 GMT 2016