Mon Aug 7 21:08:45 UTC 2017 /out/freesurfer/sub-05 /opt/freesurfer/bin/recon-all -autorecon1 -i /root/src/fmriprep/work/fmriprep_wf/single_subject_05_wf/anat_preproc_wf/t1_merge/sub-05_run-01_T1w_ras_template.nii.gz -noskullstrip -openmp 7 -subjid sub-05 -sd /out/freesurfer subjid sub-05 setenv SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux 7727740b0cba 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 15345 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 3973012 1087532 2104048 3472 781432 2523996 Swap: 4121596 947296 3174300 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:08:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:08:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:08:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-21:08:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:08:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:08:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-21:08:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-21:08:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-21:08:51-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-21:08:52-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-21:08:52-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-21:08:52-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:08:53-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:08:53-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-21:08:53-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:08:54-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:08:54-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:08:55-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:08:55-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:08:55-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:08:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-21:08:56-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:08:57-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:08:57-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:08:57-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-21:08:58-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:08:58-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-21:08:58-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:08:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:08:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:08:59-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:09:00-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:09:00-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:09:01-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:09:01-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:09:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:09:02-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:09:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-21:09:03-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: root Machine: 7727740b0cba Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/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 /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /out/freesurfer/sub-05 mri_convert /root/src/fmriprep/work/fmriprep_wf/single_subject_05_wf/anat_preproc_wf/t1_merge/sub-05_run-01_T1w_ras_template.nii.gz /out/freesurfer/sub-05/mri/orig/001.mgz mri_convert.bin /root/src/fmriprep/work/fmriprep_wf/single_subject_05_wf/anat_preproc_wf/t1_merge/sub-05_run-01_T1w_ras_template.nii.gz /out/freesurfer/sub-05/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /root/src/fmriprep/work/fmriprep_wf/single_subject_05_wf/anat_preproc_wf/t1_merge/sub-05_run-01_T1w_ras_template.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /out/freesurfer/sub-05/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon Aug 7 21:09:08 UTC 2017 Found 1 runs /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/mri/orig/001.mgz /out/freesurfer/sub-05/mri/rawavg.mgz /out/freesurfer/sub-05 mri_convert /out/freesurfer/sub-05/mri/rawavg.mgz /out/freesurfer/sub-05/mri/orig.mgz --conform mri_convert.bin /out/freesurfer/sub-05/mri/rawavg.mgz /out/freesurfer/sub-05/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /out/freesurfer/sub-05/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /out/freesurfer/sub-05/mri/orig.mgz... mri_add_xform_to_header -c /out/freesurfer/sub-05/mri/transforms/talairach.xfm /out/freesurfer/sub-05/mri/orig.mgz /out/freesurfer/sub-05/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Aug 7 21:09:17 UTC 2017 /out/freesurfer/sub-05/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /out/freesurfer/sub-05/mri /opt/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 7727740b0cba 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Mon Aug 7 21:09:17 UTC 2017 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.30299 /out/freesurfer/sub-05/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30299/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.30299/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.30299/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Aug 7 21:09:19 UTC 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.30299/nu0.mnc ./tmp.mri_nu_correct.mni.30299/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.30299/0/ -iterations 1000 -distance 50 [root@7727740b0cba:/out/freesurfer/sub-05/mri/] [2017-08-07 21:09:19] running: /opt/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.30299/0/ ./tmp.mri_nu_correct.mni.30299/nu0.mnc ./tmp.mri_nu_correct.mni.30299/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 10 CV of field change: 0.00095777 mri_convert ./tmp.mri_nu_correct.mni.30299/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.30299/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.30299/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 Aug 7 21:09:50 UTC 2017 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 Aug 7 21:09:50 UTC 2017 Ended at Mon Aug 7 21:10:37 UTC 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Aug 7 21:10:39 UTC 2017 /out/freesurfer/sub-05/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach INFO: Retrying Talairach align using 3T-based atlas... #-------------------------------------------- #@# Talairach Mon Aug 7 21:10:39 UTC 2017 /out/freesurfer/sub-05/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /out/freesurfer/sub-05/mri /opt/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 7727740b0cba 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Mon Aug 7 21:10:39 UTC 2017 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.30676 /out/freesurfer/sub-05/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30676/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.30676/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.30676/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Aug 7 21:10:41 UTC 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.30676/nu0.mnc ./tmp.mri_nu_correct.mni.30676/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.30676/0/ -iterations 1000 -distance 50 [root@7727740b0cba:/out/freesurfer/sub-05/mri/] [2017-08-07 21:10:41] running: /opt/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.30676/0/ ./tmp.mri_nu_correct.mni.30676/nu0.mnc ./tmp.mri_nu_correct.mni.30676/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 10 CV of field change: 0.00095777 mri_convert ./tmp.mri_nu_correct.mni.30676/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.30676/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.30676/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 Aug 7 21:11:11 UTC 2017 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig talairach_avi log file is transforms/talairach_avi.log... Started at Mon Aug 7 21:11:11 UTC 2017 Ended at Mon Aug 7 21:11:58 UTC 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Aug 7 21:12:00 UTC 2017 /out/freesurfer/sub-05/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0020, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach INFO: Trying MINC mritotal to perform Talairach align... #-------------------------------------------- #@# Talairach Mon Aug 7 21:12:00 UTC 2017 /out/freesurfer/sub-05/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /out/freesurfer/sub-05/mri /opt/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 7727740b0cba 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Mon Aug 7 21:12:00 UTC 2017 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.31057 /out/freesurfer/sub-05/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.31057/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.31057/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.31057/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Aug 7 21:12:02 UTC 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.31057/nu0.mnc ./tmp.mri_nu_correct.mni.31057/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.31057/0/ -iterations 1000 -distance 50 [root@7727740b0cba:/out/freesurfer/sub-05/mri/] [2017-08-07 21:12:02] running: /opt/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.31057/0/ ./tmp.mri_nu_correct.mni.31057/nu0.mnc ./tmp.mri_nu_correct.mni.31057/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 10 CV of field change: 0.00095777 mri_convert ./tmp.mri_nu_correct.mni.31057/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.31057/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.31057/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 Aug 7 21:12:32 UTC 2017 mri_nu_correct.mni done talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /out/freesurfer/sub-05/mri /opt/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.8 2016/02/16 17:17:20 zkaufman Exp $ Linux 7727740b0cba 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Mon Aug 7 21:12:32 UTC 2017 tmpdir is transforms/tmp.talairach.31297 /out/freesurfer/sub-05/mri mri_convert orig_nu.mgz transforms/tmp.talairach.31297/src.mnc mri_convert.bin orig_nu.mgz transforms/tmp.talairach.31297/src.mnc $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig_nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to transforms/tmp.talairach.31297/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /opt/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.31297/src.mnc transforms/talairach.auto.xfm Transforming slices:................................................................................................................................Done Copying chunks:......................................................................................................................................................Done. Copying chunks:..........................................................................................................Done. Transforming slices:......................................................................................................................................................Done Copying chunks:....................................................................................................................Done. Copying chunks:....................................................................................................................Done. Source volume size: 74 by 106 by 106 Source voxel size = 2.000 2.000 2.000 Source min/max real range = -0.000 236.087 Source min/max voxel= -0.000 236.087 Target volume size: 58 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.970 123.710 Target min/max voxel = -0.000 123.710 AFTER init_params() Transform matrix = 1.0000 0.0000 0.0000 -13.4625 0.0000 1.0000 0.0000 -6.2528 0.0000 0.0000 1.0000 -1.1924 Transform center = 13.790 -11.338 10.647 Transform rotations = 0.000 0.000 0.000 Transform trans = -13.462 -6.253 -1.192 Transform scale = 1.000 1.000 1.000 Transform shear = 0.000 0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -85.095 -125.510 -47.250 Lattice count = 43 55 29 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = -0.000 248.094 Source min/max voxel= -0.000 248.094 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= -0.000 144.070 Target min/max voxel = -0.000 144.070 AFTER init_params() Transform matrix = 0.0660 -1.5544 0.1417 -49.4564 0.4677 -0.1156 -1.4861 -15.8111 1.4892 0.1052 0.4605 -27.0814 Transform center = 13.790 -11.338 10.647 Transform rotations = 0.225 -1.264 1.431 Transform trans = -43.204 -12.535 -13.482 Transform scale = 1.562 1.562 1.562 Transform shear = 0.000 -0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -85.095 -125.510 -57.250 Lattice count = 43 55 34 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.068 27.336 Source min/max voxel= 0.068 27.336 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 0.0554 -1.5519 0.0821 -48.0189 0.3814 -0.0660 -1.5061 -12.5325 1.5065 0.0738 0.3783 -32.4131 Transform center = 13.790 -11.338 10.647 Transform rotations = 0.193 -1.320 1.427 Transform trans = -42.576 -11.220 -19.094 Transform scale = 1.555 1.555 1.555 Transform shear = -0.000 0.000 -0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.068 27.336 Source min/max voxel= 0.068 27.336 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 0.0215 -1.7590 -0.0108 -49.8952 0.3558 0.0150 -1.7227 -4.9524 1.7227 0.0189 0.3560 -53.4680 Transform center = 13.790 -11.338 10.647 Transform rotations = 0.053 -1.367 1.510 Transform trans = -43.560 -7.219 -36.783 Transform scale = 1.759 1.759 1.759 Transform shear = -0.000 -0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.068 27.336 Source min/max voxel= 0.068 27.336 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 0.0469 -1.8192 -0.1197 -51.0311 0.4224 0.1273 -1.7696 -2.5529 1.4979 0.0151 0.3586 -47.2724 Transform center = 13.790 -11.338 10.647 Transform rotations = 0.042 -1.336 1.460 Transform trans = -44.822 -5.673 -33.615 Transform scale = 1.824 1.824 1.540 Transform shear = -0.000 0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.068 27.336 Source min/max voxel= 0.068 27.336 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 0.0469 -1.8192 -0.1197 -51.0311 0.4224 0.1273 -1.7696 -2.5529 1.4979 0.0151 0.3586 -47.2724 Transform center = 13.790 -11.338 10.647 Transform rotations = 0.042 -1.336 1.460 Transform trans = -44.822 -5.673 -33.615 Transform scale = 1.824 1.824 1.540 Transform shear = 0.000 -0.000 -0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Mon Aug 7 21:12:39 UTC 2017 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Aug 7 21:12:41 UTC 2017 /out/freesurfer/sub-05/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach ERROR: Talairach failed! Linux 7727740b0cba 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-05 exited with ERRORS at Mon Aug 7 21:12:41 UTC 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Mon Aug 7 23:53:41 UTC 2017 /out/freesurfer/sub-05 /opt/freesurfer/bin/recon-all -autorecon1 -noskullstrip -openmp 7 -subjid sub-05 -sd /out/freesurfer -nomotioncor -notalairach subjid sub-05 setenv SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux 1d9731faa403 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 15345 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 3973012 1067808 2125536 5820 779668 2540756 Swap: 4121596 1009532 3112064 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:42-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:42-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:43-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:53:43-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:43-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:43-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:53:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:53:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:53:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:53:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:53:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:53:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:53:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:53:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:53:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:53:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:47-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:47-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:47-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:47-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:47-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:47-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:48-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:48-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:48-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:48-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:53:48-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/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 /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# Nu Intensity Correction Mon Aug 7 23:53:48 UTC 2017 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /out/freesurfer/sub-05/mri /opt/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 1d9731faa403 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Mon Aug 7 23:53:48 UTC 2017 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.4998 /out/freesurfer/sub-05/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4998/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.4998/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.4998/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Aug 7 23:53:50 UTC 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.4998/nu0.mnc ./tmp.mri_nu_correct.mni.4998/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.4998/0/ [root@1d9731faa403:/out/freesurfer/sub-05/mri/] [2017-08-07 23:53:50] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.4998/0/ ./tmp.mri_nu_correct.mni.4998/nu0.mnc ./tmp.mri_nu_correct.mni.4998/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 3 CV of field change: 0.000899708 -------------------------------------------------------- Iteration 2 Mon Aug 7 23:54:13 UTC 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.4998/nu1.mnc ./tmp.mri_nu_correct.mni.4998/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.4998/1/ [root@1d9731faa403:/out/freesurfer/sub-05/mri/] [2017-08-07 23:54:13] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.4998/1/ ./tmp.mri_nu_correct.mni.4998/nu1.mnc ./tmp.mri_nu_correct.mni.4998/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 2 CV of field change: 0.000821068 mri_binarize --i ./tmp.mri_nu_correct.mni.4998/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.4998/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /out/freesurfer/sub-05/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.4998/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.4998/ones.mgz sysname Linux hostname 1d9731faa403 machine x86_64 user root input ./tmp.mri_nu_correct.mni.4998/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.4998/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.4998/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.4998/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4998/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.4998/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.4998/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4998/input.mean.dat sysname Linux hostname 1d9731faa403 machine x86_64 user root UseRobust 0 Loading ./tmp.mri_nu_correct.mni.4998/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.4998/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4998/ones.mgz --i ./tmp.mri_nu_correct.mni.4998/nu2.mnc --sum ./tmp.mri_nu_correct.mni.4998/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4998/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.4998/ones.mgz --i ./tmp.mri_nu_correct.mni.4998/nu2.mnc --sum ./tmp.mri_nu_correct.mni.4998/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4998/output.mean.dat sysname Linux hostname 1d9731faa403 machine x86_64 user root UseRobust 0 Loading ./tmp.mri_nu_correct.mni.4998/ones.mgz Loading ./tmp.mri_nu_correct.mni.4998/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.4998/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.4998/nu2.mnc ./tmp.mri_nu_correct.mni.4998/nu2.mnc mul .97871977459016393442 Saving result to './tmp.mri_nu_correct.mni.4998/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.4998/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.4998/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.4998/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 6 seconds. mapping (13, 255) to ( 3, 110) Mon Aug 7 23:54:57 UTC 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /out/freesurfer/sub-05/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Mon Aug 7 23:54:58 UTC 2017 /out/freesurfer/sub-05/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 0.04693 -1.81917 -0.11966 -51.03114; 0.42242 0.12729 -1.76957 -2.55289; 1.49788 0.01505 0.35865 -47.27242; 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 = 4 Starting OpenSpline(): npoints = 4 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 39 white matter peak found at 20 gm peak at 14 (14), valley at 0 (-1) csf peak at 7, setting threshold to 11 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 38 white matter peak found at 50 gm peak at 35 (35), valley at 12 (12) csf peak at 12, setting threshold to 27 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 8 seconds. Started at Mon Aug 7 23:53:41 UTC 2017 Ended at Mon Aug 7 23:56:07 UTC 2017 #@#%# recon-all-run-time-hours 0.041 recon-all -s sub-05 finished without error at Mon Aug 7 23:56:07 UTC 2017 New invocation of recon-all Mon Aug 7 23:56:11 UTC 2017 /out/freesurfer/sub-05 /opt/freesurfer/bin/recon-all -autorecon2-volonly -openmp 7 -subjid sub-05 -sd /out/freesurfer subjid sub-05 setenv SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux 1d9731faa403 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 15345 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 3973012 1040520 1958360 5912 974132 2566536 Swap: 4121596 1008604 3112992 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:11-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:56:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/07-23:56:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/07-23:56:12-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/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 /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #------------------------------------- #@# EM Registration Mon Aug 7 23:56:12 UTC 2017 /out/freesurfer/sub-05/mri mri_em_register -rusage /out/freesurfer/sub-05/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /opt/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 = 7 == reading 1 input volumes... logging results to talairach.log reading '/opt/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=27.5 skull bounding box = (38, 61, 62) --> (184, 167, 216) using (87, 96, 139) as brain centroid... mean wm in atlas = 107, using box (69,83,120) --> (104, 108,157) to find MRI wm before smoothing, mri peak at 110 robust fit to distribution - 110 +- 2.2 after smoothing, mri peak at 110, scaling input intensities by 0.973 scaling channel 0 by 0.972727 initial log_p = -4.567 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.457824 @ (9.091, -9.091, -27.273) max log p = -4.388584 @ (4.545, 4.545, -4.545) max log p = -4.386587 @ (-2.273, 2.273, 2.273) max log p = -4.380059 @ (3.409, 3.409, 1.136) max log p = -4.370342 @ (0.568, 1.705, -1.705) max log p = -4.370342 @ (0.000, 0.000, 0.000) Found translation: (15.3, 2.8, -30.1): log p = -4.370 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.249, old_max_log_p =-4.370 (thresh=-4.4) 0.79781 0.63297 -0.30726 5.80713; -0.45005 0.90982 0.70569 -30.08069; 0.63508 -0.37141 0.88387 -26.99431; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.816, old_max_log_p =-4.249 (thresh=-4.2) -0.02171 1.15366 0.10778 -25.78843; -0.10072 0.01436 1.24804 -22.03071; 1.02850 -0.00936 0.05530 -16.13693; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.780, old_max_log_p =-3.816 (thresh=-3.8) -0.02171 1.15366 0.10778 -33.28843; -0.10072 0.01436 1.24804 -22.03071; 1.02850 -0.00936 0.05530 -16.13693; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.780, old_max_log_p =-3.780 (thresh=-3.8) -0.02171 1.15366 0.10778 -33.28843; -0.10072 0.01436 1.24804 -22.03071; 1.02850 -0.00936 0.05530 -16.13693; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.691, old_max_log_p =-3.780 (thresh=-3.8) -0.05441 1.13094 0.10648 -22.67738; -0.03448 0.01423 1.29583 -35.26631; 0.99294 0.02644 -0.02204 -7.28996; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.683, old_max_log_p =-3.691 (thresh=-3.7) -0.05543 1.15215 0.10848 -25.47889; -0.03448 0.01423 1.29583 -35.26631; 0.99294 0.02644 -0.02204 -7.28996; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.683, old_max_log_p =-3.683 (thresh=-3.7) -0.05543 1.15215 0.10848 -25.47889; -0.03448 0.01423 1.29583 -35.26631; 0.99294 0.02644 -0.02204 -7.28996; 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=-3.646, old_max_log_p =-3.683 (thresh=-3.7) -0.03147 1.14848 0.12864 -30.15682; -0.03380 -0.00462 1.29236 -31.60808; 0.99400 -0.00182 -0.02487 -3.03417; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.643, old_max_log_p =-3.646 (thresh=-3.6) -0.03960 1.14846 0.12883 -29.26410; -0.03384 -0.00463 1.29388 -31.78491; 0.99488 0.00758 -0.02384 -4.44274; 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 -0.03960 1.14846 0.12883 -29.26410; -0.03384 -0.00463 1.29388 -31.78491; 0.99488 0.00758 -0.02384 -4.44274; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix -0.03960 1.14846 0.12883 -29.26410; -0.03384 -0.00463 1.29388 -31.78491; 0.99488 0.00758 -0.02384 -4.44274; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: -0.03960 1.14846 0.12883 -29.26410; -0.03384 -0.00463 1.29388 -31.78491; 0.99488 0.00758 -0.02384 -4.44274; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.643 (old=-4.567) transform before final EM align: -0.03960 1.14846 0.12883 -29.26410; -0.03384 -0.00463 1.29388 -31.78491; 0.99488 0.00758 -0.02384 -4.44274; 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 -0.03960 1.14846 0.12883 -29.26410; -0.03384 -0.00463 1.29388 -31.78491; 0.99488 0.00758 -0.02384 -4.44274; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix -0.03960 1.14846 0.12883 -29.26410; -0.03384 -0.00463 1.29388 -31.78491; 0.99488 0.00758 -0.02384 -4.44274; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 013: -log(p) = 4.1 tol 0.000000 final transform: -0.03960 1.14846 0.12883 -29.26410; -0.03384 -0.00463 1.29388 -31.78491; 0.99488 0.00758 -0.02384 -4.44274; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1766.240000 mri_em_register stimesec 3.204000 mri_em_register ru_maxrss 601592 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 162169 mri_em_register ru_majflt 8 mri_em_register ru_nswap 0 mri_em_register ru_inblock 141696 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 735 mri_em_register ru_nivcsw 20697 registration took 4 minutes and 34 seconds. #-------------------------------------- #@# CA Normalize Tue Aug 8 00:00:45 UTC 2017 /out/freesurfer/sub-05/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/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 '/opt/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=27.5 skull bounding box = (38, 61, 62) --> (184, 167, 216) using (87, 96, 139) as brain centroid... mean wm in atlas = 107, using box (69,83,120) --> (104, 108,157) to find MRI wm before smoothing, mri peak at 110 robust fit to distribution - 110 +- 2.2 after smoothing, mri peak at 110, scaling input intensities by 0.973 scaling channel 0 by 0.972727 using 246344 sample points... INFO: compute sample coordinates transform -0.03960 1.14846 0.12883 -29.26410; -0.03384 -0.00463 1.29388 -31.78491; 0.99488 0.00758 -0.02384 -4.44274; 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 (33, 121, 68) --> (202, 185, 162) Left_Cerebral_White_Matter: limiting intensities to 99.0 --> 107.0 5 of 6958 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (33, 68, 68) --> (202, 130, 162) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 107.0 7 of 5083 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (55, 123, 134) --> (110, 164, 166) Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 107.0 0 of 120 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (53, 82, 134) --> (112, 123, 166) Right_Cerebellum_White_Matter: limiting intensities to 96.0 --> 107.0 0 of 59 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (90, 108, 128) --> (122, 139, 182) Brain_Stem: limiting intensities to 95.0 --> 107.0 0 of 186 (0.0%) samples deleted using 12406 total control points for intensity normalization... bias field = 0.994 +- 0.043 239 of 12394 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (33, 121, 68) --> (202, 185, 162) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 108.0 2 of 6992 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (33, 68, 68) --> (202, 130, 162) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 108.0 7 of 5104 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (55, 123, 134) --> (110, 164, 166) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 108.0 4 of 154 (2.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (53, 82, 134) --> (112, 123, 166) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 108.0 1 of 104 (1.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (90, 108, 128) --> (122, 139, 182) Brain_Stem: limiting intensities to 88.0 --> 108.0 7 of 228 (3.1%) samples deleted using 12582 total control points for intensity normalization... bias field = 1.016 +- 0.039 110 of 12469 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (33, 121, 68) --> (202, 185, 162) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 110.0 13 of 7000 (0.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (33, 68, 68) --> (202, 130, 162) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 110.0 46 of 5149 (0.9%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (55, 123, 134) --> (110, 164, 166) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 110.0 22 of 170 (12.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (53, 82, 134) --> (112, 123, 166) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 110.0 13 of 93 (14.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (90, 108, 128) --> (122, 139, 182) Brain_Stem: limiting intensities to 88.0 --> 110.0 18 of 235 (7.7%) samples deleted using 12647 total control points for intensity normalization... bias field = 1.015 +- 0.035 71 of 12444 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 9 seconds. #-------------------------------------- #@# CA Reg Tue Aug 8 00:01:54 UTC 2017 /out/freesurfer/sub-05/mri mri_ca_register -rusage /out/freesurfer/sub-05/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/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 = 7 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.48 (predicted orig area = 5.4) 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=1.114, neg=0, invalid=762 0001: dt=336.053138, rms=1.002 (10.056%), neg=0, invalid=762 0002: dt=295.936000, rms=0.955 (4.707%), neg=0, invalid=762 0003: dt=221.952000, rms=0.924 (3.227%), neg=0, invalid=762 0004: dt=247.540870, rms=0.909 (1.636%), neg=0, invalid=762 0005: dt=237.500344, rms=0.894 (1.632%), neg=0, invalid=762 0006: dt=180.844037, rms=0.887 (0.867%), neg=0, invalid=762 0007: dt=369.920000, rms=0.878 (0.908%), neg=0, invalid=762 0008: dt=137.620915, rms=0.873 (0.671%), neg=0, invalid=762 0009: dt=1183.744000, rms=0.863 (1.112%), neg=0, invalid=762 0010: dt=133.093426, rms=0.854 (1.071%), neg=0, invalid=762 0011: dt=1183.744000, rms=0.847 (0.722%), neg=0, invalid=762 0012: dt=110.976000, rms=0.843 (0.556%), neg=0, invalid=762 0013: dt=887.808000, rms=0.839 (0.438%), neg=0, invalid=762 0014: dt=129.472000, rms=0.836 (0.308%), neg=0, invalid=762 0015: dt=517.888000, rms=0.836 (0.113%), neg=0, invalid=762 0016: dt=517.888000, rms=0.833 (0.269%), neg=0, invalid=762 0017: dt=517.888000, rms=0.833 (-3.544%), neg=0, invalid=762 0018: dt=73.984000, rms=0.831 (0.228%), neg=0, invalid=762 0019: dt=27.744000, rms=0.831 (0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.833, neg=0, invalid=762 0020: dt=92.480000, rms=0.831 (0.174%), neg=0, invalid=762 0021: dt=129.472000, rms=0.831 (0.024%), neg=0, invalid=762 0022: dt=129.472000, rms=0.831 (0.014%), neg=0, invalid=762 0023: dt=129.472000, rms=0.831 (-0.007%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.840, neg=0, invalid=762 0024: dt=145.152000, rms=0.826 (1.593%), neg=0, invalid=762 0025: dt=75.182796, rms=0.810 (1.981%), neg=0, invalid=762 0026: dt=25.920000, rms=0.808 (0.212%), neg=0, invalid=762 0027: dt=25.920000, rms=0.807 (0.091%), neg=0, invalid=762 0028: dt=25.920000, rms=0.807 (0.118%), neg=0, invalid=762 0029: dt=25.920000, rms=0.802 (0.544%), neg=0, invalid=762 0030: dt=25.920000, rms=0.794 (1.037%), neg=0, invalid=762 0031: dt=25.920000, rms=0.792 (0.220%), neg=0, invalid=762 0032: dt=25.920000, rms=0.790 (0.294%), neg=0, invalid=762 0033: dt=25.920000, rms=0.787 (0.307%), neg=0, invalid=762 0034: dt=25.920000, rms=0.785 (0.321%), neg=0, invalid=762 0035: dt=25.920000, rms=0.781 (0.423%), neg=0, invalid=762 0036: dt=25.920000, rms=0.777 (0.632%), neg=0, invalid=762 0037: dt=25.920000, rms=0.775 (0.190%), neg=0, invalid=762 0038: dt=25.920000, rms=0.773 (0.204%), neg=0, invalid=762 0039: dt=25.920000, rms=0.772 (0.170%), neg=0, invalid=762 0040: dt=25.920000, rms=0.771 (0.164%), neg=0, invalid=762 0041: dt=25.920000, rms=0.769 (0.253%), neg=0, invalid=762 0042: dt=25.920000, rms=0.766 (0.406%), neg=0, invalid=762 0043: dt=25.920000, rms=0.765 (0.119%), neg=0, invalid=762 0044: dt=25.920000, rms=0.764 (0.153%), neg=0, invalid=762 0045: dt=25.920000, rms=0.763 (0.104%), neg=0, invalid=762 0046: dt=25.920000, rms=0.762 (0.083%), neg=0, invalid=762 0047: dt=36.288000, rms=0.761 (0.134%), neg=0, invalid=762 0048: dt=145.152000, rms=0.759 (0.320%), neg=0, invalid=762 0049: dt=20.736000, rms=0.759 (0.005%), neg=0, invalid=762 0050: dt=20.736000, rms=0.759 (0.020%), neg=0, invalid=762 0051: dt=20.736000, rms=0.758 (0.052%), neg=0, invalid=762 0052: dt=20.736000, rms=0.758 (0.088%), neg=0, invalid=762 0053: dt=20.736000, rms=0.757 (0.111%), neg=0, invalid=762 0054: dt=20.736000, rms=0.756 (0.154%), neg=0, invalid=762 0055: dt=20.736000, rms=0.754 (0.153%), neg=0, invalid=762 0056: dt=20.736000, rms=0.753 (0.163%), neg=0, invalid=762 0057: dt=20.736000, rms=0.752 (0.152%), neg=0, invalid=762 0058: dt=20.736000, rms=0.751 (0.160%), neg=0, invalid=762 0059: dt=20.736000, rms=0.750 (0.168%), neg=0, invalid=762 0060: dt=20.736000, rms=0.748 (0.189%), neg=0, invalid=762 0061: dt=20.736000, rms=0.747 (0.191%), neg=0, invalid=762 0062: dt=20.736000, rms=0.745 (0.174%), neg=0, invalid=762 0063: dt=20.736000, rms=0.744 (0.169%), neg=0, invalid=762 0064: dt=20.736000, rms=0.743 (0.143%), neg=0, invalid=762 0065: dt=20.736000, rms=0.742 (0.120%), neg=0, invalid=762 0066: dt=20.736000, rms=0.741 (0.132%), neg=0, invalid=762 0067: dt=20.736000, rms=0.740 (0.148%), neg=0, invalid=762 0068: dt=20.736000, rms=0.739 (0.150%), neg=0, invalid=762 0069: dt=20.736000, rms=0.738 (0.143%), neg=0, invalid=762 0070: dt=20.736000, rms=0.737 (0.122%), neg=0, invalid=762 0071: dt=20.736000, rms=0.736 (0.107%), neg=0, invalid=762 0072: dt=0.000000, rms=0.736 (0.007%), neg=0, invalid=762 0073: dt=0.450000, rms=0.736 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.737, neg=0, invalid=762 0074: dt=6.480000, rms=0.736 (0.122%), neg=0, invalid=762 0075: dt=2.268000, rms=0.736 (-0.012%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.778, neg=0, invalid=762 0076: dt=1.600000, rms=0.777 (0.103%), neg=0, invalid=762 0077: dt=0.700000, rms=0.777 (0.010%), neg=0, invalid=762 0078: dt=0.700000, rms=0.777 (0.005%), neg=0, invalid=762 0079: dt=0.700000, rms=0.777 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.778, neg=0, invalid=762 0080: dt=0.031250, rms=0.777 (0.106%), neg=0, invalid=762 0081: dt=0.000000, rms=0.777 (0.000%), neg=0, invalid=762 0082: dt=0.250000, rms=0.777 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.895, neg=0, invalid=762 0083: dt=5.973046, rms=0.869 (2.913%), neg=0, invalid=762 0084: dt=4.032000, rms=0.862 (0.809%), neg=0, invalid=762 0085: dt=3.456000, rms=0.861 (0.104%), neg=0, invalid=762 0086: dt=3.456000, rms=0.861 (0.010%), neg=0, invalid=762 0087: dt=3.456000, rms=0.861 (-0.219%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.862, neg=0, invalid=762 0088: dt=0.000000, rms=0.861 (0.098%), neg=0, invalid=762 0089: dt=0.000000, rms=0.861 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.971, neg=0, invalid=762 0090: dt=0.000000, rms=0.970 (0.077%), neg=0, invalid=762 0091: dt=0.000000, rms=0.970 (0.000%), neg=0, invalid=762 0092: dt=0.100000, rms=0.970 (-0.015%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.971, neg=0, invalid=762 0093: dt=0.112000, rms=0.970 (0.082%), neg=0, invalid=762 0094: dt=0.112000, rms=0.970 (0.003%), neg=0, invalid=762 0095: dt=0.112000, rms=0.970 (0.002%), neg=0, invalid=762 0096: dt=0.112000, rms=0.970 (-0.004%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.787, neg=0, invalid=762 0097: dt=0.384000, rms=0.769 (2.336%), neg=0, invalid=762 0098: dt=0.000000, rms=0.769 (0.001%), neg=0, invalid=762 0099: dt=0.050000, rms=0.769 (-0.198%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.770, neg=0, invalid=762 0100: dt=0.000000, rms=0.769 (0.122%), neg=0, invalid=762 0101: dt=0.000000, rms=0.769 (0.000%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.08624 (15) Left_Lateral_Ventricle (4): linear fit = 0.12 x + 0.0 (281 voxels, overlap=0.460) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (281 voxels, peak = 2), gca=8.0 gca peak = 0.15565 (16) mri peak = 0.06960 (29) Right_Lateral_Ventricle (43): linear fit = 1.84 x + 0.0 (381 voxels, overlap=0.262) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (381 voxels, peak = 29), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.11592 (102) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (535 voxels, overlap=0.998) Right_Pallidum (52): linear fit = 1.07 x + 0.0 (535 voxels, peak = 102), gca=102.2 gca peak = 0.20183 (93) mri peak = 0.42620 (101) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (664 voxels, overlap=0.090) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (664 voxels, peak = 99), gca=99.0 gca peak = 0.21683 (55) mri peak = 0.13402 (54) Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (290 voxels, overlap=0.986) Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (290 voxels, peak = 50), gca=50.3 gca peak = 0.30730 (58) mri peak = 0.09113 (56) Left_Hippocampus (17): linear fit = 0.96 x + 0.0 (229 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 0.96 x + 0.0 (229 voxels, peak = 56), gca=56.0 gca peak = 0.11430 (101) mri peak = 0.15440 (108) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (44829 voxels, overlap=0.549) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (44829 voxels, peak = 107), gca=106.6 gca peak = 0.12076 (102) mri peak = 0.26164 (106) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (44096 voxels, overlap=0.353) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (44096 voxels, peak = 105), gca=104.5 gca peak = 0.14995 (59) mri peak = 0.04968 (40) Left_Cerebral_Cortex (3): linear fit = 0.75 x + 0.0 (4808 voxels, overlap=0.001) Left_Cerebral_Cortex (3): linear fit = 0.75 x + 0.0 (4808 voxels, peak = 44), gca=44.0 gca peak = 0.15082 (58) mri peak = 0.03494 (40) Right_Cerebral_Cortex (42): linear fit = 1.51 x + 0.0 (12253 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.51 x + 0.0 (12253 voxels, peak = 88), gca=87.9 gca peak = 0.14161 (67) mri peak = 0.09910 (50) Right_Caudate (50): linear fit = 0.82 x + 0.0 (302 voxels, overlap=0.309) Right_Caudate (50): linear fit = 0.82 x + 0.0 (302 voxels, peak = 55), gca=55.3 gca peak = 0.15243 (71) mri peak = 0.08445 (65) Left_Caudate (11): linear fit = 0.90 x + 0.0 (459 voxels, overlap=0.543) Left_Caudate (11): linear fit = 0.90 x + 0.0 (459 voxels, peak = 64), gca=64.3 gca peak = 0.13336 (57) mri peak = 0.03218 (36) Left_Cerebellum_Cortex (8): linear fit = 0.80 x + 0.0 (7451 voxels, overlap=0.020) Left_Cerebellum_Cortex (8): linear fit = 0.80 x + 0.0 (7451 voxels, peak = 45), gca=45.3 gca peak = 0.13252 (56) mri peak = 0.03875 (43) Right_Cerebellum_Cortex (47): linear fit = 0.75 x + 0.0 (9529 voxels, overlap=0.062) Right_Cerebellum_Cortex (47): linear fit = 0.75 x + 0.0 (9529 voxels, peak = 42), gca=41.7 gca peak = 0.18181 (84) mri peak = 0.11936 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5441 voxels, overlap=0.893) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5441 voxels, peak = 90), gca=90.3 gca peak = 0.20573 (83) mri peak = 0.10069 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (4606 voxels, overlap=0.749) Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (4606 voxels, peak = 90), gca=90.1 gca peak = 0.21969 (57) mri peak = 0.10346 (57) Left_Amygdala (18): linear fit = 0.96 x + 0.0 (110 voxels, overlap=0.861) Left_Amygdala (18): linear fit = 0.96 x + 0.0 (110 voxels, peak = 55), gca=55.0 gca peak = 0.39313 (56) mri peak = 0.13492 (50) Right_Amygdala (54): linear fit = 0.92 x + 0.0 (219 voxels, overlap=0.859) Right_Amygdala (54): linear fit = 0.92 x + 0.0 (219 voxels, peak = 51), gca=51.2 gca peak = 0.14181 (85) mri peak = 0.15240 (102) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (3115 voxels, overlap=0.270) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (3115 voxels, peak = 96), gca=96.5 gca peak = 0.11978 (83) mri peak = 0.08468 (102) Right_Thalamus_Proper (49): linear fit = 1.17 x + 0.0 (2254 voxels, overlap=0.221) Right_Thalamus_Proper (49): linear fit = 1.17 x + 0.0 (2254 voxels, peak = 98), gca=97.5 gca peak = 0.13399 (79) mri peak = 0.05347 (84) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1075 voxels, overlap=0.494) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1075 voxels, peak = 87), gca=86.5 gca peak = 0.14159 (79) mri peak = 0.06647 (70) Right_Putamen (51): linear fit = 0.89 x + 0.0 (940 voxels, overlap=0.722) Right_Putamen (51): linear fit = 0.89 x + 0.0 (940 voxels, peak = 71), gca=70.7 gca peak = 0.10025 (80) mri peak = 0.09183 (94) Brain_Stem (16): linear fit = 1.16 x + 0.0 (7003 voxels, overlap=0.403) Brain_Stem (16): linear fit = 1.16 x + 0.0 (7003 voxels, peak = 93), gca=93.2 gca peak = 0.13281 (86) mri peak = 0.23599 (99) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1121 voxels, overlap=0.111) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1121 voxels, peak = 97), gca=96.8 gca peak = 0.12801 (89) mri peak = 0.41525 (98) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1131 voxels, overlap=0.052) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1131 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) mri peak = 0.11147 ( 3) gca peak = 0.15061 (21) mri peak = 0.04705 (51) Fourth_Ventricle (15): linear fit = 2.38 x + 0.0 (62 voxels, overlap=0.185) Fourth_Ventricle (15): linear fit = 2.38 x + 0.0 (62 voxels, peak = 50), gca=50.1 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_Cerebral_Cortex = 0.15082 (58) 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 setting label Right_Cerebral_Cortex based on Left_Cerebral_Cortex = 0.75 x + 0: 44 estimating mean gm scale to be 0.88 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.95 x + 0.0 Right_Pallidum too bright - rescaling by 1.001 (from 1.065) to 102.4 (was 102.2) 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=0.815, neg=0, invalid=762 0102: dt=78.500000, rms=0.805 (1.223%), neg=0, invalid=762 0103: dt=8.092000, rms=0.805 (0.049%), neg=0, invalid=762 0104: dt=0.505750, rms=0.805 (0.003%), neg=0, invalid=762 0105: dt=0.031609, rms=0.805 (0.000%), neg=0, invalid=762 0106: dt=0.003951, rms=0.805 (0.000%), neg=0, invalid=762 0107: dt=0.000000, rms=0.805 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.806, neg=0, invalid=762 0108: dt=0.000000, rms=0.805 (0.129%), neg=0, invalid=762 0109: dt=0.000000, rms=0.805 (0.000%), neg=0, invalid=762 0110: dt=0.001660, rms=0.805 (0.000%), neg=0, invalid=762 0111: dt=0.000830, rms=0.805 (0.000%), neg=0, invalid=762 0112: dt=0.000208, rms=0.805 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.806, neg=0, invalid=762 0113: dt=0.000000, rms=0.805 (0.129%), neg=0, invalid=762 0114: dt=0.000000, rms=0.805 (0.000%), neg=0, invalid=762 0115: dt=0.000014, rms=0.805 (0.000%), neg=0, invalid=762 0116: dt=0.000007, rms=0.805 (0.000%), neg=0, invalid=762 0117: dt=0.000000, rms=0.805 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.806, neg=0, invalid=762 0118: dt=0.000000, rms=0.805 (0.129%), neg=0, invalid=762 0119: dt=0.000000, rms=0.805 (0.000%), neg=0, invalid=762 0120: dt=0.000000, rms=0.805 (0.000%), neg=0, invalid=762 0121: dt=0.000000, rms=0.805 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.806, neg=0, invalid=762 0122: dt=0.000000, rms=0.805 (0.129%), neg=0, invalid=762 0123: dt=0.000000, rms=0.805 (0.000%), neg=0, invalid=762 0124: dt=0.000000, rms=0.805 (0.000%), neg=0, invalid=762 0125: dt=0.000000, rms=0.805 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.806, neg=0, invalid=762 0126: dt=0.000000, rms=0.805 (0.129%), neg=0, invalid=762 0127: dt=0.000000, rms=0.805 (0.000%), neg=0, invalid=762 0128: dt=0.000000, rms=0.805 (0.000%), neg=0, invalid=762 0129: dt=0.000000, rms=0.805 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.806, neg=0, invalid=762 0130: dt=0.000000, rms=0.805 (0.129%), neg=0, invalid=762 0131: dt=0.000000, rms=0.805 (0.000%), neg=0, invalid=762 0132: dt=0.000000, rms=0.805 (0.000%), neg=0, invalid=762 0133: dt=0.000000, rms=0.805 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.806, neg=0, invalid=762 0134: dt=0.000000, rms=0.805 (0.129%), neg=0, invalid=762 0135: dt=0.000000, rms=0.805 (0.000%), neg=0, invalid=762 0136: dt=0.000000, rms=0.805 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.806, neg=0, invalid=762 0137: dt=1.280000, rms=0.778 (3.508%), neg=0, invalid=762 0138: dt=0.448000, rms=0.772 (0.840%), neg=0, invalid=762 0139: dt=1.280000, rms=0.755 (2.203%), neg=0, invalid=762 0140: dt=0.448000, rms=0.751 (0.536%), neg=0, invalid=762 0141: dt=0.448000, rms=0.747 (0.486%), neg=0, invalid=762 0142: dt=0.448000, rms=0.744 (0.434%), neg=0, invalid=762 0143: dt=0.448000, rms=0.741 (0.395%), neg=0, invalid=762 0144: dt=0.448000, rms=0.738 (0.353%), neg=0, invalid=762 0145: dt=0.448000, rms=0.736 (0.317%), neg=0, invalid=762 0146: dt=0.448000, rms=0.734 (0.290%), neg=0, invalid=762 0147: dt=0.448000, rms=0.732 (0.259%), neg=0, invalid=762 0148: dt=1.187500, rms=0.727 (0.624%), neg=0, invalid=762 0149: dt=1.280000, rms=0.724 (0.490%), neg=0, invalid=762 0150: dt=1.280000, rms=0.721 (0.384%), neg=0, invalid=762 0151: dt=1.280000, rms=0.719 (0.305%), neg=0, invalid=762 0152: dt=0.448000, rms=0.718 (0.098%), neg=0, invalid=762 0153: dt=0.448000, rms=0.717 (0.095%), neg=0, invalid=762 0154: dt=0.448000, rms=0.717 (0.084%), neg=0, invalid=762 0155: dt=0.448000, rms=0.716 (0.087%), neg=0, invalid=762 0156: dt=0.448000, rms=0.715 (0.072%), neg=0, invalid=762 0157: dt=0.448000, rms=0.715 (0.072%), neg=0, invalid=762 0158: dt=0.448000, rms=0.714 (0.065%), neg=0, invalid=762 0159: dt=0.448000, rms=0.714 (0.065%), neg=0, invalid=762 0160: dt=0.448000, rms=0.714 (0.057%), neg=0, invalid=762 0161: dt=0.448000, rms=0.713 (0.057%), neg=0, invalid=762 0162: dt=0.448000, rms=0.713 (0.052%), neg=0, invalid=762 0163: dt=0.448000, rms=0.712 (0.053%), neg=0, invalid=762 0164: dt=0.448000, rms=0.712 (0.047%), neg=0, invalid=762 0165: dt=0.448000, rms=0.712 (0.047%), neg=0, invalid=762 0166: dt=0.448000, rms=0.711 (0.087%), neg=0, invalid=762 0167: dt=0.448000, rms=0.710 (0.117%), neg=0, invalid=762 0168: dt=0.448000, rms=0.709 (0.142%), neg=0, invalid=762 0169: dt=0.448000, rms=0.708 (0.164%), neg=0, invalid=762 0170: dt=0.448000, rms=0.707 (0.169%), neg=0, invalid=762 0171: dt=0.448000, rms=0.706 (0.167%), neg=0, invalid=762 0172: dt=0.448000, rms=0.705 (0.160%), neg=0, invalid=762 0173: dt=0.448000, rms=0.704 (0.156%), neg=0, invalid=762 0174: dt=0.448000, rms=0.703 (0.138%), neg=0, invalid=762 0175: dt=0.448000, rms=0.702 (0.115%), neg=0, invalid=762 0176: dt=0.448000, rms=0.701 (0.093%), neg=0, invalid=762 0177: dt=0.448000, rms=0.701 (0.085%), neg=0, invalid=762 0178: dt=0.448000, rms=0.700 (0.071%), neg=0, invalid=762 0179: dt=0.448000, rms=0.700 (0.053%), neg=0, invalid=762 0180: dt=0.448000, rms=0.699 (0.041%), neg=0, invalid=762 0181: dt=0.448000, rms=0.699 (0.029%), neg=0, invalid=762 0182: dt=0.448000, rms=0.699 (0.023%), neg=0, invalid=762 0183: dt=0.448000, rms=0.699 (0.021%), neg=0, invalid=762 0184: dt=0.000000, rms=0.699 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.700, neg=0, invalid=762 0185: dt=0.448000, rms=0.698 (0.231%), neg=0, invalid=762 0186: dt=0.448000, rms=0.698 (0.091%), neg=0, invalid=762 0187: dt=0.448000, rms=0.697 (0.078%), neg=0, invalid=762 0188: dt=0.448000, rms=0.697 (0.073%), neg=0, invalid=762 0189: dt=0.448000, rms=0.696 (0.063%), neg=0, invalid=762 0190: dt=0.448000, rms=0.696 (0.056%), neg=0, invalid=762 0191: dt=0.448000, rms=0.695 (0.052%), neg=0, invalid=762 0192: dt=0.448000, rms=0.695 (0.045%), neg=0, invalid=762 0193: dt=0.448000, rms=0.695 (0.042%), neg=0, invalid=762 0194: dt=0.448000, rms=0.694 (0.080%), neg=0, invalid=762 0195: dt=0.448000, rms=0.693 (0.098%), neg=0, invalid=762 0196: dt=0.448000, rms=0.693 (0.111%), neg=0, invalid=762 0197: dt=0.448000, rms=0.692 (0.112%), neg=0, invalid=762 0198: dt=0.448000, rms=0.691 (0.105%), neg=0, invalid=762 0199: dt=0.448000, rms=0.691 (0.086%), neg=0, invalid=762 0200: dt=0.448000, rms=0.690 (0.077%), neg=0, invalid=762 0201: dt=0.448000, rms=0.690 (0.066%), neg=0, invalid=762 0202: dt=0.448000, rms=0.689 (0.053%), neg=0, invalid=762 0203: dt=0.448000, rms=0.689 (0.039%), neg=0, invalid=762 0204: dt=0.448000, rms=0.689 (0.037%), neg=0, invalid=762 0205: dt=0.448000, rms=0.689 (0.032%), neg=0, invalid=762 0206: dt=0.448000, rms=0.688 (0.034%), neg=0, invalid=762 0207: dt=0.448000, rms=0.688 (0.039%), neg=0, invalid=762 0208: dt=0.448000, rms=0.688 (0.037%), neg=0, invalid=762 0209: dt=0.448000, rms=0.687 (0.043%), neg=0, invalid=762 0210: dt=0.448000, rms=0.687 (0.038%), neg=0, invalid=762 0211: dt=0.448000, rms=0.687 (0.045%), neg=0, invalid=762 0212: dt=0.448000, rms=0.687 (0.039%), neg=0, invalid=762 0213: dt=0.448000, rms=0.686 (0.039%), neg=0, invalid=762 0214: dt=0.448000, rms=0.686 (0.033%), neg=0, invalid=762 0215: dt=0.448000, rms=0.686 (0.029%), neg=0, invalid=762 0216: dt=0.448000, rms=0.686 (-0.002%), neg=0, invalid=762 0217: dt=0.112000, rms=0.686 (0.000%), neg=0, invalid=762 0218: dt=0.112000, rms=0.686 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.678, neg=0, invalid=762 0219: dt=0.112000, rms=0.672 (0.976%), neg=0, invalid=762 0220: dt=0.112000, rms=0.667 (0.720%), neg=0, invalid=762 0221: dt=0.112000, rms=0.663 (0.602%), neg=0, invalid=762 0222: dt=0.112000, rms=0.659 (0.508%), neg=0, invalid=762 0223: dt=0.112000, rms=0.657 (0.416%), neg=0, invalid=762 0224: dt=0.112000, rms=0.654 (0.357%), neg=0, invalid=762 0225: dt=0.112000, rms=0.652 (0.294%), neg=0, invalid=762 0226: dt=0.112000, rms=0.651 (0.256%), neg=0, invalid=762 0227: dt=0.177885, rms=0.649 (0.328%), neg=0, invalid=762 0228: dt=0.153409, rms=0.647 (0.239%), neg=0, invalid=762 0229: dt=0.112000, rms=0.646 (0.145%), neg=0, invalid=762 0230: dt=0.112000, rms=0.645 (0.130%), neg=0, invalid=762 0231: dt=0.112000, rms=0.645 (0.112%), neg=0, invalid=762 0232: dt=0.112000, rms=0.644 (0.105%), neg=0, invalid=762 0233: dt=0.112000, rms=0.643 (0.088%), neg=0, invalid=762 0234: dt=0.112000, rms=0.643 (0.086%), neg=0, invalid=762 0235: dt=0.112000, rms=0.642 (0.072%), neg=0, invalid=762 0236: dt=0.112000, rms=0.642 (0.072%), neg=0, invalid=762 0237: dt=0.112000, rms=0.641 (0.059%), neg=0, invalid=762 0238: dt=0.112000, rms=0.641 (0.065%), neg=0, invalid=762 0239: dt=0.112000, rms=0.641 (0.052%), neg=0, invalid=762 0240: dt=0.112000, rms=0.640 (0.055%), neg=0, invalid=762 0241: dt=0.112000, rms=0.640 (0.046%), neg=0, invalid=762 0242: dt=0.112000, rms=0.640 (0.047%), neg=0, invalid=762 0243: dt=0.112000, rms=0.639 (0.084%), neg=0, invalid=762 0244: dt=0.112000, rms=0.638 (0.110%), neg=0, invalid=762 0245: dt=0.112000, rms=0.638 (0.135%), neg=0, invalid=762 0246: dt=0.112000, rms=0.637 (0.153%), neg=0, invalid=762 0247: dt=0.112000, rms=0.636 (0.144%), neg=0, invalid=762 0248: dt=0.112000, rms=0.635 (0.130%), neg=0, invalid=762 0249: dt=0.112000, rms=0.634 (0.125%), neg=0, invalid=762 0250: dt=0.112000, rms=0.633 (0.107%), neg=0, invalid=762 0251: dt=0.112000, rms=0.633 (0.091%), neg=0, invalid=762 0252: dt=0.112000, rms=0.632 (0.071%), neg=0, invalid=762 0253: dt=0.112000, rms=0.632 (0.056%), neg=0, invalid=762 0254: dt=0.112000, rms=0.632 (0.047%), neg=0, invalid=762 0255: dt=0.112000, rms=0.632 (0.030%), neg=0, invalid=762 0256: dt=0.112000, rms=0.632 (-0.006%), neg=0, invalid=762 0257: dt=0.028000, rms=0.632 (0.001%), neg=0, invalid=762 0258: dt=0.064000, rms=0.632 (0.003%), neg=0, invalid=762 0259: dt=0.080000, rms=0.632 (0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.633, neg=0, invalid=762 0260: dt=0.112000, rms=0.630 (0.467%), neg=0, invalid=762 0261: dt=0.112000, rms=0.628 (0.245%), neg=0, invalid=762 0262: dt=0.130682, rms=0.627 (0.199%), neg=0, invalid=762 0263: dt=0.112000, rms=0.626 (0.136%), neg=0, invalid=762 0264: dt=0.112000, rms=0.625 (0.095%), neg=0, invalid=762 0265: dt=0.112000, rms=0.625 (0.075%), neg=0, invalid=762 0266: dt=0.112000, rms=0.625 (0.048%), neg=0, invalid=762 0267: dt=0.112000, rms=0.624 (0.044%), neg=0, invalid=762 0268: dt=0.112000, rms=0.624 (0.063%), neg=0, invalid=762 0269: dt=0.112000, rms=0.624 (0.051%), neg=0, invalid=762 0270: dt=0.112000, rms=0.623 (0.043%), neg=0, invalid=762 0271: dt=0.112000, rms=0.623 (-0.022%), neg=0, invalid=762 0272: dt=0.000000, rms=0.623 (0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.621, neg=0, invalid=762 0273: dt=23.120000, rms=0.620 (0.177%), neg=0, invalid=762 0274: dt=8.092000, rms=0.620 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.621, neg=0, invalid=762 0275: dt=32.368000, rms=0.620 (0.170%), neg=0, invalid=762 0276: dt=55.488000, rms=0.620 (0.013%), neg=0, invalid=762 0277: dt=55.488000, rms=0.620 (0.013%), neg=0, invalid=762 0278: dt=55.488000, rms=0.619 (0.006%), neg=0, invalid=762 0279: dt=55.488000, rms=0.619 (-0.017%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.621, neg=0, invalid=762 0280: dt=19.310345, rms=0.619 (0.236%), neg=0, invalid=762 0281: dt=6.480000, rms=0.619 (0.005%), neg=0, invalid=762 0282: dt=6.480000, rms=0.619 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.620, neg=0, invalid=762 0283: dt=36.288000, rms=0.618 (0.322%), neg=0, invalid=762 0284: dt=103.680000, rms=0.617 (0.142%), neg=0, invalid=762 0285: dt=103.680000, rms=0.617 (-0.406%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.618, neg=0, invalid=762 iter 0, gcam->neg = 30 after 9 iterations, nbhd size=0, neg = 0 0286: dt=31.920200, rms=0.611 (1.152%), neg=0, invalid=762 iter 0, gcam->neg = 41 after 5 iterations, nbhd size=0, neg = 0 0287: dt=19.200000, rms=0.609 (0.303%), neg=0, invalid=762 iter 0, gcam->neg = 70 after 15 iterations, nbhd size=1, neg = 0 0288: dt=25.539906, rms=0.608 (0.193%), neg=0, invalid=762 iter 0, gcam->neg = 104 after 17 iterations, nbhd size=1, neg = 0 0289: dt=25.539906, rms=0.608 (0.050%), neg=0, invalid=762 iter 0, gcam->neg = 197 after 22 iterations, nbhd size=1, neg = 0 0290: dt=25.539906, rms=0.608 (0.024%), neg=0, invalid=762 iter 0, gcam->neg = 301 after 27 iterations, nbhd size=1, neg = 0 0291: dt=25.539906, rms=0.608 (-0.209%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.609, neg=0, invalid=762 iter 0, gcam->neg = 27 after 7 iterations, nbhd size=0, neg = 0 0292: dt=30.600583, rms=0.603 (0.937%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 15 iterations, nbhd size=1, neg = 0 0293: dt=30.393013, rms=0.600 (0.556%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 2 iterations, nbhd size=0, neg = 0 0294: dt=11.200000, rms=0.598 (0.280%), neg=0, invalid=762 iter 0, gcam->neg = 42 after 7 iterations, nbhd size=0, neg = 0 0295: dt=44.800000, rms=0.596 (0.302%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 14 iterations, nbhd size=1, neg = 0 0296: dt=25.600000, rms=0.595 (0.131%), neg=0, invalid=762 iter 0, gcam->neg = 30 after 4 iterations, nbhd size=0, neg = 0 0297: dt=25.600000, rms=0.594 (0.167%), neg=0, invalid=762 iter 0, gcam->neg = 36 after 5 iterations, nbhd size=0, neg = 0 0298: dt=25.600000, rms=0.593 (0.252%), neg=0, invalid=762 iter 0, gcam->neg = 22 after 18 iterations, nbhd size=0, neg = 0 0299: dt=25.600000, rms=0.592 (0.187%), neg=0, invalid=762 iter 0, gcam->neg = 59 after 6 iterations, nbhd size=0, neg = 0 0300: dt=25.600000, rms=0.590 (0.365%), neg=0, invalid=762 iter 0, gcam->neg = 134 after 19 iterations, nbhd size=1, neg = 0 0301: dt=25.600000, rms=0.589 (0.190%), neg=0, invalid=762 iter 0, gcam->neg = 318 after 29 iterations, nbhd size=1, neg = 0 0302: dt=25.600000, rms=0.587 (0.187%), neg=0, invalid=762 iter 0, gcam->neg = 242 after 23 iterations, nbhd size=1, neg = 0 0303: dt=25.600000, rms=0.586 (0.207%), neg=0, invalid=762 iter 0, gcam->neg = 255 after 21 iterations, nbhd size=1, neg = 0 0304: dt=25.600000, rms=0.585 (0.181%), neg=0, invalid=762 iter 0, gcam->neg = 247 after 23 iterations, nbhd size=1, neg = 0 0305: dt=25.600000, rms=0.585 (0.035%), neg=0, invalid=762 iter 0, gcam->neg = 493 after 27 iterations, nbhd size=1, neg = 0 0306: dt=25.600000, rms=0.585 (-0.166%), neg=0, invalid=762 iter 0, gcam->neg = 69 after 20 iterations, nbhd size=1, neg = 0 0307: dt=21.733788, rms=0.583 (0.287%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 4 iterations, nbhd size=0, neg = 0 0308: dt=11.200000, rms=0.583 (0.065%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 3 iterations, nbhd size=0, neg = 0 0309: dt=11.200000, rms=0.583 (0.038%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 2 iterations, nbhd size=0, neg = 0 0310: dt=11.200000, rms=0.582 (0.044%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 25 iterations, nbhd size=2, neg = 0 0311: dt=11.200000, rms=0.582 (-0.085%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.591, neg=0, invalid=762 iter 0, gcam->neg = 19 after 9 iterations, nbhd size=0, neg = 0 0312: dt=5.032258, rms=0.589 (0.282%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 7 iterations, nbhd size=0, neg = 0 0313: dt=3.304348, rms=0.589 (0.027%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 10 iterations, nbhd size=0, neg = 0 0314: dt=3.304348, rms=0.589 (0.010%), neg=0, invalid=762 iter 0, gcam->neg = 36 after 17 iterations, nbhd size=1, neg = 0 0315: dt=3.304348, rms=0.589 (-0.053%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.590, neg=0, invalid=762 iter 0, gcam->neg = 5 after 4 iterations, nbhd size=0, neg = 0 0316: dt=3.000000, rms=0.589 (0.211%), neg=0, invalid=762 iter 0, gcam->neg = 52 after 8 iterations, nbhd size=0, neg = 0 0317: dt=6.666667, rms=0.588 (0.088%), neg=0, invalid=762 iter 0, gcam->neg = 48 after 21 iterations, nbhd size=1, neg = 0 0318: dt=6.666667, rms=0.588 (0.084%), neg=0, invalid=762 iter 0, gcam->neg = 56 after 18 iterations, nbhd size=1, neg = 0 0319: dt=6.666667, rms=0.587 (0.174%), neg=0, invalid=762 iter 0, gcam->neg = 95 after 20 iterations, nbhd size=1, neg = 0 0320: dt=6.666667, rms=0.586 (0.037%), neg=0, invalid=762 iter 0, gcam->neg = 143 after 20 iterations, nbhd size=1, neg = 0 0321: dt=6.666667, rms=0.585 (0.188%), neg=0, invalid=762 iter 0, gcam->neg = 193 after 18 iterations, nbhd size=1, neg = 0 0322: dt=6.666667, rms=0.583 (0.398%), neg=0, invalid=762 iter 0, gcam->neg = 286 after 28 iterations, nbhd size=1, neg = 0 0323: dt=6.666667, rms=0.580 (0.503%), neg=0, invalid=762 iter 0, gcam->neg = 331 after 26 iterations, nbhd size=1, neg = 0 0324: dt=6.666667, rms=0.577 (0.498%), neg=0, invalid=762 iter 0, gcam->neg = 427 after 29 iterations, nbhd size=2, neg = 0 0325: dt=6.666667, rms=0.576 (0.195%), neg=0, invalid=762 iter 0, gcam->neg = 497 after 25 iterations, nbhd size=1, neg = 0 0326: dt=6.666667, rms=0.575 (0.214%), neg=0, invalid=762 iter 0, gcam->neg = 666 after 24 iterations, nbhd size=1, neg = 0 0327: dt=6.666667, rms=0.574 (0.105%), neg=0, invalid=762 iter 0, gcam->neg = 808 after 27 iterations, nbhd size=1, neg = 0 0328: dt=6.666667, rms=0.574 (-0.139%), neg=0, invalid=762 iter 0, gcam->neg = 200 after 24 iterations, nbhd size=1, neg = 0 0329: dt=8.000000, rms=0.574 (0.003%), neg=0, invalid=762 iter 0, gcam->neg = 42 after 5 iterations, nbhd size=0, neg = 0 0330: dt=4.032000, rms=0.574 (0.029%), neg=0, invalid=762 0331: dt=1.008000, rms=0.574 (0.004%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.583, neg=0, invalid=762 0332: dt=0.000000, rms=0.582 (0.177%), neg=0, invalid=762 0333: dt=0.000000, rms=0.582 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.583, neg=0, invalid=762 0334: dt=0.000000, rms=0.582 (0.177%), neg=0, invalid=762 0335: dt=0.000000, rms=0.582 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.570, neg=0, invalid=762 iter 0, gcam->neg = 3860 after 22 iterations, nbhd size=1, neg = 0 0336: dt=0.776332, rms=0.557 (2.175%), neg=0, invalid=762 0337: dt=0.024000, rms=0.557 (0.009%), neg=0, invalid=762 0338: dt=0.024000, rms=0.557 (0.002%), neg=0, invalid=762 0339: dt=0.024000, rms=0.557 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.558, neg=0, invalid=762 iter 0, gcam->neg = 140 after 11 iterations, nbhd size=1, neg = 0 0340: dt=0.448000, rms=0.554 (0.715%), neg=0, invalid=762 iter 0, gcam->neg = 107 after 12 iterations, nbhd size=1, neg = 0 0341: dt=0.384000, rms=0.552 (0.415%), neg=0, invalid=762 iter 0, gcam->neg = 20 after 1 iterations, nbhd size=0, neg = 0 0342: dt=0.320000, rms=0.551 (0.246%), neg=0, invalid=762 iter 0, gcam->neg = 23 after 0 iterations, nbhd size=0, neg = 0 0343: dt=0.320000, rms=0.550 (0.125%), neg=0, invalid=762 iter 0, gcam->neg = 46 after 4 iterations, nbhd size=0, neg = 0 0344: dt=0.320000, rms=0.548 (0.272%), neg=0, invalid=762 iter 0, gcam->neg = 142 after 11 iterations, nbhd size=1, neg = 0 0345: dt=0.320000, rms=0.547 (0.200%), neg=0, invalid=762 iter 0, gcam->neg = 160 after 17 iterations, nbhd size=1, neg = 0 0346: dt=0.320000, rms=0.547 (-0.029%), neg=0, invalid=762 0347: dt=0.112000, rms=0.547 (0.091%), neg=0, invalid=762 0348: dt=0.112000, rms=0.547 (0.060%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.546, neg=0, invalid=762 0349: dt=0.505750, rms=0.546 (0.000%), neg=0, invalid=762 0350: dt=0.505750, rms=0.546 (0.000%), neg=0, invalid=762 0351: dt=0.505750, rms=0.546 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.546, neg=0, invalid=762 0352: dt=1.734000, rms=0.546 (0.000%), neg=0, invalid=762 0353: dt=1.734000, rms=0.546 (0.000%), neg=0, invalid=762 0354: dt=1.734000, rms=0.546 (0.000%), neg=0, invalid=762 0355: dt=1.734000, rms=0.546 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.546, neg=0, invalid=762 0356: dt=9.072000, rms=0.546 (0.042%), neg=0, invalid=762 0357: dt=3.888000, rms=0.546 (0.004%), neg=0, invalid=762 0358: dt=3.888000, rms=0.546 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.546, neg=0, invalid=762 0359: dt=67.047619, rms=0.545 (0.165%), neg=0, invalid=762 0360: dt=31.104000, rms=0.544 (0.068%), neg=0, invalid=762 0361: dt=31.104000, rms=0.544 (0.019%), neg=0, invalid=762 0362: dt=31.104000, rms=0.544 (0.027%), neg=0, invalid=762 0363: dt=31.104000, rms=0.544 (0.046%), neg=0, invalid=762 0364: dt=31.104000, rms=0.544 (0.035%), neg=0, invalid=762 0365: dt=31.104000, rms=0.544 (0.016%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.544, neg=0, invalid=762 0366: dt=9.600000, rms=0.543 (0.089%), neg=0, invalid=762 0367: dt=0.000000, rms=0.543 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.543, neg=0, invalid=762 0368: dt=23.388102, rms=0.542 (0.216%), neg=0, invalid=762 iter 0, gcam->neg = 155 after 21 iterations, nbhd size=1, neg = 0 0369: dt=33.806922, rms=0.540 (0.451%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0370: dt=6.400000, rms=0.539 (0.123%), neg=0, invalid=762 0371: dt=6.400000, rms=0.539 (-0.008%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.540, neg=0, invalid=762 iter 0, gcam->neg = 136 after 24 iterations, nbhd size=1, neg = 0 0372: dt=8.969199, rms=0.538 (0.350%), neg=0, invalid=762 iter 0, gcam->neg = 675 after 29 iterations, nbhd size=1, neg = 0 0373: dt=8.666667, rms=0.538 (-0.206%), neg=0, invalid=762 iter 0, gcam->neg = 675 after 29 iterations, nbhd size=1, neg = 0 0374: dt=8.666667, rms=0.538 (-0.206%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.538, neg=0, invalid=762 iter 0, gcam->neg = 611 after 24 iterations, nbhd size=1, neg = 0 0375: dt=8.732394, rms=0.536 (0.295%), neg=0, invalid=762 iter 0, gcam->neg = 73 after 22 iterations, nbhd size=1, neg = 0 0376: dt=5.150000, rms=0.535 (0.246%), neg=0, invalid=762 iter 0, gcam->neg = 44 after 16 iterations, nbhd size=1, neg = 0 0377: dt=5.150000, rms=0.532 (0.532%), neg=0, invalid=762 iter 0, gcam->neg = 52 after 16 iterations, nbhd size=1, neg = 0 0378: dt=5.150000, rms=0.531 (0.282%), neg=0, invalid=762 iter 0, gcam->neg = 108 after 20 iterations, nbhd size=1, neg = 0 0379: dt=5.150000, rms=0.530 (0.081%), neg=0, invalid=762 iter 0, gcam->neg = 180 after 21 iterations, nbhd size=1, neg = 0 0380: dt=5.150000, rms=0.529 (0.144%), neg=0, invalid=762 iter 0, gcam->neg = 306 after 32 iterations, nbhd size=1, neg = 0 0381: dt=5.150000, rms=0.528 (0.175%), neg=0, invalid=762 iter 0, gcam->neg = 407 after 24 iterations, nbhd size=1, neg = 0 0382: dt=5.150000, rms=0.527 (0.270%), neg=0, invalid=762 iter 0, gcam->neg = 625 after 33 iterations, nbhd size=1, neg = 0 0383: dt=5.150000, rms=0.527 (0.000%), neg=0, invalid=762 iter 0, gcam->neg = 736 after 30 iterations, nbhd size=1, neg = 0 0384: dt=5.150000, rms=0.527 (-0.204%), neg=0, invalid=762 iter 0, gcam->neg = 143 after 32 iterations, nbhd size=2, neg = 0 0385: dt=6.378378, rms=0.527 (-0.163%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.531, neg=0, invalid=762 0386: dt=0.000078, rms=0.531 (0.000%), neg=0, invalid=762 0387: dt=0.000000, rms=0.531 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.531, neg=0, invalid=762 0388: dt=0.000000, rms=0.531 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.524, neg=0, invalid=762 iter 0, gcam->neg = 2194 after 31 iterations, nbhd size=1, neg = 0 0389: dt=0.673780, rms=0.523 (0.186%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0390: dt=0.112000, rms=0.523 (0.096%), neg=0, invalid=762 0391: dt=0.112000, rms=0.522 (0.103%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0392: dt=0.112000, rms=0.522 (0.128%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0393: dt=0.112000, rms=0.521 (0.152%), neg=0, invalid=762 iter 0, gcam->neg = 45 after 13 iterations, nbhd size=1, neg = 0 0394: dt=0.112000, rms=0.521 (0.004%), neg=0, invalid=762 iter 0, gcam->neg = 13 after 3 iterations, nbhd size=0, neg = 0 0395: dt=0.112000, rms=0.519 (0.281%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 5 iterations, nbhd size=0, neg = 0 0396: dt=0.112000, rms=0.518 (0.348%), neg=0, invalid=762 iter 0, gcam->neg = 28 after 15 iterations, nbhd size=1, neg = 0 0397: dt=0.112000, rms=0.516 (0.325%), neg=0, invalid=762 iter 0, gcam->neg = 42 after 21 iterations, nbhd size=1, neg = 0 0398: dt=0.112000, rms=0.516 (-0.067%), neg=0, invalid=762 iter 0, gcam->neg = 72 after 6 iterations, nbhd size=0, neg = 0 0399: dt=0.256000, rms=0.515 (0.165%), neg=0, invalid=762 0400: dt=0.112000, rms=0.515 (0.072%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.515, neg=0, invalid=762 iter 0, gcam->neg = 1737 after 30 iterations, nbhd size=1, neg = 0 0401: dt=0.622137, rms=0.515 (-0.388%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 58 minutes and 54 seconds. mri_ca_register utimesec 9869.348000 mri_ca_register stimesec 5.944000 mri_ca_register ru_maxrss 1344000 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 6767670 mri_ca_register ru_majflt 8 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 1696 mri_ca_register ru_oublock 63920 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 36097 mri_ca_register ru_nivcsw 48595 FSRUNTIME@ mri_ca_register 1.9816 hours 7 threads #-------------------------------------- #@# SubCort Seg Tue Aug 8 02:00:48 UTC 2017 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname 1d9731faa403 machine x86_64 setenv SUBJECTS_DIR /out/freesurfer cd /out/freesurfer/sub-05/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 7 == 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 /opt/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 5.41 Atlas used for the 3D morph was /opt/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 = 0.10984 ( 3) Left_Lateral_Ventricle (4): linear fit = 0.09 x + 0.0 (82 voxels, overlap=0.613) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (82 voxels, peak = 2), gca=8.0 gca peak = 0.17677 (13) mri peak = 0.11112 ( 2) gca peak = 0.28129 (95) mri peak = 0.15631 (103) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (563 voxels, overlap=1.013) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (563 voxels, peak = 102), gca=102.1 gca peak = 0.16930 (96) mri peak = 0.46578 (101) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (560 voxels, overlap=0.146) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (560 voxels, peak = 100), gca=100.3 gca peak = 0.24553 (55) mri peak = 0.13369 (54) Right_Hippocampus (53): linear fit = 0.94 x + 0.0 (259 voxels, overlap=0.864) Right_Hippocampus (53): linear fit = 0.94 x + 0.0 (259 voxels, peak = 52), gca=52.0 gca peak = 0.30264 (59) mri peak = 0.09093 (54) gca peak = 0.07580 (103) mri peak = 0.19047 (108) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (37494 voxels, overlap=0.545) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (37494 voxels, peak = 105), gca=104.5 gca peak = 0.07714 (104) mri peak = 0.27787 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (42252 voxels, overlap=0.463) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (42252 voxels, peak = 105), gca=104.5 gca peak = 0.09712 (58) mri peak = 0.04803 (40) Left_Cerebral_Cortex (3): linear fit = 0.75 x + 0.0 (3779 voxels, overlap=0.020) Left_Cerebral_Cortex (3): linear fit = 0.75 x + 0.0 (3779 voxels, peak = 43), gca=43.2 gca peak = 0.11620 (58) mri peak = 0.04123 (42) Right_Cerebral_Cortex (42): linear fit = 0.74 x + 0.0 (11445 voxels, overlap=0.106) Right_Cerebral_Cortex (42): linear fit = 0.74 x + 0.0 (11445 voxels, peak = 43), gca=42.6 gca peak = 0.30970 (66) mri peak = 0.07480 (58) Right_Caudate (50): linear fit = 0.87 x + 0.0 (666 voxels, overlap=0.708) Right_Caudate (50): linear fit = 0.87 x + 0.0 (666 voxels, peak = 57), gca=57.1 gca peak = 0.15280 (69) mri peak = 0.07095 (70) Left_Caudate (11): linear fit = 0.93 x + 0.0 (451 voxels, overlap=0.702) Left_Caudate (11): linear fit = 0.93 x + 0.0 (451 voxels, peak = 64), gca=63.8 gca peak = 0.13902 (56) mri peak = 0.04147 (43) Left_Cerebellum_Cortex (8): linear fit = 0.79 x + 0.0 (5276 voxels, overlap=0.111) Left_Cerebellum_Cortex (8): linear fit = 0.79 x + 0.0 (5276 voxels, peak = 44), gca=44.0 gca peak = 0.14777 (55) mri peak = 0.04396 (42) Right_Cerebellum_Cortex (47): linear fit = 0.81 x + 0.0 (8678 voxels, overlap=0.280) Right_Cerebellum_Cortex (47): linear fit = 0.81 x + 0.0 (8678 voxels, peak = 45), gca=44.8 gca peak = 0.16765 (84) mri peak = 0.15822 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (4163 voxels, overlap=0.810) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (4163 voxels, peak = 89), gca=88.6 gca peak = 0.18739 (84) mri peak = 0.11037 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5103 voxels, overlap=0.802) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5103 voxels, peak = 90), gca=90.3 gca peak = 0.29869 (57) mri peak = 0.14056 (54) gca peak = 0.33601 (57) mri peak = 0.14159 (54) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (71 voxels, overlap=1.011) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (71 voxels, peak = 54), gca=53.9 gca peak = 0.11131 (90) mri peak = 0.16186 (102) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (2852 voxels, overlap=0.309) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (2852 voxels, peak = 101), gca=101.2 gca peak = 0.11793 (83) mri peak = 0.07491 (102) Right_Thalamus_Proper (49): linear fit = 1.17 x + 0.0 (2414 voxels, overlap=0.098) Right_Thalamus_Proper (49): linear fit = 1.17 x + 0.0 (2414 voxels, peak = 98), gca=97.5 gca peak = 0.08324 (81) mri peak = 0.05932 (84) Left_Putamen (12): linear fit = 1.05 x + 0.0 (839 voxels, overlap=0.830) Left_Putamen (12): linear fit = 1.05 x + 0.0 (839 voxels, peak = 85), gca=85.5 gca peak = 0.10360 (77) mri peak = 0.06328 (72) Right_Putamen (51): linear fit = 0.93 x + 0.0 (958 voxels, overlap=0.687) Right_Putamen (51): linear fit = 0.93 x + 0.0 (958 voxels, peak = 71), gca=71.2 gca peak = 0.08424 (78) mri peak = 0.10190 (95) Brain_Stem (16): linear fit = 1.13 x + 0.0 (7089 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.13 x + 0.0 (7089 voxels, peak = 89), gca=88.5 gca peak = 0.12631 (89) mri peak = 0.24161 (99) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1232 voxels, overlap=0.132) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1232 voxels, peak = 99), gca=99.2 gca peak = 0.14500 (87) mri peak = 0.41491 (98) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1241 voxels, overlap=0.001) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1241 voxels, peak = 98), gca=97.9 gca peak = 0.14975 (24) mri peak = 0.14316 ( 2) gca peak = 0.19357 (14) mri peak = 0.07527 ( 3) gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak Left_Hippocampus = 0.30264 (59) gca peak Left_Amygdala = 0.29869 (57) 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_Lateral_Ventricle = 0.17677 (13) 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 setting label Right_Lateral_Ventricle based on Left_Lateral_Ventricle = 0.40 x + 0: 8 setting label Left_Hippocampus based on Right_Hippocampus = 0.94 x + 0: 52 setting label Left_Amygdala based on Right_Amygdala = 0.94 x + 0: 54 estimating mean gm scale to be 0.88 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 Right_Pallidum too bright - rescaling by 0.993 (from 1.075) to 101.4 (was 102.1) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.30837 ( 7) mri peak = 0.10984 ( 3) Left_Lateral_Ventricle (4): linear fit = 0.28 x + 0.0 (82 voxels, overlap=0.927) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (82 voxels, peak = 2), gca=2.8 gca peak = 0.30173 ( 5) mri peak = 0.11112 ( 2) gca peak = 0.26931 (102) mri peak = 0.15631 (103) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (563 voxels, overlap=1.010) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (563 voxels, peak = 102), gca=102.0 gca peak = 0.15673 (100) mri peak = 0.46578 (101) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (560 voxels, overlap=0.651) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (560 voxels, peak = 100), gca=99.5 gca peak = 0.27761 (52) mri peak = 0.13369 (54) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (259 voxels, overlap=1.003) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (259 voxels, peak = 52), gca=52.0 gca peak = 0.31001 (53) mri peak = 0.09093 (54) gca peak = 0.07792 (104) mri peak = 0.19047 (108) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (37494 voxels, overlap=0.598) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (37494 voxels, peak = 104), gca=104.0 gca peak = 0.07908 (105) mri peak = 0.27787 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (42252 voxels, overlap=0.485) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (42252 voxels, peak = 106), gca=105.5 gca peak = 0.13104 (43) mri peak = 0.04803 (40) Left_Cerebral_Cortex (3): linear fit = 1.03 x + 0.0 (3779 voxels, overlap=0.940) Left_Cerebral_Cortex (3): linear fit = 1.03 x + 0.0 (3779 voxels, peak = 45), gca=44.5 gca peak = 0.15641 (43) mri peak = 0.04123 (42) Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (11445 voxels, overlap=0.740) Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (11445 voxels, peak = 45), gca=44.5 gca peak = 0.29496 (57) mri peak = 0.07480 (58) Right_Caudate (50): linear fit = 1.00 x + 0.0 (666 voxels, overlap=0.800) Right_Caudate (50): linear fit = 1.00 x + 0.0 (666 voxels, peak = 57), gca=57.0 gca peak = 0.13199 (64) mri peak = 0.07095 (70) Left_Caudate (11): linear fit = 0.95 x + 0.0 (451 voxels, overlap=1.008) Left_Caudate (11): linear fit = 0.95 x + 0.0 (451 voxels, peak = 61), gca=61.1 gca peak = 0.17961 (43) mri peak = 0.04147 (43) Left_Cerebellum_Cortex (8): linear fit = 1.03 x + 0.0 (5276 voxels, overlap=0.999) Left_Cerebellum_Cortex (8): linear fit = 1.03 x + 0.0 (5276 voxels, peak = 45), gca=44.5 gca peak = 0.17701 (45) mri peak = 0.04396 (42) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (8678 voxels, overlap=1.000) Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (8678 voxels, peak = 42), gca=42.1 gca peak = 0.16050 (89) mri peak = 0.15822 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (4163 voxels, overlap=0.962) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (4163 voxels, peak = 90), gca=90.3 gca peak = 0.14658 (90) mri peak = 0.11037 (91) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5103 voxels, overlap=0.987) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5103 voxels, peak = 89), gca=88.7 gca peak = 0.29859 (54) mri peak = 0.14056 (54) gca peak = 0.41201 (54) mri peak = 0.14159 (54) Right_Amygdala (54): linear fit = 0.98 x + 0.0 (71 voxels, overlap=0.998) Right_Amygdala (54): linear fit = 0.98 x + 0.0 (71 voxels, peak = 53), gca=52.7 gca peak = 0.10694 (101) mri peak = 0.16186 (102) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2852 voxels, overlap=0.905) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2852 voxels, peak = 101), gca=101.0 gca peak = 0.10105 (95) mri peak = 0.07491 (102) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2414 voxels, overlap=0.920) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2414 voxels, peak = 95), gca=95.0 gca peak = 0.08506 (87) mri peak = 0.05932 (84) Left_Putamen (12): linear fit = 1.00 x + 0.0 (839 voxels, overlap=0.811) Left_Putamen (12): linear fit = 1.00 x + 0.0 (839 voxels, peak = 87), gca=86.6 gca peak = 0.09183 (69) mri peak = 0.06328 (72) Right_Putamen (51): linear fit = 0.95 x + 0.0 (958 voxels, overlap=0.905) Right_Putamen (51): linear fit = 0.95 x + 0.0 (958 voxels, peak = 66), gca=65.9 gca peak = 0.07524 (89) mri peak = 0.10190 (95) Brain_Stem (16): linear fit = 0.99 x + 0.0 (7089 voxels, overlap=0.851) Brain_Stem (16): linear fit = 0.99 x + 0.0 (7089 voxels, peak = 88), gca=87.7 gca peak = 0.12080 (94) mri peak = 0.24161 (99) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1232 voxels, overlap=0.638) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1232 voxels, peak = 94), gca=94.0 gca peak = 0.13796 (96) mri peak = 0.41491 (98) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1241 voxels, overlap=0.486) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1241 voxels, peak = 97), gca=97.4 gca peak = 0.33708 (10) mri peak = 0.14316 ( 2) gca peak = 0.45928 ( 6) mri peak = 0.07527 ( 3) gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18199 (30) gca peak Left_Thalamus = 0.36646 (98) gca peak Third_Ventricle = 0.33708 (10) gca peak Fourth_Ventricle = 0.45928 ( 6) gca peak Left_Hippocampus = 0.31001 (53) gca peak Left_Amygdala = 0.29859 (54) gca peak CSF = 0.26605 (13) gca peak Left_Accumbens_area = 0.54646 (57) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.67417 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Lateral_Ventricle = 0.30173 ( 5) gca peak Right_Inf_Lat_Vent = 0.24804 (22) gca peak Right_Accumbens_area = 0.32347 (56) gca peak Right_vessel = 0.71610 (52) gca peak Right_choroid_plexus = 0.14615 (37) gca peak Fifth_Ventricle = 0.65560 (13) gca peak WM_hypointensities = 0.07298 (77) gca peak non_WM_hypointensities = 0.12093 (55) gca peak Optic_Chiasm = 0.59409 (75) not using caudate to estimate GM means setting label Right_Lateral_Ventricle based on Left_Lateral_Ventricle = 0.40 x + 0: 3 setting label Left_Hippocampus based on Right_Hippocampus = 1.00 x + 0: 52 setting label Left_Amygdala based on Right_Amygdala = 0.98 x + 0: 53 estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 Right_Pallidum too bright - rescaling by 0.996 (from 1.000) to 101.6 (was 102.0) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 73804 voxels changed in iteration 0 of unlikely voxel relabeling 258 voxels changed in iteration 1 of unlikely voxel relabeling 6 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 29018 gm and wm labels changed (%13 to gray, %87 to white out of all changed labels) 273 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 70873 changed. image ll: -2.309, PF=0.500 pass 2: 23957 changed. image ll: -2.308, PF=0.500 pass 3: 9201 changed. pass 4: 3843 changed. 46367 voxels changed in iteration 0 of unlikely voxel relabeling 337 voxels changed in iteration 1 of unlikely voxel relabeling 41 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 7721 voxels changed in iteration 0 of unlikely voxel relabeling 197 voxels changed in iteration 1 of unlikely voxel relabeling 19 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6752 voxels changed in iteration 0 of unlikely voxel relabeling 91 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 6615 voxels changed in iteration 0 of unlikely voxel relabeling 62 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 MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 3239.992000 mri_ca_label stimesec 0.668000 mri_ca_label ru_maxrss 2101164 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 866345 mri_ca_label ru_majflt 13 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 1792 mri_ca_label ru_oublock 344 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 1335 mri_ca_label ru_nivcsw 11473 auto-labeling took 52 minutes and 47 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /out/freesurfer/sub-05/mri/transforms/cc_up.lta sub-05 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /out/freesurfer/sub-05/mri/transforms/cc_up.lta reading aseg from /out/freesurfer/sub-05/mri/aseg.auto_noCCseg.mgz reading norm from /out/freesurfer/sub-05/mri/norm.mgz 295359 voxels in left wm, 406651 in right wm, xrange [32, 200] searching rotation angles z=[80 94], y=[-88 -74] searching scale 1 Z rot 79.8 searching scale 1 Z rot 80.0 searching scale 1 Z rot 80.3 searching scale 1 Z rot 80.5 searching scale 1 Z rot 80.8 searching scale 1 Z rot 81.0 searching scale 1 Z rot 81.3 searching scale 1 Z rot 81.5 searching scale 1 Z rot 81.8 searching scale 1 Z rot 82.0 searching scale 1 Z rot 82.3 searching scale 1 Z rot 82.5 searching scale 1 Z rot 82.8 searching scale 1 Z rot 83.0 searching scale 1 Z rot 83.3 searching scale 1 Z rot 83.5 searching scale 1 Z rot 83.8 searching scale 1 Z rot 84.0 searching scale 1 Z rot 84.3 searching scale 1 Z rot 84.5 searching scale 1 Z rot 84.8 searching scale 1 Z rot 85.0 searching scale 1 Z rot 85.3 searching scale 1 Z rot 85.5 searching scale 1 Z rot 85.8 searching scale 1 Z rot 86.0 searching scale 1 Z rot 86.3 searching scale 1 Z rot 86.5 searching scale 1 Z rot 86.8 global minimum found at slice 200.0, rotations (0.75, 79.75) final transformation (x=200.0, yr=0.750, zr=79.755): 0.17784 -0.98406 0.00233 217.15727; 0.98397 0.17786 0.01289 -92.76112; -0.01309 0.00000 0.99991 23.62805; 0.00000 0.00000 0.00000 1.00000; updating x range to be [59, 176] in xformed coordinates best xformed slice 111 cc center is found at 111 127 107 eigenvectors: -0.00028 0.01230 0.99992; 0.97604 -0.21759 0.00295; 0.21761 0.97596 -0.01195; writing aseg with callosum to /out/freesurfer/sub-05/mri/aseg.auto.mgz... corpus callosum segmentation took 24.1 minutes #-------------------------------------- #@# Merge ASeg Tue Aug 8 03:17:44 UTC 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue Aug 8 03:17:44 UTC 2017 /out/freesurfer/sub-05/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... 2397 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 110 gm peak at 40 (40), valley at 13 (13) csf peak at 20, setting threshold to 33 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 77 (77), valley at 14 (14) csf peak at 20, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 1 seconds. #-------------------------------------------- #@# Mask BFS Tue Aug 8 03:19:46 UTC 2017 /out/freesurfer/sub-05/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1399201 voxels in mask (pct= 8.34) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Tue Aug 8 03:19:47 UTC 2017 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 (109.0): 107.7 +- 4.6 [79.0 --> 125.0] GM (61.0) : 59.7 +- 12.6 [30.0 --> 95.0] setting bottom of white matter range to 72.3 setting top of gray matter range to 84.9 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 8103 sparsely connected voxels removed... thickening thin strands.... 20 segments, 2554 filled 97 bright non-wm voxels segmented. 3910 diagonally connected voxels added... white matter segmentation took 0.8 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 0.60 minutes reading wm segmentation from wm.seg.mgz... 1000 voxels added to wm to prevent paths from MTL structures to cortex 2910 additional wm voxels added 0 additional wm voxels added SEG EDIT: 29350 voxels turned on, 56010 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+): 56 found - 56 modified | TOTAL: 56 pass 2 (xy+): 0 found - 56 modified | TOTAL: 56 pass 1 (xy-): 53 found - 53 modified | TOTAL: 109 pass 2 (xy-): 0 found - 53 modified | TOTAL: 109 pass 1 (yz+): 50 found - 50 modified | TOTAL: 159 pass 2 (yz+): 0 found - 50 modified | TOTAL: 159 pass 1 (yz-): 56 found - 56 modified | TOTAL: 215 pass 2 (yz-): 0 found - 56 modified | TOTAL: 215 pass 1 (xz+): 42 found - 42 modified | TOTAL: 257 pass 2 (xz+): 0 found - 42 modified | TOTAL: 257 pass 1 (xz-): 54 found - 54 modified | TOTAL: 311 pass 2 (xz-): 0 found - 54 modified | TOTAL: 311 Iteration Number : 1 pass 1 (+++): 26 found - 26 modified | TOTAL: 26 pass 2 (+++): 0 found - 26 modified | TOTAL: 26 pass 1 (+++): 33 found - 33 modified | TOTAL: 59 pass 2 (+++): 0 found - 33 modified | TOTAL: 59 pass 1 (+++): 30 found - 30 modified | TOTAL: 89 pass 2 (+++): 0 found - 30 modified | TOTAL: 89 pass 1 (+++): 24 found - 24 modified | TOTAL: 113 pass 2 (+++): 0 found - 24 modified | TOTAL: 113 Iteration Number : 1 pass 1 (++): 131 found - 131 modified | TOTAL: 131 pass 2 (++): 0 found - 131 modified | TOTAL: 131 pass 1 (+-): 149 found - 149 modified | TOTAL: 280 pass 2 (+-): 0 found - 149 modified | TOTAL: 280 pass 1 (--): 155 found - 155 modified | TOTAL: 435 pass 2 (--): 1 found - 156 modified | TOTAL: 436 pass 3 (--): 0 found - 156 modified | TOTAL: 436 pass 1 (-+): 96 found - 96 modified | TOTAL: 532 pass 2 (-+): 0 found - 96 modified | TOTAL: 532 Iteration Number : 2 pass 1 (xy+): 8 found - 8 modified | TOTAL: 8 pass 2 (xy+): 0 found - 8 modified | TOTAL: 8 pass 1 (xy-): 11 found - 11 modified | TOTAL: 19 pass 2 (xy-): 0 found - 11 modified | TOTAL: 19 pass 1 (yz+): 12 found - 12 modified | TOTAL: 31 pass 2 (yz+): 0 found - 12 modified | TOTAL: 31 pass 1 (yz-): 6 found - 6 modified | TOTAL: 37 pass 2 (yz-): 0 found - 6 modified | TOTAL: 37 pass 1 (xz+): 15 found - 15 modified | TOTAL: 52 pass 2 (xz+): 0 found - 15 modified | TOTAL: 52 pass 1 (xz-): 7 found - 7 modified | TOTAL: 59 pass 2 (xz-): 0 found - 7 modified | TOTAL: 59 Iteration Number : 2 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 (+++): 2 found - 2 modified | TOTAL: 5 pass 2 (+++): 0 found - 2 modified | TOTAL: 5 pass 1 (+++): 2 found - 2 modified | TOTAL: 7 pass 2 (+++): 0 found - 2 modified | TOTAL: 7 Iteration Number : 2 pass 1 (++): 6 found - 6 modified | TOTAL: 6 pass 2 (++): 0 found - 6 modified | TOTAL: 6 pass 1 (+-): 6 found - 6 modified | TOTAL: 12 pass 2 (+-): 0 found - 6 modified | TOTAL: 12 pass 1 (--): 4 found - 4 modified | TOTAL: 16 pass 2 (--): 0 found - 4 modified | TOTAL: 16 pass 1 (-+): 6 found - 6 modified | TOTAL: 22 pass 2 (-+): 0 found - 6 modified | TOTAL: 22 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-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 1046 (out of 496557: 0.210651) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Tue Aug 8 03:21:14 UTC 2017 /out/freesurfer/sub-05/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 -0.03960 1.14846 0.12883 -29.26410; -0.03384 -0.00463 1.29388 -31.78491; 0.99488 0.00758 -0.02384 -4.44275; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform -0.03960 1.14846 0.12883 -29.26410; -0.03384 -0.00463 1.29388 -31.78491; 0.99488 0.00758 -0.02384 -4.44275; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 3002 (min = 350, max = 1400), aspect = 1.21 (min = 0.10, max = 0.75) need search nearby using seed (126, 108, 95), TAL = (2.0, -33.0, 20.0) talairach voxel to voxel transform -0.00656 0.01918 1.00554 4.88512; 0.87018 -0.08606 0.03171 22.87038; 0.00294 0.77306 0.02641 24.77517; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 108, 95) --> (2.0, -33.0, 20.0) done. writing output to filled.mgz... filling took 0.5 minutes talairach cc position changed to (2.00, -33.00, 20.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -33.00, 20.00) SRC: (101.77, 110.57, 111.09) search lh wm seed point around talairach space (-16.00, -33.00, 20.00), SRC: (101.54, 141.89, 111.20) 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 ... Started at Mon Aug 7 23:56:11 UTC 2017 Ended at Tue Aug 8 03:21:43 UTC 2017 #@#%# recon-all-run-time-hours 3.426 recon-all -s sub-05 finished without error at Tue Aug 8 03:21:43 UTC 2017 New invocation of recon-all Tue Aug 8 05:59:29 UTC 2017 /out/freesurfer/sub-05 /opt/freesurfer/bin/recon-all -autorecon3 -hemi lh -openmp 7 -subjid sub-05 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial subjid sub-05 setenv SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux 1d9731faa403 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 15345 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 3973012 1107880 1677844 6372 1187288 2493024 Swap: 4121596 983020 3138576 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-05:59:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-05:59:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-05:59:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-05:59:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-05:59:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-05:59:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-05:59:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-05:59:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-05:59:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/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 /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# Cortical ribbon mask Tue Aug 8 05:59:30 UTC 2017 /out/freesurfer/sub-05/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 sub-05 SUBJECTS_DIR is /out/freesurfer 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 = 178 writing volume /out/freesurfer/sub-05/mri/ribbon.mgz mris_volmask took 3.19 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Tue Aug 8 06:02:41 UTC 2017 /out/freesurfer/sub-05/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 sub-05 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /out/freesurfer/sub-05/mri/wm.mgz... reading input surface /out/freesurfer/sub-05/surf/lh.white... reading input pial surface /out/freesurfer/sub-05/surf/lh.pial... reading input white surface /out/freesurfer/sub-05/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 148039 Total vertex volume 146668 (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) = 380269 mm^3 (det: 5.122961 ) lhCtxGM: 145885.632 143734.000 diff= 2151.6 pctdiff= 1.475 rhCtxGM: 241063.927 239357.000 diff= 1706.9 pctdiff= 0.708 lhCtxWM: 186814.754 183207.000 diff= 3607.8 pctdiff= 1.931 rhCtxWM: 245343.213 249972.000 diff=-4628.8 pctdiff=-1.887 SubCortGMVol 47187.000 SupraTentVol 875164.527 (870298.000) diff=4866.527 pctdiff=0.556 SupraTentVolNotVent 868344.527 (863478.000) diff=4866.527 pctdiff=0.560 BrainSegVol 978847.000 (976942.000) diff=1905.000 pctdiff=0.195 BrainSegVolNotVent 969551.000 (972323.527) diff=-2772.527 pctdiff=-0.286 BrainSegVolNotVent 969551.000 CerebellumVol 106008.000 VentChorVol 6820.000 3rd4th5thCSF 2476.000 CSFVol 571.000, OptChiasmVol 65.000 MaskVol 1415899.000 1132 741 1371 1.964 0.487 0.119 0.025 11 1.2 bankssts 1222 825 1997 2.309 0.457 0.114 0.019 13 0.9 caudalanteriorcingulate 1845 1438 2854 2.093 0.645 0.169 0.049 34 4.0 caudalmiddlefrontal 786 544 1883 2.898 0.483 0.135 0.029 10 0.9 cuneus 570 357 823 2.166 0.706 0.096 0.023 4 0.6 entorhinal 2543 1767 5306 2.635 0.440 0.123 0.023 30 2.5 fusiform 5836 3981 8980 1.939 0.739 0.135 0.034 112 8.6 inferiorparietal 1658 1117 2475 2.264 0.498 0.113 0.026 13 1.5 inferiortemporal 3348 2209 5666 2.344 0.618 0.101 0.016 23 2.3 isthmuscingulate 3946 2804 8050 2.501 0.500 0.133 0.028 52 4.4 lateraloccipital 4830 3201 7343 2.189 0.560 0.128 0.029 66 5.8 lateralorbitofrontal 2354 1634 4502 2.511 0.511 0.106 0.019 20 2.0 lingual 1806 1241 3066 2.286 0.442 0.130 0.024 24 1.9 medialorbitofrontal 2137 1361 3613 2.174 0.562 0.126 0.031 31 2.9 middletemporal 2685 1778 5254 2.674 0.593 0.105 0.020 19 2.2 parahippocampal 895 626 1385 1.978 1.017 0.126 0.028 11 1.0 paracentral 1198 789 1933 2.092 0.918 0.150 0.048 33 2.3 parsopercularis 1374 877 2098 1.999 0.732 0.144 0.038 27 2.2 parsorbitalis 1309 837 1323 1.688 0.696 0.098 0.023 8 1.5 parstriangularis 766 537 1838 2.833 0.495 0.128 0.027 8 0.8 pericalcarine 2738 1800 4459 2.181 0.996 0.167 0.074 85 8.6 postcentral 3547 2464 7817 2.578 0.467 0.133 0.024 53 3.6 posteriorcingulate 2729 1717 4313 2.250 0.791 0.127 0.042 47 4.9 precentral 2381 1575 4498 2.684 0.584 0.117 0.027 26 2.3 precuneus 1399 961 2737 2.394 0.468 0.145 0.031 25 2.0 rostralanteriorcingulate 5624 3974 8007 1.848 0.601 0.142 0.040 84 10.2 rostralmiddlefrontal 10393 7264 18513 2.279 0.575 0.140 0.032 157 14.0 superiorfrontal 3794 2499 6285 2.356 0.998 0.120 0.029 48 3.9 superiorparietal 2500 1662 3539 2.035 0.764 0.118 0.031 24 3.2 superiortemporal 5807 3880 9561 2.206 0.669 0.142 0.041 112 10.4 supramarginal 214 144 369 2.561 0.965 0.099 0.014 2 0.1 frontalpole 235 142 269 1.859 0.629 0.104 0.021 2 0.2 temporalpole 340 220 692 2.777 0.371 0.102 0.021 3 0.4 transversetemporal 2446 1579 3837 2.333 0.661 0.124 0.029 29 2.9 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 sub-05 lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /out/freesurfer/sub-05/mri/wm.mgz... reading input surface /out/freesurfer/sub-05/surf/lh.pial... reading input pial surface /out/freesurfer/sub-05/surf/lh.pial... reading input white surface /out/freesurfer/sub-05/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 148039 Total vertex volume 146668 (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) = 380269 mm^3 (det: 5.122961 ) lhCtxGM: 145885.632 143734.000 diff= 2151.6 pctdiff= 1.475 rhCtxGM: 241063.927 239357.000 diff= 1706.9 pctdiff= 0.708 lhCtxWM: 186814.754 183207.000 diff= 3607.8 pctdiff= 1.931 rhCtxWM: 245343.213 249972.000 diff=-4628.8 pctdiff=-1.887 SubCortGMVol 47187.000 SupraTentVol 875164.527 (870298.000) diff=4866.527 pctdiff=0.556 SupraTentVolNotVent 868344.527 (863478.000) diff=4866.527 pctdiff=0.560 BrainSegVol 978847.000 (976942.000) diff=1905.000 pctdiff=0.195 BrainSegVolNotVent 969551.000 (972323.527) diff=-2772.527 pctdiff=-0.286 BrainSegVolNotVent 969551.000 CerebellumVol 106008.000 VentChorVol 6820.000 3rd4th5thCSF 2476.000 CSFVol 571.000, OptChiasmVol 65.000 MaskVol 1415899.000 1132 683 1371 1.964 0.487 0.121 0.033 17 1.8 bankssts 1222 911 1997 2.309 0.457 0.141 0.034 16 1.7 caudalanteriorcingulate 1845 1453 2854 2.093 0.645 0.153 0.048 38 3.9 caudalmiddlefrontal 786 733 1883 2.898 0.483 0.152 0.034 13 1.1 cuneus 570 445 823 2.166 0.706 0.116 0.026 5 0.7 entorhinal 2543 2188 5306 2.635 0.440 0.146 0.028 33 3.2 fusiform 5836 5318 8980 1.939 0.739 0.182 0.045 96 11.5 inferiorparietal 1658 1068 2475 2.264 0.498 0.129 0.036 27 2.6 inferiortemporal 3348 2511 5666 2.344 0.618 0.122 0.023 45 3.6 isthmuscingulate 3946 3514 8050 2.501 0.500 0.158 0.035 56 6.0 lateraloccipital 4830 3659 7343 2.189 0.560 0.147 0.037 68 8.6 lateralorbitofrontal 2354 1934 4502 2.511 0.511 0.129 0.026 28 2.8 lingual 1806 1422 3066 2.286 0.442 0.147 0.034 27 2.8 medialorbitofrontal 2137 1907 3613 2.174 0.562 0.164 0.038 27 3.8 middletemporal 2685 2067 5254 2.674 0.593 0.119 0.026 29 3.1 parahippocampal 895 726 1385 1.978 1.017 0.151 0.050 18 2.0 paracentral 1198 931 1933 2.092 0.918 0.153 0.054 26 3.3 parsopercularis 1374 1217 2098 1.999 0.732 0.153 0.034 14 2.3 parsorbitalis 1309 858 1323 1.688 0.696 0.103 0.027 23 1.7 parstriangularis 766 711 1838 2.833 0.495 0.165 0.034 15 1.2 pericalcarine 2738 2276 4459 2.181 0.996 0.262 0.145 49075 16.5 postcentral 3547 3466 7817 2.578 0.467 0.163 0.033 48 5.3 posteriorcingulate 2729 2255 4313 2.250 0.791 0.165 0.047 63 6.0 precentral 2381 1774 4498 2.684 0.584 0.144 0.040 57 3.9 precuneus 1399 1304 2737 2.394 0.468 0.166 0.037 17 2.4 rostralanteriorcingulate 5624 4783 8007 1.848 0.601 0.149 0.041 81 10.5 rostralmiddlefrontal 10393 9104 18513 2.279 0.575 0.162 0.039 176 18.7 superiorfrontal 3794 3338 6285 2.356 0.998 0.200 0.072 145 10.9 superiorparietal 2500 1981 3539 2.035 0.764 0.138 0.036 34 4.1 superiortemporal 5807 4858 9561 2.206 0.669 0.168 0.051 115 14.5 supramarginal 214 152 369 2.561 0.965 0.124 0.031 3 0.4 frontalpole 235 150 269 1.859 0.629 0.112 0.026 2 0.3 temporalpole 340 287 692 2.777 0.371 0.174 0.042 7 0.8 transversetemporal 2446 1775 3837 2.333 0.661 0.142 0.037 40 4.2 insula #----------------------------------------- #@# Cortical Parc 2 lh Tue Aug 8 06:03:13 UTC 2017 /out/freesurfer/sub-05/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-05 lh ../surf/lh.sphere.reg /opt/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 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/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... 1970 labels changed using aseg relabeling using gibbs priors... 000: 7088 changed, 93353 examined... 001: 1830 changed, 27325 examined... 002: 551 changed, 9266 examined... 003: 255 changed, 3035 examined... 004: 133 changed, 1453 examined... 005: 62 changed, 752 examined... 006: 50 changed, 344 examined... 007: 24 changed, 269 examined... 008: 17 changed, 132 examined... 009: 14 changed, 103 examined... 010: 10 changed, 71 examined... 011: 7 changed, 57 examined... 012: 6 changed, 39 examined... 013: 3 changed, 36 examined... 014: 6 changed, 20 examined... 015: 2 changed, 24 examined... 016: 3 changed, 10 examined... 017: 3 changed, 13 examined... 018: 1 changed, 13 examined... 019: 1 changed, 7 examined... 020: 1 changed, 7 examined... 021: 1 changed, 7 examined... 022: 1 changed, 8 examined... 023: 1 changed, 8 examined... 024: 1 changed, 7 examined... 025: 1 changed, 7 examined... 026: 0 changed, 7 examined... 769 labels changed using aseg 000: 385 total segments, 298 labels (2752 vertices) changed 001: 116 total segments, 30 labels (131 vertices) changed 002: 86 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 18 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 6595 vertices marked for relabeling... 6595 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 10 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Tue Aug 8 06:03:23 UTC 2017 /out/freesurfer/sub-05/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 sub-05 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /out/freesurfer/sub-05/mri/wm.mgz... reading input surface /out/freesurfer/sub-05/surf/lh.white... reading input pial surface /out/freesurfer/sub-05/surf/lh.pial... reading input white surface /out/freesurfer/sub-05/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 148039 Total vertex volume 146668 (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) = 380269 mm^3 (det: 5.122961 ) lhCtxGM: 145885.632 143734.000 diff= 2151.6 pctdiff= 1.475 rhCtxGM: 241063.927 239357.000 diff= 1706.9 pctdiff= 0.708 lhCtxWM: 186814.754 183207.000 diff= 3607.8 pctdiff= 1.931 rhCtxWM: 245343.213 249972.000 diff=-4628.8 pctdiff=-1.887 SubCortGMVol 47187.000 SupraTentVol 875164.527 (870298.000) diff=4866.527 pctdiff=0.556 SupraTentVolNotVent 868344.527 (863478.000) diff=4866.527 pctdiff=0.560 BrainSegVol 978847.000 (976942.000) diff=1905.000 pctdiff=0.195 BrainSegVolNotVent 969551.000 (972323.527) diff=-2772.527 pctdiff=-0.286 BrainSegVolNotVent 969551.000 CerebellumVol 106008.000 VentChorVol 6820.000 3rd4th5thCSF 2476.000 CSFVol 571.000, OptChiasmVol 65.000 MaskVol 1415899.000 483 334 652 1.896 0.661 0.102 0.023 6 0.4 G&S_frontomargin 935 636 1747 2.410 0.503 0.131 0.027 14 0.9 G&S_occipital_inf 159 115 84 0.946 0.369 0.079 0.011 1 0.1 G&S_paracentral 1231 760 1887 2.312 0.940 0.145 0.061 30 3.0 G&S_subcentral 795 517 1011 1.975 0.779 0.129 0.025 12 0.8 G&S_transv_frontopol 1900 1357 3902 2.371 0.474 0.133 0.026 31 2.0 G&S_cingul-Ant 1245 870 2324 2.407 0.529 0.126 0.022 15 1.1 G&S_cingul-Mid-Ant 1281 911 2600 2.535 0.514 0.138 0.027 20 1.4 G&S_cingul-Mid-Post 564 381 1125 2.558 0.496 0.094 0.016 4 0.3 G_cingul-Post-dorsal 641 393 1433 2.881 0.611 0.118 0.024 6 0.7 G_cingul-Post-ventral 750 516 1944 3.038 0.432 0.145 0.033 10 1.0 G_cuneus 655 430 1194 2.147 1.072 0.137 0.045 14 1.3 G_front_inf-Opercular 665 429 763 1.690 0.743 0.123 0.040 10 1.0 G_front_inf-Orbital 752 474 801 1.508 0.561 0.094 0.025 6 1.0 G_front_inf-Triangul 2909 2145 5233 2.031 0.629 0.179 0.053 66 7.3 G_front_middle 7653 5329 14363 2.293 0.607 0.143 0.033 122 10.5 G_front_sup 311 186 455 2.149 0.744 0.115 0.037 4 0.4 G_Ins_lg&S_cent_ins 301 198 390 1.898 0.620 0.120 0.024 4 0.3 G_insular_short 1515 1092 3504 2.460 0.562 0.154 0.039 31 2.2 G_occipital_middle 675 481 1587 2.821 0.522 0.132 0.029 8 0.8 G_occipital_sup 990 719 2646 2.820 0.453 0.140 0.027 16 1.2 G_oc-temp_lat-fusifor 1345 943 3138 2.581 0.635 0.134 0.027 19 1.5 G_oc-temp_med-Lingual 2875 1879 5401 2.552 0.664 0.108 0.023 23 2.6 G_oc-temp_med-Parahip 2934 1886 4480 1.971 0.618 0.135 0.034 53 4.3 G_orbital 3134 1997 4655 1.879 0.565 0.149 0.048 91 6.4 G_pariet_inf-Angular 2708 1808 4402 2.125 0.695 0.146 0.042 56 4.9 G_pariet_inf-Supramar 1040 648 1595 2.329 0.960 0.126 0.036 18 1.3 G_parietal_sup 861 539 1041 1.814 1.157 0.177 0.092 31 3.4 G_postcentral 1235 732 1770 2.006 0.685 0.109 0.038 21 2.0 G_precentral 808 508 1710 2.807 0.551 0.128 0.034 14 0.9 G_precuneus 731 490 1429 2.383 0.434 0.148 0.029 14 0.9 G_rectus 409 279 819 2.581 0.539 0.142 0.029 7 0.4 G_subcallosal 353 215 735 2.581 0.765 0.136 0.036 6 0.8 G_temp_sup-G_T_transv 862 546 1033 1.749 0.678 0.119 0.032 10 1.3 G_temp_sup-Lateral 316 204 332 1.668 0.601 0.109 0.025 2 0.3 G_temp_sup-Plan_polar 805 537 1271 2.161 0.702 0.130 0.037 8 1.2 G_temp_sup-Plan_tempo 814 539 1276 2.340 0.482 0.120 0.028 8 0.8 G_temporal_inf 1236 793 2412 2.264 0.564 0.134 0.034 22 1.8 G_temporal_middle 198 127 230 2.259 0.902 0.104 0.018 1 0.2 Lat_Fis-ant-Horizont 122 81 170 2.321 0.790 0.106 0.020 1 0.1 Lat_Fis-ant-Vertical 798 528 1220 2.753 0.387 0.114 0.023 5 0.8 Lat_Fis-post 899 668 2203 2.740 0.398 0.139 0.030 13 1.1 Pole_occipital 475 295 573 2.041 0.743 0.110 0.023 3 0.5 Pole_temporal 1168 824 2229 2.620 0.476 0.105 0.018 8 0.8 S_calcarine 346 230 1047 2.791 0.791 0.149 0.059 6 0.8 S_central 645 464 1179 2.285 0.889 0.147 0.026 9 0.8 S_cingul-Marginalis 530 340 841 2.317 0.807 0.135 0.033 8 0.7 S_circular_insula_ant 515 333 707 2.385 0.514 0.111 0.022 3 0.5 S_circular_insula_inf 978 676 1802 2.759 0.521 0.140 0.036 14 1.5 S_circular_insula_sup 441 290 596 2.235 0.532 0.098 0.020 3 0.3 S_collat_transv_ant 341 222 428 2.483 0.289 0.102 0.019 2 0.3 S_collat_transv_post 1691 1289 1848 1.645 0.552 0.150 0.040 26 3.1 S_front_inf 1082 719 1542 2.080 0.527 0.114 0.028 10 1.1 S_front_middle 2101 1448 2773 2.013 0.622 0.142 0.044 31 4.1 S_front_sup 326 230 591 2.164 0.550 0.120 0.021 2 0.3 S_interm_prim-Jensen 2392 1636 3269 1.912 1.191 0.112 0.025 26 2.3 S_intrapariet&P_trans 721 514 1311 2.437 0.538 0.117 0.019 6 0.6 S_oc_middle&Lunatus 822 569 1553 2.331 0.827 0.112 0.023 8 0.7 S_oc_sup&transversal 423 284 596 2.099 0.476 0.139 0.024 5 0.5 S_occipital_ant 439 315 885 2.486 0.382 0.127 0.027 5 0.6 S_oc-temp_lat 1824 1228 2914 2.555 0.359 0.081 0.012 8 0.9 S_oc-temp_med&Lingual 119 72 106 1.408 0.200 0.061 0.009 0 0.1 S_orbital_lateral 612 426 1115 2.236 0.474 0.123 0.031 9 0.7 S_orbital_med-olfact 1998 1342 2791 2.327 0.381 0.125 0.023 20 2.0 S_orbital-H_Shaped 872 581 1767 2.828 0.485 0.113 0.023 7 0.8 S_parieto_occipital 5551 3751 9827 2.317 0.514 0.113 0.019 55 4.5 S_pericallosal 2157 1528 3871 2.400 0.709 0.151 0.046 43 4.3 S_postcentral 858 623 1289 2.319 0.725 0.169 0.061 22 2.3 S_precentral-inf-part 464 291 589 2.222 0.623 0.133 0.037 6 0.6 S_precentral-sup-part 512 351 612 2.101 0.363 0.121 0.022 3 0.6 S_suborbital 860 573 1258 2.533 0.443 0.100 0.021 4 0.7 S_subparietal 595 396 786 2.096 0.476 0.105 0.023 3 0.5 S_temporal_inf 3465 2358 4778 2.017 0.485 0.120 0.024 38 3.6 S_temporal_sup 141 102 232 2.343 0.410 0.099 0.019 1 0.1 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Tue Aug 8 06:03:39 UTC 2017 /out/freesurfer/sub-05/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-05 lh ../surf/lh.sphere.reg /opt/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 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/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... 1970 labels changed using aseg relabeling using gibbs priors... 000: 1996 changed, 93353 examined... 001: 458 changed, 8994 examined... 002: 190 changed, 2485 examined... 003: 90 changed, 1023 examined... 004: 73 changed, 460 examined... 005: 44 changed, 321 examined... 006: 27 changed, 204 examined... 007: 26 changed, 141 examined... 008: 20 changed, 111 examined... 009: 17 changed, 95 examined... 010: 9 changed, 77 examined... 011: 10 changed, 52 examined... 012: 11 changed, 53 examined... 013: 11 changed, 53 examined... 014: 11 changed, 51 examined... 015: 11 changed, 51 examined... 016: 6 changed, 43 examined... 017: 8 changed, 33 examined... 018: 2 changed, 33 examined... 019: 1 changed, 12 examined... 020: 1 changed, 7 examined... 021: 2 changed, 9 examined... 022: 1 changed, 7 examined... 023: 1 changed, 8 examined... 024: 1 changed, 7 examined... 025: 1 changed, 7 examined... 026: 1 changed, 7 examined... 027: 0 changed, 7 examined... 890 labels changed using aseg 000: 183 total segments, 150 labels (1191 vertices) changed 001: 36 total segments, 3 labels (7 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 9 filter iterations complete (10 requested, 0 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 6380 vertices marked for relabeling... 6380 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 8 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Tue Aug 8 06:03:47 UTC 2017 /out/freesurfer/sub-05/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 sub-05 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /out/freesurfer/sub-05/mri/wm.mgz... reading input surface /out/freesurfer/sub-05/surf/lh.white... reading input pial surface /out/freesurfer/sub-05/surf/lh.pial... reading input white surface /out/freesurfer/sub-05/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 148039 Total vertex volume 146668 (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) = 380269 mm^3 (det: 5.122961 ) lhCtxGM: 145885.632 143734.000 diff= 2151.6 pctdiff= 1.475 rhCtxGM: 241063.927 239357.000 diff= 1706.9 pctdiff= 0.708 lhCtxWM: 186814.754 183207.000 diff= 3607.8 pctdiff= 1.931 rhCtxWM: 245343.213 249972.000 diff=-4628.8 pctdiff=-1.887 SubCortGMVol 47187.000 SupraTentVol 875164.527 (870298.000) diff=4866.527 pctdiff=0.556 SupraTentVolNotVent 868344.527 (863478.000) diff=4866.527 pctdiff=0.560 BrainSegVol 978847.000 (976942.000) diff=1905.000 pctdiff=0.195 BrainSegVolNotVent 969551.000 (972323.527) diff=-2772.527 pctdiff=-0.286 BrainSegVolNotVent 969551.000 CerebellumVol 106008.000 VentChorVol 6820.000 3rd4th5thCSF 2476.000 CSFVol 571.000, OptChiasmVol 65.000 MaskVol 1415899.000 1875 1313 3371 2.347 0.469 0.126 0.020 27 1.6 caudalanteriorcingulate 1997 1546 3121 2.111 0.646 0.167 0.050 36 4.2 caudalmiddlefrontal 1123 765 2512 2.862 0.479 0.130 0.027 13 1.2 cuneus 672 422 969 2.276 0.679 0.100 0.023 5 0.6 entorhinal 2418 1683 5109 2.629 0.455 0.123 0.024 29 2.4 fusiform 6021 4091 9157 1.911 0.743 0.136 0.036 119 9.2 inferiorparietal 1658 1115 2490 2.322 0.481 0.112 0.024 13 1.5 inferiortemporal 3829 2516 6849 2.410 0.592 0.104 0.017 30 2.6 isthmuscingulate 3997 2839 8241 2.515 0.502 0.133 0.027 52 4.4 lateraloccipital 5269 3467 7739 2.112 0.542 0.126 0.028 74 6.4 lateralorbitofrontal 2405 1669 4611 2.522 0.512 0.106 0.019 21 1.9 lingual 1789 1223 3142 2.324 0.472 0.131 0.025 24 1.8 medialorbitofrontal 3002 1933 4752 2.138 0.539 0.122 0.028 39 3.7 middletemporal 2342 1547 4865 2.749 0.569 0.105 0.020 17 2.0 parahippocampal 1171 804 1884 2.127 0.964 0.129 0.030 15 1.4 paracentral 1174 778 1789 2.068 0.896 0.156 0.057 34 3.0 parsopercularis 1472 968 2315 2.105 0.778 0.146 0.036 28 2.0 parsorbitalis 1422 913 1403 1.628 0.640 0.093 0.019 7 1.3 parstriangularis 791 549 1888 2.831 0.493 0.129 0.028 9 0.9 pericalcarine 3105 2043 5176 2.219 1.015 0.166 0.074 93 9.7 postcentral 3322 2338 7074 2.531 0.481 0.135 0.024 49 3.5 posteriorcingulate 2685 1704 4328 2.265 0.788 0.127 0.041 46 4.7 precentral 2258 1492 4318 2.704 0.593 0.119 0.028 25 2.3 precuneus 1640 1132 3271 2.391 0.462 0.139 0.030 29 2.1 rostralanteriorcingulate 3959 2814 5845 1.880 0.624 0.139 0.038 54 7.0 rostralmiddlefrontal 11047 7651 18681 2.208 0.611 0.140 0.033 166 15.7 superiorfrontal 3207 2126 5329 2.315 1.001 0.120 0.029 42 3.4 superiorparietal 3679 2413 4892 1.982 0.702 0.121 0.031 37 4.7 superiortemporal 5201 3486 8747 2.258 0.658 0.138 0.037 92 8.2 supramarginal 332 214 671 2.783 0.366 0.098 0.020 2 0.3 transversetemporal 1495 967 2130 2.309 0.643 0.128 0.033 17 2.0 insula #----------------------------------------- #@# WM/GM Contrast lh Tue Aug 8 06:04:03 UTC 2017 /out/freesurfer/sub-05/scripts pctsurfcon --s sub-05 --lh-only Log file is /out/freesurfer/sub-05/scripts/pctsurfcon.log Tue Aug 8 06:04:03 UTC 2017 setenv SUBJECTS_DIR /out/freesurfer cd /out/freesurfer/sub-05/scripts /opt/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux 1d9731faa403 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer mri_vol2surf --mov /out/freesurfer/sub-05/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /out/freesurfer/sub-05/surf/tmp.pctsurfcon.7519/lh.wm.mgh --regheader sub-05 --cortex srcvol = /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/label/lh.cortex.label Reading surface /out/freesurfer/sub-05/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 = 52040 Masking with /out/freesurfer/sub-05/label/lh.cortex.label Writing to /out/freesurfer/sub-05/surf/tmp.pctsurfcon.7519/lh.wm.mgh Dim: 93353 1 1 mri_vol2surf --mov /out/freesurfer/sub-05/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /out/freesurfer/sub-05/surf/tmp.pctsurfcon.7519/lh.gm.mgh --projfrac 0.3 --regheader sub-05 --cortex srcvol = /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/label/lh.cortex.label Reading surface /out/freesurfer/sub-05/surf/lh.white Done reading source surface Reading thickness /out/freesurfer/sub-05/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 = 61601 Masking with /out/freesurfer/sub-05/label/lh.cortex.label Writing to /out/freesurfer/sub-05/surf/tmp.pctsurfcon.7519/lh.gm.mgh Dim: 93353 1 1 mri_concat /out/freesurfer/sub-05/surf/tmp.pctsurfcon.7519/lh.wm.mgh /out/freesurfer/sub-05/surf/tmp.pctsurfcon.7519/lh.gm.mgh --paired-diff-norm --mul 100 --o /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/surf/lh.w-g.pct.mgh mri_segstats --in /out/freesurfer/sub-05/surf/lh.w-g.pct.mgh --annot sub-05 lh aparc --sum /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/surf/lh.w-g.pct.mgh --annot sub-05 lh aparc --sum /out/freesurfer/sub-05/stats/lh.w-g.pct.stats --snr sysname Linux hostname 1d9731faa403 machine x86_64 user root UseRobust 0 Constructing seg from annotation Reading annotation /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/surf/lh.w-g.pct.mgh Vertex Area is 0.675833 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# Relabel Hypointensities Tue Aug 8 06:04:06 UTC 2017 /out/freesurfer/sub-05/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 3369 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 8817 voxels changed to hypointensity... 11922 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Tue Aug 8 06:04:17 UTC 2017 /out/freesurfer/sub-05 mri_aparc2aseg --s sub-05 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/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: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /out/freesurfer subject sub-05 outvol /out/freesurfer/sub-05/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /out/freesurfer/sub-05/surf/lh.white Reading lh pial surface /out/freesurfer/sub-05/surf/lh.pial Loading lh annotations from /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/surf/rh.white Reading rh pial surface /out/freesurfer/sub-05/surf/rh.pial Loading rh annotations from /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/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 5.41 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 45 rescaling Left_Lateral_Ventricle from 13 --> 3 rescaling Left_Inf_Lat_Vent from 34 --> 30 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 45 rescaling Left_Thalamus from 94 --> 98 rescaling Left_Thalamus_Proper from 84 --> 101 rescaling Left_Caudate from 75 --> 61 rescaling Left_Putamen from 80 --> 87 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 4 rescaling Fourth_Ventricle from 22 --> 2 rescaling Brain_Stem from 81 --> 88 rescaling Left_Hippocampus from 57 --> 52 rescaling Left_Amygdala from 56 --> 53 rescaling CSF from 32 --> 5 rescaling Left_Accumbens_area from 62 --> 54 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 45 rescaling Right_Lateral_Ventricle from 13 --> 3 rescaling Right_Inf_Lat_Vent from 25 --> 22 rescaling Right_Cerebellum_White_Matter from 87 --> 89 rescaling Right_Cerebellum_Cortex from 59 --> 42 rescaling Right_Thalamus_Proper from 85 --> 95 rescaling Right_Caudate from 62 --> 57 rescaling Right_Putamen from 80 --> 66 rescaling Right_Pallidum from 97 --> 102 rescaling Right_Hippocampus from 53 --> 52 rescaling Right_Amygdala from 55 --> 53 rescaling Right_Accumbens_area from 65 --> 56 rescaling Right_VentralDC from 86 --> 94 rescaling Fifth_Ventricle from 40 --> 5 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 55 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 = 383021 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 853 changed. pass 2: 126 changed. pass 3: 21 changed. pass 4: 10 changed. pass 5: 4 changed. pass 6: 1 changed. pass 7: 0 changed. nchanged = 0 Writing output aseg to /out/freesurfer/sub-05/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Tue Aug 8 06:07:33 UTC 2017 /out/freesurfer/sub-05 INFO: skipping a2009s aparc2aseg #----------------------------------------- #@# AParc-to-ASeg DKTatlas Tue Aug 8 06:07:33 UTC 2017 /out/freesurfer/sub-05 INFO: skipping DKTatlas aparc2aseg #----------------------------------------- #@# APas-to-ASeg Tue Aug 8 06:07:33 UTC 2017 /out/freesurfer/sub-05/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Tue Aug 8 06:07:34 UTC 2017 setenv SUBJECTS_DIR /out/freesurfer cd /out/freesurfer/sub-05/mri /opt/freesurfer/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux 1d9731faa403 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /out/freesurfer/sub-05/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 1d9731faa403 machine x86_64 user root input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done Started at Tue Aug 8 06:07:34 UTC 2017 Ended at Tue Aug 8 06:07:38 UTC 2017 Apas2aseg-Run-Time-Sec 4 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Tue Aug 8 06:07:38 UTC 2017 /out/freesurfer/sub-05 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt --subject sub-05 $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 /opt/freesurfer/ASegStatsLUT.txt --subject sub-05 sysname Linux hostname 1d9731faa403 machine x86_64 user root UseRobust 0 atlas_icv (eTIV) = 380269 mm^3 (det: 5.122961 ) Computing euler number orig.nofix lheno = -64, rheno = -110 orig.nofix lhholes = 33, rhholes = 56 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 145885.632 143734.000 diff= 2151.6 pctdiff= 1.475 rhCtxGM: 241063.927 239357.000 diff= 1706.9 pctdiff= 0.708 lhCtxWM: 186814.754 183207.000 diff= 3607.8 pctdiff= 1.931 rhCtxWM: 245343.213 249972.000 diff=-4628.8 pctdiff=-1.887 SubCortGMVol 47187.000 SupraTentVol 875164.527 (870298.000) diff=4866.527 pctdiff=0.556 SupraTentVolNotVent 868344.527 (863478.000) diff=4866.527 pctdiff=0.560 BrainSegVol 978847.000 (976942.000) diff=1905.000 pctdiff=0.195 BrainSegVolNotVent 969551.000 (972323.527) diff=-2772.527 pctdiff=-0.286 BrainSegVolNotVent 969551.000 CerebellumVol 106008.000 VentChorVol 6820.000 3rd4th5thCSF 2476.000 CSFVol 571.000, OptChiasmVol 65.000 MaskVol 1415899.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Tue Aug 8 06:08:26 UTC 2017 /out/freesurfer/sub-05 mri_aparc2aseg --s sub-05 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /out/freesurfer subject sub-05 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /out/freesurfer/sub-05/mri/aparc+aseg.mgz Reading lh white surface /out/freesurfer/sub-05/surf/lh.white Reading lh pial surface /out/freesurfer/sub-05/surf/lh.pial Loading lh annotations from /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/surf/rh.white Reading rh pial surface /out/freesurfer/sub-05/surf/rh.pial Loading rh annotations from /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/mri/ribbon.mgz Loading filled from /out/freesurfer/sub-05/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 6966 vertices from left hemi Ripped 4921 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 /out/freesurfer/sub-05/mri/aseg.mgz Loading Ctx Seg File /out/freesurfer/sub-05/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 = 807154 Used brute-force search on 169 voxels Fixing Parahip LH WM Found 2 clusters 0 k 1.000000 1 k 5498.000000 Fixing Parahip RH WM Found 1 clusters 0 k 1810.000000 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 sub-05 --surf-wm-vol --ctab /opt/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 sub-05 --surf-wm-vol --ctab /opt/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname 1d9731faa403 machine x86_64 user root UseRobust 0 atlas_icv (eTIV) = 380269 mm^3 (det: 5.122961 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 145885.632 143734.000 diff= 2151.6 pctdiff= 1.475 rhCtxGM: 241063.927 239357.000 diff= 1706.9 pctdiff= 0.708 lhCtxWM: 186814.754 183207.000 diff= 3607.8 pctdiff= 1.931 rhCtxWM: 245343.213 249972.000 diff=-4628.8 pctdiff=-1.887 SubCortGMVol 47187.000 SupraTentVol 875164.527 (870298.000) diff=4866.527 pctdiff=0.556 SupraTentVolNotVent 868344.527 (863478.000) diff=4866.527 pctdiff=0.560 BrainSegVol 978847.000 (976942.000) diff=1905.000 pctdiff=0.195 BrainSegVolNotVent 969551.000 (972323.527) diff=-2772.527 pctdiff=-0.286 BrainSegVolNotVent 969551.000 CerebellumVol 106008.000 VentChorVol 6820.000 3rd4th5thCSF 2476.000 CSFVol 571.000, OptChiasmVol 65.000 MaskVol 1415899.000 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 /out/freesurfer/sub-05/label #-------------------------------------------- #@# BA_exvivo Labels lh Tue Aug 8 06:12:15 UTC 2017 mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA1_exvivo.label --trgsubject sub-05 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 446 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4575 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA2_exvivo.label --trgsubject sub-05 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 848 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8757 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA3a_exvivo.label --trgsubject sub-05 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 294 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4371 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA3b_exvivo.label --trgsubject sub-05 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 496 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6479 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA4a_exvivo.label --trgsubject sub-05 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 229 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6013 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA4p_exvivo.label --trgsubject sub-05 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 284 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4354 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA6_exvivo.label --trgsubject sub-05 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 580 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 14169 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA44_exvivo.label --trgsubject sub-05 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 117 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4298 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA45_exvivo.label --trgsubject sub-05 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 96 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 3518 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.V1_exvivo.label --trgsubject sub-05 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 58 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 4699 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.V2_exvivo.label --trgsubject sub-05 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 162 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 8276 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.MT_exvivo.label --trgsubject sub-05 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 53 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2071 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject sub-05 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 61 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1351 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject sub-05 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 61 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1260 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 122 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1136 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 437 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2529 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 42 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1546 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 137 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2133 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 58 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2377 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 68 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1617 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 111 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7146 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 18 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 1930 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 15 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1166 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 38 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 3443 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 75 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 3409 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 9 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 522 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 29 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 499 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject sub-05 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/lh.white Reading target registration /out/freesurfer/sub-05/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 93353 Number of reverse mapping hits = 24 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 474 mri_label2label: Done mris_label2annot --s sub-05 --hemi lh --ctab /opt/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 /opt/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 /out/freesurfer/sub-05/label cmdline mris_label2annot --s sub-05 --hemi lh --ctab /opt/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 1d9731faa403 machine x86_64 user root subject sub-05 hemi lh SUBJECTS_DIR /out/freesurfer ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /out/freesurfer/sub-05/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 67862 unhit vertices Writing annot to /out/freesurfer/sub-05/label/lh.BA_exvivo.annot mris_label2annot --s sub-05 --hemi lh --ctab /opt/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 /opt/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 /out/freesurfer/sub-05/label cmdline mris_label2annot --s sub-05 --hemi lh --ctab /opt/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 1d9731faa403 machine x86_64 user root subject sub-05 hemi lh SUBJECTS_DIR /out/freesurfer ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /out/freesurfer/sub-05/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 79397 unhit vertices Writing annot to /out/freesurfer/sub-05/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 sub-05 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /out/freesurfer/sub-05/mri/wm.mgz... reading input surface /out/freesurfer/sub-05/surf/lh.white... reading input pial surface /out/freesurfer/sub-05/surf/lh.pial... reading input white surface /out/freesurfer/sub-05/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 148039 Total vertex volume 146668 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/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) = 380269 mm^3 (det: 5.122961 ) lhCtxGM: 145885.632 143734.000 diff= 2151.6 pctdiff= 1.475 rhCtxGM: 241063.927 239357.000 diff= 1706.9 pctdiff= 0.708 lhCtxWM: 186814.754 183207.000 diff= 3607.8 pctdiff= 1.931 rhCtxWM: 245343.213 249972.000 diff=-4628.8 pctdiff=-1.887 SubCortGMVol 47187.000 SupraTentVol 875164.527 (870298.000) diff=4866.527 pctdiff=0.556 SupraTentVolNotVent 868344.527 (863478.000) diff=4866.527 pctdiff=0.560 BrainSegVol 978847.000 (976942.000) diff=1905.000 pctdiff=0.195 BrainSegVolNotVent 969551.000 (972323.527) diff=-2772.527 pctdiff=-0.286 BrainSegVolNotVent 969551.000 CerebellumVol 106008.000 VentChorVol 6820.000 3rd4th5thCSF 2476.000 CSFVol 571.000, OptChiasmVol 65.000 MaskVol 1415899.000 871 538 336 0.533 1.141 0.079 0.022 6 0.7 BA1_exvivo 3952 2636 4646 1.594 1.224 0.134 0.052 94 9.2 BA2_exvivo 792 558 735 1.180 1.343 0.137 0.054 15 1.8 BA3a_exvivo 1696 1058 900 1.199 1.322 0.114 0.075 34 5.6 BA3b_exvivo 834 593 537 0.983 1.089 0.097 0.024 9 0.6 BA4a_exvivo 849 535 515 1.159 1.155 0.123 0.051 14 2.0 BA4p_exvivo 6124 4081 9706 2.264 0.797 0.135 0.035 90 8.8 BA6_exvivo 1237 834 1689 2.126 0.878 0.154 0.055 32 3.1 BA44_exvivo 1702 1160 1692 1.462 0.512 0.109 0.027 15 2.3 BA45_exvivo 1467 1033 3532 2.760 0.508 0.140 0.029 19 1.9 V1_exvivo 3751 2670 7885 2.620 0.528 0.123 0.024 41 3.7 V2_exvivo 1185 837 2025 2.169 0.421 0.135 0.030 19 1.3 MT_exvivo 538 324 865 2.142 0.712 0.121 0.028 7 0.6 perirhinal_exvivo 493 332 961 2.543 0.623 0.094 0.017 3 0.4 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 sub-05 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /out/freesurfer/sub-05/mri/wm.mgz... reading input surface /out/freesurfer/sub-05/surf/lh.white... reading input pial surface /out/freesurfer/sub-05/surf/lh.pial... reading input white surface /out/freesurfer/sub-05/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 148039 Total vertex volume 146668 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/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) = 380269 mm^3 (det: 5.122961 ) lhCtxGM: 145885.632 143734.000 diff= 2151.6 pctdiff= 1.475 rhCtxGM: 241063.927 239357.000 diff= 1706.9 pctdiff= 0.708 lhCtxWM: 186814.754 183207.000 diff= 3607.8 pctdiff= 1.931 rhCtxWM: 245343.213 249972.000 diff=-4628.8 pctdiff=-1.887 SubCortGMVol 47187.000 SupraTentVol 875164.527 (870298.000) diff=4866.527 pctdiff=0.556 SupraTentVolNotVent 868344.527 (863478.000) diff=4866.527 pctdiff=0.560 BrainSegVol 978847.000 (976942.000) diff=1905.000 pctdiff=0.195 BrainSegVolNotVent 969551.000 (972323.527) diff=-2772.527 pctdiff=-0.286 BrainSegVolNotVent 969551.000 CerebellumVol 106008.000 VentChorVol 6820.000 3rd4th5thCSF 2476.000 CSFVol 571.000, OptChiasmVol 65.000 MaskVol 1415899.000 645 375 68 0.274 0.830 0.075 0.019 4 0.4 BA1_exvivo 1776 1175 1713 1.248 1.207 0.140 0.070 57 5.5 BA2_exvivo 530 369 118 0.618 1.055 0.125 0.043 10 0.9 BA3a_exvivo 1110 714 38 0.535 0.911 0.102 0.084 25 4.1 BA3b_exvivo 818 541 404 0.879 1.011 0.097 0.031 10 0.7 BA4a_exvivo 618 409 253 1.075 1.215 0.127 0.055 10 1.5 BA4p_exvivo 2978 1929 4856 2.285 0.947 0.118 0.033 35 3.6 BA6_exvivo 674 436 878 2.073 0.852 0.154 0.053 19 1.6 BA44_exvivo 603 395 504 1.265 0.204 0.089 0.017 4 0.5 BA45_exvivo 1540 1090 3675 2.733 0.517 0.134 0.028 18 1.9 V1_exvivo 1843 1323 4080 2.622 0.565 0.135 0.028 25 2.1 V2_exvivo 284 213 592 2.255 0.427 0.172 0.041 9 0.2 MT_exvivo 269 159 374 1.821 0.642 0.136 0.032 4 0.4 perirhinal_exvivo 268 176 564 2.556 0.739 0.089 0.020 2 0.2 entorhinal_exvivo Started at Tue Aug 8 05:59:29 UTC 2017 Ended at Tue Aug 8 06:14:41 UTC 2017 #@#%# recon-all-run-time-hours 0.253 recon-all -s sub-05 finished without error at Tue Aug 8 06:14:41 UTC 2017 New invocation of recon-all Tue Aug 8 06:14:42 UTC 2017 /out/freesurfer/sub-05 /opt/freesurfer/bin/recon-all -autorecon3 -hemi rh -openmp 7 -subjid sub-05 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortribbon -nohyporelabel -noapas2aseg -nosegstats -nowmparc subjid sub-05 setenv SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux 1d9731faa403 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 15345 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 3973012 1075088 2419924 6004 478000 2534288 Swap: 4121596 1006948 3114648 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:42-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:42-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:43-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:14:43-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:43-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:43-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:14:43-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:14:43-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:14:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:14:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:14:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:14:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:14:44-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:14:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:45-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:14:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:14:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:46-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:47-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:47-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:47-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:14:47-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/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 /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #----------------------------------------- #@# Parcellation Stats rh Tue Aug 8 06:14:47 UTC 2017 /out/freesurfer/sub-05/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 sub-05 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /out/freesurfer/sub-05/mri/wm.mgz... reading input surface /out/freesurfer/sub-05/surf/rh.white... reading input pial surface /out/freesurfer/sub-05/surf/rh.pial... reading input white surface /out/freesurfer/sub-05/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 244371 Total vertex volume 242713 (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) = 380269 mm^3 (det: 5.122961 ) lhCtxGM: 145885.632 143734.000 diff= 2151.6 pctdiff= 1.475 rhCtxGM: 241063.927 239357.000 diff= 1706.9 pctdiff= 0.708 lhCtxWM: 186814.754 183207.000 diff= 3607.8 pctdiff= 1.931 rhCtxWM: 245343.213 249972.000 diff=-4628.8 pctdiff=-1.887 SubCortGMVol 47187.000 SupraTentVol 875164.527 (870298.000) diff=4866.527 pctdiff=0.556 SupraTentVolNotVent 868344.527 (863478.000) diff=4866.527 pctdiff=0.560 BrainSegVol 978847.000 (976942.000) diff=1905.000 pctdiff=0.195 BrainSegVolNotVent 969551.000 (972323.527) diff=-2772.527 pctdiff=-0.286 BrainSegVolNotVent 969551.000 CerebellumVol 106008.000 VentChorVol 6820.000 3rd4th5thCSF 2476.000 CSFVol 571.000, OptChiasmVol 65.000 MaskVol 1415899.000 889 632 1359 2.208 0.599 0.098 0.016 4 0.6 bankssts 2183 1344 3002 2.075 0.622 0.142 0.095 46 4.7 caudalanteriorcingulate 2115 1382 3713 2.479 0.437 0.111 0.020 20 1.8 caudalmiddlefrontal 3577 2428 5312 1.867 0.473 0.161 0.058 95 9.9 cuneus 2226 1492 3968 2.582 0.492 0.111 0.021 22 1.8 entorhinal 4254 3000 8979 2.549 0.580 0.130 0.027 53 4.8 fusiform 5795 4087 11744 2.466 0.552 0.126 0.024 79 5.8 inferiorparietal 3056 2106 6099 2.575 0.506 0.115 0.019 27 2.4 inferiortemporal 1355 875 2526 2.642 0.803 0.121 0.035 17 1.7 isthmuscingulate 6341 4425 10463 2.076 0.498 0.133 0.030 109 8.1 lateraloccipital 5024 3419 9326 2.442 0.463 0.121 0.021 59 4.4 lateralorbitofrontal 3828 2706 6926 2.312 0.593 0.130 0.031 54 4.8 lingual 3076 2037 4706 2.247 0.700 0.129 0.030 38 3.9 medialorbitofrontal 3334 2256 7277 2.727 0.559 0.107 0.018 27 2.3 middletemporal 1114 756 2632 2.932 0.452 0.126 0.025 15 1.1 parahippocampal 3054 2144 6708 2.437 0.775 0.152 0.050 65 6.8 paracentral 1846 1275 3814 2.400 0.557 0.137 0.025 30 2.1 parsopercularis 1014 674 2192 2.567 0.454 0.132 0.022 12 1.0 parsorbitalis 1690 1138 2534 2.274 0.387 0.120 0.019 21 1.2 parstriangularis 2543 1807 3789 1.885 0.450 0.137 0.035 39 3.9 pericalcarine 10109 7021 19977 2.455 0.591 0.118 0.027 145 11.3 postcentral 577 338 743 1.939 1.121 0.102 0.037 12 0.9 posteriorcingulate 7130 5000 15353 2.609 0.626 0.130 0.027 108 7.9 precentral 5681 4050 10683 2.365 0.678 0.146 0.046 101 11.1 precuneus 1207 803 1831 2.217 0.759 0.134 0.041 18 2.0 rostralanteriorcingulate 5872 4032 10391 2.252 0.550 0.151 0.033 102 7.8 rostralmiddlefrontal 10455 7321 19102 2.450 0.637 0.141 0.032 166 13.8 superiorfrontal 8275 5766 16072 2.471 0.723 0.131 0.038 131 13.2 superiorparietal 4688 3157 9307 2.438 0.687 0.121 0.024 48 4.9 superiortemporal 5922 4258 14871 2.950 0.837 0.138 0.031 93 8.2 supramarginal 300 243 490 2.089 0.520 0.211 0.052 7 0.8 frontalpole 551 381 1271 2.518 0.517 0.146 0.031 10 0.8 temporalpole 460 303 722 2.375 0.524 0.125 0.028 6 0.5 transversetemporal 7862 5365 14820 2.453 0.518 0.123 0.022 106 7.2 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 sub-05 rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /out/freesurfer/sub-05/mri/wm.mgz... reading input surface /out/freesurfer/sub-05/surf/rh.pial... reading input pial surface /out/freesurfer/sub-05/surf/rh.pial... reading input white surface /out/freesurfer/sub-05/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 244371 Total vertex volume 242713 (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) = 380269 mm^3 (det: 5.122961 ) lhCtxGM: 145885.632 143734.000 diff= 2151.6 pctdiff= 1.475 rhCtxGM: 241063.927 239357.000 diff= 1706.9 pctdiff= 0.708 lhCtxWM: 186814.754 183207.000 diff= 3607.8 pctdiff= 1.931 rhCtxWM: 245343.213 249972.000 diff=-4628.8 pctdiff=-1.887 SubCortGMVol 47187.000 SupraTentVol 875164.527 (870298.000) diff=4866.527 pctdiff=0.556 SupraTentVolNotVent 868344.527 (863478.000) diff=4866.527 pctdiff=0.560 BrainSegVol 978847.000 (976942.000) diff=1905.000 pctdiff=0.195 BrainSegVolNotVent 969551.000 (972323.527) diff=-2772.527 pctdiff=-0.286 BrainSegVolNotVent 969551.000 CerebellumVol 106008.000 VentChorVol 6820.000 3rd4th5thCSF 2476.000 CSFVol 571.000, OptChiasmVol 65.000 MaskVol 1415899.000 889 614 1359 2.208 0.599 0.126 0.034 15 1.3 bankssts 2183 1605 3002 2.075 0.622 0.159 0.057 49 5.8 caudalanteriorcingulate 2115 1577 3713 2.479 0.437 0.135 0.035 33 3.3 caudalmiddlefrontal 3577 3597 5312 1.867 0.473 0.203 0.052 67 8.4 cuneus 2226 1588 3968 2.582 0.492 0.132 0.033 34 3.3 entorhinal 4254 3859 8979 2.549 0.580 0.152 0.033 64 6.1 fusiform 5795 5251 11744 2.466 0.552 0.156 0.036 77 9.4 inferiorparietal 3056 2513 6099 2.575 0.506 0.140 0.030 41 4.4 inferiortemporal 1355 1091 2526 2.642 0.803 0.195 0.074 62 3.2 isthmuscingulate 6341 5677 10463 2.076 0.498 0.166 0.037 93 10.5 lateraloccipital 5024 4102 9326 2.442 0.463 0.154 0.035 87 7.9 lateralorbitofrontal 3828 3292 6926 2.312 0.593 0.160 0.039 52 6.7 lingual 3076 2222 4706 2.247 0.700 0.143 0.041 58 5.4 medialorbitofrontal 3334 2922 7277 2.727 0.559 0.126 0.024 37 3.6 middletemporal 1114 1003 2632 2.932 0.452 0.148 0.037 14 1.8 parahippocampal 3054 3353 6708 2.437 0.775 0.213 0.059 55 8.9 paracentral 1846 1772 3814 2.400 0.557 0.176 0.034 30 3.2 parsopercularis 1014 1040 2192 2.567 0.454 0.150 0.026 9 1.3 parsorbitalis 1690 1143 2534 2.274 0.387 0.134 0.037 31 2.5 parstriangularis 2543 2269 3789 1.885 0.450 0.176 0.048 38 5.0 pericalcarine 10109 9146 19977 2.455 0.591 0.161 0.038 145 18.2 postcentral 577 470 743 1.939 1.121 0.190 0.068 17 1.7 posteriorcingulate 7130 6715 15353 2.609 0.626 0.172 0.041 121 13.6 precentral 5681 5135 10683 2.365 0.678 0.187 0.053 123 13.5 precuneus 1207 954 1831 2.217 0.759 0.152 0.060 27 3.6 rostralanteriorcingulate 5872 5232 10391 2.252 0.550 0.158 0.036 108 9.6 rostralmiddlefrontal 10455 8693 19102 2.450 0.637 0.162 0.043 192 21.2 superiorfrontal 8275 7304 16072 2.471 0.723 0.178 0.047 151 17.4 superiorparietal 4688 4109 9307 2.438 0.687 0.148 0.032 60 6.8 superiortemporal 5922 5557 14871 2.950 0.837 0.175 0.044 129 12.1 supramarginal 300 261 490 2.089 0.520 0.150 0.044 3 0.6 frontalpole 551 648 1271 2.518 0.517 0.179 0.028 7 0.7 temporalpole 460 302 722 2.375 0.524 0.140 0.038 6 0.7 transversetemporal 7862 6516 14820 2.453 0.518 0.149 0.034 122 11.8 insula #----------------------------------------- #@# Cortical Parc 2 rh Tue Aug 8 06:15:29 UTC 2017 /out/freesurfer/sub-05/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-05 rh ../surf/rh.sphere.reg /opt/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 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/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... 143 labels changed using aseg relabeling using gibbs priors... 000: 8915 changed, 132324 examined... 001: 2009 changed, 35001 examined... 002: 625 changed, 10703 examined... 003: 228 changed, 3478 examined... 004: 95 changed, 1293 examined... 005: 49 changed, 561 examined... 006: 21 changed, 300 examined... 007: 9 changed, 122 examined... 008: 6 changed, 50 examined... 009: 4 changed, 29 examined... 010: 2 changed, 21 examined... 011: 0 changed, 8 examined... 35 labels changed using aseg 000: 260 total segments, 175 labels (1665 vertices) changed 001: 88 total segments, 3 labels (20 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 32 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 6799 vertices marked for relabeling... 6799 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 13 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Tue Aug 8 06:15:42 UTC 2017 /out/freesurfer/sub-05/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 sub-05 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /out/freesurfer/sub-05/mri/wm.mgz... reading input surface /out/freesurfer/sub-05/surf/rh.white... reading input pial surface /out/freesurfer/sub-05/surf/rh.pial... reading input white surface /out/freesurfer/sub-05/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 244371 Total vertex volume 242713 (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) = 380269 mm^3 (det: 5.122961 ) lhCtxGM: 145885.632 143734.000 diff= 2151.6 pctdiff= 1.475 rhCtxGM: 241063.927 239357.000 diff= 1706.9 pctdiff= 0.708 lhCtxWM: 186814.754 183207.000 diff= 3607.8 pctdiff= 1.931 rhCtxWM: 245343.213 249972.000 diff=-4628.8 pctdiff=-1.887 SubCortGMVol 47187.000 SupraTentVol 875164.527 (870298.000) diff=4866.527 pctdiff=0.556 SupraTentVolNotVent 868344.527 (863478.000) diff=4866.527 pctdiff=0.560 BrainSegVol 978847.000 (976942.000) diff=1905.000 pctdiff=0.195 BrainSegVolNotVent 969551.000 (972323.527) diff=-2772.527 pctdiff=-0.286 BrainSegVolNotVent 969551.000 CerebellumVol 106008.000 VentChorVol 6820.000 3rd4th5thCSF 2476.000 CSFVol 571.000, OptChiasmVol 65.000 MaskVol 1415899.000 681 470 972 2.101 0.404 0.159 0.031 10 0.9 G&S_frontomargin 1060 722 2090 2.353 0.527 0.122 0.023 12 1.0 G&S_occipital_inf 2977 2094 5807 2.135 0.695 0.161 0.056 72 7.2 G&S_paracentral 1394 1000 2975 2.493 0.488 0.138 0.030 26 1.4 G&S_subcentral 974 755 1718 1.940 0.542 0.205 0.059 31 2.5 G&S_transv_frontopol 3288 2277 4766 2.071 0.608 0.139 0.039 45 5.1 G&S_cingul-Ant 2170 1346 3112 2.239 0.552 0.114 0.035 30 3.2 G&S_cingul-Mid-Ant 1263 871 2864 2.756 0.700 0.103 0.027 14 1.4 G&S_cingul-Mid-Post 418 234 360 1.658 1.219 0.115 0.060 11 0.8 G_cingul-Post-dorsal 627 414 1378 2.858 0.635 0.141 0.034 9 0.9 G_cingul-Post-ventral 3298 2254 5131 1.900 0.478 0.165 0.061 89 9.4 G_cuneus 1219 859 2936 2.535 0.573 0.157 0.032 32 1.7 G_front_inf-Opercular 358 239 714 2.575 0.356 0.117 0.017 4 0.2 G_front_inf-Orbital 525 349 877 2.229 0.368 0.131 0.026 10 0.5 G_front_inf-Triangul 3047 2032 6819 2.519 0.548 0.150 0.033 58 3.9 G_front_middle 7472 5234 14675 2.473 0.651 0.152 0.036 145 11.4 G_front_sup 1378 949 3317 2.585 0.465 0.144 0.028 29 1.7 G_Ins_lg&S_cent_ins 1403 958 2847 2.463 0.470 0.127 0.022 23 1.3 G_insular_short 1646 1172 3503 2.300 0.454 0.157 0.037 34 2.6 G_occipital_middle 1860 1311 2870 1.842 0.376 0.156 0.048 45 4.2 G_occipital_sup 2098 1502 4765 2.510 0.615 0.148 0.031 35 2.5 G_oc-temp_lat-fusifor 2351 1721 4961 2.349 0.639 0.144 0.034 34 3.3 G_oc-temp_med-Lingual 5270 3609 11036 2.695 0.519 0.120 0.023 61 4.8 G_oc-temp_med-Parahip 3069 2108 6857 2.557 0.454 0.135 0.026 48 3.4 G_orbital 2259 1633 5755 2.631 0.622 0.151 0.031 51 2.9 G_pariet_inf-Angular 3029 2255 9778 3.162 0.850 0.156 0.040 61 5.5 G_pariet_inf-Supramar 1942 1400 5037 2.766 0.916 0.141 0.050 41 4.2 G_parietal_sup 3946 2740 9195 2.589 0.651 0.126 0.028 67 4.5 G_postcentral 2564 1793 7061 2.956 0.577 0.155 0.037 56 3.9 G_precentral 2424 1754 5595 2.613 0.653 0.151 0.051 45 5.6 G_precuneus 793 524 1575 2.597 0.431 0.128 0.028 11 0.9 G_rectus 1072 680 1368 1.945 0.890 0.134 0.028 18 1.2 G_subcallosal 410 276 998 2.767 0.636 0.159 0.032 7 0.6 G_temp_sup-G_T_transv 1540 1047 4119 2.704 0.621 0.135 0.029 21 2.0 G_temp_sup-Lateral 874 604 1904 2.556 0.448 0.130 0.020 10 0.7 G_temp_sup-Plan_polar 666 492 1818 3.342 0.810 0.109 0.019 5 0.5 G_temp_sup-Plan_tempo 1508 1059 3169 2.616 0.448 0.118 0.021 15 1.2 G_temporal_inf 1832 1220 4867 2.940 0.511 0.118 0.021 20 1.4 G_temporal_middle 475 318 623 2.410 0.328 0.139 0.022 6 0.4 Lat_Fis-ant-Horizont 287 196 396 2.059 0.315 0.092 0.011 1 0.2 Lat_Fis-ant-Vertical 1296 864 1796 2.718 0.743 0.115 0.025 9 1.4 Lat_Fis-post 3471 2396 5033 1.874 0.441 0.141 0.042 86 5.9 Pole_occipital 1180 815 2728 2.559 0.669 0.120 0.021 13 1.1 Pole_temporal 2362 1711 4034 2.205 0.588 0.131 0.030 30 3.0 S_calcarine 3344 2366 5666 2.398 0.546 0.107 0.018 25 2.6 S_central 527 368 819 2.494 0.941 0.169 0.070 10 1.3 S_cingul-Marginalis 1217 812 1675 2.221 0.414 0.092 0.013 6 0.6 S_circular_insula_ant 1487 989 2003 2.182 0.350 0.102 0.017 12 1.0 S_circular_insula_inf 1538 1012 2266 2.297 0.390 0.098 0.015 12 1.0 S_circular_insula_sup 712 497 1363 2.593 0.545 0.119 0.021 5 0.6 S_collat_transv_ant 526 356 671 2.130 0.360 0.081 0.012 2 0.3 S_collat_transv_post 1213 812 1776 2.255 0.421 0.109 0.018 9 0.9 S_front_inf 1483 1027 2019 2.062 0.484 0.137 0.029 17 1.6 S_front_middle 1510 1021 2503 2.628 0.575 0.121 0.021 13 1.5 S_front_sup 154 128 514 2.927 0.787 0.144 0.029 2 0.2 S_interm_prim-Jensen 3201 2173 5249 2.523 0.546 0.115 0.023 29 3.0 S_intrapariet&P_trans 844 563 996 2.077 0.351 0.104 0.017 4 0.7 S_oc_middle&Lunatus 1186 886 2140 2.080 0.517 0.124 0.025 15 1.1 S_oc_sup&transversal 519 375 759 2.107 0.340 0.088 0.011 2 0.3 S_occipital_ant 1127 774 1911 2.474 0.446 0.107 0.017 7 0.9 S_oc-temp_lat 1558 1063 2908 2.602 0.487 0.127 0.030 18 2.1 S_oc-temp_med&Lingual 295 207 377 1.953 0.319 0.088 0.010 2 0.1 S_orbital_lateral 1257 815 1835 2.426 0.395 0.118 0.020 11 1.1 S_orbital_med-olfact 893 615 1376 2.279 0.412 0.106 0.016 6 0.6 S_orbital-H_Shaped 2948 1999 4310 1.972 0.487 0.128 0.031 49 4.1 S_parieto_occipital 1548 952 1715 2.176 0.673 0.128 0.102 24 2.4 S_pericallosal 5162 3417 8536 2.587 0.490 0.101 0.022 47 4.7 S_postcentral 1436 984 2411 2.328 0.406 0.095 0.013 10 0.9 S_precentral-inf-part 1236 861 2567 2.705 0.627 0.130 0.023 16 1.2 S_precentral-sup-part 184 123 261 2.676 0.411 0.129 0.023 1 0.3 S_suborbital 889 703 1742 2.589 0.847 0.157 0.052 13 1.7 S_subparietal 841 570 1135 2.329 0.450 0.095 0.012 4 0.5 S_temporal_inf 4791 3289 7010 2.203 0.552 0.104 0.019 31 3.6 S_temporal_sup #----------------------------------------- #@# Cortical Parc 3 rh Tue Aug 8 06:16:03 UTC 2017 /out/freesurfer/sub-05/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-05 rh ../surf/rh.sphere.reg /opt/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 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /opt/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... 635 labels changed using aseg relabeling using gibbs priors... 000: 2160 changed, 132324 examined... 001: 514 changed, 10073 examined... 002: 122 changed, 2939 examined... 003: 51 changed, 774 examined... 004: 21 changed, 303 examined... 005: 8 changed, 127 examined... 006: 7 changed, 52 examined... 007: 1 changed, 37 examined... 008: 0 changed, 5 examined... 22 labels changed using aseg 000: 69 total segments, 36 labels (382 vertices) changed 001: 35 total segments, 2 labels (11 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 10 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 5848 vertices marked for relabeling... 5848 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 10 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Tue Aug 8 06:16:13 UTC 2017 /out/freesurfer/sub-05/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 sub-05 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /out/freesurfer/sub-05/mri/wm.mgz... reading input surface /out/freesurfer/sub-05/surf/rh.white... reading input pial surface /out/freesurfer/sub-05/surf/rh.pial... reading input white surface /out/freesurfer/sub-05/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 244371 Total vertex volume 242713 (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) = 380269 mm^3 (det: 5.122961 ) lhCtxGM: 145885.632 143734.000 diff= 2151.6 pctdiff= 1.475 rhCtxGM: 241063.927 239357.000 diff= 1706.9 pctdiff= 0.708 lhCtxWM: 186814.754 183207.000 diff= 3607.8 pctdiff= 1.931 rhCtxWM: 245343.213 249972.000 diff=-4628.8 pctdiff=-1.887 SubCortGMVol 47187.000 SupraTentVol 875164.527 (870298.000) diff=4866.527 pctdiff=0.556 SupraTentVolNotVent 868344.527 (863478.000) diff=4866.527 pctdiff=0.560 BrainSegVol 978847.000 (976942.000) diff=1905.000 pctdiff=0.195 BrainSegVolNotVent 969551.000 (972323.527) diff=-2772.527 pctdiff=-0.286 BrainSegVolNotVent 969551.000 CerebellumVol 106008.000 VentChorVol 6820.000 3rd4th5thCSF 2476.000 CSFVol 571.000, OptChiasmVol 65.000 MaskVol 1415899.000 2267 1416 3209 2.072 0.603 0.137 0.088 45 4.3 caudalanteriorcingulate 2124 1401 3793 2.488 0.434 0.112 0.021 20 1.9 caudalmiddlefrontal 4382 2986 6498 1.859 0.468 0.157 0.055 108 11.3 cuneus 2393 1643 4558 2.618 0.385 0.111 0.021 23 1.9 entorhinal 4004 2830 8505 2.539 0.582 0.131 0.027 52 4.7 fusiform 5656 4005 11591 2.466 0.552 0.127 0.025 80 5.8 inferiorparietal 3339 2307 6606 2.579 0.508 0.116 0.019 30 2.6 inferiortemporal 1697 1090 3101 2.702 0.754 0.119 0.031 21 1.9 isthmuscingulate 6413 4464 10391 2.051 0.492 0.131 0.030 109 8.0 lateraloccipital 5176 3547 10169 2.466 0.468 0.127 0.023 67 4.9 lateralorbitofrontal 3725 2640 6790 2.320 0.591 0.126 0.028 45 4.3 lingual 2838 1867 4588 2.328 0.691 0.127 0.026 38 3.0 medialorbitofrontal 4042 2730 8648 2.709 0.533 0.103 0.017 30 2.7 middletemporal 1176 809 2757 2.911 0.466 0.124 0.024 14 1.1 parahippocampal 3279 2298 7118 2.462 0.772 0.146 0.047 64 6.5 paracentral 2174 1496 4538 2.412 0.537 0.134 0.024 35 2.4 parsopercularis 1025 677 2147 2.536 0.506 0.113 0.019 10 0.8 parsorbitalis 1514 1009 2083 2.245 0.378 0.122 0.021 17 1.2 parstriangularis 2579 1823 3837 1.888 0.455 0.141 0.038 48 4.4 pericalcarine 11296 7783 22095 2.462 0.590 0.119 0.027 161 12.8 postcentral 671 396 960 2.074 1.122 0.101 0.036 14 1.0 posteriorcingulate 6894 4810 14741 2.607 0.628 0.129 0.027 105 7.7 precentral 5871 4222 11346 2.406 0.671 0.148 0.047 104 11.8 precuneus 1886 1257 2883 2.248 0.706 0.141 0.048 30 3.7 rostralanteriorcingulate 4132 2764 7325 2.321 0.531 0.143 0.029 65 4.5 rostralmiddlefrontal 12291 8709 21954 2.358 0.654 0.149 0.034 208 18.0 superiorfrontal 6256 4376 12570 2.561 0.727 0.131 0.037 100 9.9 superiorparietal 7247 4934 14166 2.431 0.666 0.125 0.025 85 7.6 superiortemporal 5539 3994 14084 2.970 0.861 0.139 0.032 87 7.9 supramarginal 425 282 648 2.362 0.526 0.115 0.022 3 0.4 transversetemporal 5091 3451 9014 2.355 0.438 0.117 0.020 67 4.2 insula #----------------------------------------- #@# WM/GM Contrast rh Tue Aug 8 06:16:34 UTC 2017 /out/freesurfer/sub-05/scripts pctsurfcon --s sub-05 --rh-only Log file is /out/freesurfer/sub-05/scripts/pctsurfcon.log Tue Aug 8 06:16:34 UTC 2017 setenv SUBJECTS_DIR /out/freesurfer cd /out/freesurfer/sub-05/scripts /opt/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux 1d9731faa403 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer mri_vol2surf --mov /out/freesurfer/sub-05/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /out/freesurfer/sub-05/surf/tmp.pctsurfcon.8622/rh.wm.mgh --regheader sub-05 --cortex srcvol = /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/label/rh.cortex.label Reading surface /out/freesurfer/sub-05/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 = 74985 Masking with /out/freesurfer/sub-05/label/rh.cortex.label Writing to /out/freesurfer/sub-05/surf/tmp.pctsurfcon.8622/rh.wm.mgh Dim: 132324 1 1 mri_vol2surf --mov /out/freesurfer/sub-05/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /out/freesurfer/sub-05/surf/tmp.pctsurfcon.8622/rh.gm.mgh --projfrac 0.3 --regheader sub-05 --cortex srcvol = /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/label/rh.cortex.label Reading surface /out/freesurfer/sub-05/surf/rh.white Done reading source surface Reading thickness /out/freesurfer/sub-05/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 = 89460 Masking with /out/freesurfer/sub-05/label/rh.cortex.label Writing to /out/freesurfer/sub-05/surf/tmp.pctsurfcon.8622/rh.gm.mgh Dim: 132324 1 1 mri_concat /out/freesurfer/sub-05/surf/tmp.pctsurfcon.8622/rh.wm.mgh /out/freesurfer/sub-05/surf/tmp.pctsurfcon.8622/rh.gm.mgh --paired-diff-norm --mul 100 --o /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/surf/rh.w-g.pct.mgh mri_segstats --in /out/freesurfer/sub-05/surf/rh.w-g.pct.mgh --annot sub-05 rh aparc --sum /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/surf/rh.w-g.pct.mgh --annot sub-05 rh aparc --sum /out/freesurfer/sub-05/stats/rh.w-g.pct.stats --snr sysname Linux hostname 1d9731faa403 machine x86_64 user root UseRobust 0 Constructing seg from annotation Reading annotation /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/surf/rh.w-g.pct.mgh Vertex Area is 0.691518 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 #----------------------------------------- #@# AParc-to-ASeg aparc Tue Aug 8 06:16:39 UTC 2017 /out/freesurfer/sub-05 mri_aparc2aseg --s sub-05 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/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: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /out/freesurfer subject sub-05 outvol /out/freesurfer/sub-05/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /out/freesurfer/sub-05/surf/lh.white Reading lh pial surface /out/freesurfer/sub-05/surf/lh.pial Loading lh annotations from /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/surf/rh.white Reading rh pial surface /out/freesurfer/sub-05/surf/rh.pial Loading rh annotations from /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/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 5.41 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 45 rescaling Left_Lateral_Ventricle from 13 --> 3 rescaling Left_Inf_Lat_Vent from 34 --> 30 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 45 rescaling Left_Thalamus from 94 --> 98 rescaling Left_Thalamus_Proper from 84 --> 101 rescaling Left_Caudate from 75 --> 61 rescaling Left_Putamen from 80 --> 87 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 4 rescaling Fourth_Ventricle from 22 --> 2 rescaling Brain_Stem from 81 --> 88 rescaling Left_Hippocampus from 57 --> 52 rescaling Left_Amygdala from 56 --> 53 rescaling CSF from 32 --> 5 rescaling Left_Accumbens_area from 62 --> 54 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 45 rescaling Right_Lateral_Ventricle from 13 --> 3 rescaling Right_Inf_Lat_Vent from 25 --> 22 rescaling Right_Cerebellum_White_Matter from 87 --> 89 rescaling Right_Cerebellum_Cortex from 59 --> 42 rescaling Right_Thalamus_Proper from 85 --> 95 rescaling Right_Caudate from 62 --> 57 rescaling Right_Putamen from 80 --> 66 rescaling Right_Pallidum from 97 --> 102 rescaling Right_Hippocampus from 53 --> 52 rescaling Right_Amygdala from 55 --> 53 rescaling Right_Accumbens_area from 65 --> 56 rescaling Right_VentralDC from 86 --> 94 rescaling Fifth_Ventricle from 40 --> 5 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 55 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 = 383021 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 853 changed. pass 2: 126 changed. pass 3: 21 changed. pass 4: 10 changed. pass 5: 4 changed. pass 6: 1 changed. pass 7: 0 changed. nchanged = 0 Writing output aseg to /out/freesurfer/sub-05/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Tue Aug 8 06:19:54 UTC 2017 /out/freesurfer/sub-05 mri_aparc2aseg --s sub-05 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/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: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /out/freesurfer subject sub-05 outvol /out/freesurfer/sub-05/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /out/freesurfer/sub-05/surf/lh.white Reading lh pial surface /out/freesurfer/sub-05/surf/lh.pial Loading lh annotations from /out/freesurfer/sub-05/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /out/freesurfer/sub-05/surf/rh.white Reading rh pial surface /out/freesurfer/sub-05/surf/rh.pial Loading rh annotations from /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/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 5.41 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 45 rescaling Left_Lateral_Ventricle from 13 --> 3 rescaling Left_Inf_Lat_Vent from 34 --> 30 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 45 rescaling Left_Thalamus from 94 --> 98 rescaling Left_Thalamus_Proper from 84 --> 101 rescaling Left_Caudate from 75 --> 61 rescaling Left_Putamen from 80 --> 87 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 4 rescaling Fourth_Ventricle from 22 --> 2 rescaling Brain_Stem from 81 --> 88 rescaling Left_Hippocampus from 57 --> 52 rescaling Left_Amygdala from 56 --> 53 rescaling CSF from 32 --> 5 rescaling Left_Accumbens_area from 62 --> 54 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 45 rescaling Right_Lateral_Ventricle from 13 --> 3 rescaling Right_Inf_Lat_Vent from 25 --> 22 rescaling Right_Cerebellum_White_Matter from 87 --> 89 rescaling Right_Cerebellum_Cortex from 59 --> 42 rescaling Right_Thalamus_Proper from 85 --> 95 rescaling Right_Caudate from 62 --> 57 rescaling Right_Putamen from 80 --> 66 rescaling Right_Pallidum from 97 --> 102 rescaling Right_Hippocampus from 53 --> 52 rescaling Right_Amygdala from 55 --> 53 rescaling Right_Accumbens_area from 65 --> 56 rescaling Right_VentralDC from 86 --> 94 rescaling Fifth_Ventricle from 40 --> 5 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 55 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 = 382899 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 853 changed. pass 2: 126 changed. pass 3: 21 changed. pass 4: 10 changed. pass 5: 4 changed. pass 6: 1 changed. pass 7: 0 changed. nchanged = 0 Writing output aseg to /out/freesurfer/sub-05/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Tue Aug 8 06:23:09 UTC 2017 /out/freesurfer/sub-05 mri_aparc2aseg --s sub-05 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /out/freesurfer subject sub-05 outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /out/freesurfer/sub-05/surf/lh.white Reading lh pial surface /out/freesurfer/sub-05/surf/lh.pial Loading lh annotations from /out/freesurfer/sub-05/label/lh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading rh white surface /out/freesurfer/sub-05/surf/rh.white Reading rh pial surface /out/freesurfer/sub-05/surf/rh.pial Loading rh annotations from /out/freesurfer/sub-05/label/rh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /out/freesurfer/sub-05/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 /out/freesurfer/sub-05/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 5.41 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 106 rescaling Left_Cerebral_Cortex from 61 --> 45 rescaling Left_Lateral_Ventricle from 13 --> 3 rescaling Left_Inf_Lat_Vent from 34 --> 30 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 45 rescaling Left_Thalamus from 94 --> 98 rescaling Left_Thalamus_Proper from 84 --> 101 rescaling Left_Caudate from 75 --> 61 rescaling Left_Putamen from 80 --> 87 rescaling Left_Pallidum from 98 --> 100 rescaling Third_Ventricle from 25 --> 4 rescaling Fourth_Ventricle from 22 --> 2 rescaling Brain_Stem from 81 --> 88 rescaling Left_Hippocampus from 57 --> 52 rescaling Left_Amygdala from 56 --> 53 rescaling CSF from 32 --> 5 rescaling Left_Accumbens_area from 62 --> 54 rescaling Left_VentralDC from 87 --> 97 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 45 rescaling Right_Lateral_Ventricle from 13 --> 3 rescaling Right_Inf_Lat_Vent from 25 --> 22 rescaling Right_Cerebellum_White_Matter from 87 --> 89 rescaling Right_Cerebellum_Cortex from 59 --> 42 rescaling Right_Thalamus_Proper from 85 --> 95 rescaling Right_Caudate from 62 --> 57 rescaling Right_Putamen from 80 --> 66 rescaling Right_Pallidum from 97 --> 102 rescaling Right_Hippocampus from 53 --> 52 rescaling Right_Amygdala from 55 --> 53 rescaling Right_Accumbens_area from 65 --> 56 rescaling Right_VentralDC from 86 --> 94 rescaling Fifth_Ventricle from 40 --> 5 rescaling WM_hypointensities from 78 --> 77 rescaling non_WM_hypointensities from 40 --> 55 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 = 382899 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 853 changed. pass 2: 126 changed. pass 3: 21 changed. pass 4: 10 changed. pass 5: 4 changed. pass 6: 1 changed. pass 7: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz /out/freesurfer/sub-05/label #-------------------------------------------- #@# BA_exvivo Labels rh Tue Aug 8 06:26:23 UTC 2017 mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA1_exvivo.label --trgsubject sub-05 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 1509 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 5471 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA2_exvivo.label --trgsubject sub-05 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 2733 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 9420 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA3a_exvivo.label --trgsubject sub-05 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 450 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4430 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA3b_exvivo.label --trgsubject sub-05 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 1072 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 5594 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA4a_exvivo.label --trgsubject sub-05 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 930 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6677 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA4p_exvivo.label --trgsubject sub-05 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 547 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 5020 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA6_exvivo.label --trgsubject sub-05 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 1373 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 13629 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA44_exvivo.label --trgsubject sub-05 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 296 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7208 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA45_exvivo.label --trgsubject sub-05 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 325 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 5680 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.V1_exvivo.label --trgsubject sub-05 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 2000 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 6727 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.V2_exvivo.label --trgsubject sub-05 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 2709 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10725 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.MT_exvivo.label --trgsubject sub-05 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 186 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2118 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject sub-05 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 32 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1070 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject sub-05 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 24 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 776 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject sub-05 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 205 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 1081 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject sub-05 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 1242 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 3930 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject sub-05 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 158 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1856 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject sub-05 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 473 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2656 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject sub-05 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 450 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1838 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject sub-05 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 72 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1561 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject sub-05 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 733 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7692 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject sub-05 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 74 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1086 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject sub-05 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 59 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1237 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject sub-05 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 1481 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 4713 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject sub-05 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 1166 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4603 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject sub-05 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 22 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 290 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject sub-05 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 18 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 712 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /out/freesurfer/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject sub-05 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /out/freesurfer/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = sub-05 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 /out/freesurfer FREESURFER_HOME /opt/freesurfer Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /out/freesurfer/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /out/freesurfer/sub-05/surf/rh.white Reading target registration /out/freesurfer/sub-05/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 132324 Number of reverse mapping hits = 3 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 294 mri_label2label: Done mris_label2annot --s sub-05 --hemi rh --ctab /opt/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 /opt/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 /out/freesurfer/sub-05/label cmdline mris_label2annot --s sub-05 --hemi rh --ctab /opt/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 1d9731faa403 machine x86_64 user root subject sub-05 hemi rh SUBJECTS_DIR /out/freesurfer ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /out/freesurfer/sub-05/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 87710 unhit vertices Writing annot to /out/freesurfer/sub-05/label/rh.BA_exvivo.annot mris_label2annot --s sub-05 --hemi rh --ctab /opt/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 /opt/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 /out/freesurfer/sub-05/label cmdline mris_label2annot --s sub-05 --hemi rh --ctab /opt/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 1d9731faa403 machine x86_64 user root subject sub-05 hemi rh SUBJECTS_DIR /out/freesurfer ColorTable /opt/freesurfer/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /out/freesurfer/sub-05/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 105758 unhit vertices Writing annot to /out/freesurfer/sub-05/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 sub-05 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /out/freesurfer/sub-05/mri/wm.mgz... reading input surface /out/freesurfer/sub-05/surf/rh.white... reading input pial surface /out/freesurfer/sub-05/surf/rh.pial... reading input white surface /out/freesurfer/sub-05/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 244371 Total vertex volume 242713 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/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) = 380269 mm^3 (det: 5.122961 ) lhCtxGM: 145885.632 143734.000 diff= 2151.6 pctdiff= 1.475 rhCtxGM: 241063.927 239357.000 diff= 1706.9 pctdiff= 0.708 lhCtxWM: 186814.754 183207.000 diff= 3607.8 pctdiff= 1.931 rhCtxWM: 245343.213 249972.000 diff=-4628.8 pctdiff=-1.887 SubCortGMVol 47187.000 SupraTentVol 875164.527 (870298.000) diff=4866.527 pctdiff=0.556 SupraTentVolNotVent 868344.527 (863478.000) diff=4866.527 pctdiff=0.560 BrainSegVol 978847.000 (976942.000) diff=1905.000 pctdiff=0.195 BrainSegVolNotVent 969551.000 (972323.527) diff=-2772.527 pctdiff=-0.286 BrainSegVolNotVent 969551.000 CerebellumVol 106008.000 VentChorVol 6820.000 3rd4th5thCSF 2476.000 CSFVol 571.000, OptChiasmVol 65.000 MaskVol 1415899.000 1576 1069 3999 2.691 0.736 0.153 0.040 41 2.8 BA1_exvivo 6440 4358 11832 2.536 0.552 0.109 0.024 78 6.8 BA2_exvivo 1285 893 1739 2.215 0.494 0.131 0.030 14 1.2 BA3a_exvivo 2847 2074 6277 2.451 0.643 0.121 0.029 45 3.4 BA3b_exvivo 2140 1511 4699 2.382 0.694 0.154 0.048 47 4.5 BA4a_exvivo 1473 1053 2550 2.240 0.557 0.118 0.026 16 1.9 BA4p_exvivo 8326 5763 18577 2.782 0.570 0.136 0.028 139 9.6 BA6_exvivo 2971 2064 5759 2.439 0.533 0.130 0.024 45 2.8 BA44_exvivo 3047 2070 5580 2.393 0.450 0.127 0.022 40 2.6 BA45_exvivo 4438 3107 6826 1.934 0.482 0.139 0.040 87 7.6 V1_exvivo 7812 5477 12757 2.047 0.546 0.147 0.043 162 15.1 V2_exvivo 1550 1108 2804 2.295 0.482 0.137 0.027 22 1.7 MT_exvivo 436 306 1060 2.883 0.534 0.103 0.017 4 0.2 perirhinal_exvivo 273 210 761 2.876 0.607 0.097 0.014 1 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 sub-05 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /out/freesurfer/sub-05/mri/wm.mgz... reading input surface /out/freesurfer/sub-05/surf/rh.white... reading input pial surface /out/freesurfer/sub-05/surf/rh.pial... reading input white surface /out/freesurfer/sub-05/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 244371 Total vertex volume 242713 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /opt/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) = 380269 mm^3 (det: 5.122961 ) lhCtxGM: 145885.632 143734.000 diff= 2151.6 pctdiff= 1.475 rhCtxGM: 241063.927 239357.000 diff= 1706.9 pctdiff= 0.708 lhCtxWM: 186814.754 183207.000 diff= 3607.8 pctdiff= 1.931 rhCtxWM: 245343.213 249972.000 diff=-4628.8 pctdiff=-1.887 SubCortGMVol 47187.000 SupraTentVol 875164.527 (870298.000) diff=4866.527 pctdiff=0.556 SupraTentVolNotVent 868344.527 (863478.000) diff=4866.527 pctdiff=0.560 BrainSegVol 978847.000 (976942.000) diff=1905.000 pctdiff=0.195 BrainSegVolNotVent 969551.000 (972323.527) diff=-2772.527 pctdiff=-0.286 BrainSegVolNotVent 969551.000 CerebellumVol 106008.000 VentChorVol 6820.000 3rd4th5thCSF 2476.000 CSFVol 571.000, OptChiasmVol 65.000 MaskVol 1415899.000 939 655 3029 3.071 0.597 0.156 0.034 21 1.3 BA1_exvivo 3748 2570 6797 2.485 0.478 0.105 0.021 39 3.5 BA2_exvivo 1179 806 1565 2.210 0.505 0.127 0.025 10 1.1 BA3a_exvivo 2153 1553 4428 2.454 0.588 0.113 0.027 30 2.3 BA3b_exvivo 1597 1105 3036 2.220 0.634 0.155 0.050 36 3.6 BA4a_exvivo 987 701 1675 2.337 0.529 0.102 0.017 8 0.7 BA4p_exvivo 5414 3796 12383 2.830 0.587 0.141 0.028 103 6.4 BA6_exvivo 802 554 1926 2.599 0.569 0.150 0.029 21 1.0 BA44_exvivo 786 557 1511 2.352 0.432 0.129 0.022 13 0.8 BA45_exvivo 4245 2968 6484 1.940 0.475 0.140 0.042 86 7.5 V1_exvivo 4082 2907 6776 2.001 0.546 0.151 0.045 83 8.5 V2_exvivo 214 175 547 2.445 0.450 0.142 0.034 5 0.4 MT_exvivo 249 171 631 2.960 0.522 0.092 0.017 2 0.1 perirhinal_exvivo 171 148 535 2.972 0.575 0.107 0.012 1 0.1 entorhinal_exvivo Started at Tue Aug 8 06:14:42 UTC 2017 Ended at Tue Aug 8 06:29:26 UTC 2017 #@#%# recon-all-run-time-hours 0.246 recon-all -s sub-05 finished without error at Tue Aug 8 06:29:27 UTC 2017 New invocation of recon-all Tue Aug 8 06:29:28 UTC 2017 /out/freesurfer/sub-05 /opt/freesurfer/bin/recon-all -autorecon3 -subjid sub-05 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -noaparc2aseg -nosegstats -nowmparc -nobalabels subjid sub-05 setenv SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux 1d9731faa403 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 15345 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 3973012 1050164 2369036 5080 553812 2560072 Swap: 4121596 1026948 3094648 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:28-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:29:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:29:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:29:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:29:29-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:29:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:29:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:29:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:29:30-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:31-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:31-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:31-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:31-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:31-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:29:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:29:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/08-06:29:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/08-06:29:33-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: root Machine: 1d9731faa403 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/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 /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #----------------------------------------- #@# APas-to-ASeg Tue Aug 8 06:29:34 UTC 2017 /out/freesurfer/sub-05/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Tue Aug 8 06:29:34 UTC 2017 setenv SUBJECTS_DIR /out/freesurfer cd /out/freesurfer/sub-05/mri /opt/freesurfer/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux 1d9731faa403 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /out/freesurfer/sub-05/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 1d9731faa403 machine x86_64 user root input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done Started at Tue Aug 8 06:29:34 UTC 2017 Ended at Tue Aug 8 06:29:39 UTC 2017 Apas2aseg-Run-Time-Sec 5 apas2aseg Done Started at Tue Aug 8 06:29:28 UTC 2017 Ended at Tue Aug 8 06:29:39 UTC 2017 #@#%# recon-all-run-time-hours 0.003 recon-all -s sub-05 finished without error at Tue Aug 8 06:29:39 UTC 2017