Tue Mar 1 15:40:47 CET 2016 /dat/mw/tvb-new-dataset/tvb /opt/freesurfer/bin/recon-all -i t1_raw.nii.gz -s tvb -all subjid tvb setenv SUBJECTS_DIR /dat/mw/tvb-new-dataset FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /dat/opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20160229 Linux x220 4.3.3-300.fc23.x86_64 #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 15271 maxlocks unlimited maxsignal 15271 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 3931204 1466980 69576 238824 2394648 2139072 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.568 2016/02/25 18:47:17 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:47-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:47-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: tkregister2.c,v 1.130 2016/01/15 22:47:45 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:47-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:47-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_normalize.c,v 1.88 2015/12/23 17:30:35 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:47-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_watershed.cpp,v 1.102 2016/01/20 23:42:15 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:47-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:47-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:47-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:47-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_em_register.c,v 1.105 2016/02/11 00:50:55 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:47-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_ca_normalize.c,v 1.67 2016/01/29 18:22:07 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:47-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_ca_register.c,v 1.95 2016/01/20 23:42:15 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:47-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_ca_label.c,v 1.110 2016/01/20 23:42:14 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:47-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:47-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:47-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:47-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:47-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_fix_topology.c,v 1.50 2016/01/20 23:42:15 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_make_surfaces.c,v 1.163 2016/02/26 15:09:17 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_anatomical_stats.c,v 1.78 2015/07/06 21:58:51 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_calc.c,v 1.54 2015/12/14 23:18:58 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.53 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_robust_template.cpp,v 1.53 2016/01/20 23:36:17 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/01-14:40:48-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-02-11.gca GCASkull RB_all_withskull_2014-08-21.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /opt/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /dat/mw/tvb-new-dataset/tvb mri_convert /dat/mw/tvb-new-dataset/t1_raw.nii.gz /dat/mw/tvb-new-dataset/tvb/mri/orig/001.mgz mri_convert.bin /dat/mw/tvb-new-dataset/t1_raw.nii.gz /dat/mw/tvb-new-dataset/tvb/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /dat/mw/tvb-new-dataset/t1_raw.nii.gz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, 1) k_ras = (1, 0, 0) writing to /dat/mw/tvb-new-dataset/tvb/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Tue Mar 1 15:40:55 CET 2016 Found 1 runs /dat/mw/tvb-new-dataset/tvb/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 /dat/mw/tvb-new-dataset/tvb/mri/orig/001.mgz /dat/mw/tvb-new-dataset/tvb/mri/rawavg.mgz /dat/mw/tvb-new-dataset/tvb mri_convert /dat/mw/tvb-new-dataset/tvb/mri/rawavg.mgz /dat/mw/tvb-new-dataset/tvb/mri/orig.mgz --conform mri_convert.bin /dat/mw/tvb-new-dataset/tvb/mri/rawavg.mgz /dat/mw/tvb-new-dataset/tvb/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /dat/mw/tvb-new-dataset/tvb/mri/rawavg.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, 1) k_ras = (1, 0, 0) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /dat/mw/tvb-new-dataset/tvb/mri/orig.mgz... mri_add_xform_to_header -c /dat/mw/tvb-new-dataset/tvb/mri/transforms/talairach.xfm /dat/mw/tvb-new-dataset/tvb/mri/orig.mgz /dat/mw/tvb-new-dataset/tvb/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Mar 1 15:41:04 CET 2016 /dat/mw/tvb-new-dataset/tvb/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /dat/mw/tvb-new-dataset/tvb/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 x220 4.3.3-300.fc23.x86_64 #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Tue Mar 1 15:41:04 CET 2016 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.27051 /dat/mw/tvb-new-dataset/tvb/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27051/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.27051/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2300.00, 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.27051/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Mar 1 15:41:06 CET 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.27051/nu0.mnc ./tmp.mri_nu_correct.mni.27051/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.27051/0/ -iterations 1000 -distance 50 [mw@x220:/dat/mw/tvb-new-dataset/tvb/mri/] [2016-03-01 15:41:06] 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.27051/0/ ./tmp.mri_nu_correct.mni.27051/nu0.mnc ./tmp.mri_nu_correct.mni.27051/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 38 CV of field change: 0.000972109 mri_convert ./tmp.mri_nu_correct.mni.27051/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.27051/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.27051/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... Tue Mar 1 15:42:02 CET 2016 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Tue Mar 1 15:42:02 CET 2016 Ended at Tue Mar 1 15:42:34 CET 2016 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue Mar 1 15:42:36 CET 2016 /dat/mw/tvb-new-dataset/tvb/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4908, pval=0.1531 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /dat/mw/tvb-new-dataset/tvb/mri/transforms/talairach_avi.log tal_QC_AZS /dat/mw/tvb-new-dataset/tvb/mri/transforms/talairach_avi.log TalAviQA: 0.98083 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Tue Mar 1 15:42:36 CET 2016 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /dat/mw/tvb-new-dataset/tvb/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 x220 4.3.3-300.fc23.x86_64 #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Tue Mar 1 15:42:36 CET 2016 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.27829 /dat/mw/tvb-new-dataset/tvb/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27829/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.27829/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2300.00, 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.27829/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Mar 1 15:42:38 CET 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.27829/nu0.mnc ./tmp.mri_nu_correct.mni.27829/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.27829/0/ [mw@x220:/dat/mw/tvb-new-dataset/tvb/mri/] [2016-03-01 15:42:39] 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.27829/0/ ./tmp.mri_nu_correct.mni.27829/nu0.mnc ./tmp.mri_nu_correct.mni.27829/nu1.imp Processing:.................................................................Done 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of field change: 0.000957586 -------------------------------------------------------- Iteration 2 Tue Mar 1 15:43:21 CET 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.27829/nu1.mnc ./tmp.mri_nu_correct.mni.27829/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.27829/1/ [mw@x220:/dat/mw/tvb-new-dataset/tvb/mri/] [2016-03-01 15:43:21] 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.27829/1/ ./tmp.mri_nu_correct.mni.27829/nu1.mnc ./tmp.mri_nu_correct.mni.27829/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 33 CV of field change: 0.000969434 mri_binarize --i ./tmp.mri_nu_correct.mni.27829/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.27829/ones.mgz $Id: mri_binarize.c,v 1.42 2016/01/07 22:23:57 greve Exp $ cwd /dat/mw/tvb-new-dataset/tvb/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.27829/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.27829/ones.mgz sysname Linux hostname x220 machine x86_64 user mw input ./tmp.mri_nu_correct.mni.27829/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.27829/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.27829/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27829/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27829/input.mean.dat $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.27829/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27829/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27829/input.mean.dat sysname Linux hostname x220 machine x86_64 user mw UseRobust 0 Loading ./tmp.mri_nu_correct.mni.27829/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.27829/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.27829/ones.mgz --i ./tmp.mri_nu_correct.mni.27829/nu2.mnc --sum ./tmp.mri_nu_correct.mni.27829/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27829/output.mean.dat $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.27829/ones.mgz --i ./tmp.mri_nu_correct.mni.27829/nu2.mnc --sum ./tmp.mri_nu_correct.mni.27829/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27829/output.mean.dat sysname Linux hostname x220 machine x86_64 user mw UseRobust 0 Loading ./tmp.mri_nu_correct.mni.27829/ones.mgz Loading ./tmp.mri_nu_correct.mni.27829/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.27829/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.27829/nu2.mnc ./tmp.mri_nu_correct.mni.27829/nu2.mnc mul 1.01051549615757837758 Saving result to './tmp.mri_nu_correct.mni.27829/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.27829/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.27829/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.27829/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 7 seconds. mapping ( 5, 120) to ( 3, 110) Tue Mar 1 15:44:30 CET 2016 mri_nu_correct.mni done mri_add_xform_to_header -c /dat/mw/tvb-new-dataset/tvb/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue Mar 1 15:44:32 CET 2016 /dat/mw/tvb-new-dataset/tvb/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.99914 0.01264 -0.01755 -0.39315; -0.00268 0.88990 0.42171 6.97472; -0.00069 -0.42513 1.00011 0.95723; 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 = 18 Starting OpenSpline(): npoints = 18 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 105 gm peak at 64 (64), valley at 51 (51) csf peak at 33, setting threshold to 53 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 67 (67), valley at 42 (42) csf peak at 34, setting threshold to 56 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 8 seconds. #-------------------------------------------- #@# Skull Stripping Tue Mar 1 15:46:41 CET 2016 /dat/mw/tvb-new-dataset/tvb/mri mri_em_register -rusage /dat/mw/tvb-new-dataset/tvb/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /opt/freesurfer/average/RB_all_withskull_2014-08-21.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/freesurfer/average/RB_all_withskull_2014-08-21.gca'... average std = 23.5 using min determinant for regularization = 55.2 0 singular and 5018 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 15.9 or > 1063.6 total sample mean = 86.3 (1445 zeros) ************************************************ spacing=8, using 3388 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3388, passno 0, spacing 8 resetting wm mean[0]: 110 --> 118 resetting gm mean[0]: 70 --> 70 input volume #1 is the most T1-like using real data threshold=7.0 skull bounding box = (46, 16, 0) --> (211, 255, 246) using (101, 96, 123) as brain centroid... mean wm in atlas = 118, using box (81,66,93) --> (121, 125,153) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 106 +- 6.8 after smoothing, mri peak at 106, scaling input intensities by 1.113 scaling channel 0 by 1.11321 initial log_p = -4.436 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.380543 @ (-9.091, 9.091, -9.091) max log p = -4.276310 @ (4.545, 4.545, 4.545) max log p = -4.187532 @ (2.273, 6.818, 6.818) max log p = -4.146018 @ (1.136, -1.136, -1.136) max log p = -4.146018 @ (0.000, 0.000, 0.000) max log p = -4.138571 @ (0.852, -1.420, -3.125) Found translation: (-0.3, 17.9, -2.0): log p = -4.139 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.866, old_max_log_p =-4.139 (thresh=-4.1) 1.00000 0.00000 0.00000 -0.28409; 0.00000 1.05267 0.45704 -30.93839; 0.00000 -0.39316 1.00369 48.19064; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.866, old_max_log_p =-3.866 (thresh=-3.9) 1.07500 0.00000 0.00000 -9.81359; 0.00000 1.05267 0.45704 -30.93839; 0.00000 -0.36367 0.92842 52.72462; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.772, old_max_log_p =-3.866 (thresh=-3.9) 1.01529 0.00000 0.00000 -4.03116; 0.00000 1.08011 0.50316 -38.67525; 0.00000 -0.39281 0.89406 57.37745; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.772, old_max_log_p =-3.772 (thresh=-3.8) 1.01529 0.00000 0.00000 -4.03116; 0.00000 1.08011 0.50316 -38.67525; 0.00000 -0.39281 0.89406 57.37745; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.760, old_max_log_p =-3.772 (thresh=-3.8) 1.01291 0.00000 0.00000 -3.72458; 0.00000 1.08710 0.49758 -38.36467; 0.00000 -0.38441 0.89920 55.95819; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.756, old_max_log_p =-3.760 (thresh=-3.8) 1.01291 0.00000 0.00000 -3.72458; 0.00000 1.08710 0.49758 -38.36467; 0.00000 -0.38396 0.89815 56.01994; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.756, old_max_log_p =-3.756 (thresh=-3.8) 1.01291 0.00000 0.00000 -3.72458; 0.00000 1.08710 0.49758 -38.36467; 0.00000 -0.38396 0.89815 56.01994; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3388 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01291 0.00000 0.00000 -3.72458; 0.00000 1.08710 0.49758 -38.36467; 0.00000 -0.38396 0.89815 56.01994; 0.00000 0.00000 0.00000 1.00000; nsamples 3388 Quasinewton: input matrix 1.01291 0.00000 0.00000 -3.72458; 0.00000 1.08710 0.49758 -38.36467; 0.00000 -0.38396 0.89815 56.01994; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.01291 0.00000 0.00000 -3.72458; 0.00000 1.08710 0.49758 -38.36467; 0.00000 -0.38396 0.89815 56.01994; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.756 (old=-4.436) transform before final EM align: 1.01291 0.00000 0.00000 -3.72458; 0.00000 1.08710 0.49758 -38.36467; 0.00000 -0.38396 0.89815 56.01994; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 380366 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01291 0.00000 0.00000 -3.72458; 0.00000 1.08710 0.49758 -38.36467; 0.00000 -0.38396 0.89815 56.01994; 0.00000 0.00000 0.00000 1.00000; nsamples 380366 Quasinewton: input matrix 1.01291 0.00000 0.00000 -3.72458; 0.00000 1.08710 0.49758 -38.36467; 0.00000 -0.38396 0.89815 56.01994; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.2 tol 0.000000 final transform: 1.01291 0.00000 0.00000 -3.72458; 0.00000 1.08710 0.49758 -38.36467; 0.00000 -0.38396 0.89815 56.01994; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 887.754996 mri_em_register stimesec 2.371596 mri_em_register ru_maxrss 618256 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 916360 mri_em_register ru_majflt 65 mri_em_register ru_nswap 0 mri_em_register ru_inblock 162496 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 71 mri_em_register ru_nivcsw 31881 registration took 14 minutes and 52 seconds. mri_watershed -rusage /dat/mw/tvb-new-dataset/tvb/touch/rusage.mri_watershed.dat -T1 -brain_atlas /opt/freesurfer/average/RB_all_withskull_2014-08-21.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=128 y=89 z=105 r=93 first estimation of the main basin volume: 3393728 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=107, y=92, z=62, Imax=255 CSF=18, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=22245446712 voxels, voxel volume =1.000 = 22245446712 mmm3 = 22245447.680 cm3 done. PostAnalyze...Basin Prior 168 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=128,y=99, z=98, r=10968 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=5, CSF_MAX=32 , nb = 45388 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=26 , nb = -1029528572 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=25 , nb = -1041583568 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=33 , nb = 1059948618 LEFT_BRAIN CSF_MIN=0, CSF_intensity=7, CSF_MAX=32 , nb = 1076126540 OTHER CSF_MIN=0, CSF_intensity=14, CSF_MAX=39 , nb = 1078658978 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 32, 39, 44, 62 after analyzing : 32, 42, 44, 47 RIGHT_CER before analyzing : 26, 34, 43, 65 after analyzing : 26, 40, 43, 46 LEFT_CER before analyzing : 25, 34, 44, 66 after analyzing : 25, 40, 44, 46 RIGHT_BRAIN before analyzing : 33, 39, 44, 62 after analyzing : 33, 42, 44, 47 LEFT_BRAIN before analyzing : 32, 38, 43, 61 after analyzing : 32, 41, 43, 46 OTHER before analyzing : 39, 41, 44, 62 after analyzing : 39, 43, 44, 47 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...65 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.011 curvature mean = 72.191, std = 8.432 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 5.31, sigma = 10.54 after rotation: sse = 5.31, sigma = 10.54 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 6.65, its var is 15.62 before Erosion-Dilatation 3.39% of inacurate vertices after Erosion-Dilatation 5.11% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...44 iterations mri_strip_skull: done peeling brain Brain Size = 1833725 voxels, voxel volume = 1.000 mm3 = 1833725 mmm3 = 1833.725 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 22.916520 mri_watershed stimesec 0.523235 mri_watershed ru_maxrss 856660 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 472465 mri_watershed ru_majflt 55 mri_watershed ru_nswap 0 mri_watershed ru_inblock 184816 mri_watershed ru_oublock 3040 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 104 mri_watershed ru_nivcsw 870 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Tue Mar 1 16:01:58 CET 2016 /dat/mw/tvb-new-dataset/tvb/mri mri_em_register -rusage /dat/mw/tvb-new-dataset/tvb/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2016-02-11.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/opt/freesurfer/average/RB_all_2016-02-11.gca'... average std = 7.3 using min determinant for regularization = 5.4 0 singular and 895 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.4 or > 511.2 total sample mean = 78.3 (1020 zeros) ************************************************ spacing=8, using 2856 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2856, passno 0, spacing 8 resetting wm mean[0]: 97 --> 106 resetting gm mean[0]: 60 --> 60 input volume #1 is the most T1-like using real data threshold=26.1 skull bounding box = (56, 36, 19) --> (199, 174, 186) using (104, 82, 103) as brain centroid... mean wm in atlas = 106, using box (86,65,82) --> (121, 98,123) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 105 +- 6.1 after smoothing, mri peak at 105, scaling input intensities by 1.010 scaling channel 0 by 1.00952 initial log_p = -4.369 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.077692 @ (-9.091, 27.273, 9.091) max log p = -3.812412 @ (4.545, -4.545, -4.545) max log p = -3.773112 @ (2.273, -2.273, -2.273) max log p = -3.736454 @ (-1.136, 1.136, -1.136) max log p = -3.712395 @ (1.705, -3.977, -2.841) max log p = -3.712395 @ (0.000, 0.000, 0.000) Found translation: (-1.7, 17.6, -1.7): log p = -3.712 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.351, old_max_log_p =-3.712 (thresh=-3.7) 1.00000 0.00000 0.00000 -1.70455; 0.00000 0.99215 0.37209 -14.31480; 0.00000 -0.39034 0.83330 63.86567; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.341, old_max_log_p =-3.351 (thresh=-3.3) 1.00000 0.00000 0.00000 -1.70455; 0.00000 0.99215 0.37209 -14.31480; 0.00000 -0.41961 0.89580 60.67384; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.341, old_max_log_p =-3.341 (thresh=-3.3) 1.00000 0.00000 0.00000 -1.70455; 0.00000 0.99215 0.37209 -14.31480; 0.00000 -0.41961 0.89580 60.67384; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.235, old_max_log_p =-3.341 (thresh=-3.3) 0.99893 -0.01698 -0.04210 3.97283; 0.03570 1.04944 0.39000 -28.29395; 0.03034 -0.40157 0.86261 56.32196; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.210, old_max_log_p =-3.235 (thresh=-3.2) 0.98126 0.00263 -0.00059 0.15465; 0.00396 1.03620 0.41826 -25.67791; -0.00355 -0.43490 0.85031 67.15598; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.210, old_max_log_p =-3.210 (thresh=-3.2) 0.98126 0.00263 -0.00059 0.15465; 0.00396 1.03620 0.41826 -25.67791; -0.00355 -0.43490 0.85031 67.15598; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.177, old_max_log_p =-3.210 (thresh=-3.2) 0.98004 0.00946 -0.01460 0.06361; 0.00403 1.04563 0.40524 -25.82501; 0.01260 -0.41877 0.85892 61.65256; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.176, old_max_log_p =-3.177 (thresh=-3.2) 0.98119 0.02317 -0.00094 -2.82337; -0.01200 1.04416 0.40484 -23.07329; 0.00459 -0.41932 0.86002 62.64727; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2856 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.98119 0.02317 -0.00094 -2.82337; -0.01200 1.04416 0.40484 -23.07329; 0.00459 -0.41932 0.86002 62.64727; 0.00000 0.00000 0.00000 1.00000; nsamples 2856 Quasinewton: input matrix 0.98119 0.02317 -0.00094 -2.82337; -0.01200 1.04416 0.40484 -23.07329; 0.00459 -0.41932 0.86002 62.64727; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.98119 0.02317 -0.00094 -2.82337; -0.01200 1.04416 0.40484 -23.07329; 0.00459 -0.41932 0.86002 62.64727; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.176 (old=-4.369) transform before final EM align: 0.98119 0.02317 -0.00094 -2.82337; -0.01200 1.04416 0.40484 -23.07329; 0.00459 -0.41932 0.86002 62.64727; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 314974 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.98119 0.02317 -0.00094 -2.82337; -0.01200 1.04416 0.40484 -23.07329; 0.00459 -0.41932 0.86002 62.64727; 0.00000 0.00000 0.00000 1.00000; nsamples 314974 Quasinewton: input matrix 0.98119 0.02317 -0.00094 -2.82337; -0.01200 1.04416 0.40484 -23.07329; 0.00459 -0.41932 0.86002 62.64727; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 3.8 tol 0.000000 final transform: 0.98119 0.02317 -0.00094 -2.82337; -0.01200 1.04416 0.40484 -23.07329; 0.00459 -0.41932 0.86002 62.64727; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 825.198411 mri_em_register stimesec 1.779253 mri_em_register ru_maxrss 605888 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 788106 mri_em_register ru_majflt 37 mri_em_register ru_nswap 0 mri_em_register ru_inblock 160480 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 40 mri_em_register ru_nivcsw 7951 registration took 13 minutes and 49 seconds. #-------------------------------------- #@# CA Normalize Tue Mar 1 16:15:47 CET 2016 /dat/mw/tvb-new-dataset/tvb/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2016-02-11.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_2016-02-11.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 97 --> 106 resetting gm mean[0]: 60 --> 60 input volume #1 is the most T1-like using real data threshold=26.1 skull bounding box = (56, 36, 19) --> (199, 174, 186) using (104, 82, 103) as brain centroid... mean wm in atlas = 106, using box (86,65,82) --> (121, 98,123) to find MRI wm before smoothing, mri peak at 106 robust fit to distribution - 105 +- 6.1 after smoothing, mri peak at 105, scaling input intensities by 1.010 scaling channel 0 by 1.00952 using 246052 sample points... INFO: compute sample coordinates transform 0.98119 0.02317 -0.00094 -2.82337; -0.01200 1.04416 0.40484 -23.07329; 0.00459 -0.41932 0.86002 62.64727; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39541 control points for structure... bounding box (128, 42, 20) --> (196, 153, 190) Left_Cerebral_White_Matter: limiting intensities to 107.0 --> 132.0 10 of 23 (43.5%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39165 control points for structure... bounding box (63, 41, 22) --> (132, 146, 191) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0 0 of 12 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 2869 control points for structure... bounding box (130, 127, 60) --> (179, 165, 113) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 12 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2565 control points for structure... bounding box (83, 127, 57) --> (128, 163, 114) Right_Cerebellum_White_Matter: limiting intensities to 93.0 --> 132.0 0 of 8 (0.0%) samples deleted finding control points in Brain_Stem.... found 3504 control points for structure... bounding box (112, 109, 90) --> (147, 172, 124) Brain_Stem: limiting intensities to 88.0 --> 132.0 2 of 11 (18.2%) samples deleted using 66 total control points for intensity normalization... bias field = 0.907 +- 0.069 0 of 54 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39541 control points for structure... bounding box (128, 42, 20) --> (196, 153, 190) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 106 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39165 control points for structure... bounding box (63, 41, 22) --> (132, 146, 191) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 148 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 2869 control points for structure... bounding box (130, 127, 60) --> (179, 165, 113) Left_Cerebellum_White_Matter: limiting intensities to 92.0 --> 132.0 24 of 44 (54.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2565 control points for structure... bounding box (83, 127, 57) --> (128, 163, 114) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 15 of 39 (38.5%) samples deleted finding control points in Brain_Stem.... found 3504 control points for structure... bounding box (112, 109, 90) --> (147, 172, 124) Brain_Stem: limiting intensities to 88.0 --> 132.0 100 of 111 (90.1%) samples deleted using 448 total control points for intensity normalization... bias field = 0.991 +- 0.069 0 of 308 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39541 control points for structure... bounding box (128, 42, 20) --> (196, 153, 190) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 215 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39165 control points for structure... bounding box (63, 41, 22) --> (132, 146, 191) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 258 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 2869 control points for structure... bounding box (130, 127, 60) --> (179, 165, 113) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 36 of 69 (52.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2565 control points for structure... bounding box (83, 127, 57) --> (128, 163, 114) Right_Cerebellum_White_Matter: limiting intensities to 92.0 --> 132.0 59 of 72 (81.9%) samples deleted finding control points in Brain_Stem.... found 3504 control points for structure... bounding box (112, 109, 90) --> (147, 172, 124) Brain_Stem: limiting intensities to 88.0 --> 132.0 133 of 140 (95.0%) samples deleted using 754 total control points for intensity normalization... bias field = 1.002 +- 0.054 0 of 524 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 32 seconds. #-------------------------------------- #@# CA Reg Tue Mar 1 16:17:19 CET 2016 /dat/mw/tvb-new-dataset/tvb/mri mri_ca_register -rusage /dat/mw/tvb-new-dataset/tvb/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/average/RB_all_2016-02-11.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/opt/freesurfer/average/RB_all_2016-02-11.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.05 (predicted orig area = 7.6) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.806, neg=0, invalid=4061 0001: dt=193.307190, rms=0.723 (10.342%), neg=0, invalid=4061 0002: dt=247.111111, rms=0.704 (2.545%), neg=0, invalid=4061 0003: dt=129.472000, rms=0.693 (1.609%), neg=0, invalid=4061 0004: dt=517.888000, rms=0.684 (1.232%), neg=0, invalid=4061 0005: dt=129.472000, rms=0.681 (0.476%), neg=0, invalid=4061 0006: dt=369.920000, rms=0.679 (0.315%), neg=0, invalid=4061 0007: dt=129.472000, rms=0.677 (0.287%), neg=0, invalid=4061 0008: dt=517.888000, rms=0.675 (0.305%), neg=0, invalid=4061 0009: dt=129.472000, rms=0.673 (0.228%), neg=0, invalid=4061 0010: dt=129.472000, rms=0.673 (0.087%), neg=0, invalid=4061 0011: dt=129.472000, rms=0.672 (0.128%), neg=0, invalid=4061 0012: dt=129.472000, rms=0.671 (0.200%), neg=0, invalid=4061 0013: dt=129.472000, rms=0.669 (0.216%), neg=0, invalid=4061 0014: dt=129.472000, rms=0.668 (0.247%), neg=0, invalid=4061 0015: dt=129.472000, rms=0.666 (0.246%), neg=0, invalid=4061 0016: dt=129.472000, rms=0.664 (0.238%), neg=0, invalid=4061 0017: dt=129.472000, rms=0.663 (0.262%), neg=0, invalid=4061 0018: dt=129.472000, rms=0.661 (0.254%), neg=0, invalid=4061 0019: dt=129.472000, rms=0.659 (0.219%), neg=0, invalid=4061 0020: dt=129.472000, rms=0.658 (0.188%), neg=0, invalid=4061 0021: dt=129.472000, rms=0.657 (0.167%), neg=0, invalid=4061 0022: dt=129.472000, rms=0.656 (0.177%), neg=0, invalid=4061 0023: dt=129.472000, rms=0.655 (0.176%), neg=0, invalid=4061 0024: dt=129.472000, rms=0.654 (0.169%), neg=0, invalid=4061 0025: dt=129.472000, rms=0.653 (0.150%), neg=0, invalid=4061 0026: dt=129.472000, rms=0.652 (0.131%), neg=0, invalid=4061 0027: dt=129.472000, rms=0.651 (0.126%), neg=0, invalid=4061 0028: dt=129.472000, rms=0.650 (0.121%), neg=0, invalid=4061 0029: dt=129.472000, rms=0.649 (0.121%), neg=0, invalid=4061 0030: dt=443.904000, rms=0.649 (0.023%), neg=0, invalid=4061 0031: dt=443.904000, rms=0.649 (-0.102%), neg=0, invalid=4061 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.650, neg=0, invalid=4061 0032: dt=369.920000, rms=0.648 (0.239%), neg=0, invalid=4061 0033: dt=129.472000, rms=0.648 (0.061%), neg=0, invalid=4061 0034: dt=129.472000, rms=0.648 (0.038%), neg=0, invalid=4061 0035: dt=129.472000, rms=0.647 (0.057%), neg=0, invalid=4061 0036: dt=129.472000, rms=0.647 (0.066%), neg=0, invalid=4061 0037: dt=129.472000, rms=0.646 (0.066%), neg=0, invalid=4061 0038: dt=129.472000, rms=0.646 (0.064%), neg=0, invalid=4061 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.651, neg=0, invalid=4061 0039: dt=210.979310, rms=0.645 (0.982%), neg=0, invalid=4061 0040: dt=165.556886, rms=0.636 (1.247%), neg=0, invalid=4061 0041: dt=66.966887, rms=0.633 (0.473%), neg=0, invalid=4061 0042: dt=331.776000, rms=0.629 (0.696%), neg=0, invalid=4061 0043: dt=62.208000, rms=0.626 (0.491%), neg=0, invalid=4061 0044: dt=248.832000, rms=0.623 (0.488%), neg=0, invalid=4061 0045: dt=65.333333, rms=0.622 (0.208%), neg=0, invalid=4061 0046: dt=65.333333, rms=0.621 (0.165%), neg=0, invalid=4061 0047: dt=65.333333, rms=0.619 (0.197%), neg=0, invalid=4061 0048: dt=65.333333, rms=0.618 (0.263%), neg=0, invalid=4061 0049: dt=65.333333, rms=0.616 (0.279%), neg=0, invalid=4061 0050: dt=65.333333, rms=0.614 (0.373%), neg=0, invalid=4061 0051: dt=65.333333, rms=0.611 (0.383%), neg=0, invalid=4061 0052: dt=65.333333, rms=0.609 (0.335%), neg=0, invalid=4061 0053: dt=65.333333, rms=0.608 (0.299%), neg=0, invalid=4061 0054: dt=65.333333, rms=0.606 (0.266%), neg=0, invalid=4061 0055: dt=65.333333, rms=0.604 (0.289%), neg=0, invalid=4061 0056: dt=65.333333, rms=0.602 (0.286%), neg=0, invalid=4061 0057: dt=65.333333, rms=0.601 (0.234%), neg=0, invalid=4061 0058: dt=65.333333, rms=0.600 (0.193%), neg=0, invalid=4061 0059: dt=65.333333, rms=0.599 (0.169%), neg=0, invalid=4061 0060: dt=65.333333, rms=0.598 (0.185%), neg=0, invalid=4061 0061: dt=65.333333, rms=0.598 (0.031%), neg=0, invalid=4061 0062: dt=65.333333, rms=0.597 (0.021%), neg=0, invalid=4061 0063: dt=9.072000, rms=0.597 (-0.005%), neg=0, invalid=4061 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.598, neg=0, invalid=4061 0064: dt=9.072000, rms=0.597 (0.137%), neg=0, invalid=4061 0065: dt=2.268000, rms=0.597 (0.008%), neg=0, invalid=4061 0066: dt=1.134000, rms=0.597 (0.004%), neg=0, invalid=4061 0067: dt=0.070875, rms=0.597 (0.001%), neg=0, invalid=4061 0068: dt=0.002215, rms=0.597 (0.000%), neg=0, invalid=4061 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.619, neg=0, invalid=4061 0069: dt=0.000586, rms=0.618 (0.103%), neg=0, invalid=4061 0070: dt=0.000000, rms=0.618 (0.000%), neg=0, invalid=4061 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.619, neg=0, invalid=4061 0071: dt=0.000000, rms=0.618 (0.103%), neg=0, invalid=4061 0072: dt=0.000000, rms=0.618 (0.000%), neg=0, invalid=4061 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.683, neg=0, invalid=4061 0073: dt=6.268222, rms=0.656 (3.849%), neg=0, invalid=4061 0074: dt=4.032000, rms=0.655 (0.212%), neg=0, invalid=4061 0075: dt=4.032000, rms=0.655 (-0.011%), neg=0, invalid=4061 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.656, neg=0, invalid=4061 0076: dt=0.000141, rms=0.655 (0.080%), neg=0, invalid=4061 0077: dt=0.000000, rms=0.655 (0.000%), neg=0, invalid=4061 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.706, neg=0, invalid=4061 0078: dt=0.798535, rms=0.704 (0.314%), neg=0, invalid=4061 0079: dt=1.792000, rms=0.701 (0.458%), neg=0, invalid=4061 0080: dt=2.090909, rms=0.698 (0.395%), neg=0, invalid=4061 0081: dt=1.280000, rms=0.698 (0.072%), neg=0, invalid=4061 0082: dt=1.280000, rms=0.697 (0.041%), neg=0, invalid=4061 0083: dt=1.280000, rms=0.697 (0.010%), neg=0, invalid=4061 0084: dt=1.280000, rms=0.697 (-0.154%), neg=0, invalid=4061 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.698, neg=0, invalid=4061 0085: dt=1.536000, rms=0.696 (0.224%), neg=0, invalid=4061 0086: dt=0.000000, rms=0.696 (0.002%), neg=0, invalid=4061 0087: dt=0.100000, rms=0.696 (-0.001%), neg=0, invalid=4061 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.665, neg=0, invalid=4061 0088: dt=0.867283, rms=0.646 (2.872%), neg=0, invalid=4061 0089: dt=0.080000, rms=0.645 (0.143%), neg=0, invalid=4061 0090: dt=0.080000, rms=0.645 (-0.097%), neg=0, invalid=4061 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.646, neg=0, invalid=4061 0091: dt=0.028000, rms=0.645 (0.098%), neg=0, invalid=4061 0092: dt=0.005000, rms=0.645 (0.001%), neg=0, invalid=4061 0093: dt=0.005000, rms=0.645 (-0.000%), neg=0, invalid=4061 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.13179 (17) mri peak = 0.09128 (20) Left_Lateral_Ventricle (4): linear fit = 0.95 x + 0.0 (812 voxels, overlap=0.724) Left_Lateral_Ventricle (4): linear fit = 0.95 x + 0.0 (812 voxels, peak = 16), gca=16.2 gca peak = 0.14060 (15) mri peak = 0.08972 (17) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (670 voxels, overlap=0.871) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (670 voxels, peak = 16), gca=16.4 gca peak = 0.21831 (95) mri peak = 0.06515 (94) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (623 voxels, overlap=1.006) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (623 voxels, peak = 93), gca=92.6 gca peak = 0.21471 (96) mri peak = 0.06698 (101) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (430 voxels, overlap=1.011) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (430 voxels, peak = 100), gca=100.3 gca peak = 0.21211 (57) mri peak = 0.07338 (65) Right_Hippocampus (53): linear fit = 1.12 x + 0.0 (532 voxels, overlap=0.791) Right_Hippocampus (53): linear fit = 1.12 x + 0.0 (532 voxels, peak = 64), gca=63.6 gca peak = 0.29506 (58) mri peak = 0.08869 (66) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (458 voxels, overlap=0.997) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (458 voxels, peak = 65), gca=64.7 gca peak = 0.10708 (101) mri peak = 0.08475 (104) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (69691 voxels, overlap=0.791) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (69691 voxels, peak = 105), gca=104.5 gca peak = 0.11193 (102) mri peak = 0.08335 (105) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (67866 voxels, overlap=0.681) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (67866 voxels, peak = 108), gca=107.6 gca peak = 0.15589 (59) mri peak = 0.05749 (61) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (26812 voxels, overlap=0.989) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (26812 voxels, peak = 60), gca=60.5 gca peak = 0.15573 (58) mri peak = 0.05373 (63) Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (28564 voxels, overlap=0.963) Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (28564 voxels, peak = 61), gca=60.6 gca peak = 0.15418 (67) mri peak = 0.08266 (72) Right_Caudate (50): linear fit = 1.07 x + 0.0 (780 voxels, overlap=0.760) Right_Caudate (50): linear fit = 1.07 x + 0.0 (780 voxels, peak = 71), gca=71.4 gca peak = 0.11657 (73) mri peak = 0.07407 (76) Left_Caudate (11): linear fit = 1.03 x + 0.0 (658 voxels, overlap=0.978) Left_Caudate (11): linear fit = 1.03 x + 0.0 (658 voxels, peak = 76), gca=75.6 gca peak = 0.13135 (57) mri peak = 0.04785 (59) Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (8170 voxels, overlap=0.898) Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (8170 voxels, peak = 61), gca=60.7 gca peak = 0.13679 (56) mri peak = 0.04590 (60) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (10173 voxels, overlap=0.926) Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (10173 voxels, peak = 59), gca=58.5 gca peak = 0.17198 (84) mri peak = 0.05346 (84) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5247 voxels, overlap=0.927) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (5247 voxels, peak = 89), gca=88.6 gca peak = 0.20416 (83) mri peak = 0.06279 (83) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5533 voxels, overlap=0.976) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5533 voxels, peak = 82), gca=81.8 gca peak = 0.22988 (57) mri peak = 0.08978 (64) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (319 voxels, overlap=0.980) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (319 voxels, peak = 60), gca=59.6 gca peak = 0.39741 (56) mri peak = 0.09295 (61) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (313 voxels, overlap=0.370) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (313 voxels, peak = 64), gca=63.6 gca peak = 0.13077 (85) mri peak = 0.05625 (90) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4123 voxels, overlap=0.974) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4123 voxels, peak = 86), gca=86.3 gca peak = 0.12549 (83) mri peak = 0.05414 (85) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3742 voxels, overlap=0.881) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3742 voxels, peak = 88), gca=87.6 gca peak = 0.14242 (78) mri peak = 0.06813 (80) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1648 voxels, overlap=0.870) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1648 voxels, peak = 82), gca=81.5 gca peak = 0.11767 (75) mri peak = 0.05830 (78) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2027 voxels, overlap=0.999) Right_Putamen (51): linear fit = 1.04 x + 0.0 (2027 voxels, peak = 78), gca=78.4 gca peak = 0.09825 (80) mri peak = 0.19138 (80) Brain_Stem (16): linear fit = 1.05 x + 0.0 (9977 voxels, overlap=0.343) Brain_Stem (16): linear fit = 1.05 x + 0.0 (9977 voxels, peak = 84), gca=84.4 gca peak = 0.11703 (87) mri peak = 0.09380 (85) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (839 voxels, overlap=0.710) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (839 voxels, peak = 89), gca=89.2 gca peak = 0.11136 (89) mri peak = 0.09896 (85) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (971 voxels, overlap=0.819) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (971 voxels, peak = 88), gca=87.7 gca peak = 0.18826 (23) mri peak = 0.12121 (20) gca peak = 0.12188 (17) mri peak = 0.10673 (19) Fourth_Ventricle (15): linear fit = 0.79 x + 0.0 (202 voxels, overlap=0.611) Fourth_Ventricle (15): linear fit = 0.79 x + 0.0 (202 voxels, peak = 13), gca=13.3 gca peak Unknown = 0.94796 ( 0) gca peak Left_Inf_Lat_Vent = 0.13800 (32) gca peak Left_Thalamus = 0.70419 (95) gca peak Third_Ventricle = 0.18826 (23) gca peak CSF = 0.20601 (36) gca peak Left_Accumbens_area = 0.42073 (62) gca peak Left_undetermined = 0.95623 (27) gca peak Left_vessel = 0.34442 (53) gca peak Left_choroid_plexus = 0.10305 (45) gca peak Right_Inf_Lat_Vent = 0.20912 (26) gca peak Right_Accumbens_area = 0.28289 (64) gca peak Right_vessel = 0.48330 (52) gca peak Right_choroid_plexus = 0.13254 (41) gca peak Fifth_Ventricle = 0.56772 (36) gca peak WM_hypointensities = 0.08847 (74) gca peak non_WM_hypointensities = 0.07232 (49) gca peak Optic_Chiasm = 0.22888 (77) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.08 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.94 x + 0.0 saving intensity scales to talairach.label_intensities.txt ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.654, neg=0, invalid=4061 0094: dt=94.814815, rms=0.649 (0.798%), neg=0, invalid=4061 0095: dt=129.472000, rms=0.647 (0.316%), neg=0, invalid=4061 0096: dt=443.904000, rms=0.644 (0.506%), neg=0, invalid=4061 0097: dt=129.472000, rms=0.642 (0.233%), neg=0, invalid=4061 0098: dt=129.472000, rms=0.641 (0.129%), neg=0, invalid=4061 0099: dt=129.472000, rms=0.640 (0.195%), neg=0, invalid=4061 0100: dt=129.472000, rms=0.639 (0.226%), neg=0, invalid=4061 0101: dt=129.472000, rms=0.637 (0.188%), neg=0, invalid=4061 0102: dt=129.472000, rms=0.636 (0.192%), neg=0, invalid=4061 0103: dt=129.472000, rms=0.635 (0.151%), neg=0, invalid=4061 0104: dt=129.472000, rms=0.634 (0.150%), neg=0, invalid=4061 0105: dt=129.472000, rms=0.633 (0.134%), neg=0, invalid=4061 0106: dt=129.472000, rms=0.633 (0.132%), neg=0, invalid=4061 0107: dt=129.472000, rms=0.632 (0.107%), neg=0, invalid=4061 0108: dt=129.472000, rms=0.631 (0.075%), neg=0, invalid=4061 0109: dt=443.904000, rms=0.631 (0.072%), neg=0, invalid=4061 0110: dt=443.904000, rms=0.631 (-0.700%), neg=0, invalid=4061 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.631, neg=0, invalid=4061 0111: dt=129.472000, rms=0.630 (0.259%), neg=0, invalid=4061 0112: dt=517.888000, rms=0.629 (0.151%), neg=0, invalid=4061 0113: dt=517.888000, rms=0.629 (-0.632%), neg=0, invalid=4061 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.630, neg=0, invalid=4061 0114: dt=100.204380, rms=0.624 (0.977%), neg=0, invalid=4061 0115: dt=124.416000, rms=0.619 (0.831%), neg=0, invalid=4061 0116: dt=62.208000, rms=0.615 (0.598%), neg=0, invalid=4061 0117: dt=145.152000, rms=0.612 (0.576%), neg=0, invalid=4061 0118: dt=62.208000, rms=0.610 (0.320%), neg=0, invalid=4061 0119: dt=145.152000, rms=0.607 (0.398%), neg=0, invalid=4061 0120: dt=36.288000, rms=0.606 (0.199%), neg=0, invalid=4061 0121: dt=36.288000, rms=0.606 (0.097%), neg=0, invalid=4061 0122: dt=36.288000, rms=0.605 (0.161%), neg=0, invalid=4061 0123: dt=36.288000, rms=0.603 (0.218%), neg=0, invalid=4061 0124: dt=36.288000, rms=0.602 (0.283%), neg=0, invalid=4061 0125: dt=36.288000, rms=0.600 (0.300%), neg=0, invalid=4061 0126: dt=36.288000, rms=0.598 (0.299%), neg=0, invalid=4061 0127: dt=36.288000, rms=0.596 (0.281%), neg=0, invalid=4061 0128: dt=36.288000, rms=0.595 (0.264%), neg=0, invalid=4061 0129: dt=36.288000, rms=0.593 (0.242%), neg=0, invalid=4061 0130: dt=36.288000, rms=0.592 (0.229%), neg=0, invalid=4061 0131: dt=36.288000, rms=0.591 (0.213%), neg=0, invalid=4061 0132: dt=36.288000, rms=0.590 (0.195%), neg=0, invalid=4061 0133: dt=36.288000, rms=0.589 (0.178%), neg=0, invalid=4061 0134: dt=36.288000, rms=0.588 (0.165%), neg=0, invalid=4061 0135: dt=36.288000, rms=0.587 (0.147%), neg=0, invalid=4061 0136: dt=36.288000, rms=0.586 (0.133%), neg=0, invalid=4061 0137: dt=36.288000, rms=0.585 (0.131%), neg=0, invalid=4061 0138: dt=36.288000, rms=0.584 (0.123%), neg=0, invalid=4061 0139: dt=36.288000, rms=0.584 (0.107%), neg=0, invalid=4061 0140: dt=82.944000, rms=0.584 (0.006%), neg=0, invalid=4061 0141: dt=82.944000, rms=0.584 (0.030%), neg=0, invalid=4061 0142: dt=82.944000, rms=0.583 (0.033%), neg=0, invalid=4061 0143: dt=82.944000, rms=0.583 (0.013%), neg=0, invalid=4061 0144: dt=82.944000, rms=0.583 (0.062%), neg=0, invalid=4061 0145: dt=82.944000, rms=0.583 (0.046%), neg=0, invalid=4061 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.583, neg=0, invalid=4061 0146: dt=94.315789, rms=0.581 (0.329%), neg=0, invalid=4061 0147: dt=82.944000, rms=0.580 (0.152%), neg=0, invalid=4061 0148: dt=82.944000, rms=0.580 (-0.038%), neg=0, invalid=4061 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.594, neg=0, invalid=4061 0149: dt=11.200000, rms=0.592 (0.226%), neg=0, invalid=4061 0150: dt=8.000000, rms=0.592 (0.037%), neg=0, invalid=4061 0151: dt=8.000000, rms=0.592 (0.014%), neg=0, invalid=4061 0152: dt=8.000000, rms=0.592 (-0.041%), neg=0, invalid=4061 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.592, neg=0, invalid=4061 0153: dt=6.400000, rms=0.592 (0.107%), neg=0, invalid=4061 0154: dt=2.000000, rms=0.592 (0.002%), neg=0, invalid=4061 0155: dt=2.000000, rms=0.592 (-0.001%), neg=0, invalid=4061 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.617, neg=0, invalid=4061 0156: dt=2.791111, rms=0.615 (0.362%), neg=0, invalid=4061 0157: dt=0.864000, rms=0.615 (0.012%), neg=0, invalid=4061 0158: dt=0.864000, rms=0.615 (-0.006%), neg=0, invalid=4061 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.615, neg=0, invalid=4061 0159: dt=0.000000, rms=0.615 (0.075%), neg=0, invalid=4061 0160: dt=0.000000, rms=0.615 (0.000%), neg=0, invalid=4061 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.650, neg=0, invalid=4061 0161: dt=0.448000, rms=0.648 (0.258%), neg=0, invalid=4061 0162: dt=0.448000, rms=0.648 (0.091%), neg=0, invalid=4061 0163: dt=0.448000, rms=0.647 (0.042%), neg=0, invalid=4061 0164: dt=0.448000, rms=0.647 (-0.086%), neg=0, invalid=4061 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.648, neg=0, invalid=4061 0165: dt=0.448000, rms=0.647 (0.179%), neg=0, invalid=4061 0166: dt=0.448000, rms=0.646 (0.060%), neg=0, invalid=4061 0167: dt=0.448000, rms=0.646 (0.032%), neg=0, invalid=4061 0168: dt=0.448000, rms=0.646 (-0.036%), neg=0, invalid=4061 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.618, neg=0, invalid=4061 0169: dt=0.836638, rms=0.600 (2.919%), neg=0, invalid=4061 0170: dt=0.064000, rms=0.599 (0.133%), neg=0, invalid=4061 0171: dt=0.064000, rms=0.599 (-0.060%), neg=0, invalid=4061 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.599, neg=0, invalid=4061 0172: dt=0.028000, rms=0.599 (0.103%), neg=0, invalid=4061 0173: dt=0.004000, rms=0.599 (-0.002%), neg=0, invalid=4061 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 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.588, neg=0, invalid=4061 0174: dt=92.480000, rms=0.587 (0.044%), neg=0, invalid=4061 0175: dt=221.952000, rms=0.587 (0.084%), neg=0, invalid=4061 0176: dt=443.904000, rms=0.586 (0.125%), neg=0, invalid=4061 0177: dt=110.976000, rms=0.586 (0.053%), neg=0, invalid=4061 0178: dt=110.976000, rms=0.586 (0.004%), neg=0, invalid=4061 0179: dt=110.976000, rms=0.586 (0.025%), neg=0, invalid=4061 0180: dt=110.976000, rms=0.585 (0.066%), neg=0, invalid=4061 0181: dt=110.976000, rms=0.585 (0.048%), neg=0, invalid=4061 0182: dt=110.976000, rms=0.585 (0.036%), neg=0, invalid=4061 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.585, neg=0, invalid=4061 0183: dt=129.472000, rms=0.584 (0.156%), neg=0, invalid=4061 0184: dt=517.888000, rms=0.583 (0.150%), neg=0, invalid=4061 0185: dt=517.888000, rms=0.583 (-0.191%), neg=0, invalid=4061 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.583, neg=0, invalid=4061 0186: dt=93.992620, rms=0.581 (0.445%), neg=0, invalid=4061 0187: dt=145.152000, rms=0.577 (0.635%), neg=0, invalid=4061 0188: dt=36.288000, rms=0.576 (0.229%), neg=0, invalid=4061 0189: dt=36.288000, rms=0.575 (0.098%), neg=0, invalid=4061 0190: dt=36.288000, rms=0.574 (0.159%), neg=0, invalid=4061 0191: dt=36.288000, rms=0.573 (0.213%), neg=0, invalid=4061 0192: dt=36.288000, rms=0.572 (0.257%), neg=0, invalid=4061 0193: dt=36.288000, rms=0.570 (0.265%), neg=0, invalid=4061 0194: dt=36.288000, rms=0.569 (0.238%), neg=0, invalid=4061 0195: dt=36.288000, rms=0.567 (0.203%), neg=0, invalid=4061 0196: dt=36.288000, rms=0.566 (0.175%), neg=0, invalid=4061 0197: dt=36.288000, rms=0.566 (0.148%), neg=0, invalid=4061 0198: dt=36.288000, rms=0.565 (0.137%), neg=0, invalid=4061 0199: dt=36.288000, rms=0.564 (0.148%), neg=0, invalid=4061 0200: dt=36.288000, rms=0.563 (0.150%), neg=0, invalid=4061 0201: dt=36.288000, rms=0.562 (0.154%), neg=0, invalid=4061 0202: dt=36.288000, rms=0.561 (0.150%), neg=0, invalid=4061 0203: dt=36.288000, rms=0.561 (0.140%), neg=0, invalid=4061 0204: dt=36.288000, rms=0.560 (0.123%), neg=0, invalid=4061 0205: dt=36.288000, rms=0.559 (0.107%), neg=0, invalid=4061 0206: dt=248.832000, rms=0.559 (0.055%), neg=0, invalid=4061 0207: dt=248.832000, rms=0.559 (-0.194%), neg=0, invalid=4061 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.559, neg=0, invalid=4061 0208: dt=145.152000, rms=0.556 (0.558%), neg=0, invalid=4061 0209: dt=82.944000, rms=0.556 (0.081%), neg=0, invalid=4061 0210: dt=82.944000, rms=0.555 (0.100%), neg=0, invalid=4061 0211: dt=82.944000, rms=0.554 (0.112%), neg=0, invalid=4061 0212: dt=82.944000, rms=0.554 (0.086%), neg=0, invalid=4061 0213: dt=82.944000, rms=0.554 (0.049%), neg=0, invalid=4061 0214: dt=82.944000, rms=0.553 (0.028%), neg=0, invalid=4061 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.559, neg=0, invalid=4061 0215: dt=11.200000, rms=0.558 (0.200%), neg=0, invalid=4061 0216: dt=11.200000, rms=0.557 (0.100%), neg=0, invalid=4061 0217: dt=11.200000, rms=0.557 (0.077%), neg=0, invalid=4061 0218: dt=11.200000, rms=0.556 (0.081%), neg=0, invalid=4061 0219: dt=11.200000, rms=0.556 (0.066%), neg=0, invalid=4061 0220: dt=11.200000, rms=0.555 (0.099%), neg=0, invalid=4061 0221: dt=11.200000, rms=0.554 (0.226%), neg=0, invalid=4061 0222: dt=11.200000, rms=0.552 (0.390%), neg=0, invalid=4061 0223: dt=11.200000, rms=0.549 (0.510%), neg=0, invalid=4061 0224: dt=11.200000, rms=0.546 (0.538%), neg=0, invalid=4061 0225: dt=11.200000, rms=0.544 (0.462%), neg=0, invalid=4061 0226: dt=11.200000, rms=0.542 (0.323%), neg=0, invalid=4061 0227: dt=11.200000, rms=0.541 (0.161%), neg=0, invalid=4061 0228: dt=11.200000, rms=0.541 (0.012%), neg=0, invalid=4061 0229: dt=11.200000, rms=0.541 (-0.101%), neg=0, invalid=4061 0230: dt=0.000000, rms=0.541 (0.000%), neg=0, invalid=4061 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.541, neg=0, invalid=4061 0231: dt=9.600000, rms=0.541 (0.039%), neg=0, invalid=4061 0232: dt=0.000000, rms=0.541 (0.000%), neg=0, invalid=4061 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.557, neg=0, invalid=4061 0233: dt=0.000000, rms=0.557 (0.000%), neg=0, invalid=4061 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.557, neg=0, invalid=4061 0234: dt=0.000000, rms=0.557 (0.000%), neg=0, invalid=4061 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.591, neg=0, invalid=4061 0235: dt=0.881434, rms=0.584 (1.160%), neg=0, invalid=4061 0236: dt=0.192000, rms=0.584 (0.028%), neg=0, invalid=4061 0237: dt=0.192000, rms=0.584 (-0.008%), neg=0, invalid=4061 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.584, neg=0, invalid=4061 0238: dt=0.320000, rms=0.584 (0.044%), neg=0, invalid=4061 0239: dt=0.004000, rms=0.584 (0.000%), neg=0, invalid=4061 0240: dt=0.004000, rms=0.584 (-0.000%), neg=0, invalid=4061 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.558, neg=0, invalid=4061 0241: dt=0.776178, rms=0.543 (2.716%), neg=0, invalid=4061 0242: dt=0.048000, rms=0.542 (0.081%), neg=0, invalid=4061 0243: dt=0.048000, rms=0.542 (-0.046%), neg=0, invalid=4061 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.542, neg=0, invalid=4061 0244: dt=0.024000, rms=0.542 (0.014%), neg=0, invalid=4061 0245: dt=0.000000, rms=0.542 (0.000%), neg=0, invalid=4061 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 27 minutes and 51 seconds. mri_ca_register utimesec 5246.127744 mri_ca_register stimesec 14.399907 mri_ca_register ru_maxrss 1287836 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 15761810 mri_ca_register ru_majflt 10303 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 160696 mri_ca_register ru_oublock 63472 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 10323 mri_ca_register ru_nivcsw 78262 FSRUNTIME@ mri_ca_register 1.4641 hours 1 threads #-------------------------------------- #@# Remove Neck Tue Mar 1 17:45:10 CET 2016 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-02-11.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/opt/freesurfer/average/RB_all_2016-02-11.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... setting orig areas to linear transform determinant scaled 7.63 removing structures at least 25 mm from brain... 10630093 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 5 seconds. #-------------------------------------- #@# SubCort Seg Tue Mar 1 17:46:15 CET 2016 mri_ca_label -rusage /dat/mw/tvb-new-dataset/tvb/touch/rusage.mri_ca_label.dat -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-02-11.gca aseg.auto_noCCseg.mgz sysname Linux hostname x220 machine x86_64 setenv SUBJECTS_DIR /dat/mw/tvb-new-dataset cd /dat/mw/tvb-new-dataset/tvb/mri mri_ca_label -rusage /dat/mw/tvb-new-dataset/tvb/touch/rusage.mri_ca_label.dat -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-02-11.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /opt/freesurfer/average/RB_all_2016-02-11.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 7.63 Atlas used for the 3D morph was /opt/freesurfer/average/RB_all_2016-02-11.gca average std = 7.3 using min determinant for regularization = 5.4 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16444 (20) mri peak = 0.09147 (19) Left_Lateral_Ventricle (4): linear fit = 0.88 x + 0.0 (569 voxels, overlap=0.879) Left_Lateral_Ventricle (4): linear fit = 0.88 x + 0.0 (569 voxels, peak = 18), gca=17.7 gca peak = 0.21853 (13) mri peak = 0.07809 (17) Right_Lateral_Ventricle (43): linear fit = 1.12 x + 0.0 (466 voxels, overlap=0.627) Right_Lateral_Ventricle (43): linear fit = 1.12 x + 0.0 (466 voxels, peak = 14), gca=14.5 gca peak = 0.23579 (93) mri peak = 0.08184 (99) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (583 voxels, overlap=1.017) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (583 voxels, peak = 95), gca=95.3 gca peak = 0.15365 (91) mri peak = 0.07756 (101) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (419 voxels, overlap=1.014) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (419 voxels, peak = 96), gca=96.0 gca peak = 0.25540 (55) mri peak = 0.07627 (64) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (592 voxels, overlap=0.756) Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (592 voxels, peak = 62), gca=62.4 gca peak = 0.29884 (56) mri peak = 0.08696 (63) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (381 voxels, overlap=1.014) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (381 voxels, peak = 62), gca=62.4 gca peak = 0.07342 (103) mri peak = 0.08589 (104) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (63715 voxels, overlap=0.721) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (63715 voxels, peak = 105), gca=104.5 gca peak = 0.07502 (105) mri peak = 0.08286 (105) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (59821 voxels, overlap=0.670) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (59821 voxels, peak = 108), gca=107.6 gca peak = 0.09936 (58) mri peak = 0.05443 (60) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (32069 voxels, overlap=0.947) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (32069 voxels, peak = 59), gca=59.4 gca peak = 0.11354 (58) mri peak = 0.05182 (62) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (31734 voxels, overlap=0.922) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (31734 voxels, peak = 62), gca=62.4 gca peak = 0.23647 (67) mri peak = 0.08612 (74) Right_Caudate (50): linear fit = 1.09 x + 0.0 (778 voxels, overlap=0.652) Right_Caudate (50): linear fit = 1.09 x + 0.0 (778 voxels, peak = 73), gca=72.7 gca peak = 0.15775 (78) mri peak = 0.10705 (77) Left_Caudate (11): linear fit = 1.01 x + 0.0 (738 voxels, overlap=1.005) Left_Caudate (11): linear fit = 1.01 x + 0.0 (738 voxels, peak = 79), gca=79.2 gca peak = 0.13203 (55) mri peak = 0.05485 (59) Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (7329 voxels, overlap=0.894) Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (7329 voxels, peak = 59), gca=58.6 gca peak = 0.14108 (55) mri peak = 0.05531 (59) Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (8739 voxels, overlap=0.973) Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (8739 voxels, peak = 59), gca=58.6 gca peak = 0.16646 (84) mri peak = 0.06027 (84) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (4885 voxels, overlap=0.958) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (4885 voxels, peak = 89), gca=88.6 gca peak = 0.19062 (84) mri peak = 0.06626 (83) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5554 voxels, overlap=0.983) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5554 voxels, peak = 84), gca=83.6 gca peak = 0.32255 (58) mri peak = 0.09609 (61) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (280 voxels, overlap=1.023) Left_Amygdala (18): linear fit = 1.04 x + 0.0 (280 voxels, peak = 61), gca=60.6 gca peak = 0.43434 (57) mri peak = 0.07930 (63) Right_Amygdala (54): linear fit = 1.12 x + 0.0 (332 voxels, overlap=0.666) Right_Amygdala (54): linear fit = 1.12 x + 0.0 (332 voxels, peak = 64), gca=63.6 gca peak = 0.11365 (89) mri peak = 0.05724 (90) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3763 voxels, overlap=0.997) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3763 voxels, peak = 90), gca=90.3 gca peak = 0.10085 (80) mri peak = 0.05923 (87) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3969 voxels, overlap=0.892) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3969 voxels, peak = 84), gca=84.4 gca peak = 0.08979 (82) mri peak = 0.07615 (82) Left_Putamen (12): linear fit = 1.05 x + 0.0 (1694 voxels, overlap=0.743) Left_Putamen (12): linear fit = 1.05 x + 0.0 (1694 voxels, peak = 87), gca=86.5 gca peak = 0.10100 (75) mri peak = 0.06948 (78) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1867 voxels, overlap=0.907) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1867 voxels, peak = 78), gca=78.4 gca peak = 0.07837 (81) mri peak = 0.17385 (80) Brain_Stem (16): linear fit = 1.02 x + 0.0 (10094 voxels, overlap=0.439) Brain_Stem (16): linear fit = 1.02 x + 0.0 (10094 voxels, peak = 83), gca=83.0 gca peak = 0.13897 (88) mri peak = 0.07795 (85) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (962 voxels, overlap=0.811) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (962 voxels, peak = 91), gca=91.1 gca peak = 0.19362 (85) mri peak = 0.08848 (85) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1148 voxels, overlap=0.888) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1148 voxels, peak = 84), gca=83.7 gca peak = 0.17781 (26) mri peak = 0.15909 (20) gca peak = 0.15396 (17) mri peak = 0.12717 (19) Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (176 voxels, overlap=0.819) Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (176 voxels, peak = 18), gca=17.6 gca peak Unknown = 0.94796 ( 0) gca peak Left_Inf_Lat_Vent = 0.21623 (33) gca peak Left_Thalamus = 1.00000 (95) gca peak Third_Ventricle = 0.17781 (26) gca peak CSF = 0.19919 (30) gca peak Left_Accumbens_area = 0.78355 (62) gca peak Left_undetermined = 1.00000 (27) gca peak Left_vessel = 0.84512 (52) gca peak Left_choroid_plexus = 0.10176 (35) gca peak Right_Inf_Lat_Vent = 0.21231 (23) gca peak Right_Accumbens_area = 0.42564 (64) gca peak Right_vessel = 0.77129 (52) gca peak Right_choroid_plexus = 0.11214 (38) gca peak Fifth_Ventricle = 0.71910 (33) gca peak WM_hypointensities = 0.10829 (75) gca peak non_WM_hypointensities = 0.07461 (29) gca peak Optic_Chiasm = 0.72413 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.09 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.01 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16595 (16) mri peak = 0.09147 (19) Left_Lateral_Ventricle (4): linear fit = 1.10 x + 0.0 (569 voxels, overlap=0.940) Left_Lateral_Ventricle (4): linear fit = 1.10 x + 0.0 (569 voxels, peak = 18), gca=17.5 gca peak = 0.15982 (14) mri peak = 0.07809 (17) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (466 voxels, overlap=0.801) Right_Lateral_Ventricle (43): linear fit = 1.10 x + 0.0 (466 voxels, peak = 15), gca=15.3 gca peak = 0.24225 (97) mri peak = 0.08184 (99) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (583 voxels, overlap=1.015) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (583 voxels, peak = 98), gca=98.5 gca peak = 0.14886 (102) mri peak = 0.07756 (101) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (419 voxels, overlap=1.014) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (419 voxels, peak = 102), gca=102.0 gca peak = 0.29427 (63) mri peak = 0.07627 (64) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (592 voxels, overlap=1.009) Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (592 voxels, peak = 62), gca=62.1 gca peak = 0.30075 (63) mri peak = 0.08696 (63) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (381 voxels, overlap=1.008) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (381 voxels, peak = 62), gca=62.1 gca peak = 0.07674 (104) mri peak = 0.08589 (104) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (63715 voxels, overlap=0.780) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (63715 voxels, peak = 104), gca=104.0 gca peak = 0.07423 (107) mri peak = 0.08286 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (59821 voxels, overlap=0.778) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (59821 voxels, peak = 107), gca=107.0 gca peak = 0.09388 (58) mri peak = 0.05443 (60) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (32069 voxels, overlap=0.968) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (32069 voxels, peak = 59), gca=59.4 gca peak = 0.10514 (62) mri peak = 0.05182 (62) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (31734 voxels, overlap=0.969) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (31734 voxels, peak = 61), gca=61.1 gca peak = 0.22803 (72) mri peak = 0.08612 (74) Right_Caudate (50): linear fit = 1.01 x + 0.0 (778 voxels, overlap=1.008) Right_Caudate (50): linear fit = 1.01 x + 0.0 (778 voxels, peak = 73), gca=73.1 gca peak = 0.17559 (79) mri peak = 0.10705 (77) Left_Caudate (11): linear fit = 1.01 x + 0.0 (738 voxels, overlap=1.002) Left_Caudate (11): linear fit = 1.01 x + 0.0 (738 voxels, peak = 80), gca=80.2 gca peak = 0.13036 (58) mri peak = 0.05485 (59) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (7329 voxels, overlap=0.990) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (7329 voxels, peak = 59), gca=59.4 gca peak = 0.13566 (58) mri peak = 0.05531 (59) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (8739 voxels, overlap=0.998) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (8739 voxels, peak = 59), gca=59.4 gca peak = 0.16130 (89) mri peak = 0.06027 (84) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4885 voxels, overlap=0.993) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4885 voxels, peak = 89), gca=88.6 gca peak = 0.15200 (84) mri peak = 0.06626 (83) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5554 voxels, overlap=0.976) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5554 voxels, peak = 84), gca=83.6 gca peak = 0.30162 (61) mri peak = 0.09609 (61) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (280 voxels, overlap=1.020) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (280 voxels, peak = 60), gca=60.1 gca peak = 0.37725 (63) mri peak = 0.07930 (63) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (332 voxels, overlap=1.015) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (332 voxels, peak = 62), gca=62.1 gca peak = 0.10918 (91) mri peak = 0.05724 (90) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3763 voxels, overlap=0.997) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3763 voxels, peak = 90), gca=89.6 gca peak = 0.09372 (86) mri peak = 0.05923 (87) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3969 voxels, overlap=0.998) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3969 voxels, peak = 86), gca=85.6 gca peak = 0.07383 (85) mri peak = 0.07615 (82) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1694 voxels, overlap=0.884) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1694 voxels, peak = 85), gca=85.0 gca peak = 0.07869 (80) mri peak = 0.06948 (78) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1867 voxels, overlap=0.973) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1867 voxels, peak = 79), gca=78.8 gca peak = 0.07571 (83) mri peak = 0.17385 (80) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10094 voxels, overlap=0.531) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10094 voxels, peak = 83), gca=83.0 gca peak = 0.12315 (91) mri peak = 0.07795 (85) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (962 voxels, overlap=0.845) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (962 voxels, peak = 91), gca=90.5 gca peak = 0.16939 (84) mri peak = 0.08848 (85) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1148 voxels, overlap=0.883) Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1148 voxels, peak = 87), gca=86.9 gca peak = 0.18084 (26) mri peak = 0.15909 (20) gca peak = 0.17172 (16) mri peak = 0.12717 (19) Fourth_Ventricle (15): linear fit = 1.10 x + 0.0 (176 voxels, overlap=0.789) Fourth_Ventricle (15): linear fit = 1.10 x + 0.0 (176 voxels, peak = 18), gca=17.5 gca peak Unknown = 0.94796 ( 0) gca peak Left_Inf_Lat_Vent = 0.18731 (37) gca peak Left_Thalamus = 1.00000 (103) gca peak Third_Ventricle = 0.18084 (26) gca peak CSF = 0.20086 (37) gca peak Left_Accumbens_area = 0.74396 (63) gca peak Left_undetermined = 1.00000 (27) gca peak Left_vessel = 0.84512 (52) gca peak Left_choroid_plexus = 0.10176 (35) gca peak Right_Inf_Lat_Vent = 0.22782 (26) gca peak Right_Accumbens_area = 0.28029 (70) gca peak Right_vessel = 0.77129 (52) gca peak Right_choroid_plexus = 0.11214 (38) gca peak Fifth_Ventricle = 0.57117 (34) gca peak WM_hypointensities = 0.09852 (76) gca peak non_WM_hypointensities = 0.08058 (44) gca peak Optic_Chiasm = 0.72395 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.10 x + 0.0 Left_Pallidum too bright - rescaling by 1.003 (from 1.000) to 102.3 (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 114739 voxels changed in iteration 0 of unlikely voxel relabeling 203 voxels changed in iteration 1 of unlikely voxel relabeling 35 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 49973 gm and wm labels changed (%21 to gray, %79 to white out of all changed labels) 552 hippocampal voxels changed. 1 amygdala voxels changed. pass 1: 87757 changed. image ll: -2.169, PF=0.500 pass 2: 28663 changed. image ll: -2.169, PF=0.500 pass 3: 8282 changed. pass 4: 2794 changed. MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz... mri_ca_label utimesec 2395.025888 mri_ca_label stimesec 6.020628 mri_ca_label ru_maxrss 1651308 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 5782857 mri_ca_label ru_majflt 1430 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 72336 mri_ca_label ru_oublock 576 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 1443 mri_ca_label ru_nivcsw 61428 auto-labeling took 40 minutes and 6 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /dat/mw/tvb-new-dataset/tvb/mri/transforms/cc_up.lta tvb will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /dat/mw/tvb-new-dataset/tvb/mri/transforms/cc_up.lta reading aseg from /dat/mw/tvb-new-dataset/tvb/mri/aseg.auto_noCCseg.mgz reading norm from /dat/mw/tvb-new-dataset/tvb/mri/norm.mgz 21987 voxels in left wm, 50871 in right wm, xrange [123, 131] searching rotation angles z=[-7 7], y=[-8 6] searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.5 global minimum found at slice 128.0, rotations (-0.53, -0.21) final transformation (x=128.0, yr=-0.525, zr=-0.215): 0.99995 0.00375 -0.00917 0.52515; -0.00375 0.99999 0.00003 39.47728; 0.00917 -0.00000 0.99996 33.83053; 0.00000 0.00000 0.00000 1.00000; updating x range to be [127, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 89 93 eigenvectors: 0.00002 0.00050 1.00000; -0.23935 -0.97093 0.00049; 0.97093 -0.23935 0.00011; writing aseg with callosum to /dat/mw/tvb-new-dataset/tvb/mri/aseg.auto.mgz... corpus callosum segmentation took 0.6 minutes #-------------------------------------- #@# Merge ASeg Tue Mar 1 18:26:59 CET 2016 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue Mar 1 18:26:59 CET 2016 /dat/mw/tvb-new-dataset/tvb/mri mri_normalize -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 6808 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 113 white matter peak found at 106 gm peak at 66 (66), valley at 28 (28) csf peak at 11, setting threshold to 47 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 66 (66), valley at 24 (24) csf peak at 11, setting threshold to 47 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 3 seconds. #-------------------------------------------- #@# Mask BFS Tue Mar 1 18:30:04 CET 2016 /dat/mw/tvb-new-dataset/tvb/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1796647 voxels in mask (pct= 10.71) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Tue Mar 1 18:30:06 CET 2016 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (106.0): 106.9 +- 5.7 [80.0 --> 125.0] GM (69.0) : 68.3 +- 9.4 [30.0 --> 96.0] setting bottom of white matter range to 77.7 setting top of gray matter range to 87.0 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... 23638 sparsely connected voxels removed... thickening thin strands.... 20 segments, 6408 filled 1335 bright non-wm voxels segmented. 9219 diagonally connected voxels added... white matter segmentation took 1.4 minutes writing output to wm.seg.mgz... 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 0.45 minutes reading wm segmentation from wm.seg.mgz... 57 voxels added to wm to prevent paths from MTL structures to cortex 3164 additional wm voxels added 0 additional wm voxels added SEG EDIT: 49260 voxels turned on, 42307 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+): 37 found - 37 modified | TOTAL: 37 pass 2 (xy+): 0 found - 37 modified | TOTAL: 37 pass 1 (xy-): 32 found - 32 modified | TOTAL: 69 pass 2 (xy-): 0 found - 32 modified | TOTAL: 69 pass 1 (yz+): 51 found - 51 modified | TOTAL: 120 pass 2 (yz+): 0 found - 51 modified | TOTAL: 120 pass 1 (yz-): 28 found - 28 modified | TOTAL: 148 pass 2 (yz-): 0 found - 28 modified | TOTAL: 148 pass 1 (xz+): 36 found - 36 modified | TOTAL: 184 pass 2 (xz+): 0 found - 36 modified | TOTAL: 184 pass 1 (xz-): 37 found - 37 modified | TOTAL: 221 pass 2 (xz-): 0 found - 37 modified | TOTAL: 221 Iteration Number : 1 pass 1 (+++): 54 found - 54 modified | TOTAL: 54 pass 2 (+++): 0 found - 54 modified | TOTAL: 54 pass 1 (+++): 40 found - 40 modified | TOTAL: 94 pass 2 (+++): 0 found - 40 modified | TOTAL: 94 pass 1 (+++): 54 found - 54 modified | TOTAL: 148 pass 2 (+++): 0 found - 54 modified | TOTAL: 148 pass 1 (+++): 56 found - 56 modified | TOTAL: 204 pass 2 (+++): 0 found - 56 modified | TOTAL: 204 Iteration Number : 1 pass 1 (++): 299 found - 299 modified | TOTAL: 299 pass 2 (++): 0 found - 299 modified | TOTAL: 299 pass 1 (+-): 270 found - 270 modified | TOTAL: 569 pass 2 (+-): 0 found - 270 modified | TOTAL: 569 pass 1 (--): 332 found - 332 modified | TOTAL: 901 pass 2 (--): 1 found - 333 modified | TOTAL: 902 pass 3 (--): 0 found - 333 modified | TOTAL: 902 pass 1 (-+): 221 found - 221 modified | TOTAL: 1123 pass 2 (-+): 0 found - 221 modified | TOTAL: 1123 Iteration Number : 2 pass 1 (xy+): 16 found - 16 modified | TOTAL: 16 pass 2 (xy+): 0 found - 16 modified | TOTAL: 16 pass 1 (xy-): 11 found - 11 modified | TOTAL: 27 pass 2 (xy-): 0 found - 11 modified | TOTAL: 27 pass 1 (yz+): 20 found - 20 modified | TOTAL: 47 pass 2 (yz+): 0 found - 20 modified | TOTAL: 47 pass 1 (yz-): 10 found - 10 modified | TOTAL: 57 pass 2 (yz-): 0 found - 10 modified | TOTAL: 57 pass 1 (xz+): 16 found - 16 modified | TOTAL: 73 pass 2 (xz+): 0 found - 16 modified | TOTAL: 73 pass 1 (xz-): 9 found - 9 modified | TOTAL: 82 pass 2 (xz-): 0 found - 9 modified | TOTAL: 82 Iteration Number : 2 pass 1 (+++): 9 found - 9 modified | TOTAL: 9 pass 2 (+++): 0 found - 9 modified | TOTAL: 9 pass 1 (+++): 6 found - 6 modified | TOTAL: 15 pass 2 (+++): 0 found - 6 modified | TOTAL: 15 pass 1 (+++): 2 found - 2 modified | TOTAL: 17 pass 2 (+++): 0 found - 2 modified | TOTAL: 17 pass 1 (+++): 4 found - 4 modified | TOTAL: 21 pass 2 (+++): 0 found - 4 modified | TOTAL: 21 Iteration Number : 2 pass 1 (++): 9 found - 9 modified | TOTAL: 9 pass 2 (++): 0 found - 9 modified | TOTAL: 9 pass 1 (+-): 7 found - 7 modified | TOTAL: 16 pass 2 (+-): 0 found - 7 modified | TOTAL: 16 pass 1 (--): 10 found - 10 modified | TOTAL: 26 pass 2 (--): 0 found - 10 modified | TOTAL: 26 pass 1 (-+): 8 found - 8 modified | TOTAL: 34 pass 2 (-+): 0 found - 8 modified | TOTAL: 34 Iteration Number : 3 pass 1 (xy+): 7 found - 7 modified | TOTAL: 7 pass 2 (xy+): 0 found - 7 modified | TOTAL: 7 pass 1 (xy-): 3 found - 3 modified | TOTAL: 10 pass 2 (xy-): 0 found - 3 modified | TOTAL: 10 pass 1 (yz+): 2 found - 2 modified | TOTAL: 12 pass 2 (yz+): 0 found - 2 modified | TOTAL: 12 pass 1 (yz-): 0 found - 0 modified | TOTAL: 12 pass 1 (xz+): 3 found - 3 modified | TOTAL: 15 pass 2 (xz+): 0 found - 3 modified | TOTAL: 15 pass 1 (xz-): 4 found - 4 modified | TOTAL: 19 pass 2 (xz-): 0 found - 4 modified | TOTAL: 19 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 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 2 found - 2 modified | TOTAL: 4 pass 2 (+-): 0 found - 2 modified | TOTAL: 4 pass 1 (--): 2 found - 2 modified | TOTAL: 6 pass 2 (--): 0 found - 2 modified | TOTAL: 6 pass 1 (-+): 1 found - 1 modified | TOTAL: 7 pass 2 (-+): 0 found - 1 modified | TOTAL: 7 Iteration Number : 4 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 5 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 : 5 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 : 5 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 = 1714 (out of 638525: 0.268431) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Tue Mar 1 18:32:03 CET 2016 /dat/mw/tvb-new-dataset/tvb/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 0.98119 0.02317 -0.00094 -2.82336; -0.01200 1.04416 0.40484 -23.07330; 0.00459 -0.41932 0.86002 62.64726; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 0.98119 0.02317 -0.00094 -2.82336; -0.01200 1.04416 0.40484 -23.07330; 0.00459 -0.41932 0.86002 62.64726; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1072 (min = 350, max = 1400), aspect = 0.59 (min = 0.10, max = 0.75) no need to search using seed (125, 116, 149), TAL = (3.0, 21.0, 12.0) talairach voxel to voxel transform 1.01890 -0.01864 0.00989 1.82741; 0.01162 0.80523 -0.37903 42.35762; 0.00023 0.39271 0.97790 -52.20126; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (125, 116, 149) --> (3.0, 21.0, 12.0) done. writing output to filled.mgz... filling took 0.7 minutes talairach cc position changed to (3.00, 21.00, 12.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, 21.00, 12.00) SRC: (110.16, 80.53, 139.09) search lh wm seed point around talairach space (-15.00, 21.00, 12.00), SRC: (146.84, 80.95, 139.09) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Tue Mar 1 18:32:44 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 3 found - 3 modified | TOTAL: 4 pass 2 (xy-): 0 found - 3 modified | TOTAL: 4 pass 1 (yz+): 2 found - 2 modified | TOTAL: 6 pass 2 (yz+): 0 found - 2 modified | TOTAL: 6 pass 1 (yz-): 1 found - 1 modified | TOTAL: 7 pass 2 (yz-): 0 found - 1 modified | TOTAL: 7 pass 1 (xz+): 0 found - 0 modified | TOTAL: 7 pass 1 (xz-): 0 found - 0 modified | TOTAL: 7 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 7 (out of 311339: 0.002248) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $ slice 30: 2002 vertices, 2166 faces slice 40: 10886 vertices, 11313 faces slice 50: 24542 vertices, 25038 faces slice 60: 38513 vertices, 38982 faces slice 70: 52689 vertices, 53137 faces slice 80: 65585 vertices, 66036 faces slice 90: 77942 vertices, 78378 faces slice 100: 89959 vertices, 90411 faces slice 110: 101522 vertices, 101997 faces slice 120: 113111 vertices, 113555 faces slice 130: 124348 vertices, 124790 faces slice 140: 134724 vertices, 135119 faces slice 150: 144281 vertices, 144634 faces slice 160: 152270 vertices, 152593 faces slice 170: 158597 vertices, 158861 faces slice 180: 163307 vertices, 163488 faces slice 190: 165298 vertices, 165372 faces slice 200: 165298 vertices, 165372 faces slice 210: 165298 vertices, 165372 faces slice 220: 165298 vertices, 165372 faces slice 230: 165298 vertices, 165372 faces slice 240: 165298 vertices, 165372 faces slice 250: 165298 vertices, 165372 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 165298 voxel in cpt #1: X=-74 [v=165298,e=496116,f=330744] located at (-29.666378, -31.964331, 33.709900) For the whole surface: X=-74 [v=165298,e=496116,f=330744] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Tue Mar 1 18:32:50 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 2 found - 2 modified | TOTAL: 3 pass 2 (yz+): 0 found - 2 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 4 (out of 316586: 0.001263) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $ slice 30: 2766 vertices, 2991 faces slice 40: 11881 vertices, 12250 faces slice 50: 24225 vertices, 24696 faces slice 60: 38865 vertices, 39366 faces slice 70: 52323 vertices, 52824 faces slice 80: 65831 vertices, 66294 faces slice 90: 78559 vertices, 79004 faces slice 100: 91047 vertices, 91529 faces slice 110: 102865 vertices, 103316 faces slice 120: 114562 vertices, 115006 faces slice 130: 126015 vertices, 126463 faces slice 140: 136706 vertices, 137126 faces slice 150: 145597 vertices, 145954 faces slice 160: 153198 vertices, 153521 faces slice 170: 159686 vertices, 159971 faces slice 180: 164502 vertices, 164712 faces slice 190: 166870 vertices, 166944 faces slice 200: 166870 vertices, 166944 faces slice 210: 166870 vertices, 166944 faces slice 220: 166870 vertices, 166944 faces slice 230: 166870 vertices, 166944 faces slice 240: 166870 vertices, 166944 faces slice 250: 166870 vertices, 166944 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 166870 voxel in cpt #1: X=-74 [v=166870,e=500832,f=333888] located at (29.257374, -32.028740, 35.304886) For the whole surface: X=-74 [v=166870,e=500832,f=333888] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Tue Mar 1 18:32:56 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh Tue Mar 1 18:33:02 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Tue Mar 1 18:33:08 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 50.4 mm, total surface area = 85530 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.157 (target=0.015) step 005: RMS=0.117 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.074 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.056 (target=0.015) step 030: RMS=0.049 (target=0.015) step 035: RMS=0.045 (target=0.015) step 040: RMS=0.043 (target=0.015) step 045: RMS=0.040 (target=0.015) step 050: RMS=0.038 (target=0.015) step 055: RMS=0.038 (target=0.015) step 060: RMS=0.038 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 38.989485 mris_inflate stimesec 0.244689 mris_inflate ru_maxrss 217148 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 416000 mris_inflate ru_majflt 43 mris_inflate ru_nswap 0 mris_inflate ru_inblock 10376 mris_inflate ru_oublock 11632 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 44 mris_inflate ru_nivcsw 22 #-------------------------------------------- #@# Inflation1 rh Tue Mar 1 18:33:47 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 50.4 mm, total surface area = 86965 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.6 minutes step 000: RMS=0.156 (target=0.015) step 005: RMS=0.117 (target=0.015) step 010: RMS=0.088 (target=0.015) step 015: RMS=0.072 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.055 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.044 (target=0.015) step 040: RMS=0.042 (target=0.015) step 045: RMS=0.039 (target=0.015) step 050: RMS=0.038 (target=0.015) step 055: RMS=0.037 (target=0.015) step 060: RMS=0.036 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 38.210878 mris_inflate stimesec 0.236689 mris_inflate ru_maxrss 218756 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 419171 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11744 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 73 #-------------------------------------------- #@# QSphere lh Tue Mar 1 18:34:26 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.89 +- 0.55 (0.00-->7.59) (max @ vno 121822 --> 121847) face area 0.02 +- 0.03 (-0.11-->0.56) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.301... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.168, avgs=0 005/300: dt: 0.9000, rms radial error=174.913, avgs=0 010/300: dt: 0.9000, rms radial error=174.366, avgs=0 015/300: dt: 0.9000, rms radial error=173.647, avgs=0 020/300: dt: 0.9000, rms radial error=172.828, avgs=0 025/300: dt: 0.9000, rms radial error=171.952, avgs=0 030/300: dt: 0.9000, rms radial error=171.044, avgs=0 035/300: dt: 0.9000, rms radial error=170.118, avgs=0 040/300: dt: 0.9000, rms radial error=169.185, avgs=0 045/300: dt: 0.9000, rms radial error=168.248, avgs=0 050/300: dt: 0.9000, rms radial error=167.311, avgs=0 055/300: dt: 0.9000, rms radial error=166.376, avgs=0 060/300: dt: 0.9000, rms radial error=165.445, avgs=0 065/300: dt: 0.9000, rms radial error=164.516, avgs=0 070/300: dt: 0.9000, rms radial error=163.591, avgs=0 075/300: dt: 0.9000, rms radial error=162.670, avgs=0 080/300: dt: 0.9000, rms radial error=161.756, avgs=0 085/300: dt: 0.9000, rms radial error=160.845, avgs=0 090/300: dt: 0.9000, rms radial error=159.940, avgs=0 095/300: dt: 0.9000, rms radial error=159.039, avgs=0 100/300: dt: 0.9000, rms radial error=158.143, avgs=0 105/300: dt: 0.9000, rms radial error=157.251, avgs=0 110/300: dt: 0.9000, rms radial error=156.364, avgs=0 115/300: dt: 0.9000, rms radial error=155.483, avgs=0 120/300: dt: 0.9000, rms radial error=154.609, avgs=0 125/300: dt: 0.9000, rms radial error=153.740, avgs=0 130/300: dt: 0.9000, rms radial error=152.876, avgs=0 135/300: dt: 0.9000, rms radial error=152.016, avgs=0 140/300: dt: 0.9000, rms radial error=151.161, avgs=0 145/300: dt: 0.9000, rms radial error=150.310, avgs=0 150/300: dt: 0.9000, rms radial error=149.464, avgs=0 155/300: dt: 0.9000, rms radial error=148.623, avgs=0 160/300: dt: 0.9000, rms radial error=147.787, avgs=0 165/300: dt: 0.9000, rms radial error=146.955, avgs=0 170/300: dt: 0.9000, rms radial error=146.128, avgs=0 175/300: dt: 0.9000, rms radial error=145.306, avgs=0 180/300: dt: 0.9000, rms radial error=144.488, avgs=0 185/300: dt: 0.9000, rms radial error=143.675, avgs=0 190/300: dt: 0.9000, rms radial error=142.866, avgs=0 195/300: dt: 0.9000, rms radial error=142.062, avgs=0 200/300: dt: 0.9000, rms radial error=141.263, avgs=0 205/300: dt: 0.9000, rms radial error=140.468, avgs=0 210/300: dt: 0.9000, rms radial error=139.678, avgs=0 215/300: dt: 0.9000, rms radial error=138.892, avgs=0 220/300: dt: 0.9000, rms radial error=138.110, avgs=0 225/300: dt: 0.9000, rms radial error=137.333, avgs=0 230/300: dt: 0.9000, rms radial error=136.560, avgs=0 235/300: dt: 0.9000, rms radial error=135.791, avgs=0 240/300: dt: 0.9000, rms radial error=135.027, avgs=0 245/300: dt: 0.9000, rms radial error=134.267, avgs=0 250/300: dt: 0.9000, rms radial error=133.511, avgs=0 255/300: dt: 0.9000, rms radial error=132.759, avgs=0 260/300: dt: 0.9000, rms radial error=132.011, avgs=0 265/300: dt: 0.9000, rms radial error=131.267, avgs=0 270/300: dt: 0.9000, rms radial error=130.527, avgs=0 275/300: dt: 0.9000, rms radial error=129.792, avgs=0 280/300: dt: 0.9000, rms radial error=129.060, avgs=0 285/300: dt: 0.9000, rms radial error=128.333, avgs=0 290/300: dt: 0.9000, rms radial error=127.610, avgs=0 295/300: dt: 0.9000, rms radial error=126.890, avgs=0 300/300: dt: 0.9000, rms radial error=126.175, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 19617.31 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00017 epoch 2 (K=40.0), pass 1, starting sse = 3392.47 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00007 epoch 3 (K=160.0), pass 1, starting sse = 383.08 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00630 epoch 4 (K=640.0), pass 1, starting sse = 27.97 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.14/14 = 0.00970 final distance error %29.13 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 253.941649 mris_sphere stimesec 0.614056 mris_sphere ru_maxrss 217524 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 779545 mris_sphere ru_majflt 48 mris_sphere ru_nswap 0 mris_sphere ru_inblock 11384 mris_sphere ru_oublock 11632 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 51 mris_sphere ru_nivcsw 866 FSRUNTIME@ mris_sphere 0.0709 hours 1 threads #-------------------------------------------- #@# QSphere rh Tue Mar 1 18:38:41 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.89 +- 0.54 (0.00-->6.59) (max @ vno 123476 --> 123495) face area 0.02 +- 0.03 (-0.21-->0.57) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.295... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.566, avgs=0 005/300: dt: 0.9000, rms radial error=175.308, avgs=0 010/300: dt: 0.9000, rms radial error=174.755, avgs=0 015/300: dt: 0.9000, rms radial error=174.029, avgs=0 020/300: dt: 0.9000, rms radial error=173.202, avgs=0 025/300: dt: 0.9000, rms radial error=172.317, avgs=0 030/300: dt: 0.9000, rms radial error=171.400, avgs=0 035/300: dt: 0.9000, rms radial error=170.466, avgs=0 040/300: dt: 0.9000, rms radial error=169.524, avgs=0 045/300: dt: 0.9000, rms radial error=168.580, avgs=0 050/300: dt: 0.9000, rms radial error=167.635, avgs=0 055/300: dt: 0.9000, rms radial error=166.693, avgs=0 060/300: dt: 0.9000, rms radial error=165.755, avgs=0 065/300: dt: 0.9000, rms radial error=164.820, avgs=0 070/300: dt: 0.9000, rms radial error=163.889, avgs=0 075/300: dt: 0.9000, rms radial error=162.965, avgs=0 080/300: dt: 0.9000, rms radial error=162.049, avgs=0 085/300: dt: 0.9000, rms radial error=161.138, avgs=0 090/300: dt: 0.9000, rms radial error=160.232, avgs=0 095/300: dt: 0.9000, rms radial error=159.331, avgs=0 100/300: dt: 0.9000, rms radial error=158.435, avgs=0 105/300: dt: 0.9000, rms radial error=157.544, avgs=0 110/300: dt: 0.9000, rms radial error=156.658, avgs=0 115/300: dt: 0.9000, rms radial error=155.778, avgs=0 120/300: dt: 0.9000, rms radial error=154.902, avgs=0 125/300: dt: 0.9000, rms radial error=154.031, avgs=0 130/300: dt: 0.9000, rms radial error=153.164, avgs=0 135/300: dt: 0.9000, rms radial error=152.303, avgs=0 140/300: dt: 0.9000, rms radial error=151.446, avgs=0 145/300: dt: 0.9000, rms radial error=150.593, avgs=0 150/300: dt: 0.9000, rms radial error=149.746, avgs=0 155/300: dt: 0.9000, rms radial error=148.902, avgs=0 160/300: dt: 0.9000, rms radial error=148.064, avgs=0 165/300: dt: 0.9000, rms radial error=147.230, avgs=0 170/300: dt: 0.9000, rms radial error=146.400, avgs=0 175/300: dt: 0.9000, rms radial error=145.575, avgs=0 180/300: dt: 0.9000, rms radial error=144.755, avgs=0 185/300: dt: 0.9000, rms radial error=143.939, avgs=0 190/300: dt: 0.9000, rms radial error=143.127, avgs=0 195/300: dt: 0.9000, rms radial error=142.320, avgs=0 200/300: dt: 0.9000, rms radial error=141.518, avgs=0 205/300: dt: 0.9000, rms radial error=140.719, avgs=0 210/300: dt: 0.9000, rms radial error=139.926, avgs=0 215/300: dt: 0.9000, rms radial error=139.136, avgs=0 220/300: dt: 0.9000, rms radial error=138.351, avgs=0 225/300: dt: 0.9000, rms radial error=137.570, avgs=0 230/300: dt: 0.9000, rms radial error=136.794, avgs=0 235/300: dt: 0.9000, rms radial error=136.022, avgs=0 240/300: dt: 0.9000, rms radial error=135.254, avgs=0 245/300: dt: 0.9000, rms radial error=134.490, avgs=0 250/300: dt: 0.9000, rms radial error=133.731, avgs=0 255/300: dt: 0.9000, rms radial error=132.975, avgs=0 260/300: dt: 0.9000, rms radial error=132.224, avgs=0 265/300: dt: 0.9000, rms radial error=131.477, avgs=0 270/300: dt: 0.9000, rms radial error=130.734, avgs=0 275/300: dt: 0.9000, rms radial error=129.995, avgs=0 280/300: dt: 0.9000, rms radial error=129.261, avgs=0 285/300: dt: 0.9000, rms radial error=128.530, avgs=0 290/300: dt: 0.9000, rms radial error=127.803, avgs=0 295/300: dt: 0.9000, rms radial error=127.081, avgs=0 300/300: dt: 0.9000, rms radial error=126.363, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 19880.16 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 3467.84 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 391.00 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/11 = 0.00466 epoch 4 (K=640.0), pass 1, starting sse = 28.48 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/10 = 0.00612 final distance error %29.33 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.07 hours mris_sphere utimesec 240.794414 mris_sphere stimesec 0.565160 mris_sphere ru_maxrss 218996 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 785467 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 11744 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 0 mris_sphere ru_nivcsw 773 FSRUNTIME@ mris_sphere 0.0671 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Tue Mar 1 18:42:43 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Tue Mar 1 18:42:43 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Tue Mar 1 18:42:43 CET 2016 mris_fix_topology -rusage /dat/mw/tvb-new-dataset/tvb/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 tvb lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $ before topology correction, eno=-74 (nv=165298, nf=330744, ne=496116, g=38) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 5647 ambiguous faces found in tessellation segmenting defects... 51 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 51 defects to be corrected 0 vertices coincident reading input surface /dat/mw/tvb-new-dataset/tvb/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.8059 (-4.9030) -vertex loglikelihood: -6.5286 (-3.2643) -normal dot loglikelihood: -3.6380 (-3.6380) -quad curv loglikelihood: -6.4119 (-3.2059) Total Loglikelihood : -26.3845 CORRECTING DEFECT 0 (vertices=25, convex hull=55) After retessellation of defect 0, euler #=-46 (161949,484727,322732) : difference with theory (-48) = -2 CORRECTING DEFECT 1 (vertices=22, convex hull=53) After retessellation of defect 1, euler #=-45 (161956,484768,322767) : difference with theory (-47) = -2 CORRECTING DEFECT 2 (vertices=6, convex hull=23) After retessellation of defect 2, euler #=-44 (161956,484774,322774) : difference with theory (-46) = -2 CORRECTING DEFECT 3 (vertices=49, convex hull=83) After retessellation of defect 3, euler #=-43 (161978,484876,322855) : difference with theory (-45) = -2 CORRECTING DEFECT 4 (vertices=5, convex hull=20) After retessellation of defect 4, euler #=-42 (161978,484881,322861) : difference with theory (-44) = -2 CORRECTING DEFECT 5 (vertices=15, convex hull=32) After retessellation of defect 5, euler #=-41 (161981,484898,322876) : difference with theory (-43) = -2 CORRECTING DEFECT 6 (vertices=33, convex hull=65) After retessellation of defect 6, euler #=-40 (161990,484951,322921) : difference with theory (-42) = -2 CORRECTING DEFECT 7 (vertices=5, convex hull=27) After retessellation of defect 7, euler #=-39 (161991,484960,322930) : difference with theory (-41) = -2 CORRECTING DEFECT 8 (vertices=22, convex hull=59) After retessellation of defect 8, euler #=-38 (162004,485020,322978) : difference with theory (-40) = -2 CORRECTING DEFECT 9 (vertices=15, convex hull=32) After retessellation of defect 9, euler #=-37 (162007,485041,322997) : difference with theory (-39) = -2 CORRECTING DEFECT 10 (vertices=34, convex hull=64) After retessellation of defect 10, euler #=-36 (162014,485088,323038) : difference with theory (-38) = -2 CORRECTING DEFECT 11 (vertices=25, convex hull=66) After retessellation of defect 11, euler #=-35 (162023,485141,323083) : difference with theory (-37) = -2 CORRECTING DEFECT 12 (vertices=13, convex hull=28) After retessellation of defect 12, euler #=-34 (162023,485149,323092) : difference with theory (-36) = -2 CORRECTING DEFECT 13 (vertices=5, convex hull=20) After retessellation of defect 13, euler #=-33 (162024,485158,323101) : difference with theory (-35) = -2 CORRECTING DEFECT 14 (vertices=18, convex hull=25) After retessellation of defect 14, euler #=-32 (162026,485171,323113) : difference with theory (-34) = -2 CORRECTING DEFECT 15 (vertices=21, convex hull=49) After retessellation of defect 15, euler #=-31 (162035,485215,323149) : difference with theory (-33) = -2 CORRECTING DEFECT 16 (vertices=24, convex hull=50) After retessellation of defect 16, euler #=-30 (162044,485261,323187) : difference with theory (-32) = -2 CORRECTING DEFECT 17 (vertices=22, convex hull=43) After retessellation of defect 17, euler #=-29 (162058,485316,323229) : difference with theory (-31) = -2 CORRECTING DEFECT 18 (vertices=22, convex hull=61) After retessellation of defect 18, euler #=-28 (162067,485364,323269) : difference with theory (-30) = -2 CORRECTING DEFECT 19 (vertices=40, convex hull=55) After retessellation of defect 19, euler #=-27 (162090,485454,323337) : difference with theory (-29) = -2 CORRECTING DEFECT 20 (vertices=320, convex hull=53) After retessellation of defect 20, euler #=-26 (162103,485513,323384) : difference with theory (-28) = -2 CORRECTING DEFECT 21 (vertices=100, convex hull=45) After retessellation of defect 21, euler #=-26 (162114,485570,323430) : difference with theory (-27) = -1 CORRECTING DEFECT 22 (vertices=8, convex hull=32) After retessellation of defect 22, euler #=-25 (162115,485585,323445) : difference with theory (-26) = -1 CORRECTING DEFECT 23 (vertices=29, convex hull=60) After retessellation of defect 23, euler #=-24 (162133,485661,323504) : difference with theory (-25) = -1 CORRECTING DEFECT 24 (vertices=28, convex hull=54) After retessellation of defect 24, euler #=-23 (162151,485731,323557) : difference with theory (-24) = -1 CORRECTING DEFECT 25 (vertices=13, convex hull=36) After retessellation of defect 25, euler #=-22 (162157,485761,323582) : difference with theory (-23) = -1 CORRECTING DEFECT 26 (vertices=34, convex hull=24) After retessellation of defect 26, euler #=-21 (162162,485784,323601) : difference with theory (-22) = -1 CORRECTING DEFECT 27 (vertices=6, convex hull=43) After retessellation of defect 27, euler #=-20 (162164,485801,323617) : difference with theory (-21) = -1 CORRECTING DEFECT 28 (vertices=99, convex hull=111) After retessellation of defect 28, euler #=-19 (162201,485966,323746) : difference with theory (-20) = -1 CORRECTING DEFECT 29 (vertices=446, convex hull=74) After retessellation of defect 29, euler #=-18 (162219,486051,323814) : difference with theory (-19) = -1 CORRECTING DEFECT 30 (vertices=11, convex hull=18) After retessellation of defect 30, euler #=-17 (162223,486069,323829) : difference with theory (-18) = -1 CORRECTING DEFECT 31 (vertices=110, convex hull=40) After retessellation of defect 31, euler #=-16 (162237,486132,323879) : difference with theory (-17) = -1 CORRECTING DEFECT 32 (vertices=52, convex hull=52) After retessellation of defect 32, euler #=-15 (162250,486196,323931) : difference with theory (-16) = -1 CORRECTING DEFECT 33 (vertices=8, convex hull=15) After retessellation of defect 33, euler #=-14 (162251,486204,323939) : difference with theory (-15) = -1 CORRECTING DEFECT 34 (vertices=632, convex hull=125) After retessellation of defect 34, euler #=-14 (162287,486377,324076) : difference with theory (-14) = 0 CORRECTING DEFECT 35 (vertices=36, convex hull=85) After retessellation of defect 35, euler #=-13 (162307,486467,324147) : difference with theory (-13) = 0 CORRECTING DEFECT 36 (vertices=245, convex hull=63) After retessellation of defect 36, euler #=-12 (162329,486571,324230) : difference with theory (-12) = 0 CORRECTING DEFECT 37 (vertices=124, convex hull=155) After retessellation of defect 37, euler #=-11 (162376,486785,324398) : difference with theory (-11) = 0 CORRECTING DEFECT 38 (vertices=27, convex hull=66) After retessellation of defect 38, euler #=-10 (162385,486837,324442) : difference with theory (-10) = 0 CORRECTING DEFECT 39 (vertices=57, convex hull=55) After retessellation of defect 39, euler #=-9 (162397,486897,324491) : difference with theory (-9) = 0 CORRECTING DEFECT 40 (vertices=189, convex hull=127) After retessellation of defect 40, euler #=-8 (162461,487144,324675) : difference with theory (-8) = 0 CORRECTING DEFECT 41 (vertices=26, convex hull=26) After retessellation of defect 41, euler #=-7 (162466,487168,324695) : difference with theory (-7) = 0 CORRECTING DEFECT 42 (vertices=48, convex hull=87) After retessellation of defect 42, euler #=-6 (162499,487305,324800) : difference with theory (-6) = 0 CORRECTING DEFECT 43 (vertices=15, convex hull=38) After retessellation of defect 43, euler #=-5 (162503,487330,324822) : difference with theory (-5) = 0 CORRECTING DEFECT 44 (vertices=21, convex hull=65) After retessellation of defect 44, euler #=-4 (162511,487379,324864) : difference with theory (-4) = 0 CORRECTING DEFECT 45 (vertices=98, convex hull=45) After retessellation of defect 45, euler #=-3 (162528,487447,324916) : difference with theory (-3) = 0 CORRECTING DEFECT 46 (vertices=37, convex hull=61) After retessellation of defect 46, euler #=-2 (162538,487501,324961) : difference with theory (-2) = 0 CORRECTING DEFECT 47 (vertices=16, convex hull=55) After retessellation of defect 47, euler #=-1 (162546,487546,324999) : difference with theory (-1) = 0 CORRECTING DEFECT 48 (vertices=31, convex hull=70) After retessellation of defect 48, euler #=0 (162554,487599,325045) : difference with theory (0) = 0 CORRECTING DEFECT 49 (vertices=36, convex hull=77) After retessellation of defect 49, euler #=1 (162569,487676,325108) : difference with theory (1) = 0 CORRECTING DEFECT 50 (vertices=31, convex hull=59) After retessellation of defect 50, euler #=2 (162585,487749,325166) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.05-->8.39) (max @ vno 70737 --> 75542) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.05-->8.39) (max @ vno 70737 --> 75542) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 185 mutations (33.7%), 364 crossovers (66.3%), 172 vertices were eliminated building final representation... 2713 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=162585, nf=325166, ne=487749, g=0) writing corrected surface to /dat/mw/tvb-new-dataset/tvb/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 26.3 minutes 0 defective edges removing intersecting faces 000: 318 intersecting mris_fix_topology utimesec 1571.427603 mris_fix_topology stimesec 1.641667 mris_fix_topology ru_maxrss 508652 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 1063167 mris_fix_topology ru_majflt 53 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 12504 mris_fix_topology ru_oublock 15328 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 57 mris_fix_topology ru_nivcsw 3407 FSRUNTIME@ mris_fix_topology lh 0.4377 hours 1 threads #@# Fix Topology rh Tue Mar 1 19:08:59 CET 2016 mris_fix_topology -rusage /dat/mw/tvb-new-dataset/tvb/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 tvb rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $ before topology correction, eno=-74 (nv=166870, nf=333888, ne=500832, g=38) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 4725 ambiguous faces found in tessellation segmenting defects... 49 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 5 into 4 -merging segment 36 into 33 -merging segment 41 into 33 46 defects to be corrected 0 vertices coincident reading input surface /dat/mw/tvb-new-dataset/tvb/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.7323 (-4.8662) -vertex loglikelihood: -6.5611 (-3.2806) -normal dot loglikelihood: -3.6018 (-3.6018) -quad curv loglikelihood: -6.4121 (-3.2061) Total Loglikelihood : -26.3074 CORRECTING DEFECT 0 (vertices=25, convex hull=69) After retessellation of defect 0, euler #=-44 (163961,490696,326691) : difference with theory (-43) = 1 CORRECTING DEFECT 1 (vertices=23, convex hull=58) After retessellation of defect 1, euler #=-43 (163972,490754,326739) : difference with theory (-42) = 1 CORRECTING DEFECT 2 (vertices=8, convex hull=24) After retessellation of defect 2, euler #=-42 (163974,490770,326754) : difference with theory (-41) = 1 CORRECTING DEFECT 3 (vertices=66, convex hull=82) After retessellation of defect 3, euler #=-41 (164000,490877,326836) : difference with theory (-40) = 1 CORRECTING DEFECT 4 (vertices=98, convex hull=116) After retessellation of defect 4, euler #=-39 (164027,491009,326943) : difference with theory (-39) = 0 CORRECTING DEFECT 5 (vertices=5, convex hull=28) After retessellation of defect 5, euler #=-38 (164027,491015,326950) : difference with theory (-38) = 0 CORRECTING DEFECT 6 (vertices=23, convex hull=59) After retessellation of defect 6, euler #=-37 (164040,491077,327000) : difference with theory (-37) = 0 CORRECTING DEFECT 7 (vertices=66, convex hull=59) After retessellation of defect 7, euler #=-36 (164043,491114,327035) : difference with theory (-36) = 0 CORRECTING DEFECT 8 (vertices=122, convex hull=83) After retessellation of defect 8, euler #=-35 (164066,491221,327120) : difference with theory (-35) = 0 CORRECTING DEFECT 9 (vertices=73, convex hull=60) After retessellation of defect 9, euler #=-34 (164075,491271,327162) : difference with theory (-34) = 0 CORRECTING DEFECT 10 (vertices=37, convex hull=78) After retessellation of defect 10, euler #=-33 (164090,491344,327221) : difference with theory (-33) = 0 CORRECTING DEFECT 11 (vertices=5, convex hull=26) After retessellation of defect 11, euler #=-32 (164091,491353,327230) : difference with theory (-32) = 0 CORRECTING DEFECT 12 (vertices=61, convex hull=48) After retessellation of defect 12, euler #=-31 (164095,491383,327257) : difference with theory (-31) = 0 CORRECTING DEFECT 13 (vertices=22, convex hull=64) After retessellation of defect 13, euler #=-30 (164105,491440,327305) : difference with theory (-30) = 0 CORRECTING DEFECT 14 (vertices=17, convex hull=17) After retessellation of defect 14, euler #=-29 (164107,491450,327314) : difference with theory (-29) = 0 CORRECTING DEFECT 15 (vertices=6, convex hull=24) After retessellation of defect 15, euler #=-28 (164109,491463,327326) : difference with theory (-28) = 0 CORRECTING DEFECT 16 (vertices=21, convex hull=44) After retessellation of defect 16, euler #=-27 (164122,491517,327368) : difference with theory (-27) = 0 CORRECTING DEFECT 17 (vertices=34, convex hull=25) After retessellation of defect 17, euler #=-26 (164131,491554,327397) : difference with theory (-26) = 0 CORRECTING DEFECT 18 (vertices=34, convex hull=63) After retessellation of defect 18, euler #=-25 (164139,491604,327440) : difference with theory (-25) = 0 CORRECTING DEFECT 19 (vertices=63, convex hull=88) After retessellation of defect 19, euler #=-24 (164177,491756,327555) : difference with theory (-24) = 0 CORRECTING DEFECT 20 (vertices=6, convex hull=27) After retessellation of defect 20, euler #=-23 (164179,491772,327570) : difference with theory (-23) = 0 CORRECTING DEFECT 21 (vertices=5, convex hull=16) After retessellation of defect 21, euler #=-22 (164179,491775,327574) : difference with theory (-22) = 0 CORRECTING DEFECT 22 (vertices=25, convex hull=21) After retessellation of defect 22, euler #=-21 (164180,491785,327584) : difference with theory (-21) = 0 CORRECTING DEFECT 23 (vertices=474, convex hull=70) After retessellation of defect 23, euler #=-20 (164196,491859,327643) : difference with theory (-20) = 0 CORRECTING DEFECT 24 (vertices=5, convex hull=14) After retessellation of defect 24, euler #=-19 (164197,491867,327651) : difference with theory (-19) = 0 CORRECTING DEFECT 25 (vertices=21, convex hull=64) After retessellation of defect 25, euler #=-18 (164206,491920,327696) : difference with theory (-18) = 0 CORRECTING DEFECT 26 (vertices=35, convex hull=48) After retessellation of defect 26, euler #=-17 (164217,491970,327736) : difference with theory (-17) = 0 CORRECTING DEFECT 27 (vertices=140, convex hull=115) After retessellation of defect 27, euler #=-17 (164235,492080,327828) : difference with theory (-16) = 1 CORRECTING DEFECT 28 (vertices=30, convex hull=52) After retessellation of defect 28, euler #=-16 (164245,492126,327865) : difference with theory (-15) = 1 CORRECTING DEFECT 29 (vertices=22, convex hull=50) After retessellation of defect 29, euler #=-15 (164254,492170,327901) : difference with theory (-14) = 1 CORRECTING DEFECT 30 (vertices=30, convex hull=24) After retessellation of defect 30, euler #=-14 (164257,492187,327916) : difference with theory (-13) = 1 CORRECTING DEFECT 31 (vertices=19, convex hull=33) After retessellation of defect 31, euler #=-13 (164263,492215,327939) : difference with theory (-12) = 1 CORRECTING DEFECT 32 (vertices=282, convex hull=304) After retessellation of defect 32, euler #=-11 (164380,492744,328353) : difference with theory (-11) = 0 CORRECTING DEFECT 33 (vertices=53, convex hull=75) After retessellation of defect 33, euler #=-10 (164409,492867,328448) : difference with theory (-10) = 0 CORRECTING DEFECT 34 (vertices=10, convex hull=20) After retessellation of defect 34, euler #=-9 (164412,492881,328460) : difference with theory (-9) = 0 CORRECTING DEFECT 35 (vertices=17, convex hull=53) After retessellation of defect 35, euler #=-8 (164423,492935,328504) : difference with theory (-8) = 0 CORRECTING DEFECT 36 (vertices=228, convex hull=154) After retessellation of defect 36, euler #=-7 (164496,493221,328718) : difference with theory (-7) = 0 CORRECTING DEFECT 37 (vertices=43, convex hull=62) After retessellation of defect 37, euler #=-6 (164511,493288,328771) : difference with theory (-6) = 0 CORRECTING DEFECT 38 (vertices=277, convex hull=79) After retessellation of defect 38, euler #=-5 (164530,493387,328852) : difference with theory (-5) = 0 CORRECTING DEFECT 39 (vertices=135, convex hull=132) After retessellation of defect 39, euler #=-4 (164559,493529,328966) : difference with theory (-4) = 0 CORRECTING DEFECT 40 (vertices=71, convex hull=87) After retessellation of defect 40, euler #=-3 (164580,493632,329049) : difference with theory (-3) = 0 CORRECTING DEFECT 41 (vertices=23, convex hull=31) After retessellation of defect 41, euler #=-2 (164588,493664,329074) : difference with theory (-2) = 0 CORRECTING DEFECT 42 (vertices=81, convex hull=81) After retessellation of defect 42, euler #=-1 (164617,493783,329165) : difference with theory (-1) = 0 CORRECTING DEFECT 43 (vertices=9, convex hull=21) After retessellation of defect 43, euler #=0 (164619,493796,329177) : difference with theory (0) = 0 CORRECTING DEFECT 44 (vertices=41, convex hull=72) After retessellation of defect 44, euler #=1 (164628,493855,329228) : difference with theory (1) = 0 CORRECTING DEFECT 45 (vertices=29, convex hull=61) After retessellation of defect 45, euler #=2 (164634,493896,329264) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.09-->8.69) (max @ vno 27427 --> 34993) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.09-->8.69) (max @ vno 27427 --> 34993) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 163 mutations (34.5%), 309 crossovers (65.5%), 160 vertices were eliminated building final representation... 2236 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=164634, nf=329264, ne=493896, g=0) writing corrected surface to /dat/mw/tvb-new-dataset/tvb/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 25.3 minutes 0 defective edges removing intersecting faces 000: 293 intersecting 001: 24 intersecting 002: 2 intersecting mris_fix_topology utimesec 1511.954834 mris_fix_topology stimesec 1.499799 mris_fix_topology ru_maxrss 514488 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 1047470 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 16 mris_fix_topology ru_oublock 15496 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 2 mris_fix_topology ru_nivcsw 4026 FSRUNTIME@ mris_fix_topology rh 0.4210 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 162585 - 487749 + 325166 = 2 --> 0 holes F =2V-4: 325166 = 325170-4 (0) 2E=3F: 975498 = 975498 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 164634 - 493896 + 329264 = 2 --> 0 holes F =2V-4: 329264 = 329268-4 (0) 2E=3F: 987792 = 987792 (0) total defect index = 0 /dat/mw/tvb-new-dataset/tvb/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 39 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /dat/mw/tvb-new-dataset/tvb/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 54 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Tue Mar 1 19:34:23 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -noaparc -whiteonly -mgz -T1 brain.finalsurfs tvb lh only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.163 2016/02/26 15:09:17 fischl Exp $ $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $ reading volume /dat/mw/tvb-new-dataset/tvb/mri/filled.mgz... reading volume /dat/mw/tvb-new-dataset/tvb/mri/brain.finalsurfs.mgz... reading volume /dat/mw/tvb-new-dataset/tvb/mri/../mri/aseg.presurf.mgz... reading volume /dat/mw/tvb-new-dataset/tvb/mri/wm.mgz... 57193 bright wm thresholded. 1573 bright non-wm voxels segmented. reading original surface position from /dat/mw/tvb-new-dataset/tvb/surf/lh.orig... computing class statistics... border white: 299374 voxels (1.78%) border gray 355765 voxels (2.12%) WM (99.0): 98.6 +- 9.5 [70.0 --> 110.0] GM (69.0) : 69.2 +- 10.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 56.0 (was 70) setting MAX_BORDER_WHITE to 113.5 (was 105) setting MIN_BORDER_WHITE to 66.0 (was 85) setting MAX_CSF to 45.9 (was 40) setting MAX_GRAY to 94.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 56.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 35.9 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.03-->3.10) (max @ vno 161329 --> 161551) face area 0.27 +- 0.12 (0.00-->1.98) mean absolute distance = 0.65 +- 0.81 3472 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104+-6.1, GM=66+-6.1 mean inside = 94.0, mean outside = 72.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=77.3, 50 (50) missing vertices, mean dist 0.3 [0.5 (%33.7)->0.7 (%66.3))] %68 local maxima, %27 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= x220, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.05-->3.43) (max @ vno 107773 --> 107779) face area 0.27 +- 0.13 (0.00-->2.18) mean absolute distance = 0.33 +- 0.48 4007 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4661182.5, rms=11.312 001: dt: 0.5000, sse=2581227.8, rms=7.908 (30.098%) 002: dt: 0.5000, sse=1756256.2, rms=6.027 (23.783%) 003: dt: 0.5000, sse=1381704.0, rms=4.936 (18.097%) 004: dt: 0.5000, sse=1218477.8, rms=4.373 (11.417%) 005: dt: 0.5000, sse=1152925.6, rms=4.125 (5.670%) 006: dt: 0.5000, sse=1127394.9, rms=4.016 (2.631%) 007: dt: 0.5000, sse=1116086.5, rms=3.965 (1.264%) rms = 3.92, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=1105274.2, rms=3.919 (1.171%) 009: dt: 0.2500, sse=855996.2, rms=2.623 (33.069%) 010: dt: 0.2500, sse=792181.4, rms=2.193 (16.400%) 011: dt: 0.2500, sse=780861.4, rms=2.096 (4.415%) 012: dt: 0.2500, sse=768880.4, rms=2.010 (4.099%) rms = 1.99, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=770805.4, rms=1.985 (1.232%) 014: dt: 0.1250, sse=748078.7, rms=1.823 (8.186%) rms = 1.80, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=745960.4, rms=1.801 (1.219%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=81.8, 80 (22) missing vertices, mean dist -0.2 [0.4 (%80.2)->0.2 (%19.8))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= x220, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.24 (0.05-->3.69) (max @ vno 107773 --> 107779) face area 0.34 +- 0.16 (0.00-->2.80) mean absolute distance = 0.20 +- 0.30 3422 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1816270.2, rms=5.707 016: dt: 0.5000, sse=1248303.4, rms=3.786 (33.667%) rms = 4.04, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=1037285.9, rms=2.749 (27.382%) 018: dt: 0.2500, sse=946409.3, rms=2.135 (22.333%) 019: dt: 0.2500, sse=905138.6, rms=1.809 (15.272%) 020: dt: 0.2500, sse=894883.1, rms=1.710 (5.468%) 021: dt: 0.2500, sse=890116.1, rms=1.644 (3.851%) rms = 1.61, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=885421.0, rms=1.613 (1.912%) 023: dt: 0.1250, sse=872415.8, rms=1.489 (7.651%) rms = 1.48, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=872759.2, rms=1.480 (0.616%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=84.3, 85 (18) missing vertices, mean dist -0.1 [0.2 (%73.0)->0.2 (%27.0))] %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= x220, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.24 (0.05-->3.81) (max @ vno 107773 --> 107779) face area 0.33 +- 0.16 (0.00-->2.74) mean absolute distance = 0.17 +- 0.25 2833 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1136592.8, rms=3.388 rms = 3.52, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=951981.4, rms=2.350 (30.639%) 026: dt: 0.2500, sse=869352.1, rms=1.588 (32.395%) 027: dt: 0.2500, sse=853247.9, rms=1.478 (6.963%) rms = 1.44, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=844741.0, rms=1.436 (2.815%) 029: dt: 0.1250, sse=834392.8, rms=1.317 (8.331%) rms = 1.31, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=834517.8, rms=1.314 (0.196%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=84.9, 76 (11) missing vertices, mean dist -0.0 [0.2 (%54.8)->0.2 (%45.2))] %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= x220, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /dat/mw/tvb-new-dataset/tvb/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=848037.5, rms=1.545 rms = 2.07, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=809351.8, rms=1.083 (29.909%) 032: dt: 0.2500, sse=802639.1, rms=0.961 (11.303%) rms = 0.98, time step reduction 2 of 3 to 0.125... rms = 0.95, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=799997.3, rms=0.954 (0.703%) positioning took 0.4 minutes generating cortex label... 4 non-cortical segments detected only using segment with 7952 vertices erasing segment 1 (vno[0] = 118648) erasing segment 2 (vno[0] = 122988) erasing segment 3 (vno[0] = 124149) writing cortex label to /dat/mw/tvb-new-dataset/tvb/label/lh.cortex.label... writing curvature file /dat/mw/tvb-new-dataset/tvb/surf/lh.curv writing smoothed area to lh.area writing curvature file /dat/mw/tvb-new-dataset/tvb/surf/lh.area vertex spacing 0.88 +- 0.25 (0.05-->3.83) (max @ vno 107773 --> 107779) face area 0.33 +- 0.15 (0.00-->2.72) refinement took 4.8 minutes #-------------------------------------------- #@# Make White Surf rh Tue Mar 1 19:39:14 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -noaparc -whiteonly -mgz -T1 brain.finalsurfs tvb rh only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.163 2016/02/26 15:09:17 fischl Exp $ $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $ reading volume /dat/mw/tvb-new-dataset/tvb/mri/filled.mgz... reading volume /dat/mw/tvb-new-dataset/tvb/mri/brain.finalsurfs.mgz... reading volume /dat/mw/tvb-new-dataset/tvb/mri/../mri/aseg.presurf.mgz... reading volume /dat/mw/tvb-new-dataset/tvb/mri/wm.mgz... 57193 bright wm thresholded. 1573 bright non-wm voxels segmented. reading original surface position from /dat/mw/tvb-new-dataset/tvb/surf/rh.orig... computing class statistics... border white: 299374 voxels (1.78%) border gray 355765 voxels (2.12%) WM (99.0): 98.6 +- 9.5 [70.0 --> 110.0] GM (69.0) : 69.2 +- 10.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 57.0 (was 70) setting MAX_BORDER_WHITE to 114.5 (was 105) setting MIN_BORDER_WHITE to 67.0 (was 85) setting MAX_CSF to 46.9 (was 40) setting MAX_GRAY to 95.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 57.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.9 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.02-->3.70) (max @ vno 37809 --> 164070) face area 0.28 +- 0.12 (0.00-->1.62) mean absolute distance = 0.66 +- 0.85 3808 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-6.1, GM=67+-7.0 mean inside = 94.0, mean outside = 73.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=78.5, 64 (64) missing vertices, mean dist 0.2 [0.6 (%36.4)->0.7 (%63.6))] %68 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host= x220, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.25 (0.08-->3.35) (max @ vno 37809 --> 164070) face area 0.28 +- 0.13 (0.00-->1.95) mean absolute distance = 0.36 +- 0.51 4720 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4468571.0, rms=10.948 001: dt: 0.5000, sse=2465041.8, rms=7.591 (30.665%) 002: dt: 0.5000, sse=1685544.9, rms=5.757 (24.163%) 003: dt: 0.5000, sse=1336306.5, rms=4.706 (18.249%) 004: dt: 0.5000, sse=1191945.4, rms=4.180 (11.180%) 005: dt: 0.5000, sse=1133950.9, rms=3.935 (5.855%) 006: dt: 0.5000, sse=1107780.5, rms=3.825 (2.792%) 007: dt: 0.5000, sse=1092218.0, rms=3.768 (1.506%) rms = 3.73, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=1082452.0, rms=3.733 (0.921%) 009: dt: 0.2500, sse=849436.1, rms=2.479 (33.589%) 010: dt: 0.2500, sse=792984.2, rms=2.078 (16.192%) 011: dt: 0.2500, sse=782778.4, rms=1.995 (3.964%) 012: dt: 0.2500, sse=773454.6, rms=1.916 (3.980%) rms = 1.89, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=773279.9, rms=1.890 (1.338%) 014: dt: 0.1250, sse=755062.1, rms=1.747 (7.569%) rms = 1.73, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=753477.6, rms=1.728 (1.090%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=83.0, 79 (11) missing vertices, mean dist -0.3 [0.4 (%80.3)->0.3 (%19.7))] %84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host= x220, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.25 (0.03-->3.31) (max @ vno 128002 --> 126861) face area 0.34 +- 0.16 (0.00-->2.94) mean absolute distance = 0.21 +- 0.32 4125 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1872138.1, rms=5.798 016: dt: 0.5000, sse=1301261.8, rms=3.901 (32.723%) rms = 3.93, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=1086937.9, rms=2.944 (24.538%) 018: dt: 0.2500, sse=973976.8, rms=2.246 (23.707%) 019: dt: 0.2500, sse=928035.2, rms=1.867 (16.854%) 020: dt: 0.2500, sse=907234.8, rms=1.714 (8.231%) 021: dt: 0.2500, sse=902357.2, rms=1.605 (6.343%) rms = 1.56, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=900044.2, rms=1.560 (2.802%) 023: dt: 0.1250, sse=880471.7, rms=1.451 (6.977%) rms = 1.44, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=881695.5, rms=1.437 (0.962%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=85.5, 76 (4) missing vertices, mean dist -0.1 [0.2 (%73.0)->0.2 (%27.0))] %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host= x220, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.88 +- 0.25 (0.07-->3.40) (max @ vno 128002 --> 126861) face area 0.33 +- 0.16 (0.00-->3.50) mean absolute distance = 0.17 +- 0.27 3421 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1151083.8, rms=3.394 025: dt: 0.5000, sse=1152821.2, rms=3.319 (2.205%) rms = 3.74, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=935576.2, rms=2.126 (35.938%) 027: dt: 0.2500, sse=884731.7, rms=1.652 (22.286%) 028: dt: 0.2500, sse=862742.2, rms=1.472 (10.934%) rms = 1.46, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=853948.2, rms=1.456 (1.045%) 030: dt: 0.1250, sse=859719.4, rms=1.292 (11.297%) rms = 1.28, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=838148.1, rms=1.276 (1.235%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=86.1, 93 (3) missing vertices, mean dist -0.0 [0.2 (%55.0)->0.2 (%45.0))] %92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host= x220, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /dat/mw/tvb-new-dataset/tvb/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=852553.7, rms=1.518 rms = 2.02, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=815676.3, rms=1.060 (30.150%) 033: dt: 0.2500, sse=809558.2, rms=0.943 (11.068%) rms = 0.96, time step reduction 2 of 3 to 0.125... rms = 0.94, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=806278.1, rms=0.937 (0.684%) positioning took 0.4 minutes generating cortex label... 14 non-cortical segments detected only using segment with 7677 vertices erasing segment 1 (vno[0] = 115992) erasing segment 2 (vno[0] = 118003) erasing segment 3 (vno[0] = 119279) erasing segment 4 (vno[0] = 120369) erasing segment 5 (vno[0] = 121344) erasing segment 6 (vno[0] = 121432) erasing segment 7 (vno[0] = 121459) erasing segment 8 (vno[0] = 122444) erasing segment 9 (vno[0] = 122542) erasing segment 10 (vno[0] = 123779) erasing segment 11 (vno[0] = 124725) erasing segment 12 (vno[0] = 133803) erasing segment 13 (vno[0] = 134715) writing cortex label to /dat/mw/tvb-new-dataset/tvb/label/rh.cortex.label... writing curvature file /dat/mw/tvb-new-dataset/tvb/surf/rh.curv writing smoothed area to rh.area writing curvature file /dat/mw/tvb-new-dataset/tvb/surf/rh.area vertex spacing 0.88 +- 0.25 (0.05-->3.41) (max @ vno 126861 --> 128002) face area 0.33 +- 0.15 (0.00-->3.56) refinement took 5.1 minutes #-------------------------------------------- #@# Smooth2 lh Tue Mar 1 19:44:17 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth2 rh Tue Mar 1 19:44:22 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Tue Mar 1 19:44:28 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_inflate -rusage /dat/mw/tvb-new-dataset/tvb/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 50.7 mm, total surface area = 96828 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.177 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.091 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.041 (target=0.015) step 035: RMS=0.035 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.026 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.022 (target=0.015) step 060: RMS=0.020 (target=0.015) inflation complete. inflation took 0.6 minutes mris_inflate utimesec 36.451080 mris_inflate stimesec 0.262647 mris_inflate ru_maxrss 213888 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 409223 mris_inflate ru_majflt 3 mris_inflate ru_nswap 0 mris_inflate ru_inblock 528 mris_inflate ru_oublock 12712 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 3 mris_inflate ru_nivcsw 65 #-------------------------------------------- #@# Inflation2 rh Tue Mar 1 19:45:05 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_inflate -rusage /dat/mw/tvb-new-dataset/tvb/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 50.6 mm, total surface area = 97662 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.175 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.091 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.062 (target=0.015) step 025: RMS=0.052 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.036 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.021 (target=0.015) inflation complete. inflation took 0.6 minutes mris_inflate utimesec 36.852540 mris_inflate stimesec 0.228699 mris_inflate ru_maxrss 216052 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 413566 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 12872 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 66 #-------------------------------------------- #@# Curv .H and .K lh Tue Mar 1 19:45:42 CET 2016 /dat/mw/tvb-new-dataset/tvb/surf mris_curvature -w lh.white total integrated curvature = -3.949*4pi (-49.624) --> 5 handles ICI = 183.3, FI = 2207.4, variation=33917.018 writing Gaussian curvature to ./lh.white.K...done. writing mean curvature to ./lh.white.H...done. mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 262 vertices thresholded to be in k1 ~ [-0.16 0.37], k2 ~ [-0.09 0.05] total integrated curvature = 0.570*4pi (7.159) --> 0 handles ICI = 1.6, FI = 9.9, variation=171.802 148 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 162 vertices thresholded to be in [-0.11 0.13] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.021 done. #-------------------------------------------- #@# Curv .H and .K rh Tue Mar 1 19:46:58 CET 2016 /dat/mw/tvb-new-dataset/tvb/surf mris_curvature -w rh.white total integrated curvature = -0.907*4pi (-11.403) --> 2 handles ICI = 185.8, FI = 2244.8, variation=34405.827 writing Gaussian curvature to ./rh.white.K...done. writing mean curvature to ./rh.white.H...done. mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 206 vertices thresholded to be in k1 ~ [-0.17 0.34], k2 ~ [-0.10 0.08] total integrated curvature = 0.554*4pi (6.958) --> 0 handles ICI = 1.7, FI = 10.1, variation=176.005 165 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 163 vertices thresholded to be in [-0.11 0.12] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.021 done. #----------------------------------------- #@# Curvature Stats lh Tue Mar 1 19:48:14 CET 2016 /dat/mw/tvb-new-dataset/tvb/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm tvb lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ tvb/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 262 ] Gb_filter = 0 WARN: S lookup min: -0.366510 WARN: S explicit min: 0.000000 vertex = 415 #----------------------------------------- #@# Curvature Stats rh Tue Mar 1 19:48:18 CET 2016 /dat/mw/tvb-new-dataset/tvb/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm tvb rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ tvb/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 335 ] Gb_filter = 0 WARN: S lookup min: -0.105201 WARN: S explicit min: 0.000000 vertex = 655 #-------------------------------------------- #@# Sphere lh Tue Mar 1 19:48:22 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_sphere -rusage /dat/mw/tvb-new-dataset/tvb/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.281... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= x220, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.36 pass 1: epoch 2 of 3 starting distance error %20.35 unfolding complete - removing small folds... starting distance error %20.32 removing remaining folds... final distance error %20.33 MRISunfold() return, current seed 1234 -01: dt=0.0000, 179 negative triangles 163: dt=0.9900, 179 negative triangles 164: dt=0.9900, 58 negative triangles 165: dt=0.9900, 44 negative triangles 166: dt=0.9900, 23 negative triangles 167: dt=0.9900, 30 negative triangles 168: dt=0.9900, 23 negative triangles 169: dt=0.9900, 18 negative triangles 170: dt=0.9900, 9 negative triangles 171: dt=0.9900, 11 negative triangles 172: dt=0.9900, 6 negative triangles 173: dt=0.9900, 7 negative triangles 174: dt=0.9900, 8 negative triangles 175: dt=0.9900, 5 negative triangles 176: dt=0.9900, 3 negative triangles 177: dt=0.9900, 3 negative triangles 178: dt=0.9900, 1 negative triangles 179: dt=0.9900, 1 negative triangles 180: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.78 hours mris_sphere utimesec 2817.324712 mris_sphere stimesec 1.792553 mris_sphere ru_maxrss 292220 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 2667124 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 11440 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 0 mris_sphere ru_nivcsw 6793 FSRUNTIME@ mris_sphere 0.7842 hours 1 threads #-------------------------------------------- #@# Sphere rh Tue Mar 1 20:35:25 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_sphere -rusage /dat/mw/tvb-new-dataset/tvb/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.277... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= x220, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %21.85 pass 1: epoch 2 of 3 starting distance error %21.79 unfolding complete - removing small folds... starting distance error %21.65 removing remaining folds... final distance error %21.67 MRISunfold() return, current seed 1234 -01: dt=0.0000, 217 negative triangles 159: dt=0.9900, 217 negative triangles 160: dt=0.9900, 69 negative triangles 161: dt=0.9900, 43 negative triangles 162: dt=0.9900, 28 negative triangles 163: dt=0.9900, 36 negative triangles 164: dt=0.9900, 28 negative triangles 165: dt=0.9900, 27 negative triangles 166: dt=0.9900, 18 negative triangles 167: dt=0.9900, 24 negative triangles 168: dt=0.9900, 15 negative triangles 169: dt=0.9900, 14 negative triangles 170: dt=0.9900, 9 negative triangles 171: dt=0.9900, 14 negative triangles 172: dt=0.9900, 15 negative triangles 173: dt=0.9900, 13 negative triangles 174: dt=0.9900, 4 negative triangles 175: dt=0.9900, 8 negative triangles 176: dt=0.9900, 5 negative triangles 177: dt=0.9900, 8 negative triangles 178: dt=0.9900, 9 negative triangles 179: dt=0.9900, 7 negative triangles 180: dt=0.9900, 3 negative triangles 181: dt=0.9900, 7 negative triangles 182: dt=0.9900, 5 negative triangles 183: dt=0.9900, 7 negative triangles 184: dt=0.9900, 4 negative triangles 185: dt=0.9900, 8 negative triangles 186: dt=0.9900, 7 negative triangles 187: dt=0.9900, 4 negative triangles 188: dt=0.9900, 3 negative triangles 189: dt=0.9900, 3 negative triangles 190: dt=0.9405, 4 negative triangles 191: dt=0.9405, 2 negative triangles 192: dt=0.9405, 4 negative triangles 193: dt=0.9405, 2 negative triangles 194: dt=0.9405, 2 negative triangles 195: dt=0.9405, 3 negative triangles 196: dt=0.9405, 1 negative triangles 197: dt=0.9405, 2 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.82 hours mris_sphere utimesec 2934.221011 mris_sphere stimesec 2.545331 mris_sphere ru_maxrss 295452 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 2832078 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 11584 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 0 mris_sphere ru_nivcsw 13168 FSRUNTIME@ mris_sphere 0.8170 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Tue Mar 1 21:24:27 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_register -curv -rusage /dat/mw/tvb-new-dataset/tvb/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /dat/mw/tvb-new-dataset/tvb/scripts cmdline mris_register -curv -rusage /dat/mw/tvb-new-dataset/tvb/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /opt/freesurfer/average/lh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host= x220, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host= x220, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = -0.000, std = 5.504 curvature mean = 0.036, std = 0.937 curvature mean = 0.024, std = 0.845 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, -16.00) sse = 418018.8, tmin=1.2176 d=32.00 min @ (8.00, 8.00, 0.00) sse = 318931.3, tmin=2.4710 d=16.00 min @ (0.00, 0.00, 4.00) sse = 290195.0, tmin=3.7412 d=8.00 min @ (-2.00, 0.00, 0.00) sse = 282281.7, tmin=4.9982 d=4.00 min @ (0.00, 1.00, 0.00) sse = 281386.3, tmin=6.2634 d=2.00 min @ (0.50, 0.00, -0.50) sse = 280433.0, tmin=7.5458 d=0.50 min @ (0.00, -0.12, 0.00) sse = 280395.5, tmin=10.0985 tol=1.0e+00, sigma=0.5, host= x220, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 10.10 min curvature mean = -0.001, std = 0.924 curvature mean = 0.010, std = 0.936 curvature mean = -0.006, std = 0.934 curvature mean = 0.005, std = 0.973 curvature mean = -0.007, std = 0.936 curvature mean = 0.001, std = 0.989 2 Reading smoothwm curvature mean = -0.024, std = 0.460 curvature mean = 0.003, std = 0.067 curvature mean = 0.050, std = 0.197 curvature mean = 0.003, std = 0.079 curvature mean = 0.024, std = 0.322 curvature mean = 0.003, std = 0.084 curvature mean = 0.014, std = 0.419 curvature mean = 0.004, std = 0.086 curvature mean = 0.004, std = 0.525 MRISregister() return, current seed 0 -01: dt=0.0000, 54 negative triangles 131: dt=0.9900, 54 negative triangles 132: dt=0.9900, 49 negative triangles 133: dt=0.9900, 49 negative triangles 134: dt=0.9900, 51 negative triangles 135: dt=0.9900, 41 negative triangles 136: dt=0.9900, 35 negative triangles 137: dt=0.9900, 36 negative triangles 138: dt=0.9900, 28 negative triangles 139: dt=0.9900, 28 negative triangles 140: dt=0.9900, 29 negative triangles 141: dt=0.9900, 24 negative triangles 142: dt=0.9900, 27 negative triangles 143: dt=0.9900, 27 negative triangles 144: dt=0.9900, 27 negative triangles 145: dt=0.9900, 24 negative triangles 146: dt=0.9900, 26 negative triangles 147: dt=0.9900, 28 negative triangles 148: dt=0.9900, 23 negative triangles 149: dt=0.9900, 28 negative triangles 150: dt=0.9900, 26 negative triangles 151: dt=0.9900, 27 negative triangles 152: dt=0.9900, 26 negative triangles 153: dt=0.9900, 23 negative triangles 154: dt=0.9900, 26 negative triangles 155: dt=0.9900, 26 negative triangles 156: dt=0.9900, 28 negative triangles 157: dt=0.9900, 23 negative triangles 158: dt=0.9405, 29 negative triangles 159: dt=0.9405, 21 negative triangles 160: dt=0.9405, 27 negative triangles 161: dt=0.9405, 24 negative triangles 162: dt=0.9405, 23 negative triangles 163: dt=0.9405, 26 negative triangles 164: dt=0.9405, 19 negative triangles 165: dt=0.9405, 18 negative triangles 166: dt=0.9405, 20 negative triangles 167: dt=0.9405, 21 negative triangles 168: dt=0.9405, 18 negative triangles 169: dt=0.9405, 16 negative triangles 170: dt=0.9405, 14 negative triangles 171: dt=0.9405, 19 negative triangles 172: dt=0.9405, 15 negative triangles 173: dt=0.9405, 13 negative triangles 174: dt=0.9405, 11 negative triangles 175: dt=0.9405, 13 negative triangles 176: dt=0.9405, 13 negative triangles 177: dt=0.9405, 12 negative triangles 178: dt=0.9405, 11 negative triangles 179: dt=0.9405, 13 negative triangles 180: dt=0.9405, 10 negative triangles 181: dt=0.9405, 9 negative triangles 182: dt=0.9405, 13 negative triangles 183: dt=0.9405, 10 negative triangles 184: dt=0.9405, 11 negative triangles 185: dt=0.9405, 12 negative triangles 186: dt=0.9405, 11 negative triangles 187: dt=0.9405, 11 negative triangles 188: dt=0.9405, 9 negative triangles 189: dt=0.9405, 9 negative triangles 190: dt=0.9405, 12 negative triangles 191: dt=0.8935, 11 negative triangles 192: dt=0.8935, 12 negative triangles 193: dt=0.8935, 8 negative triangles 194: dt=0.8935, 10 negative triangles 195: dt=0.8935, 7 negative triangles 196: dt=0.8935, 9 negative triangles 197: dt=0.8935, 9 negative triangles 198: dt=0.8935, 6 negative triangles 199: dt=0.8935, 6 negative triangles 200: dt=0.8935, 10 negative triangles 201: dt=0.8935, 7 negative triangles 202: dt=0.8935, 8 negative triangles 203: dt=0.8935, 8 negative triangles 204: dt=0.8935, 6 negative triangles 205: dt=0.8935, 6 negative triangles 206: dt=0.8935, 8 negative triangles 207: dt=0.8935, 6 negative triangles 208: dt=0.8488, 6 negative triangles 209: dt=0.8488, 7 negative triangles 210: dt=0.8488, 7 negative triangles 211: dt=0.8488, 5 negative triangles 212: dt=0.8488, 6 negative triangles 213: dt=0.8488, 4 negative triangles 214: dt=0.8488, 4 negative triangles 215: dt=0.8488, 3 negative triangles 216: dt=0.8488, 4 negative triangles 217: dt=0.8488, 2 negative triangles 218: dt=0.8488, 1 negative triangles 219: dt=0.8488, 1 negative triangles 220: dt=0.8488, 1 negative triangles 221: dt=0.8488, 2 negative triangles 222: dt=0.8488, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.07 hours mris_register utimesec 3852.698517 mris_register stimesec 3.072484 mris_register ru_maxrss 268660 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 1702239 mris_register ru_majflt 53 mris_register ru_nswap 0 mris_register ru_inblock 21672 mris_register ru_oublock 11440 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 104 mris_register ru_nivcsw 12981 FSRUNTIME@ mris_register 1.0727 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Tue Mar 1 22:28:48 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_register -curv -rusage /dat/mw/tvb-new-dataset/tvb/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /opt/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /dat/mw/tvb-new-dataset/tvb/scripts cmdline mris_register -curv -rusage /dat/mw/tvb-new-dataset/tvb/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /opt/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /opt/freesurfer/average/rh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host= x220, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host= x220, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = 0.000, std = 5.514 curvature mean = 0.011, std = 0.930 curvature mean = 0.028, std = 0.841 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 478226.3, tmin=1.1847 d=32.00 min @ (-8.00, -8.00, -8.00) sse = 373478.1, tmin=2.3942 d=16.00 min @ (0.00, 0.00, 4.00) sse = 342077.3, tmin=3.6353 d=8.00 min @ (0.00, 2.00, 0.00) sse = 331599.3, tmin=4.8741 d=4.00 min @ (1.00, 0.00, 0.00) sse = 330797.4, tmin=6.1174 d=2.00 min @ (-0.50, 0.00, 0.00) sse = 330523.0, tmin=7.3640 d=1.00 min @ (0.25, 0.25, 0.00) sse = 330300.5, tmin=8.6134 tol=1.0e+00, sigma=0.5, host= x220, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 9.88 min curvature mean = -0.023, std = 0.915 curvature mean = 0.013, std = 0.932 curvature mean = -0.033, std = 0.918 curvature mean = 0.005, std = 0.969 curvature mean = -0.035, std = 0.916 curvature mean = 0.001, std = 0.986 2 Reading smoothwm curvature mean = -0.027, std = 0.312 curvature mean = 0.004, std = 0.069 curvature mean = 0.075, std = 0.294 curvature mean = 0.004, std = 0.082 curvature mean = 0.039, std = 0.470 curvature mean = 0.005, std = 0.086 curvature mean = 0.021, std = 0.614 curvature mean = 0.006, std = 0.089 curvature mean = 0.008, std = 0.732 MRISregister() return, current seed 0 -01: dt=0.0000, 76 negative triangles 134: dt=0.9900, 76 negative triangles expanding nbhd size to 1 135: dt=0.9900, 79 negative triangles 136: dt=0.9900, 42 negative triangles 137: dt=0.9900, 46 negative triangles 138: dt=0.9900, 49 negative triangles 139: dt=0.9900, 40 negative triangles 140: dt=0.9900, 39 negative triangles 141: dt=0.9900, 37 negative triangles 142: dt=0.9900, 37 negative triangles 143: dt=0.9900, 29 negative triangles 144: dt=0.9900, 28 negative triangles 145: dt=0.9900, 20 negative triangles 146: dt=0.9900, 20 negative triangles 147: dt=0.9900, 20 negative triangles 148: dt=0.9900, 20 negative triangles 149: dt=0.9900, 12 negative triangles 150: dt=0.9900, 16 negative triangles 151: dt=0.9900, 9 negative triangles 152: dt=0.9900, 9 negative triangles 153: dt=0.9900, 6 negative triangles 154: dt=0.9900, 5 negative triangles 155: dt=0.9900, 4 negative triangles 156: dt=0.9900, 1 negative triangles 157: dt=0.9900, 2 negative triangles 158: dt=0.9900, 1 negative triangles 159: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.19 hours mris_register utimesec 4288.251819 mris_register stimesec 3.272127 mris_register ru_maxrss 269788 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 1920459 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 9232 mris_register ru_oublock 11584 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 43 mris_register ru_nivcsw 20161 FSRUNTIME@ mris_register 1.1941 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Tue Mar 1 23:40:27 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Tue Mar 1 23:40:29 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Tue Mar 1 23:40:31 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mrisp_paint -a 5 /opt/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /opt/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh Tue Mar 1 23:40:33 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mrisp_paint -a 5 /opt/freesurfer/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /opt/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Tue Mar 1 23:40:34 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 tvb lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.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 1.778 2016/02/03 18:58:39 fischl Exp $ reading atlas from /opt/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1811 labels changed using aseg relabeling using gibbs priors... 000: 3467 changed, 162585 examined... 001: 799 changed, 14515 examined... 002: 178 changed, 4421 examined... 003: 71 changed, 1061 examined... 004: 36 changed, 435 examined... 005: 24 changed, 211 examined... 006: 9 changed, 142 examined... 007: 3 changed, 54 examined... 008: 2 changed, 18 examined... 009: 0 changed, 13 examined... 203 labels changed using aseg 000: 150 total segments, 104 labels (454 vertices) changed 001: 45 total segments, 5 labels (23 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 7 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2191 vertices marked for relabeling... 2191 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 14 seconds. #----------------------------------------- #@# Cortical Parc rh Tue Mar 1 23:40:49 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 tvb rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.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 1.778 2016/02/03 18:58:39 fischl Exp $ reading atlas from /opt/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1447 labels changed using aseg relabeling using gibbs priors... 000: 3373 changed, 164634 examined... 001: 824 changed, 14342 examined... 002: 212 changed, 4633 examined... 003: 66 changed, 1252 examined... 004: 33 changed, 418 examined... 005: 16 changed, 182 examined... 006: 10 changed, 96 examined... 007: 2 changed, 50 examined... 008: 2 changed, 17 examined... 009: 2 changed, 6 examined... 010: 1 changed, 12 examined... 011: 0 changed, 7 examined... 149 labels changed using aseg 000: 109 total segments, 71 labels (313 vertices) changed 001: 40 total segments, 2 labels (2 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 5 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2693 vertices marked for relabeling... 2693 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 15 seconds. #-------------------------------------------- #@# Make Pial Surf lh Tue Mar 1 23:41:04 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_make_surfaces -orig_white white -orig_pial white -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs tvb lh reading previously compute gray/white surface using white starting white location... using white starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.163 2016/02/26 15:09:17 fischl Exp $ $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $ reading volume /dat/mw/tvb-new-dataset/tvb/mri/filled.mgz... reading volume /dat/mw/tvb-new-dataset/tvb/mri/brain.finalsurfs.mgz... reading volume /dat/mw/tvb-new-dataset/tvb/mri/../mri/aseg.presurf.mgz... reading volume /dat/mw/tvb-new-dataset/tvb/mri/wm.mgz... 57193 bright wm thresholded. 1573 bright non-wm voxels segmented. reading original surface position from /dat/mw/tvb-new-dataset/tvb/surf/lh.orig... computing class statistics... border white: 299374 voxels (1.78%) border gray 355765 voxels (2.12%) WM (99.0): 98.6 +- 9.5 [70.0 --> 110.0] GM (69.0) : 69.2 +- 10.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 56.0 (was 70) setting MAX_BORDER_WHITE to 113.5 (was 105) setting MIN_BORDER_WHITE to 66.0 (was 85) setting MAX_CSF to 45.9 (was 40) setting MAX_GRAY to 94.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 56.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 35.9 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104+-6.1, GM=66+-6.1 mean inside = 94.0, mean outside = 72.3 reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... reading white vertex positions from white... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown reading initial pial vertex positions from white... mean border=53.4, 103 (103) missing vertices, mean dist 1.9 [0.0 (%0.0)->2.7 (%100.0))] %14 local maxima, %54 large gradients and %28 min vals, 141 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host= x220, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 10 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=32803278.0, rms=32.027 001: dt: 0.0500, sse=28081148.0, rms=29.572 (7.665%) 002: dt: 0.0500, sse=24913680.0, rms=27.804 (5.979%) 003: dt: 0.0500, sse=22562566.0, rms=26.415 (4.995%) 004: dt: 0.0500, sse=20713138.0, rms=25.269 (4.339%) 005: dt: 0.0500, sse=19202898.0, rms=24.293 (3.863%) 006: dt: 0.0500, sse=17935876.0, rms=23.443 (3.500%) 007: dt: 0.0500, sse=16850612.0, rms=22.689 (3.215%) 008: dt: 0.0500, sse=15905249.0, rms=22.011 (2.987%) 009: dt: 0.0500, sse=15070847.0, rms=21.395 (2.799%) 010: dt: 0.0500, sse=14327044.0, rms=20.831 (2.639%) positioning took 0.9 minutes mean border=53.2, 59 (40) missing vertices, mean dist 1.6 [0.1 (%0.0)->2.2 (%100.0))] %15 local maxima, %54 large gradients and %27 min vals, 124 gradients ignored tol=1.0e-04, sigma=2.0, host= x220, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=15098947.0, rms=21.422 011: dt: 0.0500, sse=14426470.0, rms=20.913 (2.376%) 012: dt: 0.0500, sse=13819317.0, rms=20.443 (2.249%) 013: dt: 0.0500, sse=13268051.0, rms=20.006 (2.137%) 014: dt: 0.0500, sse=12765964.0, rms=19.600 (2.031%) 015: dt: 0.0500, sse=12306869.0, rms=19.220 (1.934%) 016: dt: 0.0500, sse=11885931.0, rms=18.866 (1.844%) 017: dt: 0.0500, sse=11499591.0, rms=18.535 (1.756%) 018: dt: 0.0500, sse=11143510.0, rms=18.224 (1.677%) 019: dt: 0.0500, sse=10814003.0, rms=17.932 (1.605%) 020: dt: 0.0500, sse=10507940.0, rms=17.656 (1.539%) positioning took 0.9 minutes mean border=53.1, 62 (28) missing vertices, mean dist 1.3 [0.1 (%0.4)->1.9 (%99.6))] %16 local maxima, %54 large gradients and %27 min vals, 112 gradients ignored tol=1.0e-04, sigma=2.0, host= x220, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=10601219.0, rms=17.748 021: dt: 0.0500, sse=10311869.0, rms=17.484 (1.486%) 022: dt: 0.0500, sse=10041321.0, rms=17.234 (1.431%) 023: dt: 0.0500, sse=9786654.0, rms=16.995 (1.387%) 024: dt: 0.0500, sse=9546305.0, rms=16.766 (1.346%) 025: dt: 0.0500, sse=9318188.0, rms=16.546 (1.313%) 026: dt: 0.0500, sse=9100722.0, rms=16.334 (1.285%) 027: dt: 0.0500, sse=8891034.0, rms=16.126 (1.272%) 028: dt: 0.0500, sse=8687257.0, rms=15.921 (1.269%) 029: dt: 0.0500, sse=8489500.0, rms=15.720 (1.264%) 030: dt: 0.0500, sse=8296591.0, rms=15.521 (1.265%) positioning took 0.9 minutes mean border=53.0, 64 (18) missing vertices, mean dist 1.1 [0.1 (%3.6)->1.6 (%96.4))] %16 local maxima, %53 large gradients and %27 min vals, 127 gradients ignored tol=1.0e-04, sigma=2.0, host= x220, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=8387924.0, rms=15.618 031: dt: 0.5000, sse=6951222.0, rms=14.061 (9.971%) 032: dt: 0.5000, sse=5826492.0, rms=12.704 (9.647%) 033: dt: 0.5000, sse=4863657.0, rms=11.420 (10.109%) 034: dt: 0.5000, sse=4043514.8, rms=10.192 (10.754%) 035: dt: 0.5000, sse=3366430.8, rms=9.056 (11.143%) 036: dt: 0.5000, sse=2821487.2, rms=8.022 (11.422%) 037: dt: 0.5000, sse=2395403.5, rms=7.114 (11.318%) 038: dt: 0.5000, sse=2100659.8, rms=6.406 (9.947%) 039: dt: 0.5000, sse=1915957.5, rms=5.924 (7.525%) 040: dt: 0.5000, sse=1807720.5, rms=5.618 (5.177%) 041: dt: 0.5000, sse=1737310.8, rms=5.412 (3.652%) 042: dt: 0.5000, sse=1701307.1, rms=5.299 (2.089%) 043: dt: 0.5000, sse=1668484.1, rms=5.202 (1.832%) rms = 5.16, time step reduction 1 of 3 to 0.250... 044: dt: 0.5000, sse=1655224.0, rms=5.155 (0.907%) 045: dt: 0.2500, sse=1437543.6, rms=4.365 (15.334%) 046: dt: 0.2500, sse=1373042.6, rms=4.119 (5.631%) rms = 4.11, time step reduction 2 of 3 to 0.125... 047: dt: 0.2500, sse=1372514.1, rms=4.112 (0.170%) 048: dt: 0.1250, sse=1324479.0, rms=3.910 (4.918%) rms = 3.88, time step reduction 3 of 3 to 0.062... 049: dt: 0.1250, sse=1316895.4, rms=3.877 (0.822%) positioning took 1.9 minutes mean border=51.2, 1683 (5) missing vertices, mean dist 0.1 [0.2 (%43.7)->0.4 (%56.3))] %33 local maxima, %38 large gradients and %24 min vals, 64 gradients ignored tol=1.0e-04, sigma=1.0, host= x220, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1787566.1, rms=4.749 rms = 4.76, time step reduction 1 of 3 to 0.250... 050: dt: 0.2500, sse=1608559.4, rms=4.078 (14.140%) 051: dt: 0.2500, sse=1499266.2, rms=3.599 (11.749%) 052: dt: 0.2500, sse=1473039.5, rms=3.486 (3.118%) rms = 3.45, time step reduction 2 of 3 to 0.125... 053: dt: 0.2500, sse=1465163.2, rms=3.453 (0.966%) 054: dt: 0.1250, sse=1409563.5, rms=3.167 (8.277%) 055: dt: 0.1250, sse=1398215.6, rms=3.110 (1.805%) rms = 3.10, time step reduction 3 of 3 to 0.062... 056: dt: 0.1250, sse=1396764.6, rms=3.103 (0.207%) positioning took 0.8 minutes mean border=49.8, 1771 (5) missing vertices, mean dist 0.1 [0.1 (%41.2)->0.3 (%58.8))] %52 local maxima, %19 large gradients and %23 min vals, 58 gradients ignored tol=1.0e-04, sigma=0.5, host= x220, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1528086.2, rms=3.743 rms = 4.58, time step reduction 1 of 3 to 0.250... 057: dt: 0.2500, sse=1440575.5, rms=3.335 (10.885%) 058: dt: 0.2500, sse=1427289.4, rms=3.272 (1.906%) rms = 3.28, time step reduction 2 of 3 to 0.125... 059: dt: 0.1250, sse=1416107.6, rms=3.214 (1.777%) 060: dt: 0.1250, sse=1399915.8, rms=3.132 (2.554%) rms = 3.10, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=1394179.5, rms=3.104 (0.876%) positioning took 0.6 minutes mean border=49.0, 3461 (5) missing vertices, mean dist 0.0 [0.1 (%46.5)->0.2 (%53.5))] %55 local maxima, %16 large gradients and %23 min vals, 65 gradients ignored tol=1.0e-04, sigma=0.2, host= x220, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /dat/mw/tvb-new-dataset/tvb/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1430651.5, rms=3.290 rms = 4.03, time step reduction 1 of 3 to 0.250... 062: dt: 0.2500, sse=1400487.6, rms=3.135 (4.708%) rms = 3.09, time step reduction 2 of 3 to 0.125... 063: dt: 0.2500, sse=1387879.6, rms=3.089 (1.462%) 064: dt: 0.1250, sse=1369235.0, rms=2.984 (3.386%) rms = 2.94, time step reduction 3 of 3 to 0.062... 065: dt: 0.1250, sse=1359379.5, rms=2.937 (1.577%) positioning took 0.5 minutes writing curvature file /dat/mw/tvb-new-dataset/tvb/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /dat/mw/tvb-new-dataset/tvb/surf/lh.area.pial vertex spacing 1.01 +- 0.44 (0.09-->5.69) (max @ vno 115594 --> 115595) face area 0.40 +- 0.31 (0.00-->5.64) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 162585 vertices processed 25000 of 162585 vertices processed 50000 of 162585 vertices processed 75000 of 162585 vertices processed 100000 of 162585 vertices processed 125000 of 162585 vertices processed 150000 of 162585 vertices processed 0 of 162585 vertices processed 25000 of 162585 vertices processed 50000 of 162585 vertices processed 75000 of 162585 vertices processed 100000 of 162585 vertices processed 125000 of 162585 vertices processed 150000 of 162585 vertices processed thickness calculation complete, 234:789 truncations. 32895 vertices at 0 distance 110619 vertices at 1 distance 106158 vertices at 2 distance 43942 vertices at 3 distance 13233 vertices at 4 distance 3790 vertices at 5 distance 1140 vertices at 6 distance 343 vertices at 7 distance 120 vertices at 8 distance 77 vertices at 9 distance 48 vertices at 10 distance 35 vertices at 11 distance 18 vertices at 12 distance 8 vertices at 13 distance 9 vertices at 14 distance 13 vertices at 15 distance 5 vertices at 16 distance 7 vertices at 17 distance 7 vertices at 18 distance 4 vertices at 19 distance 7 vertices at 20 distance writing curvature file /dat/mw/tvb-new-dataset/tvb/surf/lh.thickness positioning took 8.6 minutes #-------------------------------------------- #@# Make Pial Surf rh Tue Mar 1 23:49:43 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_make_surfaces -orig_white white -orig_pial white -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs tvb rh reading previously compute gray/white surface using white starting white location... using white starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.163 2016/02/26 15:09:17 fischl Exp $ $Id: mrisurf.c,v 1.778 2016/02/03 18:58:39 fischl Exp $ reading volume /dat/mw/tvb-new-dataset/tvb/mri/filled.mgz... reading volume /dat/mw/tvb-new-dataset/tvb/mri/brain.finalsurfs.mgz... reading volume /dat/mw/tvb-new-dataset/tvb/mri/../mri/aseg.presurf.mgz... reading volume /dat/mw/tvb-new-dataset/tvb/mri/wm.mgz... 57193 bright wm thresholded. 1573 bright non-wm voxels segmented. reading original surface position from /dat/mw/tvb-new-dataset/tvb/surf/rh.orig... computing class statistics... border white: 299374 voxels (1.78%) border gray 355765 voxels (2.12%) WM (99.0): 98.6 +- 9.5 [70.0 --> 110.0] GM (69.0) : 69.2 +- 10.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 57.0 (was 70) setting MAX_BORDER_WHITE to 114.5 (was 105) setting MIN_BORDER_WHITE to 67.0 (was 85) setting MAX_CSF to 46.9 (was 40) setting MAX_GRAY to 95.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 57.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.9 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105+-6.1, GM=67+-7.0 mean inside = 94.0, mean outside = 73.0 reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... reading white vertex positions from white... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group reading initial pial vertex positions from white... mean border=54.4, 116 (116) missing vertices, mean dist 1.9 [1.6 (%0.0)->2.7 (%100.0))] %15 local maxima, %52 large gradients and %29 min vals, 161 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host= x220, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 10 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=33608528.0, rms=32.238 001: dt: 0.0500, sse=28910580.0, rms=29.842 (7.430%) 002: dt: 0.0500, sse=25773240.0, rms=28.129 (5.741%) 003: dt: 0.0500, sse=23439620.0, rms=26.784 (4.783%) 004: dt: 0.0500, sse=21605228.0, rms=25.677 (4.134%) 005: dt: 0.0500, sse=20109346.0, rms=24.737 (3.659%) 006: dt: 0.0500, sse=18854088.0, rms=23.920 (3.303%) 007: dt: 0.0500, sse=17777652.0, rms=23.196 (3.025%) 008: dt: 0.0500, sse=16838302.0, rms=22.546 (2.804%) 009: dt: 0.0500, sse=16008980.0, rms=21.956 (2.618%) 010: dt: 0.0500, sse=15268644.0, rms=21.415 (2.463%) positioning took 0.9 minutes mean border=54.3, 88 (55) missing vertices, mean dist 1.6 [0.1 (%0.0)->2.2 (%100.0))] %16 local maxima, %51 large gradients and %28 min vals, 167 gradients ignored tol=1.0e-04, sigma=2.0, host= x220, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=16066352.0, rms=22.002 011: dt: 0.0500, sse=15397316.0, rms=21.515 (2.213%) 012: dt: 0.0500, sse=14792302.0, rms=21.065 (2.092%) 013: dt: 0.0500, sse=14241700.0, rms=20.647 (1.985%) 014: dt: 0.0500, sse=13739441.0, rms=20.258 (1.884%) 015: dt: 0.0500, sse=13279946.0, rms=19.895 (1.790%) 016: dt: 0.0500, sse=12858598.0, rms=19.557 (1.701%) 017: dt: 0.0500, sse=12470569.0, rms=19.240 (1.621%) 018: dt: 0.0500, sse=12111786.0, rms=18.942 (1.549%) 019: dt: 0.0500, sse=11778987.0, rms=18.661 (1.482%) 020: dt: 0.0500, sse=11469778.0, rms=18.396 (1.419%) positioning took 0.9 minutes mean border=54.2, 105 (42) missing vertices, mean dist 1.3 [0.1 (%0.5)->1.9 (%99.5))] %17 local maxima, %51 large gradients and %28 min vals, 148 gradients ignored tol=1.0e-04, sigma=2.0, host= x220, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=11578836.0, rms=18.497 021: dt: 0.0500, sse=11284933.0, rms=18.244 (1.372%) 022: dt: 0.0500, sse=11009361.0, rms=18.002 (1.323%) 023: dt: 0.0500, sse=10748300.0, rms=17.771 (1.287%) 024: dt: 0.0500, sse=10500521.0, rms=17.548 (1.254%) 025: dt: 0.0500, sse=10263501.0, rms=17.332 (1.230%) 026: dt: 0.0500, sse=10035936.0, rms=17.122 (1.211%) 027: dt: 0.0500, sse=9814869.0, rms=16.915 (1.206%) 028: dt: 0.0500, sse=9598865.0, rms=16.711 (1.208%) 029: dt: 0.0500, sse=9386897.0, rms=16.508 (1.214%) 030: dt: 0.0500, sse=9178887.0, rms=16.307 (1.222%) positioning took 0.9 minutes mean border=54.0, 118 (35) missing vertices, mean dist 1.1 [0.1 (%3.5)->1.6 (%96.5))] %17 local maxima, %51 large gradients and %28 min vals, 123 gradients ignored tol=1.0e-04, sigma=2.0, host= x220, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=9277069.0, rms=16.405 031: dt: 0.5000, sse=7714777.0, rms=14.813 (9.700%) 032: dt: 0.5000, sse=6427467.0, rms=13.357 (9.834%) 033: dt: 0.5000, sse=5328316.0, rms=11.977 (10.332%) 034: dt: 0.5000, sse=4377617.5, rms=10.635 (11.204%) 035: dt: 0.5000, sse=3605208.8, rms=9.406 (11.555%) 036: dt: 0.5000, sse=2966012.5, rms=8.248 (12.306%) 037: dt: 0.5000, sse=2486697.5, rms=7.264 (11.938%) 038: dt: 0.5000, sse=2151233.8, rms=6.482 (10.757%) 039: dt: 0.5000, sse=1961434.4, rms=5.999 (7.461%) 040: dt: 0.5000, sse=1841318.6, rms=5.666 (5.545%) 041: dt: 0.5000, sse=1780783.9, rms=5.495 (3.021%) 042: dt: 0.5000, sse=1734270.0, rms=5.354 (2.568%) 043: dt: 0.5000, sse=1714484.5, rms=5.297 (1.060%) 044: dt: 0.5000, sse=1695912.8, rms=5.236 (1.147%) rms = 5.21, time step reduction 1 of 3 to 0.250... 045: dt: 0.5000, sse=1686803.1, rms=5.210 (0.501%) 046: dt: 0.2500, sse=1448799.0, rms=4.360 (16.305%) 047: dt: 0.2500, sse=1379114.1, rms=4.099 (5.989%) rms = 4.12, time step reduction 2 of 3 to 0.125... 048: dt: 0.1250, sse=1353288.6, rms=3.993 (2.601%) 049: dt: 0.1250, sse=1319444.4, rms=3.846 (3.669%) rms = 3.83, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=1315257.6, rms=3.826 (0.516%) positioning took 2.1 minutes mean border=52.3, 1725 (11) missing vertices, mean dist 0.1 [0.2 (%43.4)->0.4 (%56.6))] %34 local maxima, %36 large gradients and %25 min vals, 62 gradients ignored tol=1.0e-04, sigma=1.0, host= x220, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1799817.9, rms=4.748 rms = 4.89, time step reduction 1 of 3 to 0.250... 051: dt: 0.2500, sse=1619508.9, rms=4.081 (14.059%) 052: dt: 0.2500, sse=1510832.8, rms=3.612 (11.494%) 053: dt: 0.2500, sse=1488074.8, rms=3.516 (2.636%) rms = 3.50, time step reduction 2 of 3 to 0.125... 054: dt: 0.2500, sse=1483318.6, rms=3.499 (0.506%) 055: dt: 0.1250, sse=1413592.9, rms=3.148 (10.035%) 056: dt: 0.1250, sse=1399466.6, rms=3.077 (2.258%) rms = 3.06, time step reduction 3 of 3 to 0.062... 057: dt: 0.1250, sse=1395867.1, rms=3.060 (0.548%) positioning took 0.8 minutes mean border=51.0, 1876 (8) missing vertices, mean dist 0.1 [0.1 (%41.8)->0.3 (%58.2))] %53 local maxima, %18 large gradients and %24 min vals, 54 gradients ignored tol=1.0e-04, sigma=0.5, host= x220, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1518795.8, rms=3.666 rms = 4.53, time step reduction 1 of 3 to 0.250... 058: dt: 0.2500, sse=1431964.9, rms=3.258 (11.118%) 059: dt: 0.2500, sse=1416352.5, rms=3.182 (2.343%) rms = 3.19, time step reduction 2 of 3 to 0.125... 060: dt: 0.1250, sse=1404879.6, rms=3.121 (1.904%) 061: dt: 0.1250, sse=1388066.9, rms=3.034 (2.792%) rms = 3.00, time step reduction 3 of 3 to 0.062... 062: dt: 0.1250, sse=1380523.4, rms=2.997 (1.237%) positioning took 0.6 minutes mean border=50.3, 3803 (8) missing vertices, mean dist 0.0 [0.1 (%46.4)->0.2 (%53.6))] %55 local maxima, %15 large gradients and %23 min vals, 54 gradients ignored tol=1.0e-04, sigma=0.2, host= x220, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /dat/mw/tvb-new-dataset/tvb/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1409834.0, rms=3.154 rms = 3.93, time step reduction 1 of 3 to 0.250... 063: dt: 0.2500, sse=1379727.5, rms=2.993 (5.093%) rms = 2.95, time step reduction 2 of 3 to 0.125... 064: dt: 0.2500, sse=1367642.5, rms=2.948 (1.503%) 065: dt: 0.1250, sse=1349555.9, rms=2.842 (3.601%) rms = 2.80, time step reduction 3 of 3 to 0.062... 066: dt: 0.1250, sse=1340907.8, rms=2.799 (1.500%) positioning took 0.5 minutes writing curvature file /dat/mw/tvb-new-dataset/tvb/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /dat/mw/tvb-new-dataset/tvb/surf/rh.area.pial vertex spacing 1.00 +- 0.44 (0.06-->7.18) (max @ vno 115897 --> 115896) face area 0.40 +- 0.31 (0.00-->8.37) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 164634 vertices processed 25000 of 164634 vertices processed 50000 of 164634 vertices processed 75000 of 164634 vertices processed 100000 of 164634 vertices processed 125000 of 164634 vertices processed 150000 of 164634 vertices processed 0 of 164634 vertices processed 25000 of 164634 vertices processed 50000 of 164634 vertices processed 75000 of 164634 vertices processed 100000 of 164634 vertices processed 125000 of 164634 vertices processed 150000 of 164634 vertices processed thickness calculation complete, 264:1428 truncations. 33791 vertices at 0 distance 111979 vertices at 1 distance 105910 vertices at 2 distance 45354 vertices at 3 distance 13737 vertices at 4 distance 3699 vertices at 5 distance 1023 vertices at 6 distance 286 vertices at 7 distance 106 vertices at 8 distance 61 vertices at 9 distance 34 vertices at 10 distance 29 vertices at 11 distance 26 vertices at 12 distance 20 vertices at 13 distance 20 vertices at 14 distance 10 vertices at 15 distance 16 vertices at 16 distance 6 vertices at 17 distance 1 vertices at 18 distance 1 vertices at 19 distance 11 vertices at 20 distance writing curvature file /dat/mw/tvb-new-dataset/tvb/surf/rh.thickness positioning took 8.9 minutes #-------------------------------------------- #@# Surf Volume lh Tue Mar 1 23:58:35 CET 2016 /dat/mw/tvb-new-dataset/tvb/surf /dat/mw/tvb-new-dataset/tvb/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume tvb lh /dat/mw/tvb-new-dataset/tvb/surf/lh.volume masking with /dat/mw/tvb-new-dataset/tvb/label/lh.cortex.label Total face volume 308501 Total vertex volume 304395 (mask=0) #@# tvb lh 304395 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Tue Mar 1 23:58:39 CET 2016 /dat/mw/tvb-new-dataset/tvb/surf /dat/mw/tvb-new-dataset/tvb/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume tvb rh /dat/mw/tvb-new-dataset/tvb/surf/rh.volume masking with /dat/mw/tvb-new-dataset/tvb/label/rh.cortex.label Total face volume 311379 Total vertex volume 308328 (mask=0) #@# tvb rh 308328 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Tue Mar 1 23:58:42 CET 2016 /dat/mw/tvb-new-dataset/tvb/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 tvb SUBJECTS_DIR is /dat/mw/tvb-new-dataset 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 = 195 writing volume /dat/mw/tvb-new-dataset/tvb/mri/ribbon.mgz writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Wed Mar 2 00:18:49 CET 2016 /dat/mw/tvb-new-dataset/tvb/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 tvb lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /dat/mw/tvb-new-dataset/tvb/mri/wm.mgz... reading input surface /dat/mw/tvb-new-dataset/tvb/surf/lh.white... reading input pial surface /dat/mw/tvb-new-dataset/tvb/surf/lh.pial... reading input white surface /dat/mw/tvb-new-dataset/tvb/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 308501 Total vertex volume 304395 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1823453 mm^3 (det: 1.068361 ) lhCtxGM: 303030.989 302612.000 diff= 419.0 pctdiff= 0.138 rhCtxGM: 305976.827 305122.000 diff= 854.8 pctdiff= 0.279 lhCtxWM: 269979.696 270555.000 diff= -575.3 pctdiff=-0.213 rhCtxWM: 269303.513 269672.000 diff= -368.5 pctdiff=-0.137 SubCortGMVol 67172.000 SupraTentVol 1231211.025 (1227363.000) diff=3848.025 pctdiff=0.313 SupraTentVolNotVent 1219067.025 (1215219.000) diff=3848.025 pctdiff=0.316 BrainSegVol 1396386.000 (1393816.000) diff=2570.000 pctdiff=0.184 BrainSegVolNotVent 1380733.000 (1380906.025) diff=-173.025 pctdiff=-0.013 BrainSegVolNotVent 1380733.000 CerebellumVol 165357.000 VentChorVol 12144.000 3rd4th5thCSF 3509.000 CSFVol 943.000, OptChiasmVol 153.000 MaskVol 1827450.000 1607 1135 2776 2.592 0.340 0.092 0.014 7 1.0 bankssts 1494 1029 3095 2.809 0.585 0.137 0.023 29 1.3 caudalanteriorcingulate 4545 3025 8509 2.612 0.439 0.114 0.022 47 4.0 caudalmiddlefrontal 3061 1817 4575 2.192 0.473 0.134 0.038 52 4.3 cuneus 685 475 2047 3.261 0.846 0.130 0.047 8 1.3 entorhinal 5462 3644 12097 2.774 0.575 0.133 0.031 86 6.9 fusiform 9027 5993 18626 2.733 0.493 0.125 0.026 131 9.4 inferiorparietal 6682 4442 14836 2.718 0.642 0.116 0.025 102 6.4 inferiortemporal 2033 1321 3964 2.738 0.851 0.135 0.035 34 2.6 isthmuscingulate 8859 5707 15816 2.440 0.512 0.131 0.029 126 10.1 lateraloccipital 4849 3179 9769 2.741 0.617 0.125 0.033 69 6.3 lateralorbitofrontal 5925 3690 9760 2.379 0.607 0.130 0.039 85 9.1 lingual 3375 2137 6647 2.591 0.676 0.116 0.035 55 4.5 medialorbitofrontal 5642 3837 13854 2.951 0.668 0.119 0.027 87 6.3 middletemporal 924 661 2550 3.302 0.697 0.112 0.024 10 0.9 parahippocampal 2481 1402 3901 2.573 0.539 0.102 0.044 74 4.9 paracentral 2822 1891 5957 2.726 0.410 0.113 0.022 30 2.5 parsopercularis 981 680 2501 2.819 0.470 0.157 0.038 21 1.4 parsorbitalis 2348 1542 4814 2.617 0.492 0.122 0.027 31 2.4 parstriangularis 2796 1768 3364 2.025 0.443 0.118 0.034 28 3.6 pericalcarine 7904 5079 13115 2.304 0.549 0.111 0.023 82 7.3 postcentral 2494 1634 4807 2.655 0.723 0.133 0.033 40 3.2 posteriorcingulate 10311 6293 19280 2.730 0.504 0.107 0.028 96 11.3 precentral 6683 4513 12775 2.565 0.496 0.124 0.026 90 6.5 precuneus 1657 1061 3573 3.122 0.729 0.119 0.036 24 2.8 rostralanteriorcingulate 10178 6808 19358 2.461 0.431 0.136 0.031 174 12.2 rostralmiddlefrontal 13264 8909 28325 2.809 0.509 0.120 0.026 152 13.9 superiorfrontal 9675 6358 17361 2.441 0.417 0.122 0.024 133 9.2 superiorparietal 5211 3536 12596 3.043 0.610 0.113 0.024 66 4.9 superiortemporal 5488 3641 10889 2.732 0.475 0.129 0.027 88 5.6 supramarginal 306 210 988 3.045 0.493 0.178 0.039 8 0.7 frontalpole 712 470 2643 3.807 0.651 0.129 0.043 11 1.2 temporalpole 698 398 1249 2.773 0.481 0.117 0.046 10 1.4 transversetemporal 3848 2497 7980 3.074 0.746 0.121 0.043 52 6.7 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 tvb lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /dat/mw/tvb-new-dataset/tvb/mri/wm.mgz... reading input surface /dat/mw/tvb-new-dataset/tvb/surf/lh.pial... reading input pial surface /dat/mw/tvb-new-dataset/tvb/surf/lh.pial... reading input white surface /dat/mw/tvb-new-dataset/tvb/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 308501 Total vertex volume 304395 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1823453 mm^3 (det: 1.068361 ) lhCtxGM: 303030.989 302612.000 diff= 419.0 pctdiff= 0.138 rhCtxGM: 305976.827 305122.000 diff= 854.8 pctdiff= 0.279 lhCtxWM: 269979.696 270555.000 diff= -575.3 pctdiff=-0.213 rhCtxWM: 269303.513 269672.000 diff= -368.5 pctdiff=-0.137 SubCortGMVol 67172.000 SupraTentVol 1231211.025 (1227363.000) diff=3848.025 pctdiff=0.313 SupraTentVolNotVent 1219067.025 (1215219.000) diff=3848.025 pctdiff=0.316 BrainSegVol 1396386.000 (1393816.000) diff=2570.000 pctdiff=0.184 BrainSegVolNotVent 1380733.000 (1380906.025) diff=-173.025 pctdiff=-0.013 BrainSegVolNotVent 1380733.000 CerebellumVol 165357.000 VentChorVol 12144.000 3rd4th5thCSF 3509.000 CSFVol 943.000, OptChiasmVol 153.000 MaskVol 1827450.000 1607 999 2776 2.592 0.340 0.117 0.030 28 2.1 bankssts 1494 1164 3095 2.809 0.585 0.164 0.038 47 2.4 caudalanteriorcingulate 4545 3420 8509 2.612 0.439 0.132 0.028 74 5.3 caudalmiddlefrontal 3061 2352 4575 2.192 0.473 0.143 0.034 42 4.8 cuneus 685 744 2047 3.261 0.846 0.205 0.049 13 1.7 entorhinal 5462 4886 12097 2.774 0.575 0.168 0.040 101 10.0 fusiform 9027 7467 18626 2.733 0.493 0.142 0.033 117 13.1 inferiorparietal 6682 6162 14836 2.718 0.642 0.154 0.034 82 10.1 inferiortemporal 2033 1626 3964 2.738 0.851 0.165 0.048 46 4.3 isthmuscingulate 8859 7034 15816 2.440 0.512 0.147 0.034 151 13.5 lateraloccipital 4849 3787 9769 2.741 0.617 0.148 0.037 74 8.2 lateralorbitofrontal 5925 4670 9760 2.379 0.607 0.151 0.040 96 10.7 lingual 3375 2857 6647 2.591 0.676 0.151 0.039 51 5.7 medialorbitofrontal 5642 5253 13854 2.951 0.668 0.158 0.036 86 9.2 middletemporal 924 930 2550 3.302 0.697 0.177 0.039 12 1.7 parahippocampal 2481 1625 3901 2.573 0.539 0.123 0.677 885 3.3 paracentral 2822 2407 5957 2.726 0.410 0.147 0.031 39 3.8 parsopercularis 981 1027 2501 2.819 0.470 0.185 0.042 12 1.9 parsorbitalis 2348 2059 4814 2.617 0.492 0.165 0.035 41 3.6 parstriangularis 2796 1526 3364 2.025 0.443 0.109 0.029 36 3.3 pericalcarine 7904 6190 13115 2.304 0.549 0.130 0.026 95 9.1 postcentral 2494 1938 4807 2.655 0.723 0.163 0.044 85 4.7 posteriorcingulate 10311 7466 19280 2.730 0.504 0.115 0.035 120 11.7 precentral 6683 5288 12775 2.565 0.496 0.142 0.032 125 8.9 precuneus 1657 1294 3573 3.122 0.729 0.167 0.053 40 4.0 rostralanteriorcingulate 10178 8676 19358 2.461 0.431 0.160 0.034 157 15.0 rostralmiddlefrontal 13264 10737 28325 2.809 0.509 0.138 0.031 189 17.2 superiorfrontal 9675 7601 17361 2.441 0.417 0.140 0.029 148 11.8 superiorparietal 5211 4572 12596 3.043 0.610 0.147 0.034 68 7.7 superiortemporal 5488 4281 10889 2.732 0.475 0.144 0.033 96 8.0 supramarginal 306 433 988 3.045 0.493 0.233 0.040 4 0.5 frontalpole 712 917 2643 3.807 0.651 0.203 0.036 9 1.3 temporalpole 698 491 1249 2.773 0.481 0.113 0.031 7 0.9 transversetemporal 3848 2507 7980 3.074 0.746 0.153 0.054 112 10.0 insula #----------------------------------------- #@# Parcellation Stats rh Wed Mar 2 00:20:03 CET 2016 /dat/mw/tvb-new-dataset/tvb/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 tvb rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /dat/mw/tvb-new-dataset/tvb/mri/wm.mgz... reading input surface /dat/mw/tvb-new-dataset/tvb/surf/rh.white... reading input pial surface /dat/mw/tvb-new-dataset/tvb/surf/rh.pial... reading input white surface /dat/mw/tvb-new-dataset/tvb/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 311379 Total vertex volume 308328 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1823453 mm^3 (det: 1.068361 ) lhCtxGM: 303030.989 302612.000 diff= 419.0 pctdiff= 0.138 rhCtxGM: 305976.827 305122.000 diff= 854.8 pctdiff= 0.279 lhCtxWM: 269979.696 270555.000 diff= -575.3 pctdiff=-0.213 rhCtxWM: 269303.513 269672.000 diff= -368.5 pctdiff=-0.137 SubCortGMVol 67172.000 SupraTentVol 1231211.025 (1227363.000) diff=3848.025 pctdiff=0.313 SupraTentVolNotVent 1219067.025 (1215219.000) diff=3848.025 pctdiff=0.316 BrainSegVol 1396386.000 (1393816.000) diff=2570.000 pctdiff=0.184 BrainSegVolNotVent 1380733.000 (1380906.025) diff=-173.025 pctdiff=-0.013 BrainSegVolNotVent 1380733.000 CerebellumVol 165357.000 VentChorVol 12144.000 3rd4th5thCSF 3509.000 CSFVol 943.000, OptChiasmVol 153.000 MaskVol 1827450.000 1606 1141 2975 2.722 0.346 0.097 0.016 11 1.1 bankssts 1295 919 2693 2.875 0.529 0.123 0.020 19 1.0 caudalanteriorcingulate 4826 3232 9598 2.650 0.398 0.119 0.022 56 4.3 caudalmiddlefrontal 3101 1929 4963 2.286 0.457 0.148 0.040 52 4.6 cuneus 908 638 3244 3.471 0.776 0.145 0.052 22 1.8 entorhinal 4809 3250 10468 2.783 0.610 0.127 0.028 72 5.2 fusiform 10873 7315 22498 2.771 0.487 0.126 0.025 164 10.8 inferiorparietal 5677 3710 12685 2.824 0.653 0.120 0.031 97 7.0 inferiortemporal 2205 1396 4669 2.748 0.901 0.134 0.039 40 3.1 isthmuscingulate 9478 5784 17124 2.531 0.568 0.129 0.033 143 12.1 lateraloccipital 4700 3077 8945 2.631 0.689 0.128 0.033 69 6.3 lateralorbitofrontal 5579 3540 8717 2.222 0.659 0.137 0.046 88 10.2 lingual 3087 2096 6253 2.579 0.524 0.126 0.032 56 4.0 medialorbitofrontal 5723 4008 15364 3.036 0.660 0.129 0.027 113 6.3 middletemporal 1194 814 3036 3.222 0.769 0.105 0.025 9 1.1 parahippocampal 2526 1395 3965 2.619 0.508 0.099 0.032 25 3.6 paracentral 2285 1487 4483 2.746 0.371 0.111 0.023 27 1.9 parsopercularis 1368 886 3107 2.756 0.492 0.137 0.031 29 1.6 parsorbitalis 2275 1543 4526 2.573 0.443 0.125 0.024 32 2.2 parstriangularis 3342 1964 3823 2.077 0.506 0.125 0.036 41 5.0 pericalcarine 8286 5058 13307 2.356 0.499 0.103 0.021 90 6.7 postcentral 2167 1402 3983 2.524 0.781 0.135 0.033 35 2.7 posteriorcingulate 10460 6214 18419 2.775 0.453 0.101 0.028 126 12.9 precentral 8130 5408 15210 2.609 0.472 0.123 0.027 101 8.5 precuneus 1458 984 3675 3.074 0.610 0.121 0.035 20 1.9 rostralanteriorcingulate 9776 6485 17999 2.422 0.420 0.131 0.030 149 11.7 rostralmiddlefrontal 13264 8929 27933 2.709 0.500 0.120 0.026 157 13.3 superiorfrontal 10351 6731 18108 2.434 0.423 0.119 0.023 129 9.2 superiorparietal 5152 3487 12028 3.011 0.543 0.104 0.020 51 4.2 superiortemporal 4848 3174 10652 2.975 0.493 0.115 0.024 62 4.5 supramarginal 414 296 971 2.771 0.460 0.180 0.055 10 1.0 frontalpole 620 429 2856 3.986 0.678 0.136 0.047 11 1.4 temporalpole 388 240 709 2.638 0.532 0.123 0.058 6 1.0 transversetemporal 4344 2759 9343 3.124 1.046 0.116 0.037 61 6.1 insula mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab tvb rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /dat/mw/tvb-new-dataset/tvb/mri/wm.mgz... reading input surface /dat/mw/tvb-new-dataset/tvb/surf/rh.pial... reading input pial surface /dat/mw/tvb-new-dataset/tvb/surf/rh.pial... reading input white surface /dat/mw/tvb-new-dataset/tvb/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 311379 Total vertex volume 308328 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1823453 mm^3 (det: 1.068361 ) lhCtxGM: 303030.989 302612.000 diff= 419.0 pctdiff= 0.138 rhCtxGM: 305976.827 305122.000 diff= 854.8 pctdiff= 0.279 lhCtxWM: 269979.696 270555.000 diff= -575.3 pctdiff=-0.213 rhCtxWM: 269303.513 269672.000 diff= -368.5 pctdiff=-0.137 SubCortGMVol 67172.000 SupraTentVol 1231211.025 (1227363.000) diff=3848.025 pctdiff=0.313 SupraTentVolNotVent 1219067.025 (1215219.000) diff=3848.025 pctdiff=0.316 BrainSegVol 1396386.000 (1393816.000) diff=2570.000 pctdiff=0.184 BrainSegVolNotVent 1380733.000 (1380906.025) diff=-173.025 pctdiff=-0.013 BrainSegVolNotVent 1380733.000 CerebellumVol 165357.000 VentChorVol 12144.000 3rd4th5thCSF 3509.000 CSFVol 943.000, OptChiasmVol 153.000 MaskVol 1827450.000 1606 1059 2975 2.722 0.346 0.132 0.034 28 2.5 bankssts 1295 1058 2693 2.875 0.529 0.150 0.030 48 1.6 caudalanteriorcingulate 4826 3868 9598 2.650 0.398 0.132 0.025 66 5.2 caudalmiddlefrontal 3101 2504 4963 2.286 0.457 0.153 0.040 55 5.2 cuneus 908 1086 3244 3.471 0.776 0.208 0.048 18 1.9 entorhinal 4809 4071 10468 2.783 0.610 0.158 0.039 99 8.7 fusiform 10873 8636 22498 2.771 0.487 0.143 0.032 160 15.1 inferiorparietal 5677 5075 12685 2.824 0.653 0.158 0.037 83 10.1 inferiortemporal 2205 1890 4669 2.748 0.901 0.170 0.045 65 4.3 isthmuscingulate 9478 7460 17124 2.531 0.568 0.141 0.032 140 13.9 lateraloccipital 4700 3648 8945 2.631 0.689 0.150 0.037 77 7.7 lateralorbitofrontal 5579 4371 8717 2.222 0.659 0.152 0.040 100 10.3 lingual 3087 2636 6253 2.579 0.524 0.157 0.036 45 5.0 medialorbitofrontal 5723 5843 15364 3.036 0.660 0.164 0.033 74 8.5 middletemporal 1194 1043 3036 3.222 0.769 0.159 0.043 22 2.3 parahippocampal 2526 1579 3965 2.619 0.508 0.107 0.025 35 2.5 paracentral 2285 1732 4483 2.746 0.371 0.133 0.025 29 2.5 parsopercularis 1368 1342 3107 2.756 0.492 0.174 0.031 22 2.0 parsorbitalis 2275 1944 4526 2.573 0.443 0.153 0.029 29 3.1 parstriangularis 3342 1770 3823 2.077 0.506 0.107 0.029 51 4.2 pericalcarine 8286 6156 13307 2.356 0.499 0.118 0.024 77 8.4 postcentral 2167 1643 3983 2.524 0.781 0.169 0.043 85 4.1 posteriorcingulate 10460 7027 18419 2.775 0.453 0.105 0.026 124 10.9 precentral 8130 6157 15210 2.609 0.472 0.136 0.032 130 11.1 precuneus 1458 1402 3675 3.074 0.610 0.168 0.052 30 4.0 rostralanteriorcingulate 9776 8080 17999 2.422 0.420 0.154 0.031 145 13.5 rostralmiddlefrontal 13264 11103 27933 2.709 0.500 0.141 0.027 185 15.7 superiorfrontal 10351 7990 18108 2.434 0.423 0.134 0.026 144 11.3 superiorparietal 5152 4467 12028 3.011 0.543 0.141 0.030 59 6.9 superiortemporal 4848 3840 10652 2.975 0.493 0.137 0.033 74 7.0 supramarginal 414 383 971 2.771 0.460 0.184 0.056 8 1.0 frontalpole 620 946 2856 3.986 0.678 0.239 0.046 8 1.5 temporalpole 388 279 709 2.638 0.532 0.124 0.038 3 0.6 transversetemporal 4344 2980 9343 3.124 1.046 0.157 0.051 94 9.4 insula #----------------------------------------- #@# Cortical Parc 2 lh Wed Mar 2 00:21:18 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 tvb lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.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 1.778 2016/02/03 18:58:39 fischl Exp $ reading atlas from /opt/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 70 labels changed using aseg relabeling using gibbs priors... 000: 11990 changed, 162585 examined... 001: 3201 changed, 46231 examined... 002: 1035 changed, 16242 examined... 003: 455 changed, 5584 examined... 004: 238 changed, 2542 examined... 005: 155 changed, 1333 examined... 006: 94 changed, 861 examined... 007: 52 changed, 526 examined... 008: 35 changed, 280 examined... 009: 27 changed, 209 examined... 010: 13 changed, 143 examined... 011: 10 changed, 65 examined... 012: 3 changed, 54 examined... 013: 4 changed, 21 examined... 014: 3 changed, 22 examined... 015: 3 changed, 14 examined... 016: 2 changed, 16 examined... 017: 1 changed, 10 examined... 018: 1 changed, 6 examined... 019: 1 changed, 6 examined... 020: 1 changed, 8 examined... 021: 2 changed, 9 examined... 022: 2 changed, 8 examined... 023: 1 changed, 13 examined... 024: 0 changed, 7 examined... 1 labels changed using aseg 000: 643 total segments, 550 labels (5433 vertices) changed 001: 149 total segments, 57 labels (258 vertices) changed 002: 94 total segments, 2 labels (3 vertices) changed 003: 92 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 71 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1408 vertices marked for relabeling... 1408 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 19 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Wed Mar 2 00:21:37 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 tvb rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.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 1.778 2016/02/03 18:58:39 fischl Exp $ reading atlas from /opt/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 68 labels changed using aseg relabeling using gibbs priors... 000: 12312 changed, 164634 examined... 001: 3195 changed, 47165 examined... 002: 1129 changed, 16414 examined... 003: 510 changed, 6126 examined... 004: 264 changed, 2779 examined... 005: 150 changed, 1441 examined... 006: 96 changed, 823 examined... 007: 56 changed, 541 examined... 008: 25 changed, 288 examined... 009: 21 changed, 154 examined... 010: 13 changed, 110 examined... 011: 5 changed, 69 examined... 012: 1 changed, 32 examined... 013: 1 changed, 7 examined... 014: 1 changed, 7 examined... 015: 1 changed, 7 examined... 016: 0 changed, 5 examined... 30 labels changed using aseg 000: 718 total segments, 621 labels (6962 vertices) changed 001: 153 total segments, 59 labels (292 vertices) changed 002: 94 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 79 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 2061 vertices marked for relabeling... 2061 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 19 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Wed Mar 2 00:21:56 CET 2016 /dat/mw/tvb-new-dataset/tvb/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 tvb lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /dat/mw/tvb-new-dataset/tvb/mri/wm.mgz... reading input surface /dat/mw/tvb-new-dataset/tvb/surf/lh.white... reading input pial surface /dat/mw/tvb-new-dataset/tvb/surf/lh.pial... reading input white surface /dat/mw/tvb-new-dataset/tvb/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 308501 Total vertex volume 304395 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1823453 mm^3 (det: 1.068361 ) lhCtxGM: 303030.989 302612.000 diff= 419.0 pctdiff= 0.138 rhCtxGM: 305976.827 305122.000 diff= 854.8 pctdiff= 0.279 lhCtxWM: 269979.696 270555.000 diff= -575.3 pctdiff=-0.213 rhCtxWM: 269303.513 269672.000 diff= -368.5 pctdiff=-0.137 SubCortGMVol 67172.000 SupraTentVol 1231211.025 (1227363.000) diff=3848.025 pctdiff=0.313 SupraTentVolNotVent 1219067.025 (1215219.000) diff=3848.025 pctdiff=0.316 BrainSegVol 1396386.000 (1393816.000) diff=2570.000 pctdiff=0.184 BrainSegVolNotVent 1380733.000 (1380906.025) diff=-173.025 pctdiff=-0.013 BrainSegVolNotVent 1380733.000 CerebellumVol 165357.000 VentChorVol 12144.000 3rd4th5thCSF 3509.000 CSFVol 943.000, OptChiasmVol 153.000 MaskVol 1827450.000 1364 945 3222 2.654 0.531 0.146 0.037 26 2.1 G_and_S_frontomargin 2111 1364 4151 2.554 0.565 0.134 0.028 32 2.5 G_and_S_occipital_inf 1699 928 2712 2.379 0.411 0.106 0.041 50 3.0 G_and_S_paracentral 1506 967 3336 2.820 0.605 0.127 0.028 21 1.6 G_and_S_subcentral 919 631 2008 2.495 0.463 0.152 0.033 19 1.3 G_and_S_transv_frontopol 3246 2152 6979 3.006 0.489 0.119 0.025 43 3.3 G_and_S_cingul-Ant 1869 1277 3524 2.809 0.446 0.117 0.025 27 1.9 G_and_S_cingul-Mid-Ant 1693 1137 3097 2.774 0.441 0.115 0.026 15 1.6 G_and_S_cingul-Mid-Post 836 533 2373 3.286 0.651 0.161 0.041 19 1.4 G_cingul-Post-dorsal 544 349 1182 2.783 0.879 0.122 0.036 7 0.7 G_cingul-Post-ventral 3377 1975 5212 2.177 0.535 0.138 0.041 63 5.2 G_cuneus 1701 1117 4384 2.898 0.364 0.127 0.027 28 1.9 G_front_inf-Opercular 476 325 1284 2.798 0.415 0.140 0.031 10 0.5 G_front_inf-Orbital 1352 886 3185 2.720 0.503 0.135 0.033 23 1.7 G_front_inf-Triangul 5950 3920 13013 2.611 0.469 0.133 0.030 109 6.9 G_front_middle 10231 6669 23734 2.861 0.545 0.127 0.033 163 14.1 G_front_sup 592 390 1870 3.788 0.780 0.128 0.054 12 1.3 G_Ins_lg_and_S_cent_ins 1000 632 2773 3.267 0.664 0.136 0.054 20 2.1 G_insular_short 3707 2388 7916 2.730 0.522 0.139 0.032 72 4.5 G_occipital_middle 1448 945 3117 2.600 0.477 0.134 0.026 21 1.4 G_occipital_sup 1973 1294 5069 2.921 0.525 0.147 0.039 44 2.9 G_oc-temp_lat-fusifor 4150 2441 7099 2.338 0.657 0.140 0.047 74 7.5 G_oc-temp_med-Lingual 1313 900 3724 3.187 0.862 0.127 0.046 18 2.6 G_oc-temp_med-Parahip 3017 1985 7056 2.807 0.665 0.140 0.039 60 4.7 G_orbital 2870 1924 6682 2.779 0.530 0.136 0.030 49 3.5 G_pariet_inf-Angular 3625 2405 8353 2.865 0.511 0.138 0.031 72 4.3 G_pariet_inf-Supramar 3659 2401 7043 2.459 0.406 0.122 0.026 61 3.5 G_parietal_sup 3284 2089 6158 2.405 0.485 0.118 0.024 44 3.0 G_postcentral 4613 2687 10313 2.912 0.469 0.112 0.031 53 5.3 G_precentral 3704 2489 8331 2.621 0.527 0.139 0.032 69 4.3 G_precuneus 1072 649 2380 2.573 0.540 0.121 0.049 25 2.0 G_rectus 453 280 769 2.535 0.970 0.089 0.034 4 0.5 G_subcallosal 561 311 1066 2.715 0.486 0.109 0.049 9 1.2 G_temp_sup-G_T_transv 2092 1407 6098 3.079 0.626 0.134 0.031 41 2.5 G_temp_sup-Lateral 793 591 2102 3.373 0.750 0.094 0.021 4 0.6 G_temp_sup-Plan_polar 673 463 1389 2.809 0.340 0.107 0.021 5 0.6 G_temp_sup-Plan_tempo 3991 2647 10760 2.937 0.697 0.134 0.032 87 5.2 G_temporal_inf 4217 2858 11347 3.018 0.693 0.126 0.031 76 5.1 G_temporal_middle 439 283 608 2.360 0.395 0.094 0.016 2 0.3 Lat_Fis-ant-Horizont 217 150 295 2.437 0.321 0.082 0.011 1 0.1 Lat_Fis-ant-Vertical 918 605 1253 2.681 0.346 0.102 0.019 5 0.7 Lat_Fis-post 2797 1767 4858 2.310 0.553 0.132 0.031 39 3.6 Pole_occipital 2026 1365 6361 3.336 0.729 0.136 0.040 36 3.5 Pole_temporal 3418 2307 4544 2.218 0.550 0.111 0.025 27 3.3 S_calcarine 3764 2442 4492 2.135 0.514 0.099 0.025 20 4.0 S_central 1243 830 1979 2.474 0.403 0.095 0.017 7 0.7 S_cingul-Marginalis 621 398 917 2.777 0.434 0.098 0.022 3 0.5 S_circular_insula_ant 1405 918 2307 3.074 0.552 0.079 0.021 7 1.2 S_circular_insula_inf 1522 1009 2117 2.650 0.386 0.110 0.023 9 1.3 S_circular_insula_sup 795 550 1412 2.433 0.589 0.090 0.012 4 0.4 S_collat_transv_ant 659 420 1078 2.436 0.447 0.132 0.031 8 0.9 S_collat_transv_post 3454 2351 5727 2.471 0.332 0.121 0.024 34 3.3 S_front_inf 1241 837 1840 2.293 0.374 0.126 0.027 16 1.3 S_front_middle 2890 1956 4306 2.415 0.386 0.110 0.020 21 2.4 S_front_sup 601 402 1132 2.656 0.331 0.119 0.026 9 0.6 S_interm_prim-Jensen 3482 2351 5329 2.406 0.349 0.114 0.021 32 3.2 S_intrapariet_and_P_trans 1120 737 1628 2.286 0.303 0.120 0.027 12 1.0 S_oc_middle_and_Lunatus 1487 970 2113 2.397 0.335 0.100 0.017 10 0.9 S_oc_sup_and_transversal 910 604 1369 2.472 0.476 0.110 0.018 7 0.7 S_occipital_ant 1259 848 2031 2.497 0.444 0.110 0.018 11 0.9 S_oc-temp_lat 2301 1585 4082 2.731 0.497 0.113 0.023 19 2.0 S_oc-temp_med_and_Lingual 412 282 693 2.259 0.412 0.112 0.019 5 0.3 S_orbital_lateral 946 638 1301 2.420 0.498 0.091 0.015 5 0.5 S_orbital_med-olfact 1722 1128 3208 2.641 0.596 0.123 0.030 20 2.1 S_orbital-H_Shaped 2491 1658 3955 2.504 0.410 0.112 0.021 21 2.1 S_parieto_occipital 1584 991 2068 2.243 1.018 0.143 0.040 34 2.7 S_pericallosal 3416 2223 4739 2.283 0.379 0.106 0.019 30 2.7 S_postcentral 2006 1285 3095 2.743 0.364 0.099 0.019 13 1.4 S_precentral-inf-part 1813 1210 2919 2.531 0.366 0.103 0.020 14 1.4 S_precentral-sup-part 836 542 1466 2.675 0.748 0.121 0.033 11 1.1 S_suborbital 1179 783 1926 2.555 0.393 0.120 0.031 16 1.2 S_subparietal 1397 931 1994 2.426 0.349 0.093 0.014 9 0.9 S_temporal_inf 5714 3901 9971 2.675 0.443 0.105 0.019 48 4.4 S_temporal_sup 261 180 472 3.033 0.498 0.147 0.022 3 0.3 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Wed Mar 2 00:22:35 CET 2016 /dat/mw/tvb-new-dataset/tvb/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 tvb rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /dat/mw/tvb-new-dataset/tvb/mri/wm.mgz... reading input surface /dat/mw/tvb-new-dataset/tvb/surf/rh.white... reading input pial surface /dat/mw/tvb-new-dataset/tvb/surf/rh.pial... reading input white surface /dat/mw/tvb-new-dataset/tvb/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 311379 Total vertex volume 308328 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1823453 mm^3 (det: 1.068361 ) lhCtxGM: 303030.989 302612.000 diff= 419.0 pctdiff= 0.138 rhCtxGM: 305976.827 305122.000 diff= 854.8 pctdiff= 0.279 lhCtxWM: 269979.696 270555.000 diff= -575.3 pctdiff=-0.213 rhCtxWM: 269303.513 269672.000 diff= -368.5 pctdiff=-0.137 SubCortGMVol 67172.000 SupraTentVol 1231211.025 (1227363.000) diff=3848.025 pctdiff=0.313 SupraTentVolNotVent 1219067.025 (1215219.000) diff=3848.025 pctdiff=0.316 BrainSegVol 1396386.000 (1393816.000) diff=2570.000 pctdiff=0.184 BrainSegVolNotVent 1380733.000 (1380906.025) diff=-173.025 pctdiff=-0.013 BrainSegVolNotVent 1380733.000 CerebellumVol 165357.000 VentChorVol 12144.000 3rd4th5thCSF 3509.000 CSFVol 943.000, OptChiasmVol 153.000 MaskVol 1827450.000 1716 1157 3689 2.574 0.515 0.154 0.040 38 2.9 G_and_S_frontomargin 1379 878 2104 2.354 0.637 0.129 0.039 20 2.0 G_and_S_occipital_inf 1893 872 2712 2.549 0.445 0.096 0.037 25 3.1 G_and_S_paracentral 1627 1097 3440 2.787 0.359 0.120 0.022 20 1.4 G_and_S_subcentral 1820 1194 3519 2.475 0.404 0.140 0.035 35 2.6 G_and_S_transv_frontopol 3658 2502 7782 2.796 0.572 0.124 0.029 49 4.2 G_and_S_cingul-Ant 1527 1090 3584 2.810 0.430 0.110 0.020 16 1.0 G_and_S_cingul-Mid-Ant 1630 1087 3303 2.752 0.444 0.112 0.024 16 1.5 G_and_S_cingul-Mid-Post 839 540 2315 3.160 0.744 0.166 0.055 19 1.7 G_cingul-Post-dorsal 512 311 1425 3.215 0.727 0.126 0.039 8 0.6 G_cingul-Post-ventral 2729 1647 4563 2.267 0.478 0.139 0.038 45 3.7 G_cuneus 1385 912 3329 2.843 0.358 0.125 0.027 25 1.4 G_front_inf-Opercular 600 384 1467 2.856 0.392 0.123 0.028 10 0.6 G_front_inf-Orbital 1600 1066 3730 2.683 0.430 0.140 0.031 32 1.9 G_front_inf-Triangul 5673 3772 12858 2.639 0.434 0.141 0.033 107 7.3 G_front_middle 8282 5478 18661 2.781 0.509 0.123 0.027 103 8.8 G_front_sup 734 494 2206 3.726 0.952 0.113 0.039 10 1.0 G_Ins_lg_and_S_cent_ins 760 504 2504 3.532 0.601 0.139 0.042 15 1.2 G_insular_short 3728 2400 8457 2.782 0.546 0.136 0.031 77 4.3 G_occipital_middle 2467 1531 4694 2.507 0.520 0.126 0.028 36 2.5 G_occipital_sup 3037 1930 7616 2.913 0.669 0.133 0.035 59 3.8 G_oc-temp_lat-fusifor 2333 1460 4023 2.225 0.795 0.145 0.050 44 4.6 G_oc-temp_med-Lingual 2027 1338 6135 3.438 0.832 0.122 0.044 33 3.5 G_oc-temp_med-Parahip 2942 1853 6817 2.770 0.759 0.141 0.042 66 5.1 G_orbital 4758 3142 11297 2.896 0.500 0.128 0.027 85 5.1 G_pariet_inf-Angular 2463 1616 6313 3.092 0.489 0.129 0.026 45 2.6 G_pariet_inf-Supramar 3274 2158 7071 2.531 0.457 0.129 0.026 54 3.4 G_parietal_sup 3573 2054 6239 2.403 0.472 0.103 0.023 46 3.0 G_postcentral 4289 2230 8223 2.951 0.429 0.095 0.031 67 5.4 G_precentral 4441 2959 9567 2.617 0.516 0.131 0.029 70 5.2 G_precuneus 954 652 2340 2.703 0.506 0.142 0.041 26 1.7 G_rectus 711 393 979 2.061 1.367 0.104 0.059 19 1.4 G_subcallosal 333 194 668 2.658 0.602 0.123 0.066 6 0.9 G_temp_sup-G_T_transv 1741 1121 4813 3.110 0.559 0.125 0.028 32 2.0 G_temp_sup-Lateral 923 674 2553 3.121 0.712 0.103 0.021 6 0.8 G_temp_sup-Plan_polar 745 521 1530 2.861 0.449 0.083 0.013 3 0.3 G_temp_sup-Plan_tempo 3365 2188 8588 2.917 0.723 0.133 0.038 76 5.2 G_temporal_inf 3932 2720 11897 3.141 0.677 0.135 0.030 82 4.8 G_temporal_middle 270 195 367 2.349 0.311 0.095 0.013 1 0.1 Lat_Fis-ant-Horizont 204 137 364 2.924 0.404 0.104 0.026 1 0.2 Lat_Fis-ant-Vertical 1335 889 2231 2.928 0.414 0.092 0.017 6 0.9 Lat_Fis-post 5999 3434 8740 2.246 0.588 0.142 0.047 99 11.3 Pole_occipital 1812 1272 6308 3.306 0.893 0.141 0.039 33 3.0 Pole_temporal 3174 2034 4339 2.409 0.654 0.117 0.027 30 3.6 S_calcarine 3475 2213 4239 2.248 0.530 0.099 0.028 28 5.1 S_central 1135 758 1646 2.355 0.398 0.097 0.017 7 0.7 S_cingul-Marginalis 581 384 791 2.651 0.350 0.103 0.019 3 0.4 S_circular_insula_ant 1128 753 1969 3.167 0.777 0.082 0.014 4 0.6 S_circular_insula_inf 1639 1066 2514 2.786 0.400 0.107 0.023 10 1.5 S_circular_insula_sup 954 663 1504 2.601 0.296 0.089 0.012 4 0.5 S_collat_transv_ant 478 322 752 2.548 0.412 0.136 0.036 5 0.8 S_collat_transv_post 2897 1902 4283 2.390 0.366 0.106 0.019 20 2.1 S_front_inf 1187 791 1822 2.307 0.390 0.126 0.026 13 1.1 S_front_middle 3381 2316 5491 2.416 0.381 0.105 0.019 25 2.8 S_front_sup 200 125 399 2.910 0.248 0.132 0.025 4 0.2 S_interm_prim-Jensen 3176 2123 4520 2.399 0.341 0.112 0.019 27 2.5 S_intrapariet_and_P_trans 1362 905 1929 2.296 0.307 0.115 0.022 13 1.1 S_oc_middle_and_Lunatus 2092 1371 2967 2.337 0.411 0.105 0.018 16 1.5 S_oc_sup_and_transversal 1147 753 1905 2.508 0.445 0.111 0.018 29 0.8 S_occipital_ant 1092 726 2036 2.800 0.530 0.126 0.027 16 1.3 S_oc-temp_lat 1638 1165 2763 2.547 0.496 0.104 0.015 9 1.1 S_oc-temp_med_and_Lingual 310 211 335 2.091 0.317 0.128 0.019 3 0.3 S_orbital_lateral 1049 710 1431 2.321 0.738 0.093 0.014 5 0.6 S_orbital_med-olfact 1686 1144 2998 2.588 0.521 0.124 0.026 17 1.8 S_orbital-H_Shaped 3075 2012 4701 2.588 0.396 0.111 0.023 28 2.7 S_parieto_occipital 1816 1174 2181 2.149 0.843 0.134 0.028 33 1.9 S_pericallosal 3082 2001 4420 2.422 0.402 0.103 0.020 25 2.5 S_postcentral 1992 1314 3062 2.718 0.382 0.098 0.016 11 1.3 S_precentral-inf-part 2316 1548 3726 2.537 0.325 0.100 0.018 18 1.6 S_precentral-sup-part 759 509 1578 2.616 0.476 0.134 0.030 15 0.9 S_suborbital 1764 1192 3133 2.552 0.434 0.134 0.034 25 2.4 S_subparietal 1257 851 1980 2.649 0.431 0.117 0.021 11 1.1 S_temporal_inf 6391 4448 11380 2.770 0.397 0.109 0.019 53 5.1 S_temporal_sup 262 188 513 2.944 0.394 0.085 0.011 1 0.1 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Wed Mar 2 00:23:13 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 tvb lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.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 1.778 2016/02/03 18:58:39 fischl Exp $ reading atlas from /opt/freesurfer/average/lh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.007 0 singular and 293 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1264 labels changed using aseg relabeling using gibbs priors... 000: 3164 changed, 162585 examined... 001: 762 changed, 13370 examined... 002: 200 changed, 4126 examined... 003: 73 changed, 1196 examined... 004: 41 changed, 456 examined... 005: 19 changed, 243 examined... 006: 9 changed, 116 examined... 007: 5 changed, 51 examined... 008: 4 changed, 31 examined... 009: 2 changed, 25 examined... 010: 0 changed, 14 examined... 91 labels changed using aseg 000: 81 total segments, 48 labels (657 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 7 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1047 vertices marked for relabeling... 1047 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 13 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Wed Mar 2 00:23:27 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 tvb rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.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 1.778 2016/02/03 18:58:39 fischl Exp $ reading atlas from /opt/freesurfer/average/rh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.008 0 singular and 237 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1326 labels changed using aseg relabeling using gibbs priors... 000: 3121 changed, 164634 examined... 001: 783 changed, 13268 examined... 002: 229 changed, 4239 examined... 003: 83 changed, 1316 examined... 004: 35 changed, 480 examined... 005: 20 changed, 204 examined... 006: 12 changed, 120 examined... 007: 8 changed, 59 examined... 008: 6 changed, 43 examined... 009: 2 changed, 33 examined... 010: 1 changed, 12 examined... 011: 0 changed, 7 examined... 166 labels changed using aseg 000: 68 total segments, 35 labels (141 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 16 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1534 vertices marked for relabeling... 1534 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 13 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Wed Mar 2 00:23:40 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab tvb lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /dat/mw/tvb-new-dataset/tvb/mri/wm.mgz... reading input surface /dat/mw/tvb-new-dataset/tvb/surf/lh.white... reading input pial surface /dat/mw/tvb-new-dataset/tvb/surf/lh.pial... reading input white surface /dat/mw/tvb-new-dataset/tvb/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 308501 Total vertex volume 304395 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1823453 mm^3 (det: 1.068361 ) lhCtxGM: 303030.989 302612.000 diff= 419.0 pctdiff= 0.138 rhCtxGM: 305976.827 305122.000 diff= 854.8 pctdiff= 0.279 lhCtxWM: 269979.696 270555.000 diff= -575.3 pctdiff=-0.213 rhCtxWM: 269303.513 269672.000 diff= -368.5 pctdiff=-0.137 SubCortGMVol 67172.000 SupraTentVol 1231211.025 (1227363.000) diff=3848.025 pctdiff=0.313 SupraTentVolNotVent 1219067.025 (1215219.000) diff=3848.025 pctdiff=0.316 BrainSegVol 1396386.000 (1393816.000) diff=2570.000 pctdiff=0.184 BrainSegVolNotVent 1380733.000 (1380906.025) diff=-173.025 pctdiff=-0.013 BrainSegVolNotVent 1380733.000 CerebellumVol 165357.000 VentChorVol 12144.000 3rd4th5thCSF 3509.000 CSFVol 943.000, OptChiasmVol 153.000 MaskVol 1827450.000 2113 1442 4008 2.788 0.517 0.123 0.022 33 1.7 caudalanteriorcingulate 4748 3150 9069 2.628 0.446 0.113 0.022 49 4.2 caudalmiddlefrontal 4066 2488 6356 2.257 0.462 0.130 0.033 65 5.0 cuneus 645 449 1883 3.210 0.845 0.121 0.040 6 1.1 entorhinal 4953 3295 10663 2.737 0.571 0.130 0.029 74 5.7 fusiform 8559 5672 17577 2.731 0.493 0.125 0.027 120 9.1 inferiorparietal 6803 4527 15534 2.759 0.638 0.121 0.027 111 7.6 inferiortemporal 2065 1347 4027 2.724 0.859 0.134 0.035 35 2.6 isthmuscingulate 9057 5824 16259 2.440 0.517 0.132 0.029 129 10.3 lateraloccipital 5135 3391 10742 2.734 0.643 0.129 0.036 80 7.4 lateralorbitofrontal 5847 3638 9653 2.384 0.606 0.130 0.039 84 8.9 lingual 2590 1647 4897 2.506 0.642 0.110 0.033 37 3.2 medialorbitofrontal 7538 5140 17420 2.881 0.635 0.114 0.024 106 7.6 middletemporal 930 667 2560 3.307 0.698 0.113 0.024 10 0.9 parahippocampal 2980 1705 4918 2.616 0.534 0.101 0.040 78 5.3 paracentral 2433 1627 5096 2.728 0.428 0.109 0.021 24 2.1 parsopercularis 1049 714 2158 2.579 0.423 0.127 0.026 15 1.1 parsorbitalis 3050 2013 6045 2.601 0.473 0.124 0.026 41 3.1 parstriangularis 2859 1811 3473 2.026 0.446 0.119 0.035 30 3.7 pericalcarine 8701 5616 14455 2.318 0.539 0.112 0.023 90 8.1 postcentral 2623 1719 4948 2.674 0.705 0.132 0.033 40 3.3 posteriorcingulate 10119 6169 18765 2.730 0.501 0.107 0.028 95 11.1 precentral 6453 4339 12557 2.577 0.505 0.128 0.027 90 6.5 precuneus 2266 1444 4704 3.037 0.758 0.120 0.036 36 3.6 rostralanteriorcingulate 7130 4749 13771 2.503 0.443 0.141 0.033 124 9.2 rostralmiddlefrontal 15045 10118 32595 2.747 0.528 0.126 0.028 202 16.8 superiorfrontal 7693 5078 13694 2.428 0.412 0.120 0.024 106 7.3 superiorparietal 7241 4936 17569 3.039 0.664 0.115 0.026 92 7.3 superiortemporal 5396 3577 10605 2.730 0.474 0.129 0.028 85 5.5 supramarginal 700 395 1250 2.788 0.481 0.117 0.046 10 1.4 transversetemporal 3240 2098 7143 3.170 0.710 0.117 0.040 44 5.2 insula #----------------------------------------- #@# Parcellation Stats 3 rh Wed Mar 2 00:24:18 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab tvb rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /dat/mw/tvb-new-dataset/tvb/mri/wm.mgz... reading input surface /dat/mw/tvb-new-dataset/tvb/surf/rh.white... reading input pial surface /dat/mw/tvb-new-dataset/tvb/surf/rh.pial... reading input white surface /dat/mw/tvb-new-dataset/tvb/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 311379 Total vertex volume 308328 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1823453 mm^3 (det: 1.068361 ) lhCtxGM: 303030.989 302612.000 diff= 419.0 pctdiff= 0.138 rhCtxGM: 305976.827 305122.000 diff= 854.8 pctdiff= 0.279 lhCtxWM: 269979.696 270555.000 diff= -575.3 pctdiff=-0.213 rhCtxWM: 269303.513 269672.000 diff= -368.5 pctdiff=-0.137 SubCortGMVol 67172.000 SupraTentVol 1231211.025 (1227363.000) diff=3848.025 pctdiff=0.313 SupraTentVolNotVent 1219067.025 (1215219.000) diff=3848.025 pctdiff=0.316 BrainSegVol 1396386.000 (1393816.000) diff=2570.000 pctdiff=0.184 BrainSegVolNotVent 1380733.000 (1380906.025) diff=-173.025 pctdiff=-0.013 BrainSegVolNotVent 1380733.000 CerebellumVol 165357.000 VentChorVol 12144.000 3rd4th5thCSF 3509.000 CSFVol 943.000, OptChiasmVol 153.000 MaskVol 1827450.000 1352 956 2925 2.898 0.525 0.126 0.022 21 1.1 caudalanteriorcingulate 5001 3333 9975 2.658 0.392 0.119 0.023 60 4.5 caudalmiddlefrontal 3737 2360 5938 2.284 0.435 0.141 0.036 56 5.0 cuneus 974 687 3512 3.527 0.754 0.144 0.052 24 2.0 entorhinal 4207 2809 8994 2.786 0.603 0.126 0.027 64 4.5 fusiform 10342 6932 21387 2.778 0.489 0.128 0.026 161 10.5 inferiorparietal 6231 4117 14002 2.809 0.656 0.121 0.031 105 7.7 inferiortemporal 2230 1412 4693 2.744 0.896 0.134 0.039 40 3.2 isthmuscingulate 9869 6031 17959 2.536 0.579 0.128 0.032 148 12.4 lateraloccipital 5386 3543 10950 2.665 0.730 0.132 0.035 87 7.8 lateralorbitofrontal 5596 3558 8756 2.222 0.659 0.136 0.045 87 10.1 lingual 2964 1913 5687 2.431 0.830 0.124 0.039 67 4.6 medialorbitofrontal 7063 4937 17829 2.972 0.633 0.125 0.025 125 7.3 middletemporal 1134 773 2885 3.200 0.746 0.104 0.025 9 1.1 parahippocampal 2625 1467 4121 2.608 0.507 0.101 0.031 26 3.6 paracentral 2371 1554 4605 2.740 0.376 0.109 0.023 27 2.0 parsopercularis 1559 1005 3227 2.678 0.459 0.122 0.026 24 1.4 parsorbitalis 2414 1627 4589 2.531 0.442 0.130 0.025 34 2.5 parstriangularis 3375 1975 3863 2.085 0.507 0.126 0.036 42 5.2 pericalcarine 8754 5381 14023 2.346 0.503 0.103 0.021 95 7.1 postcentral 2194 1430 4037 2.527 0.775 0.135 0.033 35 2.7 posteriorcingulate 9942 5859 17487 2.784 0.457 0.101 0.028 121 12.6 precentral 8220 5467 15510 2.602 0.475 0.123 0.028 106 8.6 precuneus 1626 1109 4061 3.097 0.543 0.128 0.032 22 2.0 rostralanteriorcingulate 6279 4151 11480 2.422 0.431 0.130 0.030 96 7.1 rostralmiddlefrontal 16807 11329 34500 2.653 0.490 0.122 0.027 208 17.7 superiorfrontal 8811 5719 15677 2.462 0.414 0.118 0.023 108 7.9 superiorparietal 6892 4704 16752 3.032 0.640 0.107 0.023 71 7.0 superiortemporal 4739 3096 10323 2.983 0.478 0.116 0.024 62 4.4 supramarginal 381 238 696 2.635 0.535 0.124 0.058 6 1.0 transversetemporal 3440 2250 7886 3.344 0.755 0.110 0.030 35 3.7 insula #----------------------------------------- #@# WM/GM Contrast lh Wed Mar 2 00:24:54 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts pctsurfcon --s tvb --lh-only Log file is /dat/mw/tvb-new-dataset/tvb/scripts/pctsurfcon.log Wed Mar 2 00:24:55 CET 2016 setenv SUBJECTS_DIR /dat/mw/tvb-new-dataset cd /dat/mw/tvb-new-dataset/tvb/scripts /opt/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux x220 4.3.3-300.fc23.x86_64 #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer mri_vol2surf --mov /dat/mw/tvb-new-dataset/tvb/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /dat/mw/tvb-new-dataset/tvb/surf/tmp.pctsurfcon.18289/lh.wm.mgh --regheader tvb --cortex srcvol = /dat/mw/tvb-new-dataset/tvb/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 /dat/mw/tvb-new-dataset/tvb/mri/orig.mgz as target reference. -------- original matrix ----------- 0.00000 1.00000 0.00000 0.00000; 1.00000 0.00000 0.00000 -0.00001; 0.00000 0.00000 -1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /dat/mw/tvb-new-dataset/tvb/label/lh.cortex.label Reading surface /dat/mw/tvb-new-dataset/tvb/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 = 88110 Masking with /dat/mw/tvb-new-dataset/tvb/label/lh.cortex.label Writing to /dat/mw/tvb-new-dataset/tvb/surf/tmp.pctsurfcon.18289/lh.wm.mgh Dim: 162585 1 1 mri_vol2surf --mov /dat/mw/tvb-new-dataset/tvb/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /dat/mw/tvb-new-dataset/tvb/surf/tmp.pctsurfcon.18289/lh.gm.mgh --projfrac 0.3 --regheader tvb --cortex srcvol = /dat/mw/tvb-new-dataset/tvb/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 /dat/mw/tvb-new-dataset/tvb/mri/orig.mgz as target reference. -------- original matrix ----------- 0.00000 1.00000 0.00000 0.00000; 1.00000 0.00000 0.00000 -0.00001; 0.00000 0.00000 -1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /dat/mw/tvb-new-dataset/tvb/label/lh.cortex.label Reading surface /dat/mw/tvb-new-dataset/tvb/surf/lh.white Done reading source surface Reading thickness /dat/mw/tvb-new-dataset/tvb/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 = 108428 Masking with /dat/mw/tvb-new-dataset/tvb/label/lh.cortex.label Writing to /dat/mw/tvb-new-dataset/tvb/surf/tmp.pctsurfcon.18289/lh.gm.mgh Dim: 162585 1 1 mri_concat /dat/mw/tvb-new-dataset/tvb/surf/tmp.pctsurfcon.18289/lh.wm.mgh /dat/mw/tvb-new-dataset/tvb/surf/tmp.pctsurfcon.18289/lh.gm.mgh --paired-diff-norm --mul 100 --o /dat/mw/tvb-new-dataset/tvb/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 /dat/mw/tvb-new-dataset/tvb/surf/lh.w-g.pct.mgh mri_segstats --in /dat/mw/tvb-new-dataset/tvb/surf/lh.w-g.pct.mgh --annot tvb lh aparc --sum /dat/mw/tvb-new-dataset/tvb/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ cwd cmdline mri_segstats --in /dat/mw/tvb-new-dataset/tvb/surf/lh.w-g.pct.mgh --annot tvb lh aparc --sum /dat/mw/tvb-new-dataset/tvb/stats/lh.w-g.pct.stats --snr sysname Linux hostname x220 machine x86_64 user mw UseRobust 0 Constructing seg from annotation Reading annotation /dat/mw/tvb-new-dataset/tvb/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /dat/mw/tvb-new-dataset/tvb/surf/lh.w-g.pct.mgh Vertex Area is 0.654187 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up #----------------------------------------- #@# WM/GM Contrast rh Wed Mar 2 00:25:01 CET 2016 /dat/mw/tvb-new-dataset/tvb/scripts pctsurfcon --s tvb --rh-only Log file is /dat/mw/tvb-new-dataset/tvb/scripts/pctsurfcon.log Wed Mar 2 00:25:01 CET 2016 setenv SUBJECTS_DIR /dat/mw/tvb-new-dataset cd /dat/mw/tvb-new-dataset/tvb/scripts /opt/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux x220 4.3.3-300.fc23.x86_64 #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer mri_vol2surf --mov /dat/mw/tvb-new-dataset/tvb/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /dat/mw/tvb-new-dataset/tvb/surf/tmp.pctsurfcon.18347/rh.wm.mgh --regheader tvb --cortex srcvol = /dat/mw/tvb-new-dataset/tvb/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 /dat/mw/tvb-new-dataset/tvb/mri/orig.mgz as target reference. -------- original matrix ----------- 0.00000 1.00000 0.00000 0.00000; 1.00000 0.00000 0.00000 -0.00001; 0.00000 0.00000 -1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /dat/mw/tvb-new-dataset/tvb/label/rh.cortex.label Reading surface /dat/mw/tvb-new-dataset/tvb/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 = 88554 Masking with /dat/mw/tvb-new-dataset/tvb/label/rh.cortex.label Writing to /dat/mw/tvb-new-dataset/tvb/surf/tmp.pctsurfcon.18347/rh.wm.mgh Dim: 164634 1 1 mri_vol2surf --mov /dat/mw/tvb-new-dataset/tvb/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /dat/mw/tvb-new-dataset/tvb/surf/tmp.pctsurfcon.18347/rh.gm.mgh --projfrac 0.3 --regheader tvb --cortex srcvol = /dat/mw/tvb-new-dataset/tvb/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 /dat/mw/tvb-new-dataset/tvb/mri/orig.mgz as target reference. -------- original matrix ----------- 0.00000 1.00000 0.00000 0.00000; 1.00000 0.00000 0.00000 -0.00001; 0.00000 0.00000 -1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /dat/mw/tvb-new-dataset/tvb/label/rh.cortex.label Reading surface /dat/mw/tvb-new-dataset/tvb/surf/rh.white Done reading source surface Reading thickness /dat/mw/tvb-new-dataset/tvb/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 = 109196 Masking with /dat/mw/tvb-new-dataset/tvb/label/rh.cortex.label Writing to /dat/mw/tvb-new-dataset/tvb/surf/tmp.pctsurfcon.18347/rh.gm.mgh Dim: 164634 1 1 mri_concat /dat/mw/tvb-new-dataset/tvb/surf/tmp.pctsurfcon.18347/rh.wm.mgh /dat/mw/tvb-new-dataset/tvb/surf/tmp.pctsurfcon.18347/rh.gm.mgh --paired-diff-norm --mul 100 --o /dat/mw/tvb-new-dataset/tvb/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 /dat/mw/tvb-new-dataset/tvb/surf/rh.w-g.pct.mgh mri_segstats --in /dat/mw/tvb-new-dataset/tvb/surf/rh.w-g.pct.mgh --annot tvb rh aparc --sum /dat/mw/tvb-new-dataset/tvb/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ cwd cmdline mri_segstats --in /dat/mw/tvb-new-dataset/tvb/surf/rh.w-g.pct.mgh --annot tvb rh aparc --sum /dat/mw/tvb-new-dataset/tvb/stats/rh.w-g.pct.stats --snr sysname Linux hostname x220 machine x86_64 user mw UseRobust 0 Constructing seg from annotation Reading annotation /dat/mw/tvb-new-dataset/tvb/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /dat/mw/tvb-new-dataset/tvb/surf/rh.w-g.pct.mgh Vertex Area is 0.650251 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 Wed Mar 2 00:25:06 CET 2016 /dat/mw/tvb-new-dataset/tvb/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 175 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 359 voxels changed to hypointensity... 544 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg Wed Mar 2 00:25:28 CET 2016 /dat/mw/tvb-new-dataset/tvb mri_aparc2aseg --s tvb --volmask --aseg aseg.presurf.hypos SUBJECTS_DIR /dat/mw/tvb-new-dataset subject tvb outvol /dat/mw/tvb-new-dataset/tvb/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /dat/mw/tvb-new-dataset/tvb/surf/lh.white Reading lh pial surface /dat/mw/tvb-new-dataset/tvb/surf/lh.pial Loading lh annotations from /dat/mw/tvb-new-dataset/tvb/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /dat/mw/tvb-new-dataset/tvb/surf/rh.white Reading rh pial surface /dat/mw/tvb-new-dataset/tvb/surf/rh.pial Loading rh annotations from /dat/mw/tvb-new-dataset/tvb/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /dat/mw/tvb-new-dataset/tvb/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 /dat/mw/tvb-new-dataset/tvb/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 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 = 607609 Used brute-force search on 0 voxels Writing output aseg to /dat/mw/tvb-new-dataset/tvb/mri/aparc+aseg.mgz mri_aparc2aseg --s tvb --volmask --aseg aseg.presurf.hypos --a2009s SUBJECTS_DIR /dat/mw/tvb-new-dataset subject tvb outvol /dat/mw/tvb-new-dataset/tvb/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /dat/mw/tvb-new-dataset/tvb/surf/lh.white Reading lh pial surface /dat/mw/tvb-new-dataset/tvb/surf/lh.pial Loading lh annotations from /dat/mw/tvb-new-dataset/tvb/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Reading rh white surface /dat/mw/tvb-new-dataset/tvb/surf/rh.white Reading rh pial surface /dat/mw/tvb-new-dataset/tvb/surf/rh.pial Loading rh annotations from /dat/mw/tvb-new-dataset/tvb/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /dat/mw/tvb-new-dataset/tvb/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 /dat/mw/tvb-new-dataset/tvb/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 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 = 607609 Used brute-force search on 0 voxels Writing output aseg to /dat/mw/tvb-new-dataset/tvb/mri/aparc.a2009s+aseg.mgz mri_aparc2aseg --s tvb --volmask --aseg aseg.presurf.hypos --DKTatlas40 ERROR: Option --DKTatlas40 unknown Linux x220 4.3.3-300.fc23.x86_64 #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s tvb exited with ERRORS at Wed Mar 2 00:29:15 CET 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Wed Mar 2 14:10:52 CET 2016 /dat/mw/tvb-new-dataset/tvb /opt/freesurfer/bin/recon-all -s tvb -all subjid tvb setenv SUBJECTS_DIR /dat/mw/tvb-new-dataset FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /dat/opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20160229 Linux x220 4.3.3-300.fc23.x86_64 #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 15271 maxlocks unlimited maxsignal 15271 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 3931204 1536168 187468 231368 2207568 2068620 Swap: 3932156 685524 3246632 ######################################## program versions used $Id: recon-all,v 1.568 2016/02/25 18:47:17 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: tkregister2.c,v 1.130 2016/01/15 22:47:45 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_normalize.c,v 1.88 2015/12/23 17:30:35 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_watershed.cpp,v 1.102 2016/01/20 23:42:15 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_em_register.c,v 1.105 2016/02/11 00:50:55 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_ca_normalize.c,v 1.67 2016/01/29 18:22:07 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_ca_register.c,v 1.95 2016/01/20 23:42:15 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_ca_label.c,v 1.110 2016/01/20 23:42:14 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_fix_topology.c,v 1.50 2016/01/20 23:42:15 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:52-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:53-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:53-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_make_surfaces.c,v 1.163 2016/02/26 15:09:17 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:53-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:53-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:53-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_anatomical_stats.c,v 1.78 2015/07/06 21:58:51 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:53-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:53-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:53-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_calc.c,v 1.54 2015/12/14 23:18:58 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:53-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.53 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:53-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_robust_template.cpp,v 1.53 2016/01/20 23:36:17 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:53-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:53-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:53-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:53-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:10:53-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-02-11.gca GCASkull RB_all_withskull_2014-08-21.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /opt/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Wed Mar 2 14:10:53 CET 2016 Found 1 runs /dat/mw/tvb-new-dataset/tvb/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 /dat/mw/tvb-new-dataset/tvb/mri/orig/001.mgz /dat/mw/tvb-new-dataset/tvb/mri/rawavg.mgz /dat/mw/tvb-new-dataset/tvb mri_convert /dat/mw/tvb-new-dataset/tvb/mri/rawavg.mgz /dat/mw/tvb-new-dataset/tvb/mri/orig.mgz --conform mri_convert.bin /dat/mw/tvb-new-dataset/tvb/mri/rawavg.mgz /dat/mw/tvb-new-dataset/tvb/mri/orig.mgz --conform New invocation of recon-all Wed Mar 2 14:13:05 CET 2016 /dat/mw/tvb-new-dataset/tvb /opt/freesurfer/bin/recon-all -s tvb -aparc2aseg subjid tvb setenv SUBJECTS_DIR /dat/mw/tvb-new-dataset FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /dat/opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20160229 Linux x220 4.3.3-300.fc23.x86_64 #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 15271 maxlocks unlimited maxsignal 15271 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 3931204 1536284 85584 235372 2309336 2064576 Swap: 3932156 686748 3245408 ######################################## program versions used $Id: recon-all,v 1.568 2016/02/25 18:47:17 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: tkregister2.c,v 1.130 2016/01/15 22:47:45 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_normalize.c,v 1.88 2015/12/23 17:30:35 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_watershed.cpp,v 1.102 2016/01/20 23:42:15 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_em_register.c,v 1.105 2016/02/11 00:50:55 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_ca_normalize.c,v 1.67 2016/01/29 18:22:07 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_ca_register.c,v 1.95 2016/01/20 23:42:15 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_ca_label.c,v 1.110 2016/01/20 23:42:14 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_fix_topology.c,v 1.50 2016/01/20 23:42:15 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_make_surfaces.c,v 1.163 2016/02/26 15:09:17 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_anatomical_stats.c,v 1.78 2015/07/06 21:58:51 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_calc.c,v 1.54 2015/12/14 23:18:58 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.53 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_robust_template.cpp,v 1.53 2016/01/20 23:36:17 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:05-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-02-11.gca GCASkull RB_all_withskull_2014-08-21.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /opt/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### New invocation of recon-all Wed Mar 2 14:13:23 CET 2016 /dat/mw/tvb-new-dataset/tvb /opt/freesurfer/bin/recon-all -s tvb -aparc2aseg subjid tvb setenv SUBJECTS_DIR /dat/mw/tvb-new-dataset FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /dat/opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20160229 Linux x220 4.3.3-300.fc23.x86_64 #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 15271 maxlocks unlimited maxsignal 15271 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 3931204 1604652 49632 224204 2276920 2007572 Swap: 3932156 688996 3243160 ######################################## program versions used $Id: recon-all,v 1.568 2016/02/25 18:47:17 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: tkregister2.c,v 1.130 2016/01/15 22:47:45 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_normalize.c,v 1.88 2015/12/23 17:30:35 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_watershed.cpp,v 1.102 2016/01/20 23:42:15 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_em_register.c,v 1.105 2016/02/11 00:50:55 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_ca_normalize.c,v 1.67 2016/01/29 18:22:07 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_ca_register.c,v 1.95 2016/01/20 23:42:15 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_ca_label.c,v 1.110 2016/01/20 23:42:14 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_fix_topology.c,v 1.50 2016/01/20 23:42:15 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_make_surfaces.c,v 1.163 2016/02/26 15:09:17 fischl Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_anatomical_stats.c,v 1.78 2015/07/06 21:58:51 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mris_calc.c,v 1.54 2015/12/14 23:18:58 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.53 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_robust_template.cpp,v 1.53 2016/01/20 23:36:17 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/02-13:13:23-GMT BuildTimeStamp: Feb 29 2016 14:04:55 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: mw Machine: x220 Platform: Linux PlatformVersion: 4.3.3-300.fc23.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-02-11.gca GCASkull RB_all_withskull_2014-08-21.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /opt/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #----------------------------------------- #@# AParc-to-ASeg Wed Mar 2 14:13:23 CET 2016 /dat/mw/tvb-new-dataset/tvb mri_aparc2aseg --s tvb --volmask --aseg aseg.presurf.hypos SUBJECTS_DIR /dat/mw/tvb-new-dataset subject tvb outvol /dat/mw/tvb-new-dataset/tvb/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /dat/mw/tvb-new-dataset/tvb/surf/lh.white Reading lh pial surface /dat/mw/tvb-new-dataset/tvb/surf/lh.pial Loading lh annotations from /dat/mw/tvb-new-dataset/tvb/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /dat/mw/tvb-new-dataset/tvb/surf/rh.white Reading rh pial surface /dat/mw/tvb-new-dataset/tvb/surf/rh.pial Loading rh annotations from /dat/mw/tvb-new-dataset/tvb/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /dat/mw/tvb-new-dataset/tvb/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 /dat/mw/tvb-new-dataset/tvb/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 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 = 607609 Used brute-force search on 0 voxels Writing output aseg to /dat/mw/tvb-new-dataset/tvb/mri/aparc+aseg.mgz mri_aparc2aseg --s tvb --volmask --aseg aseg.presurf.hypos --a2009s SUBJECTS_DIR /dat/mw/tvb-new-dataset subject tvb outvol /dat/mw/tvb-new-dataset/tvb/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /dat/mw/tvb-new-dataset/tvb/surf/lh.white Reading lh pial surface /dat/mw/tvb-new-dataset/tvb/surf/lh.pial Loading lh annotations from /dat/mw/tvb-new-dataset/tvb/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Reading rh white surface /dat/mw/tvb-new-dataset/tvb/surf/rh.white Reading rh pial surface /dat/mw/tvb-new-dataset/tvb/surf/rh.pial Loading rh annotations from /dat/mw/tvb-new-dataset/tvb/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /dat/mw/tvb-new-dataset/tvb/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 /dat/mw/tvb-new-dataset/tvb/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 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 = 607609 Used brute-force search on 0 voxels Writing output aseg to /dat/mw/tvb-new-dataset/tvb/mri/aparc.a2009s+aseg.mgz mri_aparc2aseg --s tvb --volmask --aseg aseg.presurf.hypos --DKTatlas40 ERROR: Option --DKTatlas40 unknown Linux x220 4.3.3-300.fc23.x86_64 #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s tvb exited with ERRORS at Wed Mar 2 14:17:25 CET 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting