Thu Oct 6 17:16:01 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945 /usr/local/freesurfer/bin/recon-all -i Sleep_MEG_16945/02-MPRAGE/Sleep_MEG_16945-0001.dcm -s 16945 -all subjid 16945 setenv SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux jmlina2 4.4.0-38-generic #57~14.04.1-Ubuntu SMP Tue Sep 6 17:20:43 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 128212 maxlocks unlimited maxsignal 128212 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 32846740 31020056 1826684 270368 8461196 18518824 -/+ buffers/cache: 4040036 28806704 Swap: 63999996 1588 63998408 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:01-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:01-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:01-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:01-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:02-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:02-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:02-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:02-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:02-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:02-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:02-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:02-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:02-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:02-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:02-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:02-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:02-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:03-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:03-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:03-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:03-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:03-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:03-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:03-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:03-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:03-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:03-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:03-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:03-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:04-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:04-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:04-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:04-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:04-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:04-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:04-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:04-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/06-21:16:04-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: jsboucher Machine: jmlina2 Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945 mri_convert /media/jsboucher/C6C84AD8C84AC701/Users/sujets/Sleep_MEG_16945/02-MPRAGE/Sleep_MEG_16945-0001.dcm /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/orig/001.mgz mri_convert /media/jsboucher/C6C84AD8C84AC701/Users/sujets/Sleep_MEG_16945/02-MPRAGE/Sleep_MEG_16945-0001.dcm /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/jsboucher/C6C84AD8C84AC701/Users/sujets/Sleep_MEG_16945/02-MPRAGE/Sleep_MEG_16945-0001.dcm... Getting Series No INFO: Found 178 files in /media/jsboucher/C6C84AD8C84AC701/Users/sujets/Sleep_MEG_16945/02-MPRAGE INFO: Scanning for Series Number 2 Scanning Directory INFO: found 176 files in series INFO: loading series header info. RunNo = 1 INFO: sorting. INFO: (240 256 176), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /media/jsboucher/C6C84AD8C84AC701/Users/sujets/Sleep_MEG_16945/02-MPRAGE/Sleep_MEG_16945-0001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Sleep_MEG_16945 Date and time StudyDate 20141215 StudyTime 140221.546000 SeriesTime 141543.500000 AcqTime 140626.320000 Acquisition parameters PulseSeq *tfl3d1_ns Protocol MPRAGE PhEncDir ROW EchoNo 1 FlipAngle 9 EchoTime 2.91 InversionTime 900 RepetitionTime 2300 PhEncFOV 240 ReadoutFOV 256 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 256 NImageCols 240 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 86.7244 143.0871 131.8291 VolRes 1.0000 1.0000 1.0000 VolDim 240 256 176 Vc -0.0000 -1.0000 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs -1.0000 -0.0000 0.0000 VolCenter -1.2756 23.0871 3.8291 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=2300.00, TE=2.91, TI=900.00, flip angle=9.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) writing to /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Oct 6 17:16:19 EDT 2016 Found 1 runs /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/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 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/orig/001.mgz /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/rawavg.mgz /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945 mri_convert /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/rawavg.mgz /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/orig.mgz --conform mri_convert /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/rawavg.mgz /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/rawavg.mgz... TR=2300.00, TE=2.91, TI=900.00, flip angle=9.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) Original Data has (1, 1, 1) mm size and (240, 256, 176) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/orig.mgz... mri_add_xform_to_header -c /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/transforms/talairach.xfm /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/orig.mgz /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Oct 6 17:16:27 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Oct 6 17:17:45 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.8208, pval=0.8469 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/transforms/talairach_avi.log tal_QC_AZS /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/transforms/talairach_avi.log TalAviQA: 0.98114 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Thu Oct 6 17:17:45 EDT 2016 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux jmlina2 4.4.0-38-generic #57~14.04.1-Ubuntu SMP Tue Sep 6 17:20:43 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Thu Oct 6 17:17:45 EDT 2016 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.16520 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16520/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16520/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=2300.00, TE=2.91, TI=900.00, flip angle=9.00 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.16520/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Oct 6 17:17:48 EDT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.16520/nu0.mnc ./tmp.mri_nu_correct.mni.16520/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.16520/0/ defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [jsboucher@jmlina2:/media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/] [2016-10-06 17:17:48] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.16520/0/ ./tmp.mri_nu_correct.mni.16520/nu0.mnc ./tmp.mri_nu_correct.mni.16520/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 34 CV of field change: 0.000988488 [jsboucher@jmlina2:/media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/] [2016-10-06 17:18:13] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.16520/nu0.mnc ./tmp.mri_nu_correct.mni.16520/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Thu Oct 6 17:18:17 EDT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.16520/nu1.mnc ./tmp.mri_nu_correct.mni.16520/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.16520/1/ defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [jsboucher@jmlina2:/media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/] [2016-10-06 17:18:17] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.16520/1/ ./tmp.mri_nu_correct.mni.16520/nu1.mnc ./tmp.mri_nu_correct.mni.16520/nu2.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 35 CV of field change: 0.000979291 [jsboucher@jmlina2:/media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/] [2016-10-06 17:18:43] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.16520/nu1.mnc ./tmp.mri_nu_correct.mni.16520/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.16520/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.16520/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.16520/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.16520/ones.mgz sysname Linux hostname jmlina2 machine x86_64 user jsboucher input ./tmp.mri_nu_correct.mni.16520/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.16520/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.16520/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.16520/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16520/input.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.16520/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.16520/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16520/input.mean.dat sysname Linux hostname jmlina2 machine x86_64 user jsboucher UseRobust 0 Loading ./tmp.mri_nu_correct.mni.16520/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.16520/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.16520/ones.mgz --i ./tmp.mri_nu_correct.mni.16520/nu2.mnc --sum ./tmp.mri_nu_correct.mni.16520/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16520/output.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.16520/ones.mgz --i ./tmp.mri_nu_correct.mni.16520/nu2.mnc --sum ./tmp.mri_nu_correct.mni.16520/sum.junk --avgwf ./tmp.mri_nu_correct.mni.16520/output.mean.dat sysname Linux hostname jmlina2 machine x86_64 user jsboucher UseRobust 0 Loading ./tmp.mri_nu_correct.mni.16520/ones.mgz Loading ./tmp.mri_nu_correct.mni.16520/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.16520/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.16520/nu2.mnc ./tmp.mri_nu_correct.mni.16520/nu2.mnc mul 1.02391762324241019288 Saving result to './tmp.mri_nu_correct.mni.16520/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.16520/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.16520/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.16520/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 6 seconds. mapping (10, 126) to ( 3, 110) Thu Oct 6 17:19:15 EDT 2016 mri_nu_correct.mni done mri_add_xform_to_header -c /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Oct 6 17:19:16 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.115 -0.069 -0.045 1.819; 0.050 1.033 0.182 -36.556; 0.007 -0.122 1.174 -10.331; 0.000 0.000 0.000 1.000; 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 111 white matter peak found at 106 gm peak at 65 (65), valley at 41 (41) csf peak at 32, setting threshold to 54 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 63 (63), valley at 35 (35) csf peak at 31, setting threshold to 52 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 24 seconds. #-------------------------------------------- #@# Skull Stripping Thu Oct 6 17:20:40 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=10.0 skull bounding box = (56, 40, 24) --> (203, 255, 222) using (105, 112, 123) as brain centroid... mean wm in atlas = 126, using box (87,85,99) --> (123, 138,147) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 107, scaling input intensities by 1.178 scaling channel 0 by 1.17757 initial log_p = -4.7 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.550497 @ (0.000, 0.000, 0.000) max log p = -4.469434 @ (4.545, 4.545, -13.636) max log p = -4.420281 @ (-2.273, -6.818, 2.273) max log p = -4.391153 @ (-1.136, 1.136, 3.409) max log p = -4.391153 @ (0.000, 0.000, 0.000) max log p = -4.390976 @ (-1.420, -0.852, -1.420) Found translation: (-0.3, -2.0, -9.4): log p = -4.391 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.4 (thresh=-4.4) 1.236 0.000 0.000 -30.062; 0.000 1.226 0.161 -40.892; 0.000 -0.139 1.055 1.410; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-3.9) 1.144 0.000 0.000 -18.376; 0.000 1.318 0.173 -53.042; 0.000 -0.139 1.055 1.410; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.144 0.000 0.000 -18.376; 0.000 1.416 0.186 -66.104; 0.000 -0.139 1.055 1.410; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.144 0.000 0.000 -18.376; 0.000 1.416 0.186 -66.104; 0.000 -0.139 1.055 1.410; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.9 (thresh=-3.9) 1.098 -0.009 0.066 -21.135; 0.005 1.344 0.106 -49.002; -0.076 -0.053 1.081 -3.885; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.115 -0.012 0.101 -26.929; 0.002 1.316 0.138 -49.130; -0.113 -0.095 1.053 7.028; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.097 -0.009 0.065 -20.807; 0.002 1.316 0.138 -49.130; -0.077 -0.097 1.075 0.136; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.097 -0.009 0.065 -20.807; 0.002 1.316 0.138 -49.130; -0.077 -0.097 1.075 0.136; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.098 -0.009 0.074 -20.904; 0.002 1.316 0.138 -49.130; -0.087 -0.097 1.077 1.101; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 9 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.100 -0.019 0.064 -19.286; 0.011 1.313 0.147 -51.437; -0.078 -0.108 1.078 0.709; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09980 -0.01932 0.06402 -19.28550; 0.01071 1.31305 0.14739 -51.43712; -0.07774 -0.10820 1.07791 0.70946; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.09980 -0.01932 0.06402 -19.28550; 0.01071 1.31305 0.14739 -51.43712; -0.07774 -0.10820 1.07791 0.70946; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.100 -0.019 0.064 -19.286; 0.011 1.313 0.147 -51.437; -0.078 -0.108 1.078 0.709; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.8 (old=-4.7) transform before final EM align: 1.100 -0.019 0.064 -19.286; 0.011 1.313 0.147 -51.437; -0.078 -0.108 1.078 0.709; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.09980 -0.01932 0.06402 -19.28550; 0.01071 1.31305 0.14739 -51.43712; -0.07774 -0.10820 1.07791 0.70946; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.09980 -0.01932 0.06402 -19.28550; 0.01071 1.31305 0.14739 -51.43712; -0.07774 -0.10820 1.07791 0.70946; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 014: -log(p) = 4.2 tol 0.000000 final transform: 1.100 -0.019 0.064 -19.286; 0.011 1.313 0.147 -51.437; -0.078 -0.108 1.078 0.709; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 26 minutes and 50 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.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=125 y=108 z=124 r=85 first estimation of the main basin volume: 2653590 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=152, y=104, z=87, Imax=255 CSF=17, 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=20376914949 voxels, voxel volume =1.000 = 20376914949 mmm3 = 20376915.968 cm3 done. PostAnalyze...Basin Prior 56 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=126,y=116, z=115, r=10158 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=5, CSF_MAX=38 , nb = 45612 RIGHT_CER CSF_MIN=0, CSF_intensity=5, CSF_MAX=30 , nb = 3186 LEFT_CER CSF_MIN=0, CSF_intensity=5, CSF_MAX=23 , nb = 3204 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=36 , nb = 19836 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=43 , nb = 18684 OTHER CSF_MIN=0, CSF_intensity=7, CSF_MAX=25 , nb = 702 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 38, 36, 35, 61 after analyzing : 26, 36, 36, 42 RIGHT_CER before analyzing : 30, 36, 44, 73 after analyzing : 30, 41, 44, 49 LEFT_CER before analyzing : 23, 30, 39, 62 after analyzing : 23, 36, 39, 42 RIGHT_BRAIN before analyzing : 36, 34, 34, 61 after analyzing : 25, 34, 34, 40 LEFT_BRAIN before analyzing : 43, 38, 35, 60 after analyzing : 28, 38, 38, 43 OTHER before analyzing : 25, 39, 64, 94 after analyzing : 25, 55, 64, 64 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...71 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.011 curvature mean = 67.161, std = 7.784 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.97, sigma = 3.12 after rotation: sse = 1.97, sigma = 3.12 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.01, its var is 2.67 before Erosion-Dilatation 0.06% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...40 iterations mri_strip_skull: done peeling brain Brain Size = 1448181 voxels, voxel volume = 1.000 mm3 = 1448181 mmm3 = 1448.181 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Oct 6 17:47:48 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=25.0 skull bounding box = (64, 58, 37) --> (191, 183, 205) using (106, 100, 121) as brain centroid... mean wm in atlas = 107, using box (90,85,100) --> (121, 115,141) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -4.1 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.006114 @ (-9.091, 9.091, -9.091) max log p = -3.865169 @ (4.545, -4.545, -4.545) max log p = -3.819754 @ (-2.273, 2.273, -2.273) max log p = -3.799466 @ (3.409, -1.136, 1.136) max log p = -3.783011 @ (-0.568, 1.705, -1.705) max log p = -3.783011 @ (0.000, 0.000, 0.000) Found translation: (-4.0, 7.4, -16.5): log p = -3.783 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.8 (thresh=-3.8) 1.150 0.000 0.000 -23.595; 0.000 1.150 0.000 -16.835; 0.000 0.000 1.000 -16.477; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5) 1.150 0.000 0.000 -23.595; 0.000 1.150 0.000 -16.835; 0.000 0.000 1.000 -16.477; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.2, old_max_log_p =-3.5 (thresh=-3.5) 1.105 -0.009 0.062 -20.382; 0.003 1.187 0.102 -30.349; -0.078 -0.117 1.030 7.663; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.105 -0.009 0.062 -20.382; 0.003 1.187 0.102 -30.349; -0.078 -0.117 1.030 7.663; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.1, old_max_log_p =-3.2 (thresh=-3.2) 1.105 -0.009 0.062 -20.851; 0.003 1.187 0.093 -29.377; -0.078 -0.107 1.035 7.039; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.1, old_max_log_p =-3.1 (thresh=-3.1) 1.103 -0.009 0.062 -20.678; 0.003 1.186 0.093 -29.203; -0.078 -0.107 1.035 7.039; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.10321 -0.00944 0.06234 -20.67780; 0.00319 1.18550 0.09309 -29.20281; -0.07824 -0.10729 1.03473 7.03908; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.10321 -0.00944 0.06234 -20.67780; 0.00319 1.18550 0.09309 -29.20281; -0.07824 -0.10729 1.03473 7.03908; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.103 -0.009 0.062 -20.678; 0.003 1.186 0.093 -29.203; -0.078 -0.107 1.035 7.039; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.1 (old=-4.1) transform before final EM align: 1.103 -0.009 0.062 -20.678; 0.003 1.186 0.093 -29.203; -0.078 -0.107 1.035 7.039; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.10321 -0.00944 0.06234 -20.67780; 0.00319 1.18550 0.09309 -29.20281; -0.07824 -0.10729 1.03473 7.03908; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.10321 -0.00944 0.06234 -20.67780; 0.00319 1.18550 0.09309 -29.20281; -0.07824 -0.10729 1.03473 7.03908; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 009: -log(p) = 3.7 after pass:transform: ( 1.10, -0.01, 0.06, -20.68) ( 0.00, 1.19, 0.09, -29.20) ( -0.08, -0.11, 1.03, 7.04) dfp_em_step_func: 010: -log(p) = 3.7 after pass:transform: ( 1.10, -0.01, 0.06, -20.68) ( 0.00, 1.19, 0.09, -29.20) ( -0.08, -0.11, 1.03, 7.04) dfp_em_step_func: 011: -log(p) = 3.7 after pass:transform: ( 1.10, -0.01, 0.06, -20.68) ( 0.00, 1.19, 0.09, -29.20) ( -0.08, -0.11, 1.03, 7.04) dfp_em_step_func: 012: -log(p) = 3.7 after pass:transform: ( 1.10, -0.01, 0.06, -20.68) ( 0.00, 1.19, 0.09, -29.20) ( -0.08, -0.11, 1.03, 7.04) dfp_em_step_func: 013: -log(p) = 3.7 after pass:transform: ( 1.10, -0.01, 0.06, -20.68) ( 0.00, 1.19, 0.09, -29.20) ( -0.08, -0.11, 1.03, 7.04) dfp_em_step_func: 014: -log(p) = 3.7 after pass:transform: ( 1.10, -0.01, 0.06, -20.68) ( 0.00, 1.19, 0.09, -29.20) ( -0.08, -0.11, 1.03, 7.04) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 016: -log(p) = 3.7 tol 0.000000 final transform: 1.104 -0.009 0.063 -20.678; 0.004 1.186 0.094 -29.203; -0.078 -0.107 1.035 7.039; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 13 minutes and 15 seconds. #-------------------------------------- #@# CA Normalize Thu Oct 6 18:01:03 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=25.0 skull bounding box = (64, 58, 37) --> (191, 183, 205) using (106, 100, 121) as brain centroid... mean wm in atlas = 107, using box (90,85,100) --> (121, 115,141) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 using 244171 sample points... INFO: compute sample coordinates transform 1.104 -0.009 0.063 -20.678; 0.004 1.186 0.094 -29.203; -0.078 -0.107 1.035 7.039; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 59, 42) --> (188, 156, 203) Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 216.0 0 of 14 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (69, 60, 40) --> (128, 157, 202) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 216.0 0 of 18 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 130, 67) --> (174, 168, 118) Left_Cerebellum_White_Matter: limiting intensities to 84.0 --> 216.0 0 of 7 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (87, 130, 62) --> (130, 168, 116) Right_Cerebellum_White_Matter: limiting intensities to 89.0 --> 216.0 5 of 11 (45.5%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 125, 98) --> (142, 183, 128) Brain_Stem: limiting intensities to 85.0 --> 216.0 0 of 12 (0.0%) samples deleted using 62 total control points for intensity normalization... bias field = 0.993 +- 0.053 0 of 57 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 59, 42) --> (188, 156, 203) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 215.0 0 of 79 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (69, 60, 40) --> (128, 157, 202) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 215.0 0 of 100 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 130, 67) --> (174, 168, 118) Left_Cerebellum_White_Matter: limiting intensities to 85.0 --> 215.0 0 of 10 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (87, 130, 62) --> (130, 168, 116) Right_Cerebellum_White_Matter: limiting intensities to 78.0 --> 215.0 0 of 11 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 125, 98) --> (142, 183, 128) Brain_Stem: limiting intensities to 78.0 --> 215.0 0 of 41 (0.0%) samples deleted using 241 total control points for intensity normalization... bias field = 0.989 +- 0.052 0 of 241 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 59, 42) --> (188, 156, 203) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 209.0 0 of 181 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (69, 60, 40) --> (128, 157, 202) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 209.0 0 of 210 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 130, 67) --> (174, 168, 118) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 209.0 0 of 8 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (87, 130, 62) --> (130, 168, 116) Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 209.0 6 of 8 (75.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 125, 98) --> (142, 183, 128) Brain_Stem: limiting intensities to 89.0 --> 209.0 14 of 38 (36.8%) samples deleted using 445 total control points for intensity normalization... bias field = 1.005 +- 0.047 0 of 425 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 7 seconds. #-------------------------------------- #@# CA Reg Thu Oct 6 18:02:11 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.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... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.37 (predicted orig area = 5.8) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.782, neg=0, invalid=96777 0001: dt=129.472000, rms=0.710 (9.193%), neg=0, invalid=96777 0002: dt=92.480000, rms=0.701 (1.223%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.691 (1.485%), neg=0, invalid=96777 0004: dt=110.976000, rms=0.688 (0.382%), neg=0, invalid=96777 0005: dt=129.472000, rms=0.683 (0.756%), neg=0, invalid=96777 0006: dt=110.976000, rms=0.681 (0.268%), neg=0, invalid=96777 0007: dt=295.936000, rms=0.676 (0.714%), neg=0, invalid=96777 0008: dt=55.488000, rms=0.674 (0.376%), neg=0, invalid=96777 0009: dt=517.888000, rms=0.670 (0.578%), neg=0, invalid=96777 0010: dt=92.480000, rms=0.666 (0.669%), neg=0, invalid=96777 0011: dt=110.976000, rms=0.665 (0.098%), neg=0, invalid=96777 0012: dt=110.976000, rms=0.663 (0.225%), neg=0, invalid=96777 0013: dt=110.976000, rms=0.661 (0.295%), neg=0, invalid=96777 0014: dt=110.976000, rms=0.659 (0.353%), neg=0, invalid=96777 0015: dt=110.976000, rms=0.657 (0.344%), neg=0, invalid=96777 0016: dt=110.976000, rms=0.654 (0.438%), neg=0, invalid=96777 0017: dt=110.976000, rms=0.651 (0.411%), neg=0, invalid=96777 0018: dt=110.976000, rms=0.649 (0.308%), neg=0, invalid=96777 0019: dt=110.976000, rms=0.648 (0.230%), neg=0, invalid=96777 0020: dt=110.976000, rms=0.646 (0.273%), neg=0, invalid=96777 0021: dt=110.976000, rms=0.644 (0.308%), neg=0, invalid=96777 0022: dt=110.976000, rms=0.643 (0.214%), neg=0, invalid=96777 0023: dt=110.976000, rms=0.642 (0.171%), neg=0, invalid=96777 0024: dt=110.976000, rms=0.640 (0.163%), neg=0, invalid=96777 0025: dt=110.976000, rms=0.639 (0.193%), neg=0, invalid=96777 0026: dt=110.976000, rms=0.638 (0.125%), neg=0, invalid=96777 0027: dt=110.976000, rms=0.638 (0.075%), neg=0, invalid=96777 0028: dt=110.976000, rms=0.637 (0.090%), neg=0, invalid=96777 0029: dt=110.976000, rms=0.636 (0.148%), neg=0, invalid=96777 0030: dt=110.976000, rms=0.636 (0.130%), neg=0, invalid=96777 0031: dt=110.976000, rms=0.635 (0.108%), neg=0, invalid=96777 0032: dt=110.976000, rms=0.634 (0.105%), neg=0, invalid=96777 0033: dt=295.936000, rms=0.633 (0.134%), neg=0, invalid=96777 0034: dt=27.744000, rms=0.633 (0.006%), neg=0, invalid=96777 0035: dt=27.744000, rms=0.633 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.633, neg=0, invalid=96777 0036: dt=32.368000, rms=0.633 (0.011%), neg=0, invalid=96777 0037: dt=32.368000, rms=0.633 (0.011%), neg=0, invalid=96777 0038: dt=92.480000, rms=0.633 (0.013%), neg=0, invalid=96777 0039: dt=295.936000, rms=0.633 (0.055%), neg=0, invalid=96777 0040: dt=517.888000, rms=0.631 (0.280%), neg=0, invalid=96777 0041: dt=0.000000, rms=0.631 (-0.006%), neg=0, invalid=96777 0042: dt=0.850000, rms=0.631 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.636, neg=0, invalid=96777 0043: dt=124.416000, rms=0.631 (0.770%), neg=0, invalid=96777 0044: dt=36.288000, rms=0.624 (1.034%), neg=0, invalid=96777 0045: dt=31.104000, rms=0.623 (0.140%), neg=0, invalid=96777 0046: dt=31.104000, rms=0.621 (0.388%), neg=0, invalid=96777 0047: dt=31.104000, rms=0.618 (0.525%), neg=0, invalid=96777 0048: dt=31.104000, rms=0.614 (0.600%), neg=0, invalid=96777 0049: dt=31.104000, rms=0.610 (0.652%), neg=0, invalid=96777 0050: dt=31.104000, rms=0.606 (0.715%), neg=0, invalid=96777 0051: dt=31.104000, rms=0.601 (0.714%), neg=0, invalid=96777 0052: dt=31.104000, rms=0.598 (0.619%), neg=0, invalid=96777 0053: dt=31.104000, rms=0.594 (0.518%), neg=0, invalid=96777 0054: dt=31.104000, rms=0.592 (0.454%), neg=0, invalid=96777 0055: dt=31.104000, rms=0.589 (0.452%), neg=0, invalid=96777 0056: dt=31.104000, rms=0.587 (0.413%), neg=0, invalid=96777 0057: dt=31.104000, rms=0.585 (0.354%), neg=0, invalid=96777 0058: dt=31.104000, rms=0.583 (0.290%), neg=0, invalid=96777 0059: dt=31.104000, rms=0.581 (0.270%), neg=0, invalid=96777 0060: dt=31.104000, rms=0.580 (0.284%), neg=0, invalid=96777 0061: dt=31.104000, rms=0.578 (0.225%), neg=0, invalid=96777 0062: dt=31.104000, rms=0.577 (0.167%), neg=0, invalid=96777 0063: dt=31.104000, rms=0.577 (0.110%), neg=0, invalid=96777 0064: dt=31.104000, rms=0.576 (0.110%), neg=0, invalid=96777 0065: dt=145.152000, rms=0.575 (0.128%), neg=0, invalid=96777 0066: dt=9.072000, rms=0.575 (0.007%), neg=0, invalid=96777 0067: dt=9.072000, rms=0.575 (0.003%), neg=0, invalid=96777 0068: dt=9.072000, rms=0.575 (-0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.575, neg=0, invalid=96777 0069: dt=36.288000, rms=0.575 (0.055%), neg=0, invalid=96777 0070: dt=82.944000, rms=0.574 (0.093%), neg=0, invalid=96777 0071: dt=20.736000, rms=0.574 (0.017%), neg=0, invalid=96777 0072: dt=20.736000, rms=0.574 (0.018%), neg=0, invalid=96777 0073: dt=20.736000, rms=0.574 (0.031%), neg=0, invalid=96777 0074: dt=20.736000, rms=0.574 (0.031%), neg=0, invalid=96777 0075: dt=20.736000, rms=0.574 (0.023%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.593, neg=0, invalid=96777 0076: dt=5.123596, rms=0.593 (0.048%), neg=0, invalid=96777 0077: dt=2.000000, rms=0.593 (0.004%), neg=0, invalid=96777 0078: dt=2.000000, rms=0.593 (-0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.593, neg=0, invalid=96777 0079: dt=0.000000, rms=0.593 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.646, neg=0, invalid=96777 0080: dt=5.068063, rms=0.631 (2.199%), neg=0, invalid=96777 0081: dt=1.222222, rms=0.631 (0.028%), neg=0, invalid=96777 0082: dt=1.222222, rms=0.631 (-0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.631, neg=0, invalid=96777 0083: dt=0.000000, rms=0.631 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.690, neg=0, invalid=96777 0084: dt=1.248756, rms=0.685 (0.697%), neg=0, invalid=96777 0085: dt=1.924855, rms=0.680 (0.724%), neg=0, invalid=96777 0086: dt=0.448000, rms=0.680 (0.058%), neg=0, invalid=96777 0087: dt=0.448000, rms=0.679 (0.016%), neg=0, invalid=96777 0088: dt=0.448000, rms=0.679 (-0.007%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.679, neg=0, invalid=96777 0089: dt=1.280000, rms=0.678 (0.178%), neg=0, invalid=96777 0090: dt=0.000000, rms=0.678 (0.002%), neg=0, invalid=96777 0091: dt=0.100000, rms=0.678 (-0.001%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.634, neg=0, invalid=96777 0092: dt=0.448000, rms=0.618 (2.598%), neg=0, invalid=96777 0093: dt=0.000000, rms=0.618 (0.008%), neg=0, invalid=96777 0094: dt=0.050000, rms=0.618 (-0.431%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.618, neg=0, invalid=96777 0095: dt=0.000000, rms=0.618 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.09923 (14) Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (819 voxels, overlap=0.172) Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (819 voxels, peak = 13), gca=13.1 gca peak = 0.14022 (22) mri peak = 0.10955 (17) Right_Lateral_Ventricle (43): linear fit = 0.68 x + 0.0 (708 voxels, overlap=0.349) Right_Lateral_Ventricle (43): linear fit = 0.68 x + 0.0 (708 voxels, peak = 15), gca=14.9 gca peak = 0.24234 (100) mri peak = 0.07976 (98) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (310 voxels, overlap=1.005) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (310 voxels, peak = 100), gca=100.5 gca peak = 0.19192 (97) mri peak = 0.07145 (98) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (200 voxels, overlap=0.991) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (200 voxels, peak = 97), gca=97.5 gca peak = 0.24007 (63) mri peak = 0.09259 (62) Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (432 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (432 voxels, peak = 66), gca=66.5 gca peak = 0.29892 (64) mri peak = 0.09250 (63) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (400 voxels, overlap=0.990) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (400 voxels, peak = 62), gca=62.4 gca peak = 0.12541 (104) mri peak = 0.10155 (107) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (52828 voxels, overlap=0.696) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (52828 voxels, peak = 109), gca=108.7 gca peak = 0.13686 (104) mri peak = 0.07502 (109) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (52047 voxels, overlap=0.651) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (52047 voxels, peak = 110), gca=109.7 gca peak = 0.11691 (63) mri peak = 0.04707 (58) Left_Cerebral_Cortex (3): linear fit = 0.93 x + 0.0 (13484 voxels, overlap=0.814) Left_Cerebral_Cortex (3): linear fit = 0.93 x + 0.0 (13484 voxels, peak = 58), gca=58.3 gca peak = 0.13270 (63) mri peak = 0.03859 (60) Right_Cerebral_Cortex (42): linear fit = 0.95 x + 0.0 (14242 voxels, overlap=0.957) Right_Cerebral_Cortex (42): linear fit = 0.95 x + 0.0 (14242 voxels, peak = 60), gca=60.2 gca peak = 0.15182 (70) mri peak = 0.08389 (76) Right_Caudate (50): linear fit = 1.02 x + 0.0 (375 voxels, overlap=0.988) Right_Caudate (50): linear fit = 1.02 x + 0.0 (375 voxels, peak = 72), gca=71.8 gca peak = 0.14251 (76) mri peak = 0.08156 (76) Left_Caudate (11): linear fit = 0.99 x + 0.0 (554 voxels, overlap=0.960) Left_Caudate (11): linear fit = 0.99 x + 0.0 (554 voxels, peak = 75), gca=74.9 gca peak = 0.12116 (60) mri peak = 0.04061 (63) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (7065 voxels, overlap=0.789) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (7065 voxels, peak = 64), gca=64.5 gca peak = 0.12723 (61) mri peak = 0.05077 (63) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (8725 voxels, overlap=0.940) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (8725 voxels, peak = 66), gca=65.6 gca peak = 0.22684 (88) mri peak = 0.07501 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (5537 voxels, overlap=0.844) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (5537 voxels, peak = 95), gca=95.5 gca peak = 0.21067 (87) mri peak = 0.08928 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5519 voxels, overlap=0.923) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (5519 voxels, peak = 90), gca=90.0 gca peak = 0.25455 (62) mri peak = 0.10448 (63) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (200 voxels, overlap=0.994) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (200 voxels, peak = 62), gca=62.0 gca peak = 0.39668 (62) mri peak = 0.08871 (57) Right_Amygdala (54): linear fit = 0.95 x + 0.0 (259 voxels, overlap=0.949) Right_Amygdala (54): linear fit = 0.95 x + 0.0 (259 voxels, peak = 59), gca=59.2 gca peak = 0.10129 (93) mri peak = 0.05758 (94) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4239 voxels, overlap=0.904) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4239 voxels, peak = 95), gca=95.3 gca peak = 0.12071 (89) mri peak = 0.05955 (88) Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (3498 voxels, overlap=0.983) Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (3498 voxels, peak = 92), gca=92.1 gca peak = 0.13716 (82) mri peak = 0.06488 (83) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1510 voxels, overlap=0.999) Left_Putamen (12): linear fit = 1.04 x + 0.0 (1510 voxels, peak = 86), gca=85.7 gca peak = 0.15214 (84) mri peak = 0.05162 (83) Right_Putamen (51): linear fit = 0.98 x + 0.0 (1531 voxels, overlap=0.982) Right_Putamen (51): linear fit = 0.98 x + 0.0 (1531 voxels, peak = 82), gca=81.9 gca peak = 0.08983 (85) mri peak = 0.07332 (88) Brain_Stem (16): linear fit = 1.07 x + 0.0 (9559 voxels, overlap=0.778) Brain_Stem (16): linear fit = 1.07 x + 0.0 (9559 voxels, peak = 91), gca=90.5 gca peak = 0.11809 (92) mri peak = 0.06410 (93) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (614 voxels, overlap=0.641) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (614 voxels, peak = 101), gca=100.7 gca peak = 0.12914 (94) mri peak = 0.07176 (103) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (723 voxels, overlap=0.796) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (723 voxels, peak = 99), gca=99.2 gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) mri peak = 0.11196 (18) Fourth_Ventricle (15): linear fit = 0.63 x + 0.0 (212 voxels, overlap=0.134) Fourth_Ventricle (15): linear fit = 0.63 x + 0.0 (212 voxels, peak = 17), gca=17.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 0.98 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.61 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.652, neg=0, invalid=96777 0096: dt=129.472000, rms=0.647 (0.839%), neg=0, invalid=96777 0097: dt=129.472000, rms=0.644 (0.348%), neg=0, invalid=96777 0098: dt=129.472000, rms=0.643 (0.227%), neg=0, invalid=96777 0099: dt=92.480000, rms=0.642 (0.131%), neg=0, invalid=96777 0100: dt=129.472000, rms=0.641 (0.167%), neg=0, invalid=96777 0101: dt=73.984000, rms=0.640 (0.092%), neg=0, invalid=96777 0102: dt=221.952000, rms=0.639 (0.175%), neg=0, invalid=96777 0103: dt=55.488000, rms=0.639 (0.094%), neg=0, invalid=96777 0104: dt=1479.680000, rms=0.635 (0.601%), neg=0, invalid=96777 0105: dt=110.976000, rms=0.634 (0.063%), neg=0, invalid=96777 0106: dt=110.976000, rms=0.634 (0.049%), neg=0, invalid=96777 0107: dt=110.976000, rms=0.634 (0.038%), neg=0, invalid=96777 0108: dt=110.976000, rms=0.633 (0.075%), neg=0, invalid=96777 0109: dt=110.976000, rms=0.633 (0.084%), neg=0, invalid=96777 0110: dt=110.976000, rms=0.632 (0.097%), neg=0, invalid=96777 0111: dt=110.976000, rms=0.632 (0.097%), neg=0, invalid=96777 0112: dt=110.976000, rms=0.631 (0.094%), neg=0, invalid=96777 0113: dt=110.976000, rms=0.631 (0.070%), neg=0, invalid=96777 0114: dt=110.976000, rms=0.630 (0.079%), neg=0, invalid=96777 0115: dt=110.976000, rms=0.630 (0.064%), neg=0, invalid=96777 0116: dt=110.976000, rms=0.629 (0.077%), neg=0, invalid=96777 0117: dt=110.976000, rms=0.629 (0.049%), neg=0, invalid=96777 0118: dt=110.976000, rms=0.628 (0.081%), neg=0, invalid=96777 0119: dt=110.976000, rms=0.628 (0.064%), neg=0, invalid=96777 0120: dt=110.976000, rms=0.628 (0.065%), neg=0, invalid=96777 0121: dt=110.976000, rms=0.627 (0.062%), neg=0, invalid=96777 0122: dt=110.976000, rms=0.627 (0.054%), neg=0, invalid=96777 0123: dt=110.976000, rms=0.627 (0.056%), neg=0, invalid=96777 0124: dt=110.976000, rms=0.626 (0.050%), neg=0, invalid=96777 0125: dt=110.976000, rms=0.626 (0.066%), neg=0, invalid=96777 0126: dt=110.976000, rms=0.625 (0.072%), neg=0, invalid=96777 0127: dt=110.976000, rms=0.625 (0.065%), neg=0, invalid=96777 0128: dt=110.976000, rms=0.625 (0.066%), neg=0, invalid=96777 0129: dt=110.976000, rms=0.624 (0.065%), neg=0, invalid=96777 0130: dt=110.976000, rms=0.624 (0.063%), neg=0, invalid=96777 0131: dt=110.976000, rms=0.623 (0.060%), neg=0, invalid=96777 0132: dt=110.976000, rms=0.623 (0.067%), neg=0, invalid=96777 0133: dt=110.976000, rms=0.623 (0.068%), neg=0, invalid=96777 0134: dt=110.976000, rms=0.622 (0.064%), neg=0, invalid=96777 0135: dt=110.976000, rms=0.622 (0.059%), neg=0, invalid=96777 0136: dt=110.976000, rms=0.621 (0.057%), neg=0, invalid=96777 0137: dt=110.976000, rms=0.621 (0.056%), neg=0, invalid=96777 0138: dt=110.976000, rms=0.621 (0.052%), neg=0, invalid=96777 0139: dt=110.976000, rms=0.620 (0.044%), neg=0, invalid=96777 0140: dt=110.976000, rms=0.620 (0.040%), neg=0, invalid=96777 0141: dt=110.976000, rms=0.620 (0.036%), neg=0, invalid=96777 0142: dt=110.976000, rms=0.620 (0.041%), neg=0, invalid=96777 0143: dt=110.976000, rms=0.620 (0.036%), neg=0, invalid=96777 0144: dt=110.976000, rms=0.619 (0.031%), neg=0, invalid=96777 0145: dt=110.976000, rms=0.619 (0.031%), neg=0, invalid=96777 0146: dt=110.976000, rms=0.619 (0.035%), neg=0, invalid=96777 0147: dt=110.976000, rms=0.619 (0.035%), neg=0, invalid=96777 0148: dt=110.976000, rms=0.619 (0.030%), neg=0, invalid=96777 0149: dt=110.976000, rms=0.618 (0.032%), neg=0, invalid=96777 0150: dt=110.976000, rms=0.618 (0.028%), neg=0, invalid=96777 0151: dt=110.976000, rms=0.618 (0.025%), neg=0, invalid=96777 0152: dt=110.976000, rms=0.618 (0.020%), neg=0, invalid=96777 0153: dt=110.976000, rms=0.618 (0.027%), neg=0, invalid=96777 0154: dt=110.976000, rms=0.618 (0.033%), neg=0, invalid=96777 0155: dt=110.976000, rms=0.617 (0.032%), neg=0, invalid=96777 0156: dt=110.976000, rms=0.617 (0.027%), neg=0, invalid=96777 0157: dt=110.976000, rms=0.617 (0.021%), neg=0, invalid=96777 0158: dt=110.976000, rms=0.617 (0.024%), neg=0, invalid=96777 0159: dt=110.976000, rms=0.617 (0.020%), neg=0, invalid=96777 0160: dt=73.984000, rms=0.617 (0.000%), neg=0, invalid=96777 0161: dt=73.984000, rms=0.617 (0.004%), neg=0, invalid=96777 0162: dt=73.984000, rms=0.617 (0.004%), neg=0, invalid=96777 0163: dt=73.984000, rms=0.617 (0.005%), neg=0, invalid=96777 0164: dt=73.984000, rms=0.617 (0.006%), neg=0, invalid=96777 0165: dt=73.984000, rms=0.617 (0.004%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.617, neg=0, invalid=96777 0166: dt=129.472000, rms=0.616 (0.076%), neg=0, invalid=96777 0167: dt=295.936000, rms=0.616 (0.089%), neg=0, invalid=96777 0168: dt=32.368000, rms=0.615 (0.036%), neg=0, invalid=96777 0169: dt=32.368000, rms=0.615 (0.013%), neg=0, invalid=96777 0170: dt=32.368000, rms=0.615 (0.006%), neg=0, invalid=96777 0171: dt=32.368000, rms=0.615 (0.004%), neg=0, invalid=96777 0172: dt=92.480000, rms=0.615 (0.022%), neg=0, invalid=96777 0173: dt=129.472000, rms=0.615 (0.020%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.616, neg=0, invalid=96777 0174: dt=145.152000, rms=0.612 (0.706%), neg=0, invalid=96777 0175: dt=36.288000, rms=0.608 (0.559%), neg=0, invalid=96777 0176: dt=62.208000, rms=0.606 (0.382%), neg=0, invalid=96777 0177: dt=25.920000, rms=0.604 (0.257%), neg=0, invalid=96777 0178: dt=82.944000, rms=0.602 (0.312%), neg=0, invalid=96777 0179: dt=25.920000, rms=0.601 (0.256%), neg=0, invalid=96777 0180: dt=62.208000, rms=0.599 (0.232%), neg=0, invalid=96777 0181: dt=31.104000, rms=0.598 (0.181%), neg=0, invalid=96777 0182: dt=36.288000, rms=0.597 (0.160%), neg=0, invalid=96777 0183: dt=62.208000, rms=0.596 (0.179%), neg=0, invalid=96777 0184: dt=36.288000, rms=0.595 (0.167%), neg=0, invalid=96777 0185: dt=36.288000, rms=0.594 (0.138%), neg=0, invalid=96777 0186: dt=82.944000, rms=0.593 (0.193%), neg=0, invalid=96777 0187: dt=31.104000, rms=0.592 (0.155%), neg=0, invalid=96777 0188: dt=82.944000, rms=0.591 (0.163%), neg=0, invalid=96777 0189: dt=25.920000, rms=0.591 (0.136%), neg=0, invalid=96777 0190: dt=124.416000, rms=0.590 (0.191%), neg=0, invalid=96777 0191: dt=25.920000, rms=0.588 (0.179%), neg=0, invalid=96777 0192: dt=82.944000, rms=0.588 (0.152%), neg=0, invalid=96777 0193: dt=31.104000, rms=0.587 (0.107%), neg=0, invalid=96777 0194: dt=36.288000, rms=0.586 (0.091%), neg=0, invalid=96777 0195: dt=82.944000, rms=0.586 (0.109%), neg=0, invalid=96777 0196: dt=25.920000, rms=0.585 (0.119%), neg=0, invalid=96777 0197: dt=124.416000, rms=0.584 (0.148%), neg=0, invalid=96777 0198: dt=25.920000, rms=0.583 (0.137%), neg=0, invalid=96777 0199: dt=103.680000, rms=0.583 (0.112%), neg=0, invalid=96777 0200: dt=25.920000, rms=0.582 (0.098%), neg=0, invalid=96777 0201: dt=145.152000, rms=0.581 (0.207%), neg=0, invalid=96777 0202: dt=25.920000, rms=0.581 (0.067%), neg=0, invalid=96777 0203: dt=124.416000, rms=0.580 (0.089%), neg=0, invalid=96777 0204: dt=31.104000, rms=0.579 (0.122%), neg=0, invalid=96777 0205: dt=31.104000, rms=0.579 (0.046%), neg=0, invalid=96777 0206: dt=31.104000, rms=0.579 (0.057%), neg=0, invalid=96777 0207: dt=31.104000, rms=0.578 (0.086%), neg=0, invalid=96777 0208: dt=31.104000, rms=0.578 (0.117%), neg=0, invalid=96777 0209: dt=31.104000, rms=0.577 (0.136%), neg=0, invalid=96777 0210: dt=31.104000, rms=0.576 (0.166%), neg=0, invalid=96777 0211: dt=31.104000, rms=0.575 (0.171%), neg=0, invalid=96777 0212: dt=31.104000, rms=0.574 (0.188%), neg=0, invalid=96777 0213: dt=31.104000, rms=0.573 (0.202%), neg=0, invalid=96777 0214: dt=31.104000, rms=0.571 (0.197%), neg=0, invalid=96777 0215: dt=31.104000, rms=0.570 (0.193%), neg=0, invalid=96777 0216: dt=31.104000, rms=0.570 (0.031%), neg=0, invalid=96777 0217: dt=31.104000, rms=0.570 (0.054%), neg=0, invalid=96777 0218: dt=31.104000, rms=0.569 (0.078%), neg=0, invalid=96777 0219: dt=31.104000, rms=0.569 (0.093%), neg=0, invalid=96777 0220: dt=31.104000, rms=0.568 (0.097%), neg=0, invalid=96777 0221: dt=31.104000, rms=0.568 (0.112%), neg=0, invalid=96777 0222: dt=31.104000, rms=0.567 (0.121%), neg=0, invalid=96777 0223: dt=31.104000, rms=0.566 (0.126%), neg=0, invalid=96777 0224: dt=7.776000, rms=0.566 (0.005%), neg=0, invalid=96777 0225: dt=7.776000, rms=0.566 (0.004%), neg=0, invalid=96777 0226: dt=2.268000, rms=0.566 (0.002%), neg=0, invalid=96777 0227: dt=0.567000, rms=0.566 (0.000%), neg=0, invalid=96777 0228: dt=0.567000, rms=0.566 (0.000%), neg=0, invalid=96777 0229: dt=0.017719, rms=0.566 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.566, neg=0, invalid=96777 0230: dt=0.008859, rms=0.566 (0.000%), neg=0, invalid=96777 0231: dt=0.001898, rms=0.566 (0.000%), neg=0, invalid=96777 0232: dt=0.000119, rms=0.566 (0.000%), neg=0, invalid=96777 0233: dt=0.000059, rms=0.566 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.572, neg=0, invalid=96777 0234: dt=44.800000, rms=0.557 (2.547%), neg=0, invalid=96777 0235: dt=44.800000, rms=0.548 (1.667%), neg=0, invalid=96777 0236: dt=11.200000, rms=0.546 (0.318%), neg=0, invalid=96777 0237: dt=44.800000, rms=0.541 (0.950%), neg=0, invalid=96777 0238: dt=8.000000, rms=0.539 (0.358%), neg=0, invalid=96777 0239: dt=8.000000, rms=0.538 (0.201%), neg=0, invalid=96777 0240: dt=153.600000, rms=0.526 (2.129%), neg=0, invalid=96777 0241: dt=2.800000, rms=0.525 (0.193%), neg=0, invalid=96777 0242: dt=11.162791, rms=0.523 (0.383%), neg=0, invalid=96777 0243: dt=11.200000, rms=0.523 (0.147%), neg=0, invalid=96777 0244: dt=32.000000, rms=0.522 (0.172%), neg=0, invalid=96777 0245: dt=6.567164, rms=0.521 (0.116%), neg=0, invalid=96777 0246: dt=44.800000, rms=0.519 (0.325%), neg=0, invalid=96777 0247: dt=11.200000, rms=0.519 (0.112%), neg=0, invalid=96777 0248: dt=38.400000, rms=0.518 (0.116%), neg=0, invalid=96777 0249: dt=6.400000, rms=0.517 (0.130%), neg=0, invalid=96777 0250: dt=44.800000, rms=0.516 (0.239%), neg=0, invalid=96777 0251: dt=9.600000, rms=0.516 (0.093%), neg=0, invalid=96777 0252: dt=11.200000, rms=0.515 (0.062%), neg=0, invalid=96777 0253: dt=25.600000, rms=0.515 (0.098%), neg=0, invalid=96777 0254: dt=8.000000, rms=0.515 (0.061%), neg=0, invalid=96777 0255: dt=76.800000, rms=0.514 (0.204%), neg=0, invalid=96777 0256: dt=6.849315, rms=0.513 (0.163%), neg=0, invalid=96777 0257: dt=25.600000, rms=0.512 (0.083%), neg=0, invalid=96777 0258: dt=9.600000, rms=0.512 (0.075%), neg=0, invalid=96777 0259: dt=9.600000, rms=0.512 (0.030%), neg=0, invalid=96777 0260: dt=9.600000, rms=0.512 (0.051%), neg=0, invalid=96777 0261: dt=9.600000, rms=0.511 (0.062%), neg=0, invalid=96777 0262: dt=9.600000, rms=0.511 (0.093%), neg=0, invalid=96777 0263: dt=9.600000, rms=0.510 (0.118%), neg=0, invalid=96777 0264: dt=9.600000, rms=0.509 (0.143%), neg=0, invalid=96777 0265: dt=9.600000, rms=0.509 (0.157%), neg=0, invalid=96777 0266: dt=9.600000, rms=0.508 (0.167%), neg=0, invalid=96777 0267: dt=9.600000, rms=0.507 (0.166%), neg=0, invalid=96777 0268: dt=9.600000, rms=0.506 (0.165%), neg=0, invalid=96777 0269: dt=9.600000, rms=0.505 (0.167%), neg=0, invalid=96777 0270: dt=9.600000, rms=0.504 (0.169%), neg=0, invalid=96777 0271: dt=9.600000, rms=0.504 (0.160%), neg=0, invalid=96777 0272: dt=9.600000, rms=0.503 (0.150%), neg=0, invalid=96777 0273: dt=9.600000, rms=0.502 (0.144%), neg=0, invalid=96777 0274: dt=9.600000, rms=0.501 (0.152%), neg=0, invalid=96777 0275: dt=9.600000, rms=0.501 (0.148%), neg=0, invalid=96777 0276: dt=9.600000, rms=0.500 (0.123%), neg=0, invalid=96777 0277: dt=9.600000, rms=0.499 (0.126%), neg=0, invalid=96777 0278: dt=9.600000, rms=0.499 (0.116%), neg=0, invalid=96777 0279: dt=9.600000, rms=0.498 (0.107%), neg=0, invalid=96777 0280: dt=9.600000, rms=0.498 (0.092%), neg=0, invalid=96777 0281: dt=9.600000, rms=0.497 (0.087%), neg=0, invalid=96777 0282: dt=9.600000, rms=0.497 (0.091%), neg=0, invalid=96777 0283: dt=9.600000, rms=0.496 (0.078%), neg=0, invalid=96777 0284: dt=9.600000, rms=0.496 (0.083%), neg=0, invalid=96777 0285: dt=9.600000, rms=0.496 (0.074%), neg=0, invalid=96777 0286: dt=9.600000, rms=0.495 (0.072%), neg=0, invalid=96777 0287: dt=9.600000, rms=0.495 (0.065%), neg=0, invalid=96777 0288: dt=9.600000, rms=0.495 (0.063%), neg=0, invalid=96777 0289: dt=9.600000, rms=0.494 (0.050%), neg=0, invalid=96777 0290: dt=9.600000, rms=0.494 (0.050%), neg=0, invalid=96777 0291: dt=9.600000, rms=0.494 (0.058%), neg=0, invalid=96777 0292: dt=9.600000, rms=0.494 (0.054%), neg=0, invalid=96777 0293: dt=9.600000, rms=0.493 (0.053%), neg=0, invalid=96777 0294: dt=9.600000, rms=0.493 (0.047%), neg=0, invalid=96777 0295: dt=9.600000, rms=0.493 (0.042%), neg=0, invalid=96777 0296: dt=9.600000, rms=0.493 (0.046%), neg=0, invalid=96777 0297: dt=9.600000, rms=0.493 (0.037%), neg=0, invalid=96777 0298: dt=9.600000, rms=0.492 (0.041%), neg=0, invalid=96777 0299: dt=9.600000, rms=0.492 (0.037%), neg=0, invalid=96777 0300: dt=9.600000, rms=0.492 (0.031%), neg=0, invalid=96777 0301: dt=9.600000, rms=0.492 (0.039%), neg=0, invalid=96777 0302: dt=9.600000, rms=0.492 (0.043%), neg=0, invalid=96777 0303: dt=9.600000, rms=0.491 (0.034%), neg=0, invalid=96777 0304: dt=9.600000, rms=0.491 (0.029%), neg=0, invalid=96777 0305: dt=9.600000, rms=0.491 (0.027%), neg=0, invalid=96777 0306: dt=9.600000, rms=0.491 (0.029%), neg=0, invalid=96777 0307: dt=9.600000, rms=0.491 (0.026%), neg=0, invalid=96777 0308: dt=9.600000, rms=0.491 (0.030%), neg=0, invalid=96777 0309: dt=9.600000, rms=0.491 (0.021%), neg=0, invalid=96777 0310: dt=9.600000, rms=0.490 (0.029%), neg=0, invalid=96777 0311: dt=9.600000, rms=0.490 (0.027%), neg=0, invalid=96777 0312: dt=9.600000, rms=0.490 (0.028%), neg=0, invalid=96777 0313: dt=9.600000, rms=0.490 (0.024%), neg=0, invalid=96777 0314: dt=9.600000, rms=0.490 (0.022%), neg=0, invalid=96777 0315: dt=32.000000, rms=0.490 (0.006%), neg=0, invalid=96777 0316: dt=32.000000, rms=0.490 (-0.007%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.490, neg=0, invalid=96777 0317: dt=32.000000, rms=0.488 (0.326%), neg=0, invalid=96777 0318: dt=11.200000, rms=0.488 (0.090%), neg=0, invalid=96777 0319: dt=11.200000, rms=0.488 (0.026%), neg=0, invalid=96777 0320: dt=11.200000, rms=0.488 (0.051%), neg=0, invalid=96777 0321: dt=11.200000, rms=0.487 (0.049%), neg=0, invalid=96777 0322: dt=11.200000, rms=0.487 (0.042%), neg=0, invalid=96777 0323: dt=11.200000, rms=0.487 (0.032%), neg=0, invalid=96777 0324: dt=11.200000, rms=0.487 (0.023%), neg=0, invalid=96777 0325: dt=11.200000, rms=0.487 (-0.009%), neg=0, invalid=96777 0326: dt=11.200000, rms=0.487 (0.005%), neg=0, invalid=96777 0327: dt=38.400000, rms=0.487 (0.038%), neg=0, invalid=96777 0328: dt=6.400000, rms=0.487 (0.009%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.508, neg=0, invalid=96777 0329: dt=0.000000, rms=0.508 (0.001%), neg=0, invalid=96777 0330: dt=0.000000, rms=0.508 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.508, neg=0, invalid=96777 0331: dt=0.000000, rms=0.508 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.550, neg=0, invalid=96777 0332: dt=1.228916, rms=0.546 (0.737%), neg=0, invalid=96777 0333: dt=0.320000, rms=0.545 (0.022%), neg=0, invalid=96777 0334: dt=0.320000, rms=0.545 (-0.016%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.545, neg=0, invalid=96777 0335: dt=0.786667, rms=0.545 (0.134%), neg=0, invalid=96777 0336: dt=0.256000, rms=0.545 (0.007%), neg=0, invalid=96777 0337: dt=0.256000, rms=0.545 (-0.006%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.502, neg=0, invalid=96777 0338: dt=0.112000, rms=0.498 (0.830%), neg=0, invalid=96777 0339: dt=0.146111, rms=0.494 (0.851%), neg=0, invalid=96777 0340: dt=0.112000, rms=0.491 (0.480%), neg=0, invalid=96777 0341: dt=0.028000, rms=0.491 (0.095%), neg=0, invalid=96777 0342: dt=0.116111, rms=0.489 (0.384%), neg=0, invalid=96777 0343: dt=0.112000, rms=0.488 (0.303%), neg=0, invalid=96777 0344: dt=0.112000, rms=0.486 (0.248%), neg=0, invalid=96777 0345: dt=0.112000, rms=0.485 (0.206%), neg=0, invalid=96777 0346: dt=0.112000, rms=0.484 (0.180%), neg=0, invalid=96777 0347: dt=0.112000, rms=0.484 (0.148%), neg=0, invalid=96777 0348: dt=0.112000, rms=0.483 (0.133%), neg=0, invalid=96777 0349: dt=0.112000, rms=0.483 (0.112%), neg=0, invalid=96777 0350: dt=0.320000, rms=0.481 (0.281%), neg=0, invalid=96777 0351: dt=0.028000, rms=0.481 (0.016%), neg=0, invalid=96777 0352: dt=0.028000, rms=0.481 (0.018%), neg=0, invalid=96777 0353: dt=0.028000, rms=0.481 (0.030%), neg=0, invalid=96777 0354: dt=0.028000, rms=0.481 (0.046%), neg=0, invalid=96777 0355: dt=0.028000, rms=0.480 (0.055%), neg=0, invalid=96777 0356: dt=0.028000, rms=0.480 (0.063%), neg=0, invalid=96777 0357: dt=0.028000, rms=0.480 (0.069%), neg=0, invalid=96777 0358: dt=0.028000, rms=0.479 (0.068%), neg=0, invalid=96777 0359: dt=0.028000, rms=0.479 (0.072%), neg=0, invalid=96777 0360: dt=0.028000, rms=0.479 (0.072%), neg=0, invalid=96777 0361: dt=0.028000, rms=0.478 (0.069%), neg=0, invalid=96777 0362: dt=0.028000, rms=0.478 (0.071%), neg=0, invalid=96777 0363: dt=0.028000, rms=0.478 (0.065%), neg=0, invalid=96777 0364: dt=0.028000, rms=0.477 (0.065%), neg=0, invalid=96777 0365: dt=0.028000, rms=0.477 (0.060%), neg=0, invalid=96777 0366: dt=0.028000, rms=0.477 (0.053%), neg=0, invalid=96777 0367: dt=0.028000, rms=0.477 (0.046%), neg=0, invalid=96777 0368: dt=0.028000, rms=0.477 (0.045%), neg=0, invalid=96777 0369: dt=0.028000, rms=0.476 (0.040%), neg=0, invalid=96777 0370: dt=0.028000, rms=0.476 (0.001%), neg=0, invalid=96777 0371: dt=0.028000, rms=0.476 (-0.001%), neg=0, invalid=96777 0372: dt=0.000000, rms=0.476 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.476, neg=0, invalid=96777 0373: dt=0.112000, rms=0.475 (0.295%), neg=0, invalid=96777 0374: dt=0.320000, rms=0.472 (0.621%), neg=0, invalid=96777 0375: dt=0.096000, rms=0.472 (0.058%), neg=0, invalid=96777 0376: dt=0.112000, rms=0.471 (0.053%), neg=0, invalid=96777 0377: dt=0.112000, rms=0.471 (0.043%), neg=0, invalid=96777 0378: dt=0.112000, rms=0.471 (0.027%), neg=0, invalid=96777 0379: dt=0.112000, rms=0.471 (0.027%), neg=0, invalid=96777 0380: dt=0.112000, rms=0.471 (0.017%), neg=0, invalid=96777 0381: dt=0.112000, rms=0.471 (0.034%), neg=0, invalid=96777 0382: dt=0.112000, rms=0.471 (0.034%), neg=0, invalid=96777 0383: dt=0.112000, rms=0.471 (0.004%), neg=0, invalid=96777 0384: dt=0.056000, rms=0.471 (-0.000%), neg=0, invalid=96777 0385: dt=0.028000, rms=0.471 (0.001%), neg=0, invalid=96777 0386: dt=0.112000, rms=0.471 (0.003%), neg=0, invalid=96777 0387: dt=0.112000, rms=0.471 (-0.000%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ******************************** ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.469, neg=0, invalid=96777 0388: dt=0.000000, rms=0.469 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.469, neg=0, invalid=96777 0389: dt=295.936000, rms=0.468 (0.083%), neg=0, invalid=96777 0390: dt=55.488000, rms=0.468 (0.020%), neg=0, invalid=96777 0391: dt=55.488000, rms=0.468 (0.012%), neg=0, invalid=96777 0392: dt=55.488000, rms=0.468 (0.003%), neg=0, invalid=96777 0393: dt=55.488000, rms=0.468 (0.004%), neg=0, invalid=96777 0394: dt=55.488000, rms=0.468 (0.010%), neg=0, invalid=96777 0395: dt=55.488000, rms=0.468 (0.020%), neg=0, invalid=96777 0396: dt=55.488000, rms=0.468 (0.016%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.468, neg=0, invalid=96777 0397: dt=31.104000, rms=0.468 (0.053%), neg=0, invalid=96777 0398: dt=31.104000, rms=0.467 (0.033%), neg=0, invalid=96777 0399: dt=31.104000, rms=0.467 (0.016%), neg=0, invalid=96777 0400: dt=31.104000, rms=0.467 (0.007%), neg=0, invalid=96777 0401: dt=31.104000, rms=0.467 (-0.048%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.467, neg=0, invalid=96777 0402: dt=103.680000, rms=0.465 (0.428%), neg=0, invalid=96777 0403: dt=36.288000, rms=0.465 (0.108%), neg=0, invalid=96777 0404: dt=36.288000, rms=0.465 (0.052%), neg=0, invalid=96777 0405: dt=36.288000, rms=0.464 (0.072%), neg=0, invalid=96777 0406: dt=36.288000, rms=0.464 (0.099%), neg=0, invalid=96777 0407: dt=36.288000, rms=0.463 (0.116%), neg=0, invalid=96777 0408: dt=36.288000, rms=0.463 (0.079%), neg=0, invalid=96777 0409: dt=36.288000, rms=0.462 (0.117%), neg=0, invalid=96777 0410: dt=36.288000, rms=0.462 (0.082%), neg=0, invalid=96777 0411: dt=20.736000, rms=0.462 (0.015%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.462, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0412: dt=32.000000, rms=0.460 (0.511%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0413: dt=32.000000, rms=0.458 (0.299%), neg=0, invalid=96777 0414: dt=7.496855, rms=0.458 (0.189%), neg=0, invalid=96777 0415: dt=7.496855, rms=0.457 (0.105%), neg=0, invalid=96777 0416: dt=7.496855, rms=0.457 (0.108%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0417: dt=7.496855, rms=0.456 (0.155%), neg=0, invalid=96777 0418: dt=7.496855, rms=0.455 (0.158%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0419: dt=7.496855, rms=0.454 (0.143%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 5 iterations, nbhd size=0, neg = 0 0420: dt=7.496855, rms=0.454 (0.139%), neg=0, invalid=96777 iter 0, gcam->neg = 12 after 6 iterations, nbhd size=0, neg = 0 0421: dt=7.496855, rms=0.453 (0.090%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 4 iterations, nbhd size=0, neg = 0 0422: dt=7.496855, rms=0.453 (0.053%), neg=0, invalid=96777 0423: dt=0.000000, rms=0.453 (0.009%), neg=0, invalid=96777 0424: dt=0.250000, rms=0.453 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.453, neg=0, invalid=96777 iter 0, gcam->neg = 44 after 7 iterations, nbhd size=0, neg = 0 0425: dt=32.000000, rms=0.451 (0.486%), neg=0, invalid=96777 0426: dt=11.200000, rms=0.450 (0.299%), neg=0, invalid=96777 0427: dt=11.200000, rms=0.449 (0.221%), neg=0, invalid=96777 0428: dt=11.200000, rms=0.448 (0.203%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0429: dt=11.200000, rms=0.447 (0.261%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0430: dt=11.200000, rms=0.446 (0.214%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0431: dt=11.200000, rms=0.445 (0.189%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 3 iterations, nbhd size=0, neg = 0 0432: dt=11.200000, rms=0.444 (0.147%), neg=0, invalid=96777 0433: dt=11.200000, rms=0.443 (0.140%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0434: dt=11.200000, rms=0.443 (0.095%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0435: dt=11.200000, rms=0.443 (0.072%), neg=0, invalid=96777 0436: dt=32.000000, rms=0.442 (0.163%), neg=0, invalid=96777 0437: dt=8.000000, rms=0.442 (0.069%), neg=0, invalid=96777 0438: dt=8.000000, rms=0.442 (0.028%), neg=0, invalid=96777 0439: dt=8.000000, rms=0.441 (0.032%), neg=0, invalid=96777 0440: dt=8.000000, rms=0.441 (0.051%), neg=0, invalid=96777 0441: dt=8.000000, rms=0.441 (0.047%), neg=0, invalid=96777 0442: dt=8.000000, rms=0.441 (0.058%), neg=0, invalid=96777 0443: dt=8.000000, rms=0.441 (0.050%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.444, neg=0, invalid=96777 0444: dt=4.032000, rms=0.443 (0.063%), neg=0, invalid=96777 0445: dt=2.880000, rms=0.443 (0.014%), neg=0, invalid=96777 0446: dt=2.880000, rms=0.443 (0.011%), neg=0, invalid=96777 0447: dt=2.880000, rms=0.443 (-0.061%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.443, neg=0, invalid=96777 iter 0, gcam->neg = 9 after 2 iterations, nbhd size=0, neg = 0 0448: dt=5.333333, rms=0.443 (0.117%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 10 iterations, nbhd size=1, neg = 0 0449: dt=4.266667, rms=0.443 (0.080%), neg=0, invalid=96777 0450: dt=4.266667, rms=0.442 (0.120%), neg=0, invalid=96777 iter 0, gcam->neg = 31 after 10 iterations, nbhd size=1, neg = 0 0451: dt=4.266667, rms=0.441 (0.181%), neg=0, invalid=96777 iter 0, gcam->neg = 32 after 10 iterations, nbhd size=1, neg = 0 0452: dt=4.266667, rms=0.441 (0.097%), neg=0, invalid=96777 iter 0, gcam->neg = 53 after 14 iterations, nbhd size=1, neg = 0 0453: dt=4.266667, rms=0.440 (0.138%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0454: dt=4.266667, rms=0.439 (0.182%), neg=0, invalid=96777 iter 0, gcam->neg = 15 after 8 iterations, nbhd size=1, neg = 0 0455: dt=4.266667, rms=0.438 (0.295%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 1 iterations, nbhd size=0, neg = 0 0456: dt=4.266667, rms=0.436 (0.391%), neg=0, invalid=96777 iter 0, gcam->neg = 19 after 7 iterations, nbhd size=1, neg = 0 0457: dt=4.266667, rms=0.435 (0.388%), neg=0, invalid=96777 iter 0, gcam->neg = 42 after 12 iterations, nbhd size=1, neg = 0 0458: dt=4.266667, rms=0.433 (0.381%), neg=0, invalid=96777 iter 0, gcam->neg = 80 after 13 iterations, nbhd size=1, neg = 0 0459: dt=4.266667, rms=0.432 (0.278%), neg=0, invalid=96777 iter 0, gcam->neg = 60 after 15 iterations, nbhd size=1, neg = 0 0460: dt=4.266667, rms=0.431 (0.196%), neg=0, invalid=96777 iter 0, gcam->neg = 52 after 15 iterations, nbhd size=1, neg = 0 0461: dt=4.266667, rms=0.430 (0.113%), neg=0, invalid=96777 iter 0, gcam->neg = 40 after 10 iterations, nbhd size=1, neg = 0 0462: dt=4.266667, rms=0.430 (-0.021%), neg=0, invalid=96777 0463: dt=0.000000, rms=0.430 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.436, neg=0, invalid=96777 0464: dt=0.000000, rms=0.436 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.436, neg=0, invalid=96777 0465: dt=0.000000, rms=0.436 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.427, neg=0, invalid=96777 iter 0, gcam->neg = 619 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.007, neg=1, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 1, delta 0, rms=0.004 (38.050%) iter 2, dt=0.000983: new neg 1, old_neg 1, delta 0, rms=0.003 (38.476%) iter 3, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.002 (11.472%) 0466: dt=1.609195, rms=0.398 (6.810%), neg=0, invalid=96777 0467: dt=0.000000, rms=0.398 (-0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 32 after 6 iterations, nbhd size=1, neg = 0 0468: dt=0.050000, rms=0.398 (-0.282%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.398, neg=0, invalid=96777 0469: dt=0.000000, rms=0.398 (0.000%), neg=0, invalid=96777 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 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.388, neg=0, invalid=96777 0470: dt=0.000000, rms=0.389 (-0.257%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.389, neg=0, invalid=96777 0471: dt=8.092000, rms=0.389 (0.000%), neg=0, invalid=96777 0472: dt=0.022594, rms=0.389 (0.000%), neg=0, invalid=96777 0473: dt=0.022594, rms=0.389 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.389, neg=0, invalid=96777 0474: dt=0.000000, rms=0.389 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.389, neg=0, invalid=96777 0475: dt=20.736000, rms=0.389 (0.010%), neg=0, invalid=96777 0476: dt=9.072000, rms=0.389 (0.001%), neg=0, invalid=96777 0477: dt=9.072000, rms=0.389 (0.001%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... iter 1, dt=0.000219: new neg 0, old_neg 1, delta 1, rms=0.002 (8.503%) 0478: dt=9.072000, rms=0.389 (-0.002%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.390, neg=0, invalid=96777 iter 0, gcam->neg = 7 after 200 iterations, nbhd size=3, neg = 5 starting rms=0.009, neg=5, removing folds in lattice.... iter 1, dt=0.000023: new neg 3, old_neg 5, delta 2, rms=0.006 (38.790%) iter 2, dt=0.000036: new neg 1, old_neg 3, delta 2, rms=0.003 (53.059%) iter 3, dt=0.002294: new neg 0, old_neg 1, delta 1, rms=0.002 (31.134%) 0479: dt=6.400000, rms=0.389 (0.038%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 200 iterations, nbhd size=1, neg = 7 starting rms=0.010, neg=7, removing folds in lattice.... iter 1, dt=0.000023: new neg 2, old_neg 7, delta 5, rms=0.003 (69.772%) iter 2, dt=0.000036: new neg 1, old_neg 2, delta 1, rms=0.002 (26.573%) iter 3, dt=0.002294: new neg 0, old_neg 1, delta 1, rms=0.002 (25.000%) 0480: dt=6.400000, rms=0.389 (0.011%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 200 iterations, nbhd size=4, neg = 4 starting rms=0.008, neg=4, removing folds in lattice.... iter 1, dt=0.000055: new neg 0, old_neg 4, delta 4, rms=0.002 (76.007%) 0481: dt=6.400000, rms=0.389 (0.001%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 200 iterations, nbhd size=3, neg = 8 starting rms=0.013, neg=8, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 8, delta 7, rms=0.003 (80.001%) iter 2, dt=0.002294: new neg 0, old_neg 1, delta 1, rms=0.002 (36.989%) 0482: dt=6.400000, rms=0.389 (-0.038%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.389, neg=0, invalid=96777 iter 0, gcam->neg = 13 after 200 iterations, nbhd size=3, neg = 9 starting rms=0.014, neg=9, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 9, delta 8, rms=0.003 (79.740%) iter 2, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.002 (36.278%) 0483: dt=44.800000, rms=0.388 (0.413%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 200 iterations, nbhd size=3, neg = 10 starting rms=0.016, neg=10, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 10, delta 9, rms=0.003 (81.843%) iter 2, dt=0.000102: new neg 1, old_neg 1, delta 0, rms=0.002 (15.710%) iter 3, dt=0.000143: new neg 0, old_neg 1, delta 1, rms=0.002 (20.802%) 0484: dt=25.600000, rms=0.387 (0.165%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 200 iterations, nbhd size=1, neg = 5 starting rms=0.010, neg=5, removing folds in lattice.... iter 1, dt=0.000031: new neg 0, old_neg 5, delta 5, rms=0.002 (80.342%) 0485: dt=25.600000, rms=0.387 (0.088%), neg=0, invalid=96777 iter 0, gcam->neg = 9 after 200 iterations, nbhd size=4, neg = 10 starting rms=0.016, neg=10, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 10, delta 9, rms=0.003 (81.834%) iter 2, dt=0.000036: new neg 1, old_neg 1, delta 0, rms=0.003 (6.473%) iter 3, dt=0.002294: new neg 0, old_neg 1, delta 1, rms=0.002 (37.194%) 0486: dt=25.600000, rms=0.387 (0.069%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 200 iterations, nbhd size=3, neg = 6 starting rms=0.012, neg=6, removing folds in lattice.... iter 1, dt=0.000025: new neg 0, old_neg 6, delta 6, rms=0.002 (85.520%) 0487: dt=25.600000, rms=0.386 (0.073%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 200 iterations, nbhd size=4, neg = 6 starting rms=0.012, neg=6, removing folds in lattice.... iter 1, dt=0.000023: new neg 0, old_neg 6, delta 6, rms=0.002 (85.223%) 0488: dt=25.600000, rms=0.386 (0.060%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 200 iterations, nbhd size=4, neg = 5 starting rms=0.011, neg=5, removing folds in lattice.... iter 1, dt=0.000023: new neg 0, old_neg 5, delta 5, rms=0.002 (83.339%) 0489: dt=9.600000, rms=0.386 (0.023%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.388, neg=0, invalid=96777 iter 0, gcam->neg = 6 after 200 iterations, nbhd size=4, neg = 6 starting rms=0.013, neg=6, removing folds in lattice.... iter 1, dt=0.000023: new neg 0, old_neg 6, delta 6, rms=0.002 (85.944%) 0490: dt=0.864000, rms=0.388 (0.028%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 200 iterations, nbhd size=1, neg = 5 starting rms=0.011, neg=5, removing folds in lattice.... iter 1, dt=0.000023: new neg 0, old_neg 5, delta 5, rms=0.002 (84.363%) 0491: dt=0.576000, rms=0.387 (0.019%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 200 iterations, nbhd size=1, neg = 5 starting rms=0.011, neg=5, removing folds in lattice.... iter 1, dt=0.000023: new neg 0, old_neg 5, delta 5, rms=0.002 (84.376%) 0492: dt=0.576000, rms=0.387 (0.017%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 200 iterations, nbhd size=1, neg = 6 starting rms=0.013, neg=6, removing folds in lattice.... iter 1, dt=0.000023: new neg 0, old_neg 6, delta 6, rms=0.002 (85.950%) 0493: dt=0.576000, rms=0.387 (0.011%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 200 iterations, nbhd size=1, neg = 5 starting rms=0.011, neg=5, removing folds in lattice.... iter 1, dt=0.000031: new neg 0, old_neg 5, delta 5, rms=0.002 (84.215%) 0494: dt=0.576000, rms=0.387 (0.014%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0495: dt=0.576000, rms=0.387 (0.015%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 200 iterations, nbhd size=4, neg = 9 starting rms=0.015, neg=9, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 9, delta 8, rms=0.003 (83.020%) iter 2, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.002 (38.944%) 0496: dt=0.576000, rms=0.387 (0.007%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.387, neg=0, invalid=96777 iter 0, gcam->neg = 53 after 200 iterations, nbhd size=2, neg = 10 starting rms=0.016, neg=10, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 10, delta 9, rms=0.002 (84.615%) iter 2, dt=0.000036: new neg 1, old_neg 1, delta 0, rms=0.002 (9.001%) iter 3, dt=0.002294: new neg 0, old_neg 1, delta 1, rms=0.001 (44.466%) 0497: dt=6.912000, rms=0.386 (0.311%), neg=0, invalid=96777 iter 0, gcam->neg = 42 after 200 iterations, nbhd size=3, neg = 10 starting rms=0.015, neg=10, removing folds in lattice.... iter 1, dt=0.000023: new neg 2, old_neg 10, delta 8, rms=0.003 (81.360%) iter 2, dt=0.000036: new neg 1, old_neg 2, delta 1, rms=0.003 (11.557%) iter 3, dt=0.000160: new neg 0, old_neg 1, delta 1, rms=0.002 (31.790%) 0498: dt=5.647059, rms=0.385 (0.182%), neg=0, invalid=96777 iter 0, gcam->neg = 46 after 200 iterations, nbhd size=3, neg = 10 starting rms=0.015, neg=10, removing folds in lattice.... iter 1, dt=0.000023: new neg 2, old_neg 10, delta 8, rms=0.003 (82.931%) iter 2, dt=0.000036: new neg 1, old_neg 2, delta 1, rms=0.002 (10.906%) iter 3, dt=0.002294: new neg 0, old_neg 1, delta 1, rms=0.001 (45.042%) 0499: dt=5.647059, rms=0.385 (0.040%), neg=0, invalid=96777 iter 0, gcam->neg = 56 after 200 iterations, nbhd size=3, neg = 10 starting rms=0.015, neg=10, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 10, delta 9, rms=0.002 (83.942%) iter 2, dt=0.000102: new neg 1, old_neg 1, delta 0, rms=0.002 (25.590%) iter 3, dt=0.002294: new neg 0, old_neg 1, delta 1, rms=0.001 (32.707%) 0500: dt=5.647059, rms=0.385 (0.151%), neg=0, invalid=96777 iter 0, gcam->neg = 41 after 200 iterations, nbhd size=3, neg = 10 starting rms=0.015, neg=10, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 10, delta 9, rms=0.002 (84.271%) iter 2, dt=0.000184: new neg 0, old_neg 1, delta 1, rms=0.001 (43.406%) 0501: dt=5.647059, rms=0.384 (0.111%), neg=0, invalid=96777 iter 0, gcam->neg = 30 after 200 iterations, nbhd size=3, neg = 10 starting rms=0.015, neg=10, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 10, delta 9, rms=0.002 (84.238%) iter 2, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.001 (46.406%) 0502: dt=5.647059, rms=0.384 (0.064%), neg=0, invalid=96777 iter 0, gcam->neg = 15 after 200 iterations, nbhd size=4, neg = 10 starting rms=0.015, neg=10, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 10, delta 9, rms=0.002 (84.868%) iter 2, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.001 (46.548%) 0503: dt=3.456000, rms=0.384 (0.044%), neg=0, invalid=96777 iter 0, gcam->neg = 14 after 200 iterations, nbhd size=3, neg = 10 starting rms=0.015, neg=10, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 10, delta 9, rms=0.002 (84.761%) iter 2, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.001 (45.915%) 0504: dt=3.456000, rms=0.384 (0.042%), neg=0, invalid=96777 iter 0, gcam->neg = 14 after 200 iterations, nbhd size=4, neg = 10 starting rms=0.015, neg=10, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 10, delta 9, rms=0.002 (84.797%) iter 2, dt=0.001638: new neg 0, old_neg 1, delta 1, rms=0.001 (47.192%) 0505: dt=3.456000, rms=0.383 (0.035%), neg=0, invalid=96777 iter 0, gcam->neg = 19 after 200 iterations, nbhd size=4, neg = 10 starting rms=0.015, neg=10, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 10, delta 9, rms=0.002 (84.768%) iter 2, dt=0.001966: new neg 0, old_neg 1, delta 1, rms=0.001 (47.488%) 0506: dt=3.456000, rms=0.383 (0.031%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.387, neg=0, invalid=96777 0507: dt=0.000000, rms=0.387 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.387, neg=0, invalid=96777 0508: dt=0.000000, rms=0.387 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.381, neg=0, invalid=96777 iter 0, gcam->neg = 234 after 22 iterations, nbhd size=2, neg = 0 0509: dt=0.480699, rms=0.374 (1.837%), neg=0, invalid=96777 0510: dt=0.007000, rms=0.374 (0.001%), neg=0, invalid=96777 0511: dt=0.007000, rms=0.374 (0.001%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0512: dt=0.007000, rms=0.374 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0513: dt=0.007000, rms=0.374 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0514: dt=0.007000, rms=0.374 (0.001%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0515: dt=0.007000, rms=0.374 (0.002%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0516: dt=0.007000, rms=0.374 (0.001%), neg=0, invalid=96777 0517: dt=0.007000, rms=0.374 (0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.374, neg=0, invalid=96777 iter 0, gcam->neg = 122 after 21 iterations, nbhd size=2, neg = 0 0518: dt=0.287109, rms=0.371 (0.628%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0519: dt=0.005000, rms=0.371 (0.005%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0520: dt=0.005000, rms=0.371 (0.004%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0521: dt=0.005000, rms=0.371 (0.008%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0522: dt=0.005000, rms=0.371 (0.012%), neg=0, invalid=96777 0523: dt=0.005000, rms=0.371 (0.015%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0524: dt=0.005000, rms=0.371 (0.017%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0525: dt=0.005000, rms=0.371 (0.020%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0526: dt=0.005000, rms=0.371 (0.022%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0527: dt=0.005000, rms=0.371 (0.023%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0528: dt=0.005000, rms=0.371 (0.024%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0529: dt=0.005000, rms=0.371 (0.025%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0530: dt=0.005000, rms=0.371 (0.025%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0531: dt=0.005000, rms=0.370 (0.025%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0532: dt=0.005000, rms=0.370 (0.025%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0533: dt=0.005000, rms=0.370 (0.025%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0534: dt=0.012000, rms=0.370 (0.004%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 2 hours, 24 minutes and 19 seconds. #-------------------------------------- #@# CA Reg Inv Thu Oct 6 20:26:30 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Thu Oct 6 20:27:12 EDT 2016 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... removing structures at least 25 mm from brain... 11582687 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 0 minutes and 46 seconds. #-------------------------------------- #@# SkullLTA Thu Oct 6 20:27:58 EDT 2016 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=9.0 skull bounding box = (52, 40, 23) --> (201, 216, 226) using (102, 99, 125) as brain centroid... mean wm in atlas = 126, using box (84,77,100) --> (120, 120,150) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 107, scaling input intensities by 1.178 scaling channel 0 by 1.17757 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.8, old_max_log_p =-3.9 (thresh=-3.9) 1.104 -0.009 0.063 -20.678; 0.004 1.262 0.100 -38.785; -0.084 -0.115 1.113 -0.386; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.104 -0.009 0.063 -20.678; 0.004 1.262 0.100 -38.785; -0.077 -0.106 1.029 7.596; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.124 -0.053 0.059 -17.710; 0.037 1.279 0.136 -49.357; -0.078 -0.149 1.025 13.077; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.124 -0.053 0.059 -17.710; 0.037 1.279 0.136 -49.357; -0.078 -0.149 1.025 13.077; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.124 -0.031 0.053 -19.925; 0.021 1.283 0.102 -43.688; -0.067 -0.108 1.028 5.578; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.124 -0.031 0.053 -19.925; 0.021 1.283 0.102 -43.688; -0.067 -0.108 1.028 5.578; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.12360 -0.03080 0.05267 -19.92549; 0.02091 1.28269 0.10183 -43.68766; -0.06704 -0.10774 1.02839 5.57813; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.12360 -0.03080 0.05267 -19.92549; 0.02091 1.28269 0.10183 -43.68766; -0.06704 -0.10774 1.02839 5.57813; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.124 -0.031 0.053 -19.925; 0.021 1.283 0.102 -43.688; -0.067 -0.108 1.028 5.578; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.8 (old=-3.9) transform before final EM align: 1.124 -0.031 0.053 -19.925; 0.021 1.283 0.102 -43.688; -0.067 -0.108 1.028 5.578; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.12360 -0.03080 0.05267 -19.92549; 0.02091 1.28269 0.10183 -43.68766; -0.06704 -0.10774 1.02839 5.57813; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.12360 -0.03080 0.05267 -19.92549; 0.02091 1.28269 0.10183 -43.68766; -0.06704 -0.10774 1.02839 5.57813; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 008: -log(p) = 4.2 after pass:transform: ( 1.12, -0.03, 0.05, -19.93) ( 0.02, 1.28, 0.10, -43.69) ( -0.07, -0.11, 1.03, 5.58) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.2 tol 0.000000 final transform: 1.124 -0.031 0.053 -19.925; 0.021 1.283 0.102 -43.688; -0.067 -0.108 1.028 5.578; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 16 minutes and 34 seconds. #-------------------------------------- #@# SubCort Seg Thu Oct 6 20:44:32 EDT 2016 mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname jmlina2 machine x86_64 setenv SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets cd /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /usr/local/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.11133 (16) Left_Lateral_Ventricle (4): linear fit = 0.56 x + 0.0 (622 voxels, overlap=0.177) Left_Lateral_Ventricle (4): linear fit = 0.56 x + 0.0 (622 voxels, peak = 15), gca=15.3 gca peak = 0.14982 (20) mri peak = 0.11061 (18) Right_Lateral_Ventricle (43): linear fit = 0.71 x + 0.0 (648 voxels, overlap=0.415) Right_Lateral_Ventricle (43): linear fit = 0.71 x + 0.0 (648 voxels, peak = 14), gca=14.3 gca peak = 0.28003 (97) mri peak = 0.08647 (100) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (266 voxels, overlap=1.023) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (266 voxels, peak = 97), gca=97.5 gca peak = 0.18160 (96) mri peak = 0.09412 (100) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (289 voxels, overlap=0.864) Left_Pallidum (13): linear fit = 1.03 x + 0.0 (289 voxels, peak = 99), gca=99.4 gca peak = 0.27536 (62) mri peak = 0.09208 (67) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (388 voxels, overlap=1.008) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (388 voxels, peak = 62), gca=62.0 gca peak = 0.32745 (63) mri peak = 0.08220 (63) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (380 voxels, overlap=1.010) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (380 voxels, peak = 62), gca=62.1 gca peak = 0.08597 (105) mri peak = 0.10069 (108) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (27397 voxels, overlap=0.653) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (27397 voxels, peak = 108), gca=107.6 gca peak = 0.09209 (106) mri peak = 0.08712 (111) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (27983 voxels, overlap=0.613) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (27983 voxels, peak = 111), gca=110.8 gca peak = 0.07826 (63) mri peak = 0.04752 (58) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (11008 voxels, overlap=0.748) Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (11008 voxels, peak = 58), gca=57.6 gca peak = 0.08598 (64) mri peak = 0.04227 (60) Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (10619 voxels, overlap=0.729) Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (10619 voxels, peak = 59), gca=58.6 gca peak = 0.24164 (71) mri peak = 0.08623 (76) Right_Caudate (50): linear fit = 1.03 x + 0.0 (773 voxels, overlap=1.007) Right_Caudate (50): linear fit = 1.03 x + 0.0 (773 voxels, peak = 73), gca=73.5 gca peak = 0.18227 (75) mri peak = 0.09175 (77) Left_Caudate (11): linear fit = 0.99 x + 0.0 (914 voxels, overlap=0.945) Left_Caudate (11): linear fit = 0.99 x + 0.0 (914 voxels, peak = 74), gca=73.9 gca peak = 0.10629 (62) mri peak = 0.05041 (63) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (5981 voxels, overlap=0.903) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (5981 voxels, peak = 67), gca=66.7 gca peak = 0.11668 (59) mri peak = 0.05937 (63) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (7691 voxels, overlap=0.926) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (7691 voxels, peak = 63), gca=63.4 gca peak = 0.17849 (88) mri peak = 0.07882 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (3954 voxels, overlap=0.922) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (3954 voxels, peak = 92), gca=92.0 gca peak = 0.16819 (86) mri peak = 0.09533 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (4176 voxels, overlap=0.944) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (4176 voxels, peak = 89), gca=89.0 gca peak = 0.41688 (64) mri peak = 0.09722 (63) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (140 voxels, overlap=1.036) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (140 voxels, peak = 65), gca=65.0 gca peak = 0.42394 (62) mri peak = 0.10658 (62) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (154 voxels, overlap=1.046) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (154 voxels, peak = 61), gca=61.1 gca peak = 0.10041 (96) mri peak = 0.07065 (94) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3330 voxels, overlap=0.957) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3330 voxels, peak = 96), gca=96.0 gca peak = 0.13978 (88) mri peak = 0.06532 (93) Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (3612 voxels, overlap=0.988) Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (3612 voxels, peak = 91), gca=91.1 gca peak = 0.08514 (81) mri peak = 0.06772 (83) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1413 voxels, overlap=0.964) Left_Putamen (12): linear fit = 1.01 x + 0.0 (1413 voxels, peak = 82), gca=82.2 gca peak = 0.09624 (82) mri peak = 0.06494 (83) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1291 voxels, overlap=0.977) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1291 voxels, peak = 81), gca=80.8 gca peak = 0.07543 (88) mri peak = 0.07263 (88) Brain_Stem (16): linear fit = 1.03 x + 0.0 (8686 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.03 x + 0.0 (8686 voxels, peak = 91), gca=91.1 gca peak = 0.12757 (95) mri peak = 0.07595 (96) Right_VentralDC (60): linear fit = 1.04 x + 0.0 (671 voxels, overlap=0.723) Right_VentralDC (60): linear fit = 1.04 x + 0.0 (671 voxels, peak = 99), gca=99.3 gca peak = 0.17004 (92) mri peak = 0.07403 (103) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (824 voxels, overlap=0.888) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (824 voxels, peak = 96), gca=96.1 gca peak = 0.21361 (36) mri peak = 1.00000 (16) gca peak = 0.26069 (23) mri peak = 0.15385 (18) Fourth_Ventricle (15): linear fit = 0.73 x + 0.0 (78 voxels, overlap=0.074) Fourth_Ventricle (15): linear fit = 0.73 x + 0.0 (78 voxels, peak = 17), gca=16.7 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.97 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 0.67 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.21843 (15) mri peak = 0.11133 (16) Left_Lateral_Ventricle (4): linear fit = 1.11 x + 0.0 (622 voxels, overlap=0.999) Left_Lateral_Ventricle (4): linear fit = 1.11 x + 0.0 (622 voxels, peak = 17), gca=16.6 gca peak = 0.19394 (15) mri peak = 0.11061 (18) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (648 voxels, overlap=0.913) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (648 voxels, peak = 16), gca=15.5 gca peak = 0.29719 (98) mri peak = 0.08647 (100) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (266 voxels, overlap=1.019) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (266 voxels, peak = 98), gca=98.5 gca peak = 0.18331 (99) mri peak = 0.09412 (100) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (289 voxels, overlap=1.003) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (289 voxels, peak = 99), gca=99.5 gca peak = 0.27302 (62) mri peak = 0.09208 (67) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (388 voxels, overlap=1.008) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (388 voxels, peak = 62), gca=62.0 gca peak = 0.29241 (62) mri peak = 0.08220 (63) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (380 voxels, overlap=1.008) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (380 voxels, peak = 62), gca=62.0 gca peak = 0.08345 (108) mri peak = 0.10069 (108) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (27397 voxels, overlap=0.757) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (27397 voxels, peak = 109), gca=108.5 gca peak = 0.08576 (111) mri peak = 0.08712 (111) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (27983 voxels, overlap=0.753) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (27983 voxels, peak = 111), gca=111.0 gca peak = 0.08263 (58) mri peak = 0.04752 (58) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (11008 voxels, overlap=0.977) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (11008 voxels, peak = 58), gca=58.0 gca peak = 0.09561 (58) mri peak = 0.04227 (60) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (10619 voxels, overlap=0.973) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (10619 voxels, peak = 59), gca=59.4 gca peak = 0.29688 (76) mri peak = 0.08623 (76) Right_Caudate (50): linear fit = 1.00 x + 0.0 (773 voxels, overlap=1.009) Right_Caudate (50): linear fit = 1.00 x + 0.0 (773 voxels, peak = 76), gca=76.0 gca peak = 0.17616 (74) mri peak = 0.09175 (77) Left_Caudate (11): linear fit = 1.00 x + 0.0 (914 voxels, overlap=1.002) Left_Caudate (11): linear fit = 1.00 x + 0.0 (914 voxels, peak = 74), gca=74.0 gca peak = 0.09721 (65) mri peak = 0.05041 (63) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (5981 voxels, overlap=0.995) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (5981 voxels, peak = 65), gca=65.0 gca peak = 0.12072 (64) mri peak = 0.05937 (63) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (7691 voxels, overlap=0.997) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (7691 voxels, peak = 63), gca=63.0 gca peak = 0.17369 (92) mri peak = 0.07882 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3954 voxels, overlap=0.995) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3954 voxels, peak = 92), gca=91.5 gca peak = 0.16430 (89) mri peak = 0.09533 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4176 voxels, overlap=0.995) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4176 voxels, peak = 89), gca=88.6 gca peak = 0.32957 (64) mri peak = 0.09722 (63) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (140 voxels, overlap=1.027) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (140 voxels, peak = 64), gca=64.0 gca peak = 0.44034 (62) mri peak = 0.10658 (62) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (154 voxels, overlap=1.046) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (154 voxels, peak = 62), gca=62.0 gca peak = 0.11183 (96) mri peak = 0.07065 (94) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3330 voxels, overlap=0.957) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3330 voxels, peak = 97), gca=97.4 gca peak = 0.13039 (91) mri peak = 0.06532 (93) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3612 voxels, overlap=0.942) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3612 voxels, peak = 91), gca=91.0 gca peak = 0.07944 (82) mri peak = 0.06772 (83) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1413 voxels, overlap=0.997) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1413 voxels, peak = 82), gca=81.6 gca peak = 0.10801 (75) mri peak = 0.06494 (83) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1291 voxels, overlap=0.999) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1291 voxels, peak = 76), gca=76.1 gca peak = 0.07088 (91) mri peak = 0.07263 (88) Brain_Stem (16): linear fit = 1.00 x + 0.0 (8686 voxels, overlap=0.835) Brain_Stem (16): linear fit = 1.00 x + 0.0 (8686 voxels, peak = 91), gca=90.5 gca peak = 0.13434 (99) mri peak = 0.07595 (96) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (671 voxels, overlap=0.802) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (671 voxels, peak = 101), gca=101.5 gca peak = 0.15198 (96) mri peak = 0.07403 (103) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (824 voxels, overlap=0.933) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (824 voxels, peak = 96), gca=96.5 gca peak = 0.25344 (24) mri peak = 1.00000 (16) gca peak = 0.24206 (17) mri peak = 0.15385 (18) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (78 voxels, overlap=0.750) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (78 voxels, peak = 17), gca=16.6 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.23355 (35) gca peak Third_Ventricle = 0.25344 (24) gca peak CSF = 0.25014 (26) gca peak Left_Accumbens_area = 0.51641 (69) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.58977 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.32960 (32) gca peak Right_Accumbens_area = 0.40248 (74) gca peak Right_vessel = 0.71181 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.45329 (29) gca peak WM_hypointensities = 0.14483 (84) gca peak non_WM_hypointensities = 0.10275 (55) gca peak Optic_Chiasm = 0.34840 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.04 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 14772 gm and wm labels changed (%14 to gray, %86 to white out of all changed labels) 262 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 83551 changed. image ll: -2.151, PF=1.000 pass 2: 13181 changed. image ll: -2.149, PF=1.000 pass 3: 4076 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 13 minutes and 9 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/transforms/cc_up.lta 16945 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/transforms/cc_up.lta reading aseg from /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/aseg.auto_noCCseg.mgz reading norm from /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/norm.mgz 44176 voxels in left wm, 42854 in right wm, xrange [121, 132] searching rotation angles z=[-5 9], y=[-4 10] searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.8 searching scale 1 Z rot 7.0 searching scale 1 Z rot 7.3 searching scale 1 Z rot 7.5 searching scale 1 Z rot 7.8 searching scale 1 Z rot 8.0 searching scale 1 Z rot 8.3 searching scale 1 Z rot 8.5 searching scale 1 Z rot 8.8 global minimum found at slice 126.3, rotations (3.20, 2.01) final transformation (x=126.3, yr=3.199, zr=2.009): 0.998 -0.035 0.056 -0.873; 0.035 0.999 0.002 21.417; -0.056 -0.000 0.998 20.229; 0.000 0.000 0.000 1.000; updating x range to be [126, 130] in xformed coordinates best xformed slice 129 cc center is found at 129 145 166 eigenvectors: 0.001 0.001 1.000; 0.028 -1.000 0.001; 1.000 0.028 -0.001; error in mid anterior detected - correcting... writing aseg with callosum to /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.6 minutes #-------------------------------------- #@# Merge ASeg Thu Oct 6 20:58:16 EDT 2016 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Oct 6 20:58:16 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri mri_normalize -aseg aseg.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.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 4060 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 111 white matter peak found at 108 gm peak at 66 (66), valley at 30 (30) 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 111 white matter peak found at 110 gm peak at 65 (65), valley at 31 (31) 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 2 minutes and 8 seconds. #-------------------------------------------- #@# Mask BFS Thu Oct 6 21:00:24 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1420743 voxels in mask (pct= 8.47) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Oct 6 21:00:26 EDT 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 (107.0): 107.2 +- 5.3 [80.0 --> 125.0] GM (69.0) : 68.2 +- 9.5 [30.0 --> 96.0] setting bottom of white matter range to 77.7 setting top of gray matter range to 87.2 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 14493 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5813 filled 268 bright non-wm voxels segmented. 5825 diagonally connected voxels added... white matter segmentation took 1.0 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.33 minutes reading wm segmentation from wm.seg.mgz... 34 voxels added to wm to prevent paths from MTL structures to cortex 1075 additional wm voxels added 0 additional wm voxels added SEG EDIT: 39136 voxels turned on, 43528 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 104 new 104 115,126,128 old 104 new 104 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 13 found - 13 modified | TOTAL: 13 pass 2 (xy+): 0 found - 13 modified | TOTAL: 13 pass 1 (xy-): 15 found - 15 modified | TOTAL: 28 pass 2 (xy-): 0 found - 15 modified | TOTAL: 28 pass 1 (yz+): 21 found - 21 modified | TOTAL: 49 pass 2 (yz+): 0 found - 21 modified | TOTAL: 49 pass 1 (yz-): 10 found - 10 modified | TOTAL: 59 pass 2 (yz-): 0 found - 10 modified | TOTAL: 59 pass 1 (xz+): 16 found - 16 modified | TOTAL: 75 pass 2 (xz+): 0 found - 16 modified | TOTAL: 75 pass 1 (xz-): 19 found - 19 modified | TOTAL: 94 pass 2 (xz-): 0 found - 19 modified | TOTAL: 94 Iteration Number : 1 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 16 found - 16 modified | TOTAL: 22 pass 2 (+++): 0 found - 16 modified | TOTAL: 22 pass 1 (+++): 14 found - 14 modified | TOTAL: 36 pass 2 (+++): 0 found - 14 modified | TOTAL: 36 pass 1 (+++): 12 found - 12 modified | TOTAL: 48 pass 2 (+++): 0 found - 12 modified | TOTAL: 48 Iteration Number : 1 pass 1 (++): 186 found - 186 modified | TOTAL: 186 pass 2 (++): 0 found - 186 modified | TOTAL: 186 pass 1 (+-): 197 found - 197 modified | TOTAL: 383 pass 2 (+-): 0 found - 197 modified | TOTAL: 383 pass 1 (--): 133 found - 133 modified | TOTAL: 516 pass 2 (--): 0 found - 133 modified | TOTAL: 516 pass 1 (-+): 201 found - 201 modified | TOTAL: 717 pass 2 (-+): 0 found - 201 modified | TOTAL: 717 Iteration Number : 2 pass 1 (xy+): 8 found - 8 modified | TOTAL: 8 pass 2 (xy+): 0 found - 8 modified | TOTAL: 8 pass 1 (xy-): 1 found - 1 modified | TOTAL: 9 pass 2 (xy-): 0 found - 1 modified | TOTAL: 9 pass 1 (yz+): 3 found - 3 modified | TOTAL: 12 pass 2 (yz+): 0 found - 3 modified | TOTAL: 12 pass 1 (yz-): 4 found - 4 modified | TOTAL: 16 pass 2 (yz-): 0 found - 4 modified | TOTAL: 16 pass 1 (xz+): 2 found - 2 modified | TOTAL: 18 pass 2 (xz+): 0 found - 2 modified | TOTAL: 18 pass 1 (xz-): 2 found - 2 modified | TOTAL: 20 pass 2 (xz-): 0 found - 2 modified | TOTAL: 20 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 1 found - 1 modified | TOTAL: 3 pass 2 (+++): 0 found - 1 modified | TOTAL: 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 3 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 2 found - 2 modified | TOTAL: 3 pass 2 (+-): 0 found - 2 modified | TOTAL: 3 pass 1 (--): 2 found - 2 modified | TOTAL: 5 pass 2 (--): 0 found - 2 modified | TOTAL: 5 pass 1 (-+): 2 found - 2 modified | TOTAL: 7 pass 2 (-+): 0 found - 2 modified | TOTAL: 7 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 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-): 1 found - 1 modified | TOTAL: 3 pass 2 (xz-): 0 found - 1 modified | TOTAL: 3 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 893 (out of 494528: 0.180576) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Oct 6 21:01:49 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/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 1.104 -0.009 0.063 -20.678; 0.004 1.186 0.094 -29.203; -0.078 -0.107 1.035 7.039; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.104 -0.009 0.063 -20.678; 0.004 1.186 0.094 -29.203; -0.078 -0.107 1.035 7.039; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1266 (min = 350, max = 1400), aspect = 0.52 (min = 0.10, max = 0.75) no need to search using seed (126, 110, 90), TAL = (2.0, -38.0, 18.0) talairach voxel to voxel transform 0.902 0.002 -0.055 19.096; -0.008 0.836 -0.075 24.785; 0.067 0.087 0.954 -2.800; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 110, 90) --> (2.0, -38.0, 18.0) done. writing output to filled.mgz... filling took 0.5 minutes talairach cc position changed to (2.00, -38.00, 18.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -38.00, 18.00) SRC: (111.78, 109.15, 99.86) search lh wm seed point around talairach space (-16.00, -38.00, 18.00), SRC: (144.26, 108.86, 102.28) 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 Thu Oct 6 21:02:18 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 3 found - 3 modified | TOTAL: 4 pass 2 (yz+): 0 found - 3 modified | TOTAL: 4 pass 1 (yz-): 0 found - 0 modified | TOTAL: 4 pass 1 (xz+): 2 found - 2 modified | TOTAL: 6 pass 2 (xz+): 0 found - 2 modified | TOTAL: 6 pass 1 (xz-): 1 found - 1 modified | TOTAL: 7 pass 2 (xz-): 0 found - 1 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 0 found - 0 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 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 = 10 (out of 236655: 0.004226) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 40: 136 vertices, 168 faces slice 50: 4440 vertices, 4660 faces slice 60: 11853 vertices, 12131 faces slice 70: 21639 vertices, 21977 faces slice 80: 31621 vertices, 31999 faces slice 90: 41683 vertices, 42013 faces slice 100: 52123 vertices, 52485 faces slice 110: 63671 vertices, 64063 faces slice 120: 74772 vertices, 75212 faces slice 130: 85501 vertices, 85917 faces slice 140: 96132 vertices, 96565 faces slice 150: 105789 vertices, 106164 faces slice 160: 114207 vertices, 114518 faces slice 170: 121743 vertices, 122052 faces slice 180: 128324 vertices, 128617 faces slice 190: 133737 vertices, 133966 faces slice 200: 136732 vertices, 136838 faces slice 210: 136866 vertices, 136934 faces slice 220: 136866 vertices, 136934 faces slice 230: 136866 vertices, 136934 faces slice 240: 136866 vertices, 136934 faces slice 250: 136866 vertices, 136934 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 136866 voxel in cpt #1: X=-68 [v=136866,e=410802,f=273868] located at (-24.561556, -13.443222, 19.200758) For the whole surface: X=-68 [v=136866,e=410802,f=273868] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Oct 6 21:02:22 EDT 2016 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Thu Oct 6 21:02:25 EDT 2016 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts avg radius = 46.1 mm, total surface area = 69771 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.3 minutes Not saving sulc step 000: RMS=0.105 (target=0.015) step 005: RMS=0.077 (target=0.015) step 010: RMS=0.057 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.041 (target=0.015) step 025: RMS=0.037 (target=0.015) step 030: RMS=0.032 (target=0.015) step 035: RMS=0.029 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.026 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.024 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Thu Oct 6 21:02:43 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/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 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.98 +- 0.59 (0.00-->7.33) (max @ vno 48748 --> 49778) face area 0.02 +- 0.03 (-0.16-->0.71) scaling brain by 0.305... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.210, avgs=0 005/300: dt: 0.9000, rms radial error=176.952, avgs=0 010/300: dt: 0.9000, rms radial error=176.397, avgs=0 015/300: dt: 0.9000, rms radial error=175.669, avgs=0 020/300: dt: 0.9000, rms radial error=174.838, avgs=0 025/300: dt: 0.9000, rms radial error=173.950, avgs=0 030/300: dt: 0.9000, rms radial error=173.029, avgs=0 035/300: dt: 0.9000, rms radial error=172.092, avgs=0 040/300: dt: 0.9000, rms radial error=171.146, avgs=0 045/300: dt: 0.9000, rms radial error=170.197, avgs=0 050/300: dt: 0.9000, rms radial error=169.249, avgs=0 055/300: dt: 0.9000, rms radial error=168.303, avgs=0 060/300: dt: 0.9000, rms radial error=167.361, avgs=0 065/300: dt: 0.9000, rms radial error=166.422, avgs=0 070/300: dt: 0.9000, rms radial error=165.488, avgs=0 075/300: dt: 0.9000, rms radial error=164.560, avgs=0 080/300: dt: 0.9000, rms radial error=163.636, avgs=0 085/300: dt: 0.9000, rms radial error=162.718, avgs=0 090/300: dt: 0.9000, rms radial error=161.804, avgs=0 095/300: dt: 0.9000, rms radial error=160.895, avgs=0 100/300: dt: 0.9000, rms radial error=159.991, avgs=0 105/300: dt: 0.9000, rms radial error=159.092, avgs=0 110/300: dt: 0.9000, rms radial error=158.197, avgs=0 115/300: dt: 0.9000, rms radial error=157.308, avgs=0 120/300: dt: 0.9000, rms radial error=156.423, avgs=0 125/300: dt: 0.9000, rms radial error=155.543, avgs=0 130/300: dt: 0.9000, rms radial error=154.668, avgs=0 135/300: dt: 0.9000, rms radial error=153.798, avgs=0 140/300: dt: 0.9000, rms radial error=152.932, avgs=0 145/300: dt: 0.9000, rms radial error=152.071, avgs=0 150/300: dt: 0.9000, rms radial error=151.215, avgs=0 155/300: dt: 0.9000, rms radial error=150.364, avgs=0 160/300: dt: 0.9000, rms radial error=149.518, avgs=0 165/300: dt: 0.9000, rms radial error=148.677, avgs=0 170/300: dt: 0.9000, rms radial error=147.840, avgs=0 175/300: dt: 0.9000, rms radial error=147.008, avgs=0 180/300: dt: 0.9000, rms radial error=146.181, avgs=0 185/300: dt: 0.9000, rms radial error=145.358, avgs=0 190/300: dt: 0.9000, rms radial error=144.540, avgs=0 195/300: dt: 0.9000, rms radial error=143.726, avgs=0 200/300: dt: 0.9000, rms radial error=142.916, avgs=0 205/300: dt: 0.9000, rms radial error=142.111, avgs=0 210/300: dt: 0.9000, rms radial error=141.311, avgs=0 215/300: dt: 0.9000, rms radial error=140.515, avgs=0 220/300: dt: 0.9000, rms radial error=139.723, avgs=0 225/300: dt: 0.9000, rms radial error=138.935, avgs=0 230/300: dt: 0.9000, rms radial error=138.152, avgs=0 235/300: dt: 0.9000, rms radial error=137.374, avgs=0 240/300: dt: 0.9000, rms radial error=136.599, avgs=0 245/300: dt: 0.9000, rms radial error=135.829, avgs=0 250/300: dt: 0.9000, rms radial error=135.063, avgs=0 255/300: dt: 0.9000, rms radial error=134.302, avgs=0 260/300: dt: 0.9000, rms radial error=133.545, avgs=0 265/300: dt: 0.9000, rms radial error=132.792, avgs=0 270/300: dt: 0.9000, rms radial error=132.043, avgs=0 275/300: dt: 0.9000, rms radial error=131.298, avgs=0 280/300: dt: 0.9000, rms radial error=130.558, avgs=0 285/300: dt: 0.9000, rms radial error=129.821, avgs=0 290/300: dt: 0.9000, rms radial error=129.089, avgs=0 295/300: dt: 0.9000, rms radial error=128.361, avgs=0 300/300: dt: 0.9000, rms radial error=127.637, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16204.48 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 = 2776.50 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00005 epoch 3 (K=160.0), pass 1, starting sse = 310.87 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00645 epoch 4 (K=640.0), pass 1, starting sse = 21.25 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/14 = 0.00739 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.04 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Thu Oct 6 21:05:16 EDT 2016 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 16945 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 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-68 (nv=136866, nf=273868, ne=410802, g=35) 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 10 iterations marking ambiguous vertices... 3882 ambiguous faces found in tessellation segmenting defects... 39 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 34 into 23 -merging segment 26 into 27 -merging segment 32 into 30 36 defects to be corrected 0 vertices coincident reading input surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5035 (-4.7518) -vertex loglikelihood: -6.5591 (-3.2796) -normal dot loglikelihood: -3.5762 (-3.5762) -quad curv loglikelihood: -6.5955 (-3.2978) Total Loglikelihood : -26.2344 CORRECTING DEFECT 0 (vertices=76, convex hull=97) After retessellation of defect 0, euler #=-36 (134527,402626,268063) : difference with theory (-33) = 3 CORRECTING DEFECT 1 (vertices=25, convex hull=63) After retessellation of defect 1, euler #=-35 (134537,402683,268111) : difference with theory (-32) = 3 CORRECTING DEFECT 2 (vertices=25, convex hull=42) After retessellation of defect 2, euler #=-34 (134543,402717,268140) : difference with theory (-31) = 3 CORRECTING DEFECT 3 (vertices=23, convex hull=49) After retessellation of defect 3, euler #=-33 (134555,402774,268186) : difference with theory (-30) = 3 CORRECTING DEFECT 4 (vertices=21, convex hull=41) After retessellation of defect 4, euler #=-32 (134564,402816,268220) : difference with theory (-29) = 3 CORRECTING DEFECT 5 (vertices=45, convex hull=29) After retessellation of defect 5, euler #=-31 (134567,402833,268235) : difference with theory (-28) = 3 CORRECTING DEFECT 6 (vertices=19, convex hull=39) After retessellation of defect 6, euler #=-30 (134571,402861,268260) : difference with theory (-27) = 3 CORRECTING DEFECT 7 (vertices=43, convex hull=88) After retessellation of defect 7, euler #=-29 (134599,402985,268357) : difference with theory (-26) = 3 CORRECTING DEFECT 8 (vertices=42, convex hull=70) After retessellation of defect 8, euler #=-28 (134627,403098,268443) : difference with theory (-25) = 3 CORRECTING DEFECT 9 (vertices=18, convex hull=42) After retessellation of defect 9, euler #=-27 (134634,403129,268468) : difference with theory (-24) = 3 CORRECTING DEFECT 10 (vertices=43, convex hull=71) After retessellation of defect 10, euler #=-26 (134656,403226,268544) : difference with theory (-23) = 3 CORRECTING DEFECT 11 (vertices=125, convex hull=108) After retessellation of defect 11, euler #=-25 (134713,403442,268704) : difference with theory (-22) = 3 CORRECTING DEFECT 12 (vertices=48, convex hull=60) After retessellation of defect 12, euler #=-24 (134728,403515,268763) : difference with theory (-21) = 3 CORRECTING DEFECT 13 (vertices=173, convex hull=113) After retessellation of defect 13, euler #=-23 (134782,403731,268926) : difference with theory (-20) = 3 CORRECTING DEFECT 14 (vertices=32, convex hull=57) After retessellation of defect 14, euler #=-22 (134803,403818,268993) : difference with theory (-19) = 3 CORRECTING DEFECT 15 (vertices=17, convex hull=34) After retessellation of defect 15, euler #=-21 (134812,403856,269023) : difference with theory (-18) = 3 CORRECTING DEFECT 16 (vertices=9, convex hull=19) After retessellation of defect 16, euler #=-20 (134813,403863,269030) : difference with theory (-17) = 3 CORRECTING DEFECT 17 (vertices=40, convex hull=34) After retessellation of defect 17, euler #=-19 (134822,403902,269061) : difference with theory (-16) = 3 CORRECTING DEFECT 18 (vertices=23, convex hull=26) After retessellation of defect 18, euler #=-18 (134825,403918,269075) : difference with theory (-15) = 3 CORRECTING DEFECT 19 (vertices=77, convex hull=83) After retessellation of defect 19, euler #=-17 (134857,404050,269176) : difference with theory (-14) = 3 CORRECTING DEFECT 20 (vertices=28, convex hull=54) After retessellation of defect 20, euler #=-16 (134867,404101,269218) : difference with theory (-13) = 3 CORRECTING DEFECT 21 (vertices=19, convex hull=34) After retessellation of defect 21, euler #=-15 (134869,404120,269236) : difference with theory (-12) = 3 CORRECTING DEFECT 22 (vertices=5, convex hull=17) After retessellation of defect 22, euler #=-14 (134871,404129,269244) : difference with theory (-11) = 3 CORRECTING DEFECT 23 (vertices=819, convex hull=366) After retessellation of defect 23, euler #=-12 (135099,405002,269891) : difference with theory (-10) = 2 CORRECTING DEFECT 24 (vertices=18, convex hull=29) After retessellation of defect 24, euler #=-11 (135104,405022,269907) : difference with theory (-9) = 2 CORRECTING DEFECT 25 (vertices=14, convex hull=34) After retessellation of defect 25, euler #=-10 (135108,405045,269927) : difference with theory (-8) = 2 CORRECTING DEFECT 26 (vertices=51, convex hull=80) After retessellation of defect 26, euler #=-8 (135124,405125,269993) : difference with theory (-7) = 1 CORRECTING DEFECT 27 (vertices=8, convex hull=22) After retessellation of defect 27, euler #=-7 (135126,405137,270004) : difference with theory (-6) = 1 CORRECTING DEFECT 28 (vertices=65, convex hull=39) After retessellation of defect 28, euler #=-6 (135136,405180,270038) : difference with theory (-5) = 1 CORRECTING DEFECT 29 (vertices=200, convex hull=158) After retessellation of defect 29, euler #=-4 (135198,405446,270244) : difference with theory (-4) = 0 CORRECTING DEFECT 30 (vertices=32, convex hull=68) After retessellation of defect 30, euler #=-3 (135207,405501,270291) : difference with theory (-3) = 0 CORRECTING DEFECT 31 (vertices=45, convex hull=56) After retessellation of defect 31, euler #=-2 (135219,405562,270341) : difference with theory (-2) = 0 CORRECTING DEFECT 32 (vertices=84, convex hull=97) After retessellation of defect 32, euler #=-1 (135249,405690,270440) : difference with theory (-1) = 0 CORRECTING DEFECT 33 (vertices=6, convex hull=25) After retessellation of defect 33, euler #=0 (135250,405699,270449) : difference with theory (0) = 0 CORRECTING DEFECT 34 (vertices=25, convex hull=60) After retessellation of defect 34, euler #=1 (135258,405745,270488) : difference with theory (1) = 0 CORRECTING DEFECT 35 (vertices=19, convex hull=59) After retessellation of defect 35, euler #=2 (135267,405795,270530) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.87 +- 0.23 (0.05-->8.24) (max @ vno 91060 --> 99328) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.87 +- 0.23 (0.05-->8.24) (max @ vno 91060 --> 99328) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 125 mutations (35.3%), 229 crossovers (64.7%), 54 vertices were eliminated building final representation... 1599 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=135267, nf=270530, ne=405795, g=0) writing corrected surface to /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 11.7 minutes 0 defective edges removing intersecting faces 000: 320 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 135267 - 405795 + 270530 = 2 --> 0 holes F =2V-4: 270530 = 270534-4 (0) 2E=3F: 811590 = 811590 (0) total defect index = 0 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 78 intersecting 001: 7 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Oct 6 21:17:01 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs 16945 lh only generating white matter surface 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 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/filled.mgz... reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/brain.finalsurfs.mgz... reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/wm.mgz... 21319 bright wm thresholded. 319 bright non-wm voxels segmented. reading original surface position from /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.orig... computing class statistics... border white: 246340 voxels (1.47%) border gray 280577 voxels (1.67%) WM (92.0): 93.5 +- 9.6 [70.0 --> 110.0] GM (78.0) : 75.8 +- 12.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 52.8 (was 70) setting MAX_BORDER_WHITE to 113.6 (was 105) setting MIN_BORDER_WHITE to 65.0 (was 85) setting MAX_CSF to 40.6 (was 40) setting MAX_GRAY to 94.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 58.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 28.3 (was 40) repositioning cortical surface to gray/white boundary reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.22 (0.02-->3.49) (max @ vno 91060 --> 99328) face area 0.27 +- 0.12 (0.00-->2.77) mean absolute distance = 0.67 +- 0.83 3178 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=65 mean inside = 93.3, mean outside = 72.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group mean border=77.3, 75 (75) missing vertices, mean dist 0.3 [0.6 (%35.4)->0.7 (%64.6))] %68 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=jmlin, 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 0.90 +- 0.27 (0.10-->3.98) (max @ vno 100561 --> 100554) face area 0.27 +- 0.13 (0.00-->2.71) mean absolute distance = 0.34 +- 0.53 3416 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5748776.0, rms=11.17 001: dt: 0.5000, sse=6938695.0, rms=7.958 (0.000%) 002: dt: 0.5000, sse=7622417.0, rms=6.186 (0.000%) 003: dt: 0.5000, sse=8035618.0, rms=5.203 (0.000%) 004: dt: 0.5000, sse=8372381.5, rms=4.642 (0.000%) 005: dt: 0.5000, sse=8534732.0, rms=4.394 (0.000%) 006: dt: 0.5000, sse=8636741.0, rms=4.222 (0.000%) 007: dt: 0.5000, sse=8672364.0, rms=4.166 (0.000%) 008: dt: 0.5000, sse=8692549.0, rms=4.086 (0.000%) rms = 4.07, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=8657049.0, rms=4.073 (0.000%) 010: dt: 0.2500, sse=5629353.5, rms=2.953 (0.000%) 011: dt: 0.2500, sse=5240016.5, rms=2.570 (0.000%) 012: dt: 0.2500, sse=4950560.5, rms=2.490 (0.000%) 013: dt: 0.2500, sse=4886045.5, rms=2.417 (0.000%) rms = 2.39, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=4801194.5, rms=2.389 (0.000%) 015: dt: 0.1250, sse=4657236.5, rms=2.284 (0.000%) rms = 2.27, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4615698.0, rms=2.272 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=81.0, 65 (22) missing vertices, mean dist -0.2 [0.4 (%73.7)->0.3 (%26.3))] %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=jmlin, 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 +- 0.26 (0.06-->4.28) (max @ vno 100561 --> 100554) face area 0.34 +- 0.17 (0.00-->3.29) mean absolute distance = 0.25 +- 0.35 3770 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5288095.5, rms=5.19 017: dt: 0.5000, sse=5648945.0, rms=3.580 (0.000%) rms = 3.94, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5203555.5, rms=2.690 (0.000%) 019: dt: 0.2500, sse=5046323.5, rms=2.225 (0.000%) 020: dt: 0.2500, sse=4951439.0, rms=1.979 (0.000%) 021: dt: 0.2500, sse=4915652.5, rms=1.923 (0.000%) rms = 1.89, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=4858297.0, rms=1.886 (0.000%) 023: dt: 0.1250, sse=4761923.5, rms=1.786 (0.000%) rms = 1.78, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4716918.0, rms=1.785 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... mean border=83.5, 43 (8) missing vertices, mean dist -0.1 [0.3 (%68.9)->0.2 (%31.1))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=jmlin, 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 +- 0.26 (0.06-->4.14) (max @ vno 135119 --> 135116) face area 0.33 +- 0.16 (0.00-->3.12) mean absolute distance = 0.22 +- 0.30 3700 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4948710.0, rms=3.60 025: dt: 0.5000, sse=5438494.5, rms=3.408 (0.000%) rms = 3.82, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5015021.0, rms=2.312 (0.000%) 027: dt: 0.2500, sse=4998113.0, rms=1.905 (0.000%) 028: dt: 0.2500, sse=4987605.0, rms=1.743 (0.000%) rms = 1.75, time step reduction 2 of 3 to 0.125... 029: dt: 0.1250, sse=4923199.5, rms=1.674 (0.000%) 030: dt: 0.1250, sse=4832503.0, rms=1.585 (0.000%) rms = 1.59, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4832503.0, rms=1.585 (0.004%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=84.2, 62 (8) missing vertices, mean dist -0.0 [0.2 (%55.3)->0.2 (%44.7))] %90 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=jmlin, 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 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=4848227.5, rms=1.88 rms = 2.39, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=4984834.0, rms=1.361 (0.000%) 033: dt: 0.2500, sse=5226163.5, rms=1.171 (0.000%) rms = 1.18, time step reduction 2 of 3 to 0.125... rms = 1.16, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5221977.0, rms=1.163 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group generating cortex label... 12 non-cortical segments detected only using segment with 1954 vertices erasing segment 1 (vno[0] = 81244) erasing segment 2 (vno[0] = 82251) erasing segment 3 (vno[0] = 87523) erasing segment 4 (vno[0] = 94992) erasing segment 5 (vno[0] = 95965) erasing segment 6 (vno[0] = 97171) erasing segment 7 (vno[0] = 98126) erasing segment 8 (vno[0] = 99013) erasing segment 9 (vno[0] = 99820) erasing segment 10 (vno[0] = 99998) erasing segment 11 (vno[0] = 105090) writing cortex label to /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/label/lh.cortex.label... writing curvature file /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.curv writing smoothed area to lh.area writing curvature file /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.area vertex spacing 0.88 +- 0.26 (0.03-->3.60) (max @ vno 104112 --> 105026) face area 0.33 +- 0.16 (0.00-->3.12) refinement took 3.6 minutes #-------------------------------------------- #@# Smooth2 lh Thu Oct 6 21:20:39 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts 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 Thu Oct 6 21:20:41 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 46.2 mm, total surface area = 79848 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.121 (target=0.015) step 005: RMS=0.082 (target=0.015) step 010: RMS=0.060 (target=0.015) step 015: RMS=0.048 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.019 (target=0.015) step 045: RMS=0.017 (target=0.015) step 050: RMS=0.016 (target=0.015) inflation complete. inflation took 0.3 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 219 vertices thresholded to be in k1 ~ [-0.20 0.47], k2 ~ [-0.10 0.05] total integrated curvature = 0.569*4pi (7.154) --> 0 handles ICI = 1.6, FI = 10.8, variation=181.187 102 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 160 vertices thresholded to be in [-0.13 0.21] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.025 done. #----------------------------------------- #@# Curvature Stats lh Thu Oct 6 21:21:52 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 16945 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 [ 16945/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 [ 245 ] Gb_filter = 0 WARN: S lookup min: -0.607546 WARN: S explicit min: 0.000000 vertex = 263 #-------------------------------------------- #@# Sphere lh Thu Oct 6 21:21:55 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.284... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=jmlin, 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 %20.24 pass 1: epoch 2 of 3 starting distance error %20.20 unfolding complete - removing small folds... starting distance error %20.17 removing remaining folds... final distance error %20.18 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.45 hours #-------------------------------------------- #@# Surf Reg lh Thu Oct 6 21:48:48 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/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=jmlin, 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=jmlin, 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 = 0.568 curvature mean = 0.014, std = 0.931 curvature mean = 0.024, std = 0.854 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (0.00, -8.00, 8.00) sse = 280655.6, tmin=1.1477 d=16.00 min @ (0.00, 4.00, -4.00) sse = 253585.5, tmin=1.7271 d=8.00 min @ (0.00, 0.00, 2.00) sse = 253056.2, tmin=2.3256 d=4.00 min @ (-1.00, 0.00, -1.00) sse = 250900.0, tmin=2.9333 d=2.00 min @ (0.00, -0.50, 0.00) sse = 250745.8, tmin=3.5495 d=1.00 min @ (0.00, 0.00, 0.25) sse = 250707.2, tmin=4.1556 d=0.50 min @ (0.00, 0.12, -0.12) sse = 250699.9, tmin=4.7599 tol=1.0e+00, sigma=0.5, host=jmlin, 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 4.76 min curvature mean = -0.010, std = 0.942 curvature mean = 0.012, std = 0.932 curvature mean = -0.011, std = 0.954 curvature mean = 0.005, std = 0.966 curvature mean = -0.011, std = 0.956 curvature mean = 0.001, std = 0.983 2 Reading smoothwm curvature mean = -0.026, std = 0.307 curvature mean = 0.003, std = 0.067 curvature mean = 0.071, std = 0.322 curvature mean = 0.003, std = 0.079 curvature mean = 0.032, std = 0.512 curvature mean = 0.003, std = 0.085 curvature mean = 0.018, std = 0.654 curvature mean = 0.004, std = 0.088 curvature mean = 0.007, std = 0.766 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Thu Oct 6 22:03:15 EDT 2016 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 #-------------------------------------------- #@# AvgCurv lh Thu Oct 6 22:03:16 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mrisp_paint -a 5 /usr/local/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 /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Thu Oct 6 22:03:17 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 16945 lh ../surf/lh.sphere.reg /usr/local/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.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/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... 962 labels changed using aseg relabeling using gibbs priors... 000: 3020 changed, 135267 examined... 001: 686 changed, 12976 examined... 002: 178 changed, 3832 examined... 003: 53 changed, 1083 examined... 004: 22 changed, 318 examined... 005: 14 changed, 128 examined... 006: 10 changed, 91 examined... 007: 6 changed, 54 examined... 008: 4 changed, 32 examined... 009: 0 changed, 14 examined... 234 labels changed using aseg 000: 103 total segments, 52 labels (199 vertices) changed 001: 49 total segments, 9 labels (20 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 34 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1449 vertices marked for relabeling... 1449 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 30 seconds. #-------------------------------------------- #@# Make Pial Surf lh Thu Oct 6 22:03:48 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs 16945 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/filled.mgz... reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/brain.finalsurfs.mgz... reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/wm.mgz... 21319 bright wm thresholded. 319 bright non-wm voxels segmented. reading original surface position from /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.orig... computing class statistics... border white: 246340 voxels (1.47%) border gray 280577 voxels (1.67%) WM (92.0): 93.5 +- 9.6 [70.0 --> 110.0] GM (78.0) : 75.8 +- 12.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 52.8 (was 70) setting MAX_BORDER_WHITE to 113.6 (was 105) setting MIN_BORDER_WHITE to 65.0 (was 85) setting MAX_CSF to 40.6 (was 40) setting MAX_GRAY to 94.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 58.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 28.3 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=65 mean inside = 93.3, mean outside = 72.1 smoothing surface for 5 iterations... 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/white boundary reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.22 (0.02-->3.49) (max @ vno 91060 --> 99328) face area 0.27 +- 0.12 (0.00-->2.77) mean absolute distance = 0.67 +- 0.83 3203 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 27 points - only 0.00% unknown deleting segment 3 with 775 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown deleting segment 7 with 10 points - only 0.00% unknown mean border=77.3, 75 (75) missing vertices, mean dist 0.3 [0.6 (%35.4)->0.7 (%64.6))] %69 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=jmlin, 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 0.90 +- 0.27 (0.10-->3.98) (max @ vno 100561 --> 100554) face area 0.27 +- 0.13 (0.00-->2.71) mean absolute distance = 0.34 +- 0.53 3458 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5769134.0, rms=11.16 001: dt: 0.5000, sse=6973927.0, rms=7.944 (0.000%) 002: dt: 0.5000, sse=7658848.5, rms=6.175 (0.000%) 003: dt: 0.5000, sse=8080630.5, rms=5.194 (0.000%) 004: dt: 0.5000, sse=8415445.0, rms=4.635 (0.000%) 005: dt: 0.5000, sse=8585770.0, rms=4.387 (0.000%) 006: dt: 0.5000, sse=8681801.0, rms=4.217 (0.000%) 007: dt: 0.5000, sse=8729190.0, rms=4.161 (0.000%) 008: dt: 0.5000, sse=8739957.0, rms=4.083 (0.000%) rms = 4.07, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=8714709.0, rms=4.069 (0.000%) 010: dt: 0.2500, sse=5661232.5, rms=2.949 (0.000%) 011: dt: 0.2500, sse=5270219.0, rms=2.567 (0.000%) 012: dt: 0.2500, sse=4977344.5, rms=2.486 (0.000%) 013: dt: 0.2500, sse=4914212.0, rms=2.414 (0.000%) rms = 2.39, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=4829563.0, rms=2.386 (0.000%) 015: dt: 0.1250, sse=4685449.5, rms=2.282 (0.000%) rms = 2.27, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4643605.5, rms=2.270 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 53 points - only 0.00% unknown deleting segment 1 with 13 points - only 0.00% unknown deleting segment 3 with 739 points - only 0.00% unknown deleting segment 7 with 7 points - only 0.00% unknown deleting segment 8 with 59 points - only 52.54% unknown deleting segment 9 with 6 points - only 0.00% unknown mean border=80.9, 98 (32) missing vertices, mean dist -0.2 [0.4 (%73.8)->0.3 (%26.2))] %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=jmlin, 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 +- 0.26 (0.09-->4.18) (max @ vno 100561 --> 100554) face area 0.34 +- 0.17 (0.00-->3.29) mean absolute distance = 0.25 +- 0.36 3822 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5336667.5, rms=5.21 017: dt: 0.5000, sse=5694608.0, rms=3.596 (0.000%) rms = 3.95, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5247378.5, rms=2.712 (0.000%) 019: dt: 0.2500, sse=5089296.5, rms=2.250 (0.000%) 020: dt: 0.2500, sse=4994001.0, rms=2.005 (0.000%) 021: dt: 0.2500, sse=4959427.5, rms=1.947 (0.000%) rms = 1.91, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=4902230.0, rms=1.910 (0.000%) 023: dt: 0.1250, sse=4805869.0, rms=1.810 (0.000%) rms = 1.80, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4757590.0, rms=1.805 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 52 points - only 0.00% unknown deleting segment 1 with 11 points - only 0.00% unknown deleting segment 2 with 776 points - only 0.00% unknown deleting segment 3 with 7 points - only 0.00% unknown deleting segment 4 with 130 points - only 58.46% unknown deleting segment 5 with 13 points - only 0.00% unknown mean border=83.4, 97 (21) missing vertices, mean dist -0.1 [0.3 (%68.9)->0.2 (%31.1))] %89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=jmlin, 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 +- 0.26 (0.06-->4.34) (max @ vno 100561 --> 100554) face area 0.33 +- 0.16 (0.00-->3.12) mean absolute distance = 0.22 +- 0.30 3750 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4993553.5, rms=3.60 025: dt: 0.5000, sse=5482967.0, rms=3.407 (0.000%) rms = 3.82, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5059085.0, rms=2.316 (0.000%) 027: dt: 0.2500, sse=5042877.5, rms=1.909 (0.000%) 028: dt: 0.2500, sse=5033192.0, rms=1.747 (0.000%) rms = 1.76, time step reduction 2 of 3 to 0.125... 029: dt: 0.1250, sse=4968027.0, rms=1.679 (0.000%) 030: dt: 0.1250, sse=4875354.5, rms=1.590 (0.000%) rms = 1.60, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4875354.5, rms=1.590 (0.004%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 51 points - only 0.00% unknown deleting segment 1 with 13 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 782 points - only 0.00% unknown deleting segment 7 with 7 points - only 0.00% unknown deleting segment 8 with 87 points - only 51.72% unknown deleting segment 9 with 15 points - only 0.00% unknown mean border=84.2, 117 (16) missing vertices, mean dist -0.0 [0.2 (%55.3)->0.2 (%44.7))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=jmlin, 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 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4891638.0, rms=1.89 rms = 2.39, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=5030390.0, rms=1.368 (0.000%) 033: dt: 0.2500, sse=5277345.0, rms=1.177 (0.000%) rms = 1.19, time step reduction 2 of 3 to 0.125... rms = 1.17, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5272848.5, rms=1.169 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=54.7, 92 (92) missing vertices, mean dist 1.7 [0.2 (%0.0)->2.5 (%100.0))] %19 local maxima, %46 large gradients and %30 min vals, 1566 gradients ignored tol=1.0e-04, sigma=2.0, host=jmlin, 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=24860348.0, rms=29.25 001: dt: 0.5000, sse=18495424.0, rms=24.661 (0.000%) 002: dt: 0.5000, sse=13956730.0, rms=20.804 (0.000%) 003: dt: 0.5000, sse=10888144.0, rms=17.634 (0.000%) 004: dt: 0.5000, sse=9041322.0, rms=15.095 (0.000%) 005: dt: 0.5000, sse=8026896.5, rms=13.118 (0.000%) 006: dt: 0.5000, sse=7470908.0, rms=11.598 (0.000%) 007: dt: 0.5000, sse=7209186.5, rms=10.310 (0.000%) 008: dt: 0.5000, sse=7022315.5, rms=9.136 (0.000%) 009: dt: 0.5000, sse=6978128.0, rms=8.040 (0.000%) 010: dt: 0.5000, sse=6966598.0, rms=7.092 (0.000%) 011: dt: 0.5000, sse=7094233.5, rms=6.272 (0.000%) 012: dt: 0.5000, sse=7167779.5, rms=5.645 (0.000%) 013: dt: 0.5000, sse=7347430.0, rms=5.183 (0.000%) 014: dt: 0.5000, sse=7414065.5, rms=4.881 (0.000%) 015: dt: 0.5000, sse=7529778.5, rms=4.675 (0.000%) 016: dt: 0.5000, sse=7580832.0, rms=4.555 (0.000%) 017: dt: 0.5000, sse=7628582.0, rms=4.476 (0.000%) 018: dt: 0.5000, sse=7653604.0, rms=4.421 (0.000%) rms = 4.38, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=7663649.0, rms=4.384 (0.000%) 020: dt: 0.2500, sse=5423642.0, rms=3.641 (0.000%) 021: dt: 0.2500, sse=5293026.5, rms=3.410 (0.000%) rms = 3.40, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5118111.0, rms=3.401 (0.000%) 023: dt: 0.1250, sse=4844542.0, rms=3.239 (0.000%) rms = 3.21, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4804430.5, rms=3.213 (0.000%) positioning took 1.5 minutes mean border=52.3, 1256 (13) missing vertices, mean dist 0.2 [0.2 (%44.3)->0.5 (%55.7))] %40 local maxima, %31 large gradients and %24 min vals, 608 gradients ignored tol=1.0e-04, sigma=1.0, host=jmlin, 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=5419018.5, rms=5.10 025: dt: 0.5000, sse=5774966.0, rms=4.418 (0.000%) rms = 4.37, time step reduction 1 of 3 to 0.250... 026: dt: 0.5000, sse=7518325.0, rms=4.372 (0.000%) 027: dt: 0.2500, sse=5554217.5, rms=3.517 (0.000%) 028: dt: 0.2500, sse=5702263.5, rms=3.268 (0.000%) rms = 3.24, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=5497425.5, rms=3.245 (0.000%) 030: dt: 0.1250, sse=5273081.5, rms=3.013 (0.000%) rms = 2.97, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=5251669.0, rms=2.967 (0.000%) positioning took 0.5 minutes mean border=50.6, 1465 (10) missing vertices, mean dist 0.1 [0.2 (%40.9)->0.4 (%59.1))] %55 local maxima, %16 large gradients and %24 min vals, 652 gradients ignored tol=1.0e-04, sigma=0.5, host=jmlin, 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=5426246.5, rms=3.85 rms = 4.24, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=5230411.0, rms=3.377 (0.000%) 033: dt: 0.2500, sse=5274592.5, rms=3.151 (0.000%) rms = 3.11, time step reduction 2 of 3 to 0.125... 034: dt: 0.2500, sse=5473955.5, rms=3.114 (0.000%) 035: dt: 0.1250, sse=5289357.5, rms=2.940 (0.000%) rms = 2.90, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=5300101.0, rms=2.902 (0.000%) positioning took 0.4 minutes mean border=49.9, 2733 (10) missing vertices, mean dist 0.0 [0.2 (%47.7)->0.3 (%52.3))] %56 local maxima, %14 large gradients and %23 min vals, 532 gradients ignored tol=1.0e-04, sigma=0.2, host=jmlin, 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 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=5332168.0, rms=3.12 rms = 3.81, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=5251443.0, rms=2.941 (0.000%) rms = 2.89, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=5507276.5, rms=2.891 (0.000%) 039: dt: 0.1250, sse=5373821.5, rms=2.803 (0.000%) rms = 2.76, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=5420117.5, rms=2.765 (0.000%) positioning took 0.3 minutes writing curvature file /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.area.pial vertex spacing 0.98 +- 0.42 (0.08-->10.18) (max @ vno 92777 --> 93823) face area 0.38 +- 0.29 (0.00-->7.15) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 135267 vertices processed 25000 of 135267 vertices processed 50000 of 135267 vertices processed 75000 of 135267 vertices processed 100000 of 135267 vertices processed 125000 of 135267 vertices processed 0 of 135267 vertices processed 25000 of 135267 vertices processed 50000 of 135267 vertices processed 75000 of 135267 vertices processed 100000 of 135267 vertices processed 125000 of 135267 vertices processed thickness calculation complete, 293:324 truncations. 26781 vertices at 0 distance 87382 vertices at 1 distance 87012 vertices at 2 distance 39454 vertices at 3 distance 12620 vertices at 4 distance 3680 vertices at 5 distance 1133 vertices at 6 distance 363 vertices at 7 distance 124 vertices at 8 distance 50 vertices at 9 distance 25 vertices at 10 distance 26 vertices at 11 distance 14 vertices at 12 distance 19 vertices at 13 distance 12 vertices at 14 distance 11 vertices at 15 distance 19 vertices at 16 distance 7 vertices at 17 distance 10 vertices at 18 distance 8 vertices at 19 distance 4 vertices at 20 distance writing curvature file /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.thickness positioning took 7.0 minutes #-------------------------------------------- #@# Surf Volume lh Thu Oct 6 22:10:50 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/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_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast lh Thu Oct 6 22:10:50 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts pctsurfcon --s 16945 --lh-only Log file is /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts/pctsurfcon.log Thu Oct 6 22:10:51 EDT 2016 setenv SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets cd /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux jmlina2 4.4.0-38-generic #57~14.04.1-Ubuntu SMP Tue Sep 6 17:20:43 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/tmp.pctsurfcon.18932/lh.wm.mgh --regheader 16945 --cortex srcvol = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/orig.mgz as target reference. Loading label /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/label/lh.cortex.label Reading surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/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 = 71662 Masking with /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/label/lh.cortex.label Writing to /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/tmp.pctsurfcon.18932/lh.wm.mgh Dim: 135267 1 1 mri_vol2surf --mov /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/tmp.pctsurfcon.18932/lh.gm.mgh --projfrac 0.3 --regheader 16945 --cortex srcvol = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/orig.mgz as target reference. Loading label /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/label/lh.cortex.label Reading surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Done reading source surface Reading thickness /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/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 = 88684 Masking with /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/label/lh.cortex.label Writing to /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/tmp.pctsurfcon.18932/lh.gm.mgh Dim: 135267 1 1 mri_concat /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/tmp.pctsurfcon.18932/lh.wm.mgh /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/tmp.pctsurfcon.18932/lh.gm.mgh --paired-diff-norm --mul 100 --o /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/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 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.w-g.pct.mgh mri_segstats --in /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.w-g.pct.mgh --annot 16945 lh aparc --sum /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.w-g.pct.mgh --annot 16945 lh aparc --sum /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/stats/lh.w-g.pct.stats --snr sysname Linux hostname jmlina2 machine x86_64 user jsboucher UseRobust 0 Constructing seg from annotation Reading annotation 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 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.w-g.pct.mgh Vertex Area is 0.652865 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1440 992.534 2 1002 caudalanteriorcingulate 849 550.098 3 1003 caudalmiddlefrontal 2765 1828.371 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 1979 1270.226 6 1006 entorhinal 591 397.610 7 1007 fusiform 5169 3432.930 8 1008 inferiorparietal 5806 3899.874 9 1009 inferiortemporal 4915 3297.872 10 1010 isthmuscingulate 1699 1072.493 11 1011 lateraloccipital 6525 4009.294 12 1012 lateralorbitofrontal 4440 2902.796 13 1013 lingual 6352 4078.948 14 1014 medialorbitofrontal 2673 1777.047 15 1015 middletemporal 4392 3004.908 16 1016 parahippocampal 987 620.772 17 1017 paracentral 1715 1081.395 18 1018 parsopercularis 3372 2230.731 19 1019 parsorbitalis 1067 719.012 20 1020 parstriangularis 2261 1505.261 21 1021 pericalcarine 2756 1811.775 22 1022 postcentral 7046 4573.338 23 1023 posteriorcingulate 1751 1171.392 24 1024 precentral 6932 4285.636 25 1025 precuneus 6483 4252.721 26 1026 rostralanteriorcingulate 1317 887.572 27 1027 rostralmiddlefrontal 7901 5313.879 28 1028 superiorfrontal 9744 6485.484 29 1029 superiorparietal 9066 5830.847 30 1030 superiortemporal 5085 3326.927 31 1031 supramarginal 5223 3516.199 32 1032 frontalpole 310 205.390 33 1033 temporalpole 583 401.538 34 1034 transversetemporal 769 449.008 35 1035 insula 3171 1995.153 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Thu Oct 6 22:10:55 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 16945 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/wm.mgz... reading input surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white... reading input pial surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.pial... reading input white surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. 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 1440 993 2445 2.551 0.362 0.124 0.036 14 2.1 bankssts 849 550 1612 2.643 0.423 0.152 0.053 15 1.6 caudalanteriorcingulate 2765 1828 5085 2.539 0.426 0.151 0.068 42 7.6 caudalmiddlefrontal 1979 1270 2339 1.638 0.481 0.190 0.112 115 9.6 cuneus 591 398 1654 3.029 0.720 0.149 0.050 9 1.2 entorhinal 5169 3433 10236 2.602 0.526 0.175 0.084 147 17.5 fusiform 5806 3900 10582 2.469 0.431 0.168 0.108 283 26.8 inferiorparietal 4915 3298 9727 2.614 0.608 0.165 0.083 126 16.7 inferiortemporal 1699 1072 2698 2.471 0.749 0.170 0.083 41 5.4 isthmuscingulate 6525 4009 8853 2.063 0.495 0.171 0.098 300 24.2 lateraloccipital 4440 2903 8363 2.581 0.671 0.177 0.160 215 19.4 lateralorbitofrontal 6352 4079 9090 2.041 0.593 0.182 0.111 308 26.5 lingual 2673 1777 4736 2.356 0.746 0.155 0.091 82 10.4 medialorbitofrontal 4392 3005 10705 2.880 0.593 0.176 0.082 111 15.5 middletemporal 987 621 1887 2.648 0.649 0.157 0.107 31 5.8 parahippocampal 1715 1081 2683 2.304 0.525 0.137 0.054 21 4.3 paracentral 3372 2231 6870 2.687 0.462 0.150 0.059 60 8.5 parsopercularis 1067 719 2553 2.876 0.710 0.183 0.087 27 4.0 parsorbitalis 2261 1505 4276 2.517 0.507 0.161 0.076 59 6.7 parstriangularis 2756 1812 2505 1.561 0.439 0.178 0.088 58 10.6 pericalcarine 7046 4573 10847 2.129 0.582 0.162 0.103 162 21.2 postcentral 1751 1171 3367 2.677 0.582 0.179 0.076 43 5.5 posteriorcingulate 6932 4286 11703 2.585 0.514 0.151 0.074 199 22.5 precentral 6483 4253 9846 2.157 0.477 0.163 0.087 147 23.7 precuneus 1317 888 3011 2.871 0.569 0.190 0.119 41 7.0 rostralanteriorcingulate 7901 5314 14054 2.319 0.556 0.175 0.089 195 28.3 rostralmiddlefrontal 9744 6485 20081 2.775 0.594 0.167 0.095 218 33.0 superiorfrontal 9066 5831 13291 2.106 0.448 0.155 0.069 170 26.7 superiorparietal 5085 3327 10096 2.755 0.600 0.148 0.063 87 12.9 superiortemporal 5223 3516 9945 2.616 0.438 0.167 0.073 112 16.0 supramarginal 310 205 870 2.941 0.533 0.223 0.107 12 1.2 frontalpole 583 402 1872 3.331 0.624 0.190 0.105 13 2.5 temporalpole 769 449 1192 2.494 0.382 0.167 0.081 17 2.6 transversetemporal 3171 1995 6046 3.022 0.666 0.143 0.117 90 15.9 insula #----------------------------------------- #@# Cortical Parc 2 lh Thu Oct 6 22:11:05 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 16945 lh ../surf/lh.sphere.reg /usr/local/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.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/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... 83 labels changed using aseg relabeling using gibbs priors... 000: 9448 changed, 135267 examined... 001: 2303 changed, 36266 examined... 002: 717 changed, 11763 examined... 003: 319 changed, 4055 examined... 004: 158 changed, 1761 examined... 005: 91 changed, 902 examined... 006: 51 changed, 522 examined... 007: 27 changed, 290 examined... 008: 8 changed, 154 examined... 009: 4 changed, 46 examined... 010: 3 changed, 30 examined... 011: 2 changed, 15 examined... 012: 2 changed, 15 examined... 013: 3 changed, 13 examined... 014: 2 changed, 15 examined... 015: 0 changed, 8 examined... 39 labels changed using aseg 000: 312 total segments, 233 labels (3085 vertices) changed 001: 100 total segments, 21 labels (80 vertices) changed 002: 79 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 152 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 624 vertices marked for relabeling... 624 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 41 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Thu Oct 6 22:11:46 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_anatomical_stats -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 16945 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/wm.mgz... reading input surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white... reading input pial surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.pial... reading input white surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. 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 1124 768 1974 2.246 0.620 0.192 0.091 33 4.3 G_and_S_frontomargin 1571 1028 2798 2.362 0.515 0.172 0.071 34 4.3 G_and_S_occipital_inf 1428 834 2306 2.290 0.508 0.160 0.077 44 4.7 G_and_S_paracentral 1353 890 2808 2.739 0.520 0.163 0.063 25 3.7 G_and_S_subcentral 468 320 866 2.098 0.640 0.203 0.145 17 3.2 G_and_S_transv_frontopol 2231 1504 4353 2.691 0.571 0.167 0.092 54 9.1 G_and_S_cingul-Ant 1367 928 2584 2.668 0.449 0.145 0.050 19 2.8 G_and_S_cingul-Mid-Ant 1229 823 2166 2.634 0.478 0.153 0.061 21 3.2 G_and_S_cingul-Mid-Post 626 404 1413 2.939 0.662 0.204 0.099 17 2.5 G_cingul-Post-dorsal 382 230 577 2.486 0.838 0.158 0.064 9 0.9 G_cingul-Post-ventral 2101 1341 2307 1.545 0.494 0.197 0.119 120 10.7 G_cuneus 1735 1138 4409 2.885 0.396 0.169 0.073 41 5.1 G_front_inf-Opercular 383 243 1035 3.163 0.482 0.201 0.089 14 1.5 G_front_inf-Orbital 1331 871 2872 2.626 0.509 0.187 0.104 51 5.0 G_front_inf-Triangul 3722 2446 8188 2.580 0.517 0.184 0.108 109 15.0 G_front_middle 6955 4596 15916 2.892 0.594 0.179 0.111 186 25.5 G_front_sup 481 289 1008 3.183 0.641 0.149 0.075 11 1.6 G_Ins_lg_and_S_cent_ins 725 427 2008 3.541 0.591 0.162 0.262 29 9.4 G_insular_short 1488 928 2756 2.394 0.447 0.174 0.093 43 5.4 G_occipital_middle 2259 1411 3153 1.945 0.438 0.177 0.097 58 9.3 G_occipital_sup 2010 1286 4600 2.783 0.518 0.190 0.100 62 8.3 G_oc-temp_lat-fusifor 4393 2746 6187 1.951 0.637 0.197 0.131 281 21.5 G_oc-temp_med-Lingual 1087 690 2802 2.946 0.686 0.162 0.105 34 6.2 G_oc-temp_med-Parahip 2780 1783 6233 2.670 0.715 0.203 0.218 187 14.3 G_orbital 2243 1501 4983 2.610 0.438 0.190 0.184 223 18.0 G_pariet_inf-Angular 2680 1803 5878 2.705 0.418 0.178 0.084 67 9.9 G_pariet_inf-Supramar 3430 2185 5431 2.129 0.433 0.154 0.070 69 10.0 G_parietal_sup 2800 1748 4488 2.134 0.506 0.173 0.163 85 9.9 G_postcentral 2594 1553 5498 2.775 0.531 0.161 0.088 56 10.0 G_precentral 4046 2623 6791 2.210 0.469 0.170 0.097 108 16.9 G_precuneus 1025 651 2501 2.713 0.613 0.191 0.135 58 6.1 G_rectus 416 265 679 2.448 1.039 0.164 0.138 15 2.6 G_subcallosal 527 293 914 2.461 0.332 0.158 0.084 13 1.8 G_temp_sup-G_T_transv 1875 1203 4905 2.940 0.579 0.171 0.084 50 6.1 G_temp_sup-Lateral 599 379 1409 3.189 0.568 0.152 0.082 14 1.8 G_temp_sup-Plan_polar 854 589 1586 2.554 0.547 0.149 0.059 13 1.9 G_temp_sup-Plan_tempo 2704 1853 6525 2.691 0.633 0.192 0.110 101 12.0 G_temporal_inf 2845 1943 8140 3.058 0.568 0.192 0.098 85 12.1 G_temporal_middle 442 296 717 2.467 0.479 0.135 0.044 6 0.9 Lat_Fis-ant-Horizont 317 207 423 2.344 0.414 0.125 0.040 2 0.5 Lat_Fis-ant-Vertical 1192 797 1585 2.449 0.419 0.147 0.052 16 2.7 Lat_Fis-post 2387 1343 2715 1.799 0.436 0.189 0.144 220 13.1 Pole_occipital 1522 1073 4252 3.069 0.699 0.199 0.110 65 6.4 Pole_temporal 3468 2290 3692 1.831 0.566 0.166 0.086 72 12.7 S_calcarine 3157 2061 3532 1.976 0.541 0.147 0.069 107 9.7 S_central 1152 771 1570 2.104 0.419 0.141 0.052 15 2.6 S_cingul-Marginalis 765 503 1330 2.819 0.540 0.140 0.081 17 2.4 S_circular_insula_ant 1361 895 2047 2.753 0.609 0.113 0.039 10 2.1 S_circular_insula_inf 1788 1190 2723 2.692 0.471 0.118 0.037 15 2.8 S_circular_insula_sup 831 549 1215 2.227 0.487 0.142 0.059 12 2.2 S_collat_transv_ant 553 371 782 2.078 0.359 0.144 0.045 7 1.1 S_collat_transv_post 2735 1817 4406 2.409 0.381 0.153 0.068 48 8.3 S_front_inf 1845 1258 2853 2.198 0.550 0.161 0.069 32 5.6 S_front_middle 2100 1436 3266 2.398 0.470 0.143 0.052 22 4.7 S_front_sup 197 141 369 2.638 0.508 0.190 0.079 5 0.7 S_interm_prim-Jensen 2198 1467 3079 2.285 0.397 0.140 0.046 25 4.3 S_intrapariet_and_P_trans 715 482 842 2.009 0.358 0.141 0.044 7 1.4 S_oc_middle_and_Lunatus 1648 1080 2177 2.106 0.411 0.152 0.071 27 5.0 S_oc_sup_and_transversal 1031 685 1356 2.382 0.346 0.145 0.056 12 2.1 S_occipital_ant 1187 781 1660 2.352 0.391 0.135 0.046 13 2.3 S_oc-temp_lat 2713 1831 4288 2.457 0.454 0.152 0.062 41 6.6 S_oc-temp_med_and_Lingual 527 347 656 1.982 0.367 0.134 0.047 5 1.0 S_orbital_lateral 979 690 1465 2.257 0.681 0.131 0.068 30 1.9 S_orbital_med-olfact 1533 1033 2651 2.468 0.712 0.161 0.085 33 6.3 S_orbital-H_Shaped 1521 1024 1914 1.951 0.497 0.156 0.068 25 3.8 S_parieto_occipital 1067 633 1236 2.272 0.746 0.166 0.070 26 2.7 S_pericallosal 3352 2209 4672 2.244 0.431 0.147 0.059 56 8.0 S_postcentral 1640 1090 2420 2.522 0.410 0.135 0.049 18 3.4 S_precentral-inf-part 1032 681 1358 2.456 0.406 0.120 0.035 7 1.6 S_precentral-sup-part 624 435 883 2.225 0.687 0.133 0.039 6 1.1 S_suborbital 1037 697 1641 2.284 0.485 0.158 0.063 17 2.9 S_subparietal 1332 883 1990 2.608 0.454 0.143 0.061 20 3.2 S_temporal_inf 4972 3377 7781 2.477 0.408 0.140 0.047 67 9.5 S_temporal_sup 347 243 528 2.718 0.442 0.160 0.058 5 0.9 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Thu Oct 6 22:11:55 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 16945 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/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... 1072 labels changed using aseg relabeling using gibbs priors... 000: 2789 changed, 135267 examined... 001: 651 changed, 11888 examined... 002: 183 changed, 3629 examined... 003: 74 changed, 1076 examined... 004: 42 changed, 457 examined... 005: 23 changed, 257 examined... 006: 11 changed, 126 examined... 007: 8 changed, 60 examined... 008: 2 changed, 45 examined... 009: 2 changed, 13 examined... 010: 0 changed, 9 examined... 181 labels changed using aseg 000: 73 total segments, 40 labels (283 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 39 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 437 vertices marked for relabeling... 437 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 31 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Thu Oct 6 22:12:26 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_anatomical_stats -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 16945 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/wm.mgz... reading input surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white... reading input pial surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.pial... reading input white surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. 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 1499 979 2855 2.692 0.431 0.146 0.050 24 2.8 caudalanteriorcingulate 2902 1921 5344 2.536 0.426 0.149 0.067 44 7.9 caudalmiddlefrontal 2996 1912 3566 1.679 0.488 0.182 0.107 138 13.3 cuneus 567 383 1582 3.000 0.766 0.147 0.048 9 1.1 entorhinal 4741 3110 9174 2.595 0.503 0.170 0.079 109 15.5 fusiform 5557 3711 10162 2.471 0.430 0.170 0.111 283 26.5 inferiorparietal 5074 3440 10319 2.616 0.615 0.173 0.088 161 18.2 inferiortemporal 1691 1068 2704 2.479 0.751 0.171 0.083 41 5.4 isthmuscingulate 7030 4336 9405 2.036 0.492 0.171 0.097 310 26.0 lateraloccipital 4620 3036 8801 2.525 0.715 0.183 0.165 247 20.9 lateralorbitofrontal 6332 4068 9031 2.037 0.590 0.183 0.111 308 26.6 lingual 2347 1554 4511 2.454 0.714 0.158 0.088 79 8.9 medialorbitofrontal 5701 3891 12949 2.815 0.575 0.166 0.075 125 18.1 middletemporal 1020 646 1967 2.660 0.645 0.157 0.105 31 5.9 parahippocampal 1984 1256 3113 2.346 0.521 0.140 0.056 25 5.0 paracentral 2993 1968 6287 2.735 0.450 0.152 0.062 57 7.8 parsopercularis 1254 824 2836 2.920 0.592 0.166 0.071 29 3.9 parsorbitalis 2862 1902 5100 2.435 0.486 0.159 0.073 67 8.3 parstriangularis 2637 1727 2406 1.571 0.442 0.179 0.089 56 10.3 pericalcarine 7871 5116 12215 2.157 0.579 0.161 0.099 175 23.4 postcentral 1843 1232 3433 2.656 0.582 0.178 0.075 44 5.7 posteriorcingulate 6873 4248 11579 2.582 0.513 0.150 0.074 197 22.0 precentral 6581 4297 10019 2.156 0.471 0.163 0.085 147 24.1 precuneus 1661 1112 3518 2.810 0.610 0.191 0.123 53 9.1 rostralanteriorcingulate 5435 3634 9700 2.341 0.537 0.175 0.092 133 20.1 rostralmiddlefrontal 10847 7277 22210 2.692 0.649 0.171 0.097 256 37.9 superiorfrontal 6789 4399 10232 2.154 0.428 0.153 0.068 128 19.3 superiorparietal 6854 4525 14093 2.782 0.605 0.151 0.065 123 17.9 superiortemporal 5006 3381 9318 2.589 0.430 0.164 0.070 102 14.6 supramarginal 759 440 1162 2.485 0.370 0.167 0.081 17 2.6 transversetemporal 2808 1785 5528 3.062 0.668 0.135 0.110 55 14.0 insula #-------------------------------------------- #@# Tessellate rh Thu Oct 6 22:12:35 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/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-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 4 found - 4 modified | TOTAL: 7 pass 2 (yz+): 0 found - 4 modified | TOTAL: 7 pass 1 (yz-): 0 found - 0 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 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 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 = 10 (out of 237457: 0.004211) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 40: 424 vertices, 496 faces slice 50: 5059 vertices, 5272 faces slice 60: 12305 vertices, 12587 faces slice 70: 22233 vertices, 22612 faces slice 80: 32964 vertices, 33358 faces slice 90: 43930 vertices, 44289 faces slice 100: 54948 vertices, 55354 faces slice 110: 66945 vertices, 67366 faces slice 120: 78430 vertices, 78849 faces slice 130: 89537 vertices, 89939 faces slice 140: 99790 vertices, 100157 faces slice 150: 109101 vertices, 109448 faces slice 160: 116869 vertices, 117203 faces slice 170: 124419 vertices, 124693 faces slice 180: 130428 vertices, 130685 faces slice 190: 135431 vertices, 135642 faces slice 200: 137988 vertices, 138065 faces slice 210: 138014 vertices, 138076 faces slice 220: 138014 vertices, 138076 faces slice 230: 138014 vertices, 138076 faces slice 240: 138014 vertices, 138076 faces slice 250: 138014 vertices, 138076 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 138014 voxel in cpt #1: X=-62 [v=138014,e=414228,f=276152] located at (27.567682, -15.370310, 19.194675) For the whole surface: X=-62 [v=138014,e=414228,f=276152] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Thu Oct 6 22:12:39 EDT 2016 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Thu Oct 6 22:12:42 EDT 2016 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts avg radius = 45.7 mm, total surface area = 70194 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.3 minutes Not saving sulc step 000: RMS=0.105 (target=0.015) step 005: RMS=0.077 (target=0.015) step 010: RMS=0.057 (target=0.015) step 015: RMS=0.048 (target=0.015) step 020: RMS=0.041 (target=0.015) step 025: RMS=0.036 (target=0.015) step 030: RMS=0.033 (target=0.015) step 035: RMS=0.030 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.026 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Thu Oct 6 22:13:01 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/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 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.98 +- 0.58 (0.00-->6.69) (max @ vno 53553 --> 54643) face area 0.02 +- 0.03 (-0.14-->0.70) scaling brain by 0.304... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.237, avgs=0 005/300: dt: 0.9000, rms radial error=176.976, avgs=0 010/300: dt: 0.9000, rms radial error=176.415, avgs=0 015/300: dt: 0.9000, rms radial error=175.679, avgs=0 020/300: dt: 0.9000, rms radial error=174.840, avgs=0 025/300: dt: 0.9000, rms radial error=173.944, avgs=0 030/300: dt: 0.9000, rms radial error=173.016, avgs=0 035/300: dt: 0.9000, rms radial error=172.072, avgs=0 040/300: dt: 0.9000, rms radial error=171.120, avgs=0 045/300: dt: 0.9000, rms radial error=170.167, avgs=0 050/300: dt: 0.9000, rms radial error=169.214, avgs=0 055/300: dt: 0.9000, rms radial error=168.267, avgs=0 060/300: dt: 0.9000, rms radial error=167.324, avgs=0 065/300: dt: 0.9000, rms radial error=166.386, avgs=0 070/300: dt: 0.9000, rms radial error=165.453, avgs=0 075/300: dt: 0.9000, rms radial error=164.526, avgs=0 080/300: dt: 0.9000, rms radial error=163.604, avgs=0 085/300: dt: 0.9000, rms radial error=162.688, avgs=0 090/300: dt: 0.9000, rms radial error=161.776, avgs=0 095/300: dt: 0.9000, rms radial error=160.869, avgs=0 100/300: dt: 0.9000, rms radial error=159.966, avgs=0 105/300: dt: 0.9000, rms radial error=159.069, avgs=0 110/300: dt: 0.9000, rms radial error=158.176, avgs=0 115/300: dt: 0.9000, rms radial error=157.289, avgs=0 120/300: dt: 0.9000, rms radial error=156.406, avgs=0 125/300: dt: 0.9000, rms radial error=155.527, avgs=0 130/300: dt: 0.9000, rms radial error=154.654, avgs=0 135/300: dt: 0.9000, rms radial error=153.785, avgs=0 140/300: dt: 0.9000, rms radial error=152.921, avgs=0 145/300: dt: 0.9000, rms radial error=152.061, avgs=0 150/300: dt: 0.9000, rms radial error=151.207, avgs=0 155/300: dt: 0.9000, rms radial error=150.356, avgs=0 160/300: dt: 0.9000, rms radial error=149.511, avgs=0 165/300: dt: 0.9000, rms radial error=148.669, avgs=0 170/300: dt: 0.9000, rms radial error=147.833, avgs=0 175/300: dt: 0.9000, rms radial error=147.000, avgs=0 180/300: dt: 0.9000, rms radial error=146.173, avgs=0 185/300: dt: 0.9000, rms radial error=145.350, avgs=0 190/300: dt: 0.9000, rms radial error=144.531, avgs=0 195/300: dt: 0.9000, rms radial error=143.717, avgs=0 200/300: dt: 0.9000, rms radial error=142.907, avgs=0 205/300: dt: 0.9000, rms radial error=142.102, avgs=0 210/300: dt: 0.9000, rms radial error=141.301, avgs=0 215/300: dt: 0.9000, rms radial error=140.505, avgs=0 220/300: dt: 0.9000, rms radial error=139.713, avgs=0 225/300: dt: 0.9000, rms radial error=138.926, avgs=0 230/300: dt: 0.9000, rms radial error=138.143, avgs=0 235/300: dt: 0.9000, rms radial error=137.364, avgs=0 240/300: dt: 0.9000, rms radial error=136.589, avgs=0 245/300: dt: 0.9000, rms radial error=135.819, avgs=0 250/300: dt: 0.9000, rms radial error=135.053, avgs=0 255/300: dt: 0.9000, rms radial error=134.291, avgs=0 260/300: dt: 0.9000, rms radial error=133.533, avgs=0 265/300: dt: 0.9000, rms radial error=132.780, avgs=0 270/300: dt: 0.9000, rms radial error=132.030, avgs=0 275/300: dt: 0.9000, rms radial error=131.285, avgs=0 280/300: dt: 0.9000, rms radial error=130.544, avgs=0 285/300: dt: 0.9000, rms radial error=129.808, avgs=0 290/300: dt: 0.9000, rms radial error=129.075, avgs=0 295/300: dt: 0.9000, rms radial error=128.346, avgs=0 300/300: dt: 0.9000, rms radial error=127.622, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16352.41 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 2 (K=40.0), pass 1, starting sse = 2798.37 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00005 epoch 3 (K=160.0), pass 1, starting sse = 307.38 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/12 = 0.00613 epoch 4 (K=640.0), pass 1, starting sse = 21.09 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/13 = 0.00940 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.04 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Thu Oct 6 22:15:33 EDT 2016 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 16945 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 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-62 (nv=138014, nf=276152, ne=414228, g=32) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 3173 ambiguous faces found in tessellation segmenting defects... 39 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 19 into 18 38 defects to be corrected 0 vertices coincident reading input surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.6046 (-4.8023) -vertex loglikelihood: -6.6002 (-3.3001) -normal dot loglikelihood: -3.5876 (-3.5876) -quad curv loglikelihood: -6.5886 (-3.2943) Total Loglikelihood : -26.3809 CORRECTING DEFECT 0 (vertices=43, convex hull=70) After retessellation of defect 0, euler #=-36 (136027,407115,271052) : difference with theory (-35) = 1 CORRECTING DEFECT 1 (vertices=23, convex hull=42) After retessellation of defect 1, euler #=-35 (136036,407157,271086) : difference with theory (-34) = 1 CORRECTING DEFECT 2 (vertices=25, convex hull=73) After retessellation of defect 2, euler #=-34 (136047,407216,271135) : difference with theory (-33) = 1 CORRECTING DEFECT 3 (vertices=42, convex hull=64) After retessellation of defect 3, euler #=-33 (136058,407276,271185) : difference with theory (-32) = 1 CORRECTING DEFECT 4 (vertices=18, convex hull=47) After retessellation of defect 4, euler #=-32 (136066,407315,271217) : difference with theory (-31) = 1 CORRECTING DEFECT 5 (vertices=46, convex hull=72) After retessellation of defect 5, euler #=-31 (136076,407377,271270) : difference with theory (-30) = 1 CORRECTING DEFECT 6 (vertices=14, convex hull=24) After retessellation of defect 6, euler #=-30 (136076,407384,271278) : difference with theory (-29) = 1 CORRECTING DEFECT 7 (vertices=343, convex hull=291) After retessellation of defect 7, euler #=-29 (136229,407987,271729) : difference with theory (-28) = 1 CORRECTING DEFECT 8 (vertices=39, convex hull=84) After retessellation of defect 8, euler #=-28 (136244,408065,271793) : difference with theory (-27) = 1 CORRECTING DEFECT 9 (vertices=128, convex hull=61) After retessellation of defect 9, euler #=-27 (136261,408137,271849) : difference with theory (-26) = 1 CORRECTING DEFECT 10 (vertices=25, convex hull=48) After retessellation of defect 10, euler #=-26 (136270,408182,271886) : difference with theory (-25) = 1 CORRECTING DEFECT 11 (vertices=22, convex hull=57) After retessellation of defect 11, euler #=-25 (136279,408230,271926) : difference with theory (-24) = 1 CORRECTING DEFECT 12 (vertices=34, convex hull=65) After retessellation of defect 12, euler #=-24 (136295,408304,271985) : difference with theory (-23) = 1 CORRECTING DEFECT 13 (vertices=40, convex hull=69) After retessellation of defect 13, euler #=-23 (136307,408366,272036) : difference with theory (-22) = 1 CORRECTING DEFECT 14 (vertices=55, convex hull=89) After retessellation of defect 14, euler #=-22 (136325,408457,272110) : difference with theory (-21) = 1 CORRECTING DEFECT 15 (vertices=27, convex hull=61) After retessellation of defect 15, euler #=-21 (136338,408515,272156) : difference with theory (-20) = 1 CORRECTING DEFECT 16 (vertices=152, convex hull=83) After retessellation of defect 16, euler #=-20 (136366,408631,272245) : difference with theory (-19) = 1 CORRECTING DEFECT 17 (vertices=28, convex hull=40) After retessellation of defect 17, euler #=-19 (136377,408679,272283) : difference with theory (-18) = 1 CORRECTING DEFECT 18 (vertices=159, convex hull=71) After retessellation of defect 18, euler #=-17 (136386,408739,272336) : difference with theory (-17) = 0 CORRECTING DEFECT 19 (vertices=25, convex hull=45) After retessellation of defect 19, euler #=-16 (136395,408784,272373) : difference with theory (-16) = 0 CORRECTING DEFECT 20 (vertices=39, convex hull=30) After retessellation of defect 20, euler #=-15 (136401,408813,272397) : difference with theory (-15) = 0 CORRECTING DEFECT 21 (vertices=23, convex hull=28) After retessellation of defect 21, euler #=-14 (136404,408835,272417) : difference with theory (-14) = 0 CORRECTING DEFECT 22 (vertices=48, convex hull=70) After retessellation of defect 22, euler #=-13 (136425,408928,272490) : difference with theory (-13) = 0 CORRECTING DEFECT 23 (vertices=19, convex hull=36) After retessellation of defect 23, euler #=-12 (136431,408956,272513) : difference with theory (-12) = 0 CORRECTING DEFECT 24 (vertices=90, convex hull=116) After retessellation of defect 24, euler #=-11 (136485,409171,272675) : difference with theory (-11) = 0 CORRECTING DEFECT 25 (vertices=13, convex hull=27) After retessellation of defect 25, euler #=-10 (136486,409183,272687) : difference with theory (-10) = 0 CORRECTING DEFECT 26 (vertices=49, convex hull=36) After retessellation of defect 26, euler #=-9 (136494,409217,272714) : difference with theory (-9) = 0 CORRECTING DEFECT 27 (vertices=5, convex hull=16) After retessellation of defect 27, euler #=-8 (136495,409226,272723) : difference with theory (-8) = 0 CORRECTING DEFECT 28 (vertices=25, convex hull=67) After retessellation of defect 28, euler #=-7 (136504,409277,272766) : difference with theory (-7) = 0 CORRECTING DEFECT 29 (vertices=51, convex hull=60) After retessellation of defect 29, euler #=-6 (136522,409356,272828) : difference with theory (-6) = 0 CORRECTING DEFECT 30 (vertices=87, convex hull=58) After retessellation of defect 30, euler #=-5 (136532,409411,272874) : difference with theory (-5) = 0 CORRECTING DEFECT 31 (vertices=43, convex hull=70) After retessellation of defect 31, euler #=-4 (136551,409498,272943) : difference with theory (-4) = 0 CORRECTING DEFECT 32 (vertices=38, convex hull=71) After retessellation of defect 32, euler #=-3 (136567,409576,273006) : difference with theory (-3) = 0 CORRECTING DEFECT 33 (vertices=58, convex hull=97) After retessellation of defect 33, euler #=-2 (136583,409663,273078) : difference with theory (-2) = 0 CORRECTING DEFECT 34 (vertices=17, convex hull=56) After retessellation of defect 34, euler #=-1 (136594,409718,273123) : difference with theory (-1) = 0 CORRECTING DEFECT 35 (vertices=19, convex hull=51) After retessellation of defect 35, euler #=0 (136602,409759,273157) : difference with theory (0) = 0 CORRECTING DEFECT 36 (vertices=26, convex hull=38) After retessellation of defect 36, euler #=1 (136605,409782,273178) : difference with theory (1) = 0 CORRECTING DEFECT 37 (vertices=58, convex hull=72) After retessellation of defect 37, euler #=2 (136619,409851,273234) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.87 +- 0.23 (0.07-->6.24) (max @ vno 51298 --> 52224) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.87 +- 0.23 (0.07-->6.24) (max @ vno 51298 --> 52224) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 146 mutations (35.5%), 265 crossovers (64.5%), 128 vertices were eliminated building final representation... 1395 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=136619, nf=273234, ne=409851, g=0) writing corrected surface to /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 15.4 minutes 0 defective edges removing intersecting faces 000: 225 intersecting 001: 3 intersecting 002: 2 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 136619 - 409851 + 273234 = 2 --> 0 holes F =2V-4: 273234 = 273238-4 (0) 2E=3F: 819702 = 819702 (0) total defect index = 0 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 28 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Thu Oct 6 22:30:59 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs 16945 rh only generating white matter surface 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 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/filled.mgz... reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/brain.finalsurfs.mgz... reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/wm.mgz... 20229 bright wm thresholded. 316 bright non-wm voxels segmented. reading original surface position from /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.orig... computing class statistics... border white: 246340 voxels (1.47%) border gray 280577 voxels (1.67%) WM (92.0): 93.5 +- 9.4 [70.0 --> 110.0] GM (78.0) : 75.9 +- 12.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 54.7 (was 70) setting MAX_BORDER_WHITE to 113.4 (was 105) setting MIN_BORDER_WHITE to 67.0 (was 85) setting MAX_CSF to 42.3 (was 40) setting MAX_GRAY to 94.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 60.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 30.0 (was 40) repositioning cortical surface to gray/white boundary reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.22 (0.04-->3.19) (max @ vno 22237 --> 136118) face area 0.27 +- 0.12 (0.00-->2.70) mean absolute distance = 0.66 +- 0.83 2878 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=67 mean inside = 92.9, mean outside = 72.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=78.3, 66 (66) missing vertices, mean dist 0.2 [0.6 (%37.9)->0.7 (%62.1))] %63 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=jmlin, 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 0.89 +- 0.26 (0.08-->4.49) (max @ vno 99773 --> 98838) face area 0.27 +- 0.13 (0.00-->2.64) mean absolute distance = 0.35 +- 0.56 3609 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5485898.0, rms=10.60 001: dt: 0.5000, sse=6884764.5, rms=7.363 (0.000%) 002: dt: 0.5000, sse=7630158.0, rms=5.726 (0.000%) 003: dt: 0.5000, sse=8060431.0, rms=4.886 (0.000%) 004: dt: 0.5000, sse=8408440.0, rms=4.420 (0.000%) 005: dt: 0.5000, sse=8547145.0, rms=4.218 (0.000%) 006: dt: 0.5000, sse=8658883.0, rms=4.072 (0.000%) rms = 4.03, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=8646189.0, rms=4.034 (0.000%) 008: dt: 0.2500, sse=5604122.0, rms=2.898 (0.000%) 009: dt: 0.2500, sse=5231770.0, rms=2.514 (0.000%) 010: dt: 0.2500, sse=4953301.5, rms=2.423 (0.000%) 011: dt: 0.2500, sse=4888267.0, rms=2.350 (0.000%) rms = 2.32, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=4802563.0, rms=2.323 (0.000%) 013: dt: 0.1250, sse=4648142.5, rms=2.192 (0.000%) rms = 2.18, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=4605070.5, rms=2.177 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=81.8, 79 (31) missing vertices, mean dist -0.2 [0.4 (%72.2)->0.2 (%27.8))] %77 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=jmlin, 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 0.88 +- 0.26 (0.07-->4.58) (max @ vno 99773 --> 98838) face area 0.33 +- 0.16 (0.00-->3.49) mean absolute distance = 0.26 +- 0.38 4342 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5254321.5, rms=4.99 015: dt: 0.5000, sse=5688928.5, rms=3.552 (0.000%) rms = 3.90, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=5219676.0, rms=2.666 (0.000%) 017: dt: 0.2500, sse=5056214.0, rms=2.211 (0.000%) 018: dt: 0.2500, sse=4963879.0, rms=1.963 (0.000%) rms = 1.91, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=4933519.5, rms=1.914 (0.000%) 020: dt: 0.1250, sse=4802709.0, rms=1.788 (0.000%) rms = 1.77, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=4757320.0, rms=1.772 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=84.2, 60 (21) missing vertices, mean dist -0.1 [0.3 (%68.2)->0.2 (%31.8))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=jmlin, 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 (0.09-->4.61) (max @ vno 99773 --> 98838) face area 0.33 +- 0.16 (0.00-->3.47) mean absolute distance = 0.23 +- 0.32 3502 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4974353.0, rms=3.46 022: dt: 0.5000, sse=5460049.5, rms=3.324 (0.000%) rms = 3.78, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=5044956.0, rms=2.272 (0.000%) 024: dt: 0.2500, sse=5030750.0, rms=1.883 (0.000%) 025: dt: 0.2500, sse=5015173.0, rms=1.738 (0.000%) rms = 1.74, time step reduction 2 of 3 to 0.125... 026: dt: 0.1250, sse=4956170.0, rms=1.671 (0.000%) 027: dt: 0.1250, sse=4871195.0, rms=1.582 (0.000%) rms = 1.59, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=4871195.0, rms=1.582 (0.003%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=85.0, 66 (14) missing vertices, mean dist -0.0 [0.2 (%55.0)->0.2 (%45.0))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=jmlin, 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 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4894720.5, rms=1.93 rms = 2.38, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=5028828.5, rms=1.403 (0.000%) 030: dt: 0.2500, sse=5282411.5, rms=1.190 (0.000%) rms = 1.20, time step reduction 2 of 3 to 0.125... rms = 1.18, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=5276650.0, rms=1.181 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group generating cortex label... 19 non-cortical segments detected only using segment with 1784 vertices erasing segment 1 (vno[0] = 57308) erasing segment 2 (vno[0] = 65800) erasing segment 3 (vno[0] = 93283) erasing segment 4 (vno[0] = 94396) erasing segment 5 (vno[0] = 95260) erasing segment 6 (vno[0] = 98909) erasing segment 7 (vno[0] = 98910) erasing segment 8 (vno[0] = 98915) erasing segment 9 (vno[0] = 100804) erasing segment 10 (vno[0] = 101666) erasing segment 11 (vno[0] = 101687) erasing segment 12 (vno[0] = 102756) erasing segment 13 (vno[0] = 107038) erasing segment 14 (vno[0] = 107041) erasing segment 15 (vno[0] = 107836) erasing segment 16 (vno[0] = 108688) erasing segment 17 (vno[0] = 110215) erasing segment 18 (vno[0] = 136382) writing cortex label to /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/label/rh.cortex.label... writing curvature file /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.curv writing smoothed area to rh.area writing curvature file /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.area vertex spacing 0.88 +- 0.26 (0.03-->4.65) (max @ vno 99773 --> 98838) face area 0.32 +- 0.16 (0.00-->3.39) refinement took 3.4 minutes #-------------------------------------------- #@# Smooth2 rh Thu Oct 6 22:34:25 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts 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 rh Thu Oct 6 22:34:27 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 45.8 mm, total surface area = 79838 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.120 (target=0.015) step 005: RMS=0.082 (target=0.015) step 010: RMS=0.060 (target=0.015) step 015: RMS=0.050 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.021 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: RMS=0.015 (target=0.015) inflation complete. inflation took 0.3 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 158 vertices thresholded to be in k1 ~ [-0.32 0.29], k2 ~ [-0.16 0.11] total integrated curvature = 0.555*4pi (6.974) --> 0 handles ICI = 1.4, FI = 8.6, variation=148.220 124 vertices thresholded to be in [-0.03 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 122 vertices thresholded to be in [-0.14 0.14] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.021 done. #----------------------------------------- #@# Curvature Stats rh Thu Oct 6 22:35:40 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 16945 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 [ 16945/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 [ 247 ] Gb_filter = 0 WARN: S lookup min: -0.268916 WARN: S explicit min: 0.000000 vertex = 600 #-------------------------------------------- #@# Sphere rh Thu Oct 6 22:35:43 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.283... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=jmlin, 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 %42.39 pass 1: epoch 2 of 3 starting distance error %20.13 unfolding complete - removing small folds... starting distance error %19.99 removing remaining folds... final distance error %20.01 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.27 hours #-------------------------------------------- #@# Surf Reg rh Thu Oct 6 22:51:48 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/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=jmlin, 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=jmlin, 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 = 0.579 curvature mean = 0.019, std = 0.933 curvature mean = 0.027, std = 0.854 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, 16.00) sse = 407615.7, tmin=0.5789 d=32.00 min @ (8.00, -8.00, -8.00) sse = 316287.5, tmin=1.1613 d=16.00 min @ (-4.00, 0.00, 0.00) sse = 309381.9, tmin=1.7514 d=8.00 min @ (2.00, 0.00, 0.00) sse = 306716.7, tmin=2.3440 d=4.00 min @ (0.00, 1.00, 0.00) sse = 305200.7, tmin=2.9412 d=2.00 min @ (-0.50, -0.50, 0.00) sse = 305127.3, tmin=3.5412 d=1.00 min @ (0.25, 0.25, 0.25) sse = 304959.7, tmin=4.1440 tol=1.0e+00, sigma=0.5, host=jmlin, 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 4.77 min curvature mean = -0.008, std = 0.943 curvature mean = 0.009, std = 0.935 curvature mean = -0.013, std = 0.952 curvature mean = 0.004, std = 0.969 curvature mean = -0.015, std = 0.950 curvature mean = 0.001, std = 0.986 2 Reading smoothwm curvature mean = -0.027, std = 0.306 curvature mean = 0.005, std = 0.070 curvature mean = 0.064, std = 0.336 curvature mean = 0.004, std = 0.084 curvature mean = 0.031, std = 0.524 curvature mean = 0.005, std = 0.090 curvature mean = 0.017, std = 0.663 curvature mean = 0.005, std = 0.093 curvature mean = 0.006, std = 0.776 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Thu Oct 6 23:06:41 EDT 2016 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 rh Thu Oct 6 23:06:42 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mrisp_paint -a 5 /usr/local/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 /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Thu Oct 6 23:06:43 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 16945 rh ../surf/rh.sphere.reg /usr/local/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.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/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... 890 labels changed using aseg relabeling using gibbs priors... 000: 2951 changed, 136619 examined... 001: 706 changed, 12579 examined... 002: 182 changed, 3969 examined... 003: 56 changed, 1075 examined... 004: 22 changed, 334 examined... 005: 6 changed, 132 examined... 006: 5 changed, 44 examined... 007: 4 changed, 27 examined... 008: 4 changed, 25 examined... 009: 1 changed, 16 examined... 010: 0 changed, 7 examined... 150 labels changed using aseg 000: 91 total segments, 51 labels (368 vertices) changed 001: 41 total segments, 1 labels (1 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 45 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1380 vertices marked for relabeling... 1380 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 31 seconds. #-------------------------------------------- #@# Make Pial Surf rh Thu Oct 6 23:07:15 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs 16945 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/filled.mgz... reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/brain.finalsurfs.mgz... reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/wm.mgz... 20229 bright wm thresholded. 316 bright non-wm voxels segmented. reading original surface position from /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.orig... computing class statistics... border white: 246340 voxels (1.47%) border gray 280577 voxels (1.67%) WM (92.0): 93.5 +- 9.4 [70.0 --> 110.0] GM (78.0) : 75.9 +- 12.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 54.7 (was 70) setting MAX_BORDER_WHITE to 113.4 (was 105) setting MIN_BORDER_WHITE to 67.0 (was 85) setting MAX_CSF to 42.3 (was 40) setting MAX_GRAY to 94.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 60.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 30.0 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=67 mean inside = 92.9, mean outside = 72.1 smoothing surface for 5 iterations... 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/white boundary reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.22 (0.04-->3.19) (max @ vno 22237 --> 136118) face area 0.27 +- 0.12 (0.00-->2.70) mean absolute distance = 0.66 +- 0.83 2905 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 440 points - only 0.00% unknown removing 3 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 23 points - only 0.00% unknown deleting segment 8 with 8 points - only 0.00% unknown mean border=78.3, 66 (66) missing vertices, mean dist 0.2 [0.6 (%37.9)->0.7 (%62.1))] %63 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=jmlin, 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 0.89 +- 0.26 (0.08-->4.49) (max @ vno 99773 --> 98838) face area 0.27 +- 0.13 (0.00-->2.64) mean absolute distance = 0.35 +- 0.56 3621 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5496648.0, rms=10.59 001: dt: 0.5000, sse=6904505.0, rms=7.356 (0.000%) 002: dt: 0.5000, sse=7652937.0, rms=5.721 (0.000%) 003: dt: 0.5000, sse=8087735.0, rms=4.883 (0.000%) 004: dt: 0.5000, sse=8436767.0, rms=4.418 (0.000%) 005: dt: 0.5000, sse=8581001.0, rms=4.216 (0.000%) 006: dt: 0.5000, sse=8688645.0, rms=4.071 (0.000%) rms = 4.03, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=8684529.0, rms=4.033 (0.000%) 008: dt: 0.2500, sse=5624108.5, rms=2.897 (0.000%) 009: dt: 0.2500, sse=5252066.5, rms=2.514 (0.000%) 010: dt: 0.2500, sse=4971734.0, rms=2.422 (0.000%) 011: dt: 0.2500, sse=4907474.0, rms=2.350 (0.000%) rms = 2.32, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=4821591.0, rms=2.323 (0.000%) 013: dt: 0.1250, sse=4666437.5, rms=2.192 (0.000%) rms = 2.18, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=4623089.5, rms=2.177 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 1 with 367 points - only 0.00% unknown deleting segment 2 with 10 points - only 0.00% unknown removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown deleting segment 8 with 38 points - only 0.00% unknown deleting segment 9 with 8 points - only 0.00% unknown mean border=81.8, 81 (31) missing vertices, mean dist -0.2 [0.4 (%72.3)->0.2 (%27.7))] %77 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=jmlin, 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 0.88 +- 0.25 (0.07-->4.58) (max @ vno 99773 --> 98838) face area 0.33 +- 0.16 (0.00-->3.49) mean absolute distance = 0.26 +- 0.38 4363 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5274639.0, rms=4.99 015: dt: 0.5000, sse=5709793.0, rms=3.551 (0.000%) rms = 3.90, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=5240000.0, rms=2.664 (0.000%) 017: dt: 0.2500, sse=5077563.5, rms=2.210 (0.000%) 018: dt: 0.2500, sse=4983589.0, rms=1.962 (0.000%) rms = 1.91, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=4954166.5, rms=1.914 (0.000%) 020: dt: 0.1250, sse=4823123.0, rms=1.788 (0.000%) rms = 1.77, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=4777328.0, rms=1.772 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 1 with 429 points - only 0.00% unknown removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 34 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 8 points - only 0.00% unknown mean border=84.2, 61 (21) missing vertices, mean dist -0.1 [0.3 (%68.2)->0.2 (%31.8))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=jmlin, 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 (0.09-->4.61) (max @ vno 99773 --> 98838) face area 0.33 +- 0.16 (0.00-->3.47) mean absolute distance = 0.23 +- 0.32 3512 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4994655.5, rms=3.46 022: dt: 0.5000, sse=5482080.0, rms=3.322 (0.000%) rms = 3.78, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=5066244.0, rms=2.271 (0.000%) 024: dt: 0.2500, sse=5052458.0, rms=1.883 (0.000%) 025: dt: 0.2500, sse=5035820.5, rms=1.739 (0.000%) rms = 1.74, time step reduction 2 of 3 to 0.125... 026: dt: 0.1250, sse=4976819.5, rms=1.672 (0.000%) 027: dt: 0.1250, sse=4891865.0, rms=1.583 (0.000%) rms = 1.59, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=4891865.0, rms=1.583 (0.003%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 436 points - only 0.00% unknown removing 3 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 11 points - only 0.00% unknown deleting segment 8 with 11 points - only 0.00% unknown deleting segment 9 with 34 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown deleting segment 11 with 8 points - only 0.00% unknown mean border=85.0, 66 (14) missing vertices, mean dist -0.0 [0.2 (%55.0)->0.2 (%45.0))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=jmlin, 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 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4915942.5, rms=1.93 rms = 2.37, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=5051804.5, rms=1.402 (0.000%) 030: dt: 0.2500, sse=5307520.0, rms=1.190 (0.000%) rms = 1.20, time step reduction 2 of 3 to 0.125... rms = 1.18, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=5301665.0, rms=1.181 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group smoothing surface for 5 iterations... mean border=56.3, 114 (114) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.4 (%100.0))] %21 local maxima, %48 large gradients and %27 min vals, 1796 gradients ignored tol=1.0e-04, sigma=2.0, host=jmlin, 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=23815662.0, rms=28.38 001: dt: 0.5000, sse=17723658.0, rms=23.897 (0.000%) 002: dt: 0.5000, sse=13433659.0, rms=20.159 (0.000%) 003: dt: 0.5000, sse=10656993.0, rms=17.116 (0.000%) 004: dt: 0.5000, sse=9048528.0, rms=14.663 (0.000%) 005: dt: 0.5000, sse=8103919.0, rms=12.698 (0.000%) 006: dt: 0.5000, sse=7585847.0, rms=11.140 (0.000%) 007: dt: 0.5000, sse=7288307.5, rms=9.833 (0.000%) 008: dt: 0.5000, sse=7148270.5, rms=8.673 (0.000%) 009: dt: 0.5000, sse=7073769.5, rms=7.673 (0.000%) 010: dt: 0.5000, sse=7128776.5, rms=6.808 (0.000%) 011: dt: 0.5000, sse=7228637.0, rms=6.092 (0.000%) 012: dt: 0.5000, sse=7333557.5, rms=5.503 (0.000%) 013: dt: 0.5000, sse=7478344.5, rms=5.086 (0.000%) 014: dt: 0.5000, sse=7553741.5, rms=4.813 (0.000%) 015: dt: 0.5000, sse=7681743.5, rms=4.647 (0.000%) 016: dt: 0.5000, sse=7702556.0, rms=4.546 (0.000%) 017: dt: 0.5000, sse=7769790.5, rms=4.477 (0.000%) 018: dt: 0.5000, sse=7750174.5, rms=4.424 (0.000%) rms = 4.39, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=7815067.5, rms=4.388 (0.000%) 020: dt: 0.2500, sse=5555540.5, rms=3.664 (0.000%) 021: dt: 0.2500, sse=5413234.0, rms=3.446 (0.000%) rms = 3.42, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5238091.0, rms=3.420 (0.000%) 023: dt: 0.1250, sse=4978112.0, rms=3.261 (0.000%) rms = 3.23, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4938783.5, rms=3.233 (0.000%) positioning took 1.6 minutes mean border=53.7, 1111 (15) missing vertices, mean dist 0.2 [0.2 (%42.9)->0.6 (%57.1))] %42 local maxima, %32 large gradients and %22 min vals, 600 gradients ignored tol=1.0e-04, sigma=1.0, host=jmlin, 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=5661402.0, rms=5.45 025: dt: 0.5000, sse=5930522.5, rms=4.640 (0.000%) 026: dt: 0.5000, sse=7582631.0, rms=4.516 (0.000%) rms = 4.49, time step reduction 1 of 3 to 0.250... 027: dt: 0.5000, sse=7236434.0, rms=4.491 (0.000%) 028: dt: 0.2500, sse=5879335.5, rms=3.561 (0.000%) 029: dt: 0.2500, sse=5789342.5, rms=3.252 (0.000%) rms = 3.25, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=5651720.5, rms=3.250 (0.000%) 031: dt: 0.1250, sse=5376383.5, rms=3.004 (0.000%) rms = 2.96, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=5347268.5, rms=2.956 (0.000%) positioning took 0.5 minutes mean border=52.1, 1328 (9) missing vertices, mean dist 0.1 [0.2 (%40.3)->0.4 (%59.7))] %56 local maxima, %17 large gradients and %22 min vals, 701 gradients ignored tol=1.0e-04, sigma=0.5, host=jmlin, 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=5533912.5, rms=3.88 rms = 4.17, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=5337566.5, rms=3.402 (0.000%) 034: dt: 0.2500, sse=5347061.5, rms=3.140 (0.000%) 035: dt: 0.2500, sse=5545418.5, rms=3.081 (0.000%) rms = 3.05, time step reduction 2 of 3 to 0.125... 036: dt: 0.2500, sse=5643607.0, rms=3.053 (0.000%) 037: dt: 0.1250, sse=5414941.0, rms=2.864 (0.000%) rms = 2.82, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=5422778.5, rms=2.817 (0.000%) positioning took 0.4 minutes mean border=51.3, 2535 (7) missing vertices, mean dist 0.0 [0.2 (%46.7)->0.3 (%53.3))] %58 local maxima, %15 large gradients and %21 min vals, 580 gradients ignored tol=1.0e-04, sigma=0.2, host=jmlin, 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 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=5460220.5, rms=3.08 rms = 3.69, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=5374921.0, rms=2.874 (0.000%) 040: dt: 0.2500, sse=5611980.0, rms=2.821 (0.000%) rms = 2.83, time step reduction 2 of 3 to 0.125... rms = 2.78, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=5552121.5, rms=2.779 (0.000%) positioning took 0.3 minutes writing curvature file /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.area.pial vertex spacing 0.99 +- 0.42 (0.03-->5.91) (max @ vno 70089 --> 71218) face area 0.39 +- 0.29 (0.00-->4.76) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 136619 vertices processed 25000 of 136619 vertices processed 50000 of 136619 vertices processed 75000 of 136619 vertices processed 100000 of 136619 vertices processed 125000 of 136619 vertices processed 0 of 136619 vertices processed 25000 of 136619 vertices processed 50000 of 136619 vertices processed 75000 of 136619 vertices processed 100000 of 136619 vertices processed 125000 of 136619 vertices processed thickness calculation complete, 278:539 truncations. 28516 vertices at 0 distance 90219 vertices at 1 distance 87061 vertices at 2 distance 39187 vertices at 3 distance 12016 vertices at 4 distance 3538 vertices at 5 distance 1096 vertices at 6 distance 340 vertices at 7 distance 131 vertices at 8 distance 73 vertices at 9 distance 52 vertices at 10 distance 32 vertices at 11 distance 34 vertices at 12 distance 35 vertices at 13 distance 16 vertices at 14 distance 18 vertices at 15 distance 12 vertices at 16 distance 3 vertices at 17 distance 12 vertices at 18 distance 10 vertices at 19 distance 7 vertices at 20 distance writing curvature file /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.thickness positioning took 7.0 minutes #-------------------------------------------- #@# Surf Volume rh Thu Oct 6 23:14:14 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/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_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast rh Thu Oct 6 23:14:15 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts pctsurfcon --s 16945 --rh-only Log file is /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts/pctsurfcon.log Thu Oct 6 23:14:15 EDT 2016 setenv SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets cd /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux jmlina2 4.4.0-38-generic #57~14.04.1-Ubuntu SMP Tue Sep 6 17:20:43 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/tmp.pctsurfcon.19535/rh.wm.mgh --regheader 16945 --cortex srcvol = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/orig.mgz as target reference. Loading label /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/label/rh.cortex.label Reading surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/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 = 71274 Masking with /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/label/rh.cortex.label Writing to /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/tmp.pctsurfcon.19535/rh.wm.mgh Dim: 136619 1 1 mri_vol2surf --mov /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/tmp.pctsurfcon.19535/rh.gm.mgh --projfrac 0.3 --regheader 16945 --cortex srcvol = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/orig.mgz as target reference. Loading label /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/label/rh.cortex.label Reading surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Done reading source surface Reading thickness /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/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 = 89592 Masking with /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/label/rh.cortex.label Writing to /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/tmp.pctsurfcon.19535/rh.gm.mgh Dim: 136619 1 1 mri_concat /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/tmp.pctsurfcon.19535/rh.wm.mgh /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/tmp.pctsurfcon.19535/rh.gm.mgh --paired-diff-norm --mul 100 --o /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/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 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.w-g.pct.mgh mri_segstats --in /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.w-g.pct.mgh --annot 16945 rh aparc --sum /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.w-g.pct.mgh --annot 16945 rh aparc --sum /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/stats/rh.w-g.pct.stats --snr sysname Linux hostname jmlina2 machine x86_64 user jsboucher UseRobust 0 Constructing seg from annotation Reading annotation 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 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.w-g.pct.mgh Vertex Area is 0.645338 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1223 851.142 2 2002 caudalanteriorcingulate 1194 794.983 3 2003 caudalmiddlefrontal 3189 2106.855 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2098 1286.354 6 2006 entorhinal 558 368.441 7 2007 fusiform 5454 3577.255 8 2008 inferiorparietal 8127 5275.348 9 2009 inferiortemporal 4740 3021.256 10 2010 isthmuscingulate 1256 788.750 11 2011 lateraloccipital 7789 4755.660 12 2012 lateralorbitofrontal 3926 2614.338 13 2013 lingual 5443 3514.734 14 2014 medialorbitofrontal 3061 1988.347 15 2015 middletemporal 4925 3272.710 16 2016 parahippocampal 1101 687.115 17 2017 paracentral 2274 1452.229 18 2018 parsopercularis 2739 1842.173 19 2019 parsorbitalis 1240 836.774 20 2020 parstriangularis 2497 1648.537 21 2021 pericalcarine 2806 1810.107 22 2022 postcentral 5480 3466.278 23 2023 posteriorcingulate 1863 1224.406 24 2024 precentral 7513 4712.405 25 2025 precuneus 6261 4076.902 26 2026 rostralanteriorcingulate 828 543.179 27 2027 rostralmiddlefrontal 7686 5121.054 28 2028 superiorfrontal 9436 6176.307 29 2029 superiorparietal 9202 5799.448 30 2030 superiortemporal 5232 3325.063 31 2031 supramarginal 5212 3382.059 32 2032 frontalpole 410 264.501 33 2033 temporalpole 690 460.625 34 2034 transversetemporal 557 314.558 35 2035 insula 2969 1959.399 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Thu Oct 6 23:14:20 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 16945 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/wm.mgz... reading input surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white... reading input pial surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.pial... reading input white surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. 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 1223 851 2068 2.466 0.364 0.124 0.040 11 2.1 bankssts 1194 795 2333 2.817 0.546 0.163 0.064 25 3.2 caudalanteriorcingulate 3189 2107 5802 2.438 0.538 0.150 0.071 106 10.0 caudalmiddlefrontal 2098 1286 2647 1.824 0.489 0.190 0.136 154 9.2 cuneus 558 368 1710 3.168 1.055 0.173 0.081 10 2.1 entorhinal 5454 3577 11150 2.705 0.621 0.161 0.076 114 17.2 fusiform 8127 5275 14162 2.440 0.493 0.157 0.069 157 23.3 inferiorparietal 4740 3021 9121 2.568 0.642 0.164 0.082 115 16.2 inferiortemporal 1256 789 2064 2.435 0.757 0.165 0.112 49 7.2 isthmuscingulate 7789 4756 10831 2.047 0.472 0.173 0.147 316 38.4 lateraloccipital 3926 2614 7296 2.415 0.673 0.167 0.081 103 13.2 lateralorbitofrontal 5443 3515 8124 2.120 0.574 0.174 0.097 126 20.1 lingual 3061 1988 5360 2.267 0.728 0.171 0.097 97 12.0 medialorbitofrontal 4925 3273 11709 2.856 0.639 0.162 0.072 106 14.1 middletemporal 1101 687 2269 2.953 0.728 0.165 0.103 25 4.9 parahippocampal 2274 1452 3663 2.393 0.488 0.146 0.060 37 5.9 paracentral 2739 1842 5219 2.460 0.552 0.165 0.070 55 8.0 parsopercularis 1240 837 2596 2.374 0.635 0.178 0.085 32 4.2 parsorbitalis 2497 1649 4211 2.124 0.584 0.163 0.075 52 7.8 parstriangularis 2806 1810 2728 1.674 0.464 0.180 0.122 77 12.0 pericalcarine 5480 3466 7846 2.059 0.618 0.160 0.131 185 19.7 postcentral 1863 1224 3495 2.654 0.616 0.169 0.068 42 5.3 posteriorcingulate 7513 4712 11804 2.380 0.504 0.160 0.116 270 37.7 precentral 6261 4077 9760 2.282 0.575 0.165 0.087 173 20.2 precuneus 828 543 1625 2.847 0.609 0.168 0.076 18 2.5 rostralanteriorcingulate 7686 5121 13163 2.196 0.609 0.173 0.084 182 26.8 rostralmiddlefrontal 9436 6176 18755 2.709 0.630 0.172 0.115 283 39.2 superiorfrontal 9202 5799 12953 2.062 0.425 0.160 0.088 264 32.7 superiorparietal 5232 3325 9513 2.486 0.549 0.140 0.081 176 15.0 superiortemporal 5212 3382 9156 2.514 0.530 0.160 0.078 99 15.8 supramarginal 410 265 944 2.488 0.683 0.226 0.137 27 2.6 frontalpole 690 461 1751 2.885 0.801 0.250 0.496 513 5.4 temporalpole 557 315 679 2.103 0.404 0.167 0.103 14 2.4 transversetemporal 2969 1959 6185 3.050 0.851 0.149 0.085 67 9.3 insula #----------------------------------------- #@# Cortical Parc 2 rh Thu Oct 6 23:14:29 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 16945 rh ../surf/rh.sphere.reg /usr/local/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.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/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... 4 labels changed using aseg relabeling using gibbs priors... 000: 10075 changed, 136619 examined... 001: 2370 changed, 38153 examined... 002: 762 changed, 12056 examined... 003: 287 changed, 4138 examined... 004: 136 changed, 1594 examined... 005: 96 changed, 800 examined... 006: 66 changed, 525 examined... 007: 39 changed, 370 examined... 008: 24 changed, 212 examined... 009: 7 changed, 130 examined... 010: 1 changed, 41 examined... 011: 1 changed, 5 examined... 012: 3 changed, 9 examined... 013: 0 changed, 11 examined... 13 labels changed using aseg 000: 292 total segments, 205 labels (2786 vertices) changed 001: 110 total segments, 24 labels (133 vertices) changed 002: 87 total segments, 1 labels (1 vertices) changed 003: 86 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 123 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 724 vertices marked for relabeling... 724 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 42 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Thu Oct 6 23:15:11 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_anatomical_stats -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 16945 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/wm.mgz... reading input surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white... reading input pial surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.pial... reading input white surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. 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 1010 695 1884 2.142 0.726 0.185 0.085 30 3.9 G_and_S_frontomargin 1117 724 1946 2.395 0.436 0.170 0.073 21 3.4 G_and_S_occipital_inf 1438 828 2155 2.190 0.523 0.171 0.183 92 8.6 G_and_S_paracentral 1109 742 2312 2.752 0.407 0.161 0.067 21 3.0 G_and_S_subcentral 923 618 1788 2.237 0.666 0.199 0.110 29 4.1 G_and_S_transv_frontopol 2438 1637 4447 2.504 0.624 0.151 0.061 35 6.0 G_and_S_cingul-Ant 1438 964 2727 2.703 0.458 0.148 0.062 22 3.7 G_and_S_cingul-Mid-Ant 1406 950 2540 2.520 0.526 0.155 0.062 23 3.6 G_and_S_cingul-Mid-Post 656 411 1544 2.929 0.762 0.210 0.112 25 3.3 G_cingul-Post-dorsal 211 137 513 3.192 0.705 0.197 0.099 6 0.8 G_cingul-Post-ventral 1955 1201 2362 1.727 0.524 0.197 0.146 153 8.9 G_cuneus 1428 968 3197 2.574 0.568 0.184 0.085 37 4.9 G_front_inf-Opercular 346 231 646 2.344 0.644 0.214 0.105 13 1.6 G_front_inf-Orbital 1592 1037 3112 2.267 0.609 0.174 0.083 39 5.6 G_front_inf-Triangul 3703 2434 7488 2.418 0.624 0.184 0.106 156 16.3 G_front_middle 7006 4528 15516 2.809 0.646 0.192 0.143 280 35.8 G_front_sup 463 296 1308 3.672 0.818 0.164 0.127 16 2.2 G_Ins_lg_and_S_cent_ins 524 338 1704 3.698 0.831 0.169 0.131 23 2.1 G_insular_short 1913 1216 4092 2.580 0.450 0.176 0.087 46 6.4 G_occipital_middle 2442 1480 3605 2.075 0.427 0.171 0.092 75 9.5 G_occipital_sup 2300 1437 5217 2.812 0.633 0.185 0.100 69 9.9 G_oc-temp_lat-fusifor 3622 2276 5763 2.158 0.600 0.192 0.112 108 15.6 G_oc-temp_med-Lingual 1786 1139 4671 3.152 0.923 0.192 0.248 531 9.8 G_oc-temp_med-Parahip 2619 1723 6369 2.658 0.663 0.196 0.112 104 11.7 G_orbital 2898 1872 6161 2.609 0.537 0.177 0.086 80 10.2 G_pariet_inf-Angular 2757 1750 5779 2.626 0.557 0.174 0.097 69 9.9 G_pariet_inf-Supramar 3024 1874 4791 2.155 0.421 0.163 0.109 109 12.1 G_parietal_sup 1963 1157 3189 2.163 0.584 0.175 0.226 114 9.0 G_postcentral 2913 1711 5579 2.527 0.541 0.183 0.151 113 18.9 G_precentral 3654 2360 6035 2.157 0.543 0.178 0.094 137 13.9 G_precuneus 921 555 1860 2.354 0.670 0.203 0.154 56 5.9 G_rectus 281 189 496 2.616 0.925 0.081 0.041 3 0.3 G_subcallosal 460 256 642 2.128 0.445 0.161 0.114 12 2.1 G_temp_sup-G_T_transv 1825 1087 3882 2.665 0.580 0.159 0.141 134 7.7 G_temp_sup-Lateral 715 487 1512 2.610 0.666 0.145 0.069 10 2.1 G_temp_sup-Plan_polar 658 448 1114 2.426 0.517 0.139 0.050 8 1.4 G_temp_sup-Plan_tempo 2409 1488 5488 2.683 0.675 0.184 0.100 83 10.1 G_temporal_inf 3015 1976 8099 3.013 0.604 0.175 0.087 83 10.1 G_temporal_middle 355 236 507 2.046 0.491 0.129 0.040 4 0.6 Lat_Fis-ant-Horizont 188 125 317 2.700 0.486 0.157 0.076 3 0.4 Lat_Fis-ant-Vertical 1360 897 1744 2.410 0.448 0.141 0.053 16 3.0 Lat_Fis-post 4883 2814 5751 1.853 0.468 0.178 0.203 270 30.8 Pole_occipital 1825 1217 5003 2.854 0.875 0.210 0.132 66 9.6 Pole_temporal 2695 1810 3082 1.940 0.642 0.173 0.107 63 10.2 S_calcarine 3036 2019 3371 1.932 0.547 0.148 0.112 93 14.6 S_central 1496 998 2067 2.267 0.400 0.133 0.049 16 3.1 S_cingul-Marginalis 532 355 813 2.605 0.531 0.139 0.046 6 1.1 S_circular_insula_ant 1170 758 1651 2.404 0.562 0.099 0.035 8 1.7 S_circular_insula_inf 1377 913 2007 2.537 0.425 0.122 0.038 11 2.3 S_circular_insula_sup 1129 766 1774 2.347 0.499 0.131 0.046 14 2.3 S_collat_transv_ant 623 419 749 2.102 0.449 0.150 0.063 7 1.5 S_collat_transv_post 2490 1659 3552 2.135 0.462 0.148 0.059 36 5.9 S_front_inf 1511 1000 2330 2.079 0.566 0.146 0.061 29 3.8 S_front_middle 2201 1465 3057 2.274 0.525 0.144 0.055 25 5.3 S_front_sup 471 313 594 2.161 0.455 0.147 0.047 6 1.0 S_interm_prim-Jensen 3515 2296 4355 2.029 0.425 0.149 0.065 58 9.3 S_intrapariet_and_P_trans 1186 775 1355 1.978 0.371 0.151 0.056 16 2.8 S_oc_middle_and_Lunatus 1586 1025 2051 2.090 0.367 0.142 0.053 23 3.7 S_oc_sup_and_transversal 685 455 982 2.260 0.381 0.149 0.071 10 2.3 S_occipital_ant 1362 892 1911 2.505 0.378 0.124 0.040 10 2.4 S_oc-temp_lat 2027 1394 3332 2.617 0.484 0.127 0.040 15 3.6 S_oc-temp_med_and_Lingual 530 348 720 1.812 0.523 0.179 0.089 12 2.2 S_orbital_lateral 875 600 1262 2.134 0.710 0.113 0.029 6 1.1 S_orbital_med-olfact 1548 1049 2413 2.185 0.493 0.162 0.071 30 4.8 S_orbital-H_Shaped 1853 1204 2509 2.311 0.530 0.151 0.058 26 4.5 S_parieto_occipital 1375 830 1533 2.479 0.802 0.164 0.098 53 6.8 S_pericallosal 2145 1425 2657 2.147 0.497 0.144 0.050 23 4.6 S_postcentral 1912 1280 3084 2.369 0.466 0.140 0.054 23 4.8 S_precentral-inf-part 1618 1073 2028 2.141 0.367 0.135 0.055 40 3.7 S_precentral-sup-part 396 266 534 2.164 0.848 0.150 0.045 5 0.7 S_suborbital 970 649 1392 2.338 0.491 0.142 0.052 10 2.1 S_subparietal 1310 862 1746 2.409 0.495 0.139 0.050 14 3.0 S_temporal_inf 5556 3739 8590 2.375 0.421 0.130 0.045 62 10.5 S_temporal_sup 250 172 337 2.348 0.350 0.186 0.089 6 1.2 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Thu Oct 6 23:15:21 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 16945 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/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... 963 labels changed using aseg relabeling using gibbs priors... 000: 2693 changed, 136619 examined... 001: 653 changed, 11548 examined... 002: 172 changed, 3564 examined... 003: 64 changed, 1043 examined... 004: 33 changed, 397 examined... 005: 17 changed, 177 examined... 006: 9 changed, 99 examined... 007: 9 changed, 51 examined... 008: 10 changed, 52 examined... 009: 8 changed, 50 examined... 010: 5 changed, 41 examined... 011: 2 changed, 26 examined... 012: 3 changed, 13 examined... 013: 1 changed, 13 examined... 014: 2 changed, 7 examined... 015: 2 changed, 11 examined... 016: 2 changed, 10 examined... 017: 2 changed, 10 examined... 018: 4 changed, 14 examined... 019: 4 changed, 19 examined... 020: 4 changed, 18 examined... 021: 1 changed, 18 examined... 022: 1 changed, 7 examined... 023: 0 changed, 7 examined... 223 labels changed using aseg 000: 57 total segments, 24 labels (332 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 44 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 480 vertices marked for relabeling... 480 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 30 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Thu Oct 6 23:15:51 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/scripts mris_anatomical_stats -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 16945 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/wm.mgz... reading input surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white... reading input pial surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.pial... reading input white surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. 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 1174 784 2314 2.827 0.539 0.164 0.064 25 3.2 caudalanteriorcingulate 3299 2172 5980 2.446 0.535 0.150 0.072 107 10.4 caudalmiddlefrontal 2483 1545 3066 1.843 0.478 0.184 0.123 158 10.0 cuneus 571 382 1739 3.145 1.082 0.173 0.078 10 2.0 entorhinal 4894 3191 9848 2.717 0.606 0.156 0.070 94 14.5 fusiform 7669 4992 13602 2.442 0.502 0.157 0.069 152 21.6 inferiorparietal 5260 3373 10384 2.584 0.661 0.168 0.087 134 19.3 inferiortemporal 1255 787 2051 2.426 0.757 0.165 0.112 49 7.2 isthmuscingulate 8146 4982 11295 2.054 0.468 0.173 0.145 323 40.0 lateraloccipital 4514 3000 8600 2.416 0.707 0.175 0.087 134 16.6 lateralorbitofrontal 5492 3551 8188 2.114 0.576 0.174 0.097 127 20.1 lingual 2401 1549 4298 2.275 0.742 0.170 0.099 88 9.7 medialorbitofrontal 5854 3921 13230 2.802 0.618 0.158 0.067 117 15.8 middletemporal 1083 681 2209 2.913 0.708 0.167 0.102 25 4.8 parahippocampal 2361 1526 3826 2.406 0.494 0.148 0.061 38 6.2 paracentral 2912 1953 5533 2.463 0.547 0.164 0.070 59 8.4 parsopercularis 1174 787 2355 2.391 0.582 0.169 0.075 28 3.5 parsorbitalis 2698 1785 4633 2.126 0.587 0.168 0.079 58 9.1 parstriangularis 2773 1785 2691 1.674 0.465 0.180 0.123 76 12.1 pericalcarine 5926 3756 8449 2.075 0.618 0.160 0.130 208 22.4 postcentral 1873 1232 3507 2.656 0.614 0.170 0.068 43 5.3 posteriorcingulate 7158 4485 11399 2.394 0.504 0.161 0.119 266 36.7 precentral 6601 4267 10316 2.277 0.567 0.166 0.089 186 21.7 precuneus 941 618 1776 2.814 0.622 0.169 0.076 19 2.8 rostralanteriorcingulate 4956 3267 8321 2.185 0.573 0.173 0.087 121 17.4 rostralmiddlefrontal 12453 8193 23831 2.579 0.677 0.171 0.107 345 49.4 superiorfrontal 7948 5007 11373 2.061 0.428 0.159 0.088 221 27.5 superiorparietal 7044 4535 13081 2.516 0.587 0.153 0.121 713 23.5 superiortemporal 4800 3102 8312 2.508 0.535 0.158 0.077 87 14.5 supramarginal 574 323 692 2.079 0.422 0.170 0.109 15 2.5 transversetemporal 2692 1786 5792 3.092 0.791 0.139 0.073 51 7.4 insula #-------------------------------------------- #@# Cortical ribbon mask Thu Oct 6 23:16:01 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 16945 SUBJECTS_DIR is /media/jsboucher/C6C84AD8C84AC701/Users/sujets 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 = 63 writing volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Thu Oct 6 23:24:37 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject 16945 $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject 16945 sysname Linux hostname jmlina2 machine x86_64 user jsboucher UseRobust 0 atlas_icv (eTIV) = 1409347 mm^3 (det: 1.382275 ) Computing euler number orig.nofix lheno = -68, rheno = -62 orig.nofix lhholes = 35, rhholes = 32 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 222538.050 222091.000 diff= 447.0 pctdiff= 0.201 rhCtxGM: 220420.019 219664.000 diff= 756.0 pctdiff= 0.343 lhCtxWM: 198845.307 198841.500 diff= 3.8 pctdiff= 0.002 rhCtxWM: 196603.299 197337.500 diff= -734.2 pctdiff=-0.373 SubCortGMVol 59981.000 SupraTentVol 913455.675 (912071.000) diff=1384.675 pctdiff=0.152 SupraTentVolNotVent 899563.675 (898179.000) diff=1384.675 pctdiff=0.154 BrainSegVol 1048070.000 (1045689.000) diff=2381.000 pctdiff=0.227 BrainSegVolNotVent 1030844.000 (1031070.675) diff=-226.675 pctdiff=-0.022 BrainSegVolNotVent 1030844.000 CerebellumVol 132419.000 VentChorVol 13892.000 3rd4th5thCSF 3334.000 CSFVol 976.000, OptChiasmVol 223.000 MaskVol 1445267.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation 3 4 Left-Lateral-Ventricle 5548 5548.458 4 5 Left-Inf-Lat-Vent 125 124.968 5 7 Left-Cerebellum-White-Matter 15990 15990.075 6 8 Left-Cerebellum-Cortex 50248 50248.445 7 10 Left-Thalamus-Proper 8058 8057.827 8 11 Left-Caudate 4216 4216.329 9 12 Left-Putamen 5573 5572.924 10 13 Left-Pallidum 1835 1835.329 11 14 3rd-Ventricle 850 849.883 12 15 4th-Ventricle 1698 1697.696 13 16 Brain-Stem 21297 21297.057 14 17 Left-Hippocampus 3951 3951.135 15 18 Left-Amygdala 1481 1481.393 16 24 CSF 981 981.119 17 26 Left-Accumbens-area 649 649.003 18 28 Left-VentralDC 4160 4160.101 19 30 Left-vessel 99 98.988 20 31 Left-choroid-plexus 1123 1122.729 23 43 Right-Lateral-Ventricle 5647 5646.856 24 44 Right-Inf-Lat-Vent 142 142.116 25 46 Right-Cerebellum-White-Matter 15755 15754.698 26 47 Right-Cerebellum-Cortex 52027 52027.320 27 49 Right-Thalamus-Proper 7872 7871.779 28 50 Right-Caudate 4627 4627.371 29 51 Right-Putamen 4827 4826.604 30 52 Right-Pallidum 1501 1500.728 31 53 Right-Hippocampus 3841 3840.907 32 54 Right-Amygdala 1236 1235.903 33 58 Right-Accumbens-area 634 633.968 34 60 Right-VentralDC 3988 3987.905 35 62 Right-vessel 149 148.839 36 63 Right-choroid-plexus 1327 1327.211 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 496 496.198 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 24 24.152 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 244 243.726 45 251 CC_Posterior 951 950.653 46 252 CC_Mid_Posterior 389 389.304 47 253 CC_Central 424 424.050 48 254 CC_Mid_Anterior 386 385.808 49 255 CC_Anterior 748 747.962 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Thu Oct 6 23:26:25 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945 mri_aparc2aseg --s 16945 --volmask SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets subject 16945 outvol /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading lh pial surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.pial Loading lh annotations from /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/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 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading rh pial surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.pial Loading rh annotations from /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/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 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/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 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- 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 = 440523 Used brute-force search on 0 voxels Writing output aseg to /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/aparc+aseg.mgz /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945 mri_aparc2aseg --s 16945 --volmask --a2009s SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets subject 16945 outvol /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading lh pial surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.pial Loading lh annotations from /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/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 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading rh pial surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.pial Loading rh annotations from /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/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 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/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 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- 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 = 440523 Used brute-force search on 0 voxels Writing output aseg to /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Thu Oct 6 23:28:07 EDT 2016 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945 mri_aparc2aseg --s 16945 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets subject 16945 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/aparc+aseg.mgz Reading lh white surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading lh pial surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.pial Loading lh annotations from /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/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 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading rh pial surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.pial Loading rh annotations from /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/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 /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/ribbon.mgz Loading filled from /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/filled.mgz Ripping vertices labeled as unkown Ripped 8133 vertices from left hemi Ripped 7640 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/aseg.mgz Loading Ctx Seg File /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- 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 = 834896 Used brute-force search on 119 voxels Fixing Parahip LH WM Found 6 clusters 0 k 1.000000 1 k 1.000000 2 k 1.000000 3 k 1204.000000 4 k 1.000000 5 k 1.000000 Fixing Parahip RH WM Found 5 clusters 0 k 1.000000 1 k 1.000000 2 k 10.000000 3 k 1.000000 4 k 1510.000000 Writing output aseg to mri/wmparc.mgz /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 16945 --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 16945 --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname jmlina2 machine x86_64 user jsboucher UseRobust 0 atlas_icv (eTIV) = 1409347 mm^3 (det: 1.382275 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 222538.050 222091.000 diff= 447.0 pctdiff= 0.201 rhCtxGM: 220420.019 219664.000 diff= 756.0 pctdiff= 0.343 lhCtxWM: 198845.307 198841.500 diff= 3.8 pctdiff= 0.002 rhCtxWM: 196603.299 197337.500 diff= -734.2 pctdiff=-0.373 SubCortGMVol 59981.000 SupraTentVol 913455.675 (912071.000) diff=1384.675 pctdiff=0.152 SupraTentVolNotVent 899563.675 (898179.000) diff=1384.675 pctdiff=0.154 BrainSegVol 1048070.000 (1045689.000) diff=2381.000 pctdiff=0.227 BrainSegVolNotVent 1030844.000 (1031070.675) diff=-226.675 pctdiff=-0.022 BrainSegVolNotVent 1030844.000 CerebellumVol 132419.000 VentChorVol 13892.000 3rd4th5thCSF 3334.000 CSFVol 976.000, OptChiasmVol 223.000 MaskVol 1445267.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation 0 3000 wm-lh-unknown 0 0.000 1 3001 wm-lh-bankssts 2813 2813.488 2 3002 wm-lh-caudalanteriorcingulate 2332 2332.332 3 3003 wm-lh-caudalmiddlefrontal 4929 4929.047 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 1414 1414.063 6 3006 wm-lh-entorhinal 897 896.847 7 3007 wm-lh-fusiform 6189 6189.311 8 3008 wm-lh-inferiorparietal 6834 6834.046 9 3009 wm-lh-inferiortemporal 5293 5293.494 10 3010 wm-lh-isthmuscingulate 3858 3858.377 11 3011 wm-lh-lateraloccipital 7406 7406.128 12 3012 wm-lh-lateralorbitofrontal 6711 6710.589 13 3013 wm-lh-lingual 6384 6384.249 14 3014 wm-lh-medialorbitofrontal 3391 3391.366 15 3015 wm-lh-middletemporal 4221 4220.650 16 3016 wm-lh-parahippocampal 1259 1259.405 17 3017 wm-lh-paracentral 2802 2802.325 18 3018 wm-lh-parsopercularis 4619 4618.828 19 3019 wm-lh-parsorbitalis 1017 1016.796 20 3020 wm-lh-parstriangularis 3146 3145.574 21 3021 wm-lh-pericalcarine 3666 3665.579 22 3022 wm-lh-postcentral 7321 7321.381 23 3023 wm-lh-posteriorcingulate 3811 3811.271 24 3024 wm-lh-precentral 11291 11291.124 25 3025 wm-lh-precuneus 8138 8138.089 26 3026 wm-lh-rostralanteriorcingulate 2192 2192.494 27 3027 wm-lh-rostralmiddlefrontal 11259 11259.121 28 3028 wm-lh-superiorfrontal 15790 15789.530 29 3029 wm-lh-superiorparietal 11847 11847.426 30 3030 wm-lh-superiortemporal 6069 6068.789 31 3031 wm-lh-supramarginal 7434 7433.597 32 3032 wm-lh-frontalpole 179 179.037 33 3033 wm-lh-temporalpole 471 470.509 34 3034 wm-lh-transversetemporal 772 772.313 35 3035 wm-lh-insula 7754 7754.287 36 3100 wm-lh-Unknown 0 0.000 37 3101 wm-lh-Corpus_callosum 0 0.000 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 0.000 39 3103 wm-lh-G_cingulate-Isthmus 0 0.000 40 3104 wm-lh-G_cingulate-Main_part 0 0.000 41 3105 wm-lh-G_cuneus 0 0.000 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 0.000 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 0.000 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 0.000 45 3109 wm-lh-G_frontal_middle 0 0.000 46 3110 wm-lh-G_frontal_superior 0 0.000 47 3111 wm-lh-G_frontomarginal 0 0.000 48 3112 wm-lh-G_insular_long 0 0.000 49 3113 wm-lh-G_insular_short 0 0.000 50 3114 wm-lh-G_and_S_occipital_inferior 0 0.000 51 3115 wm-lh-G_occipital_middle 0 0.000 52 3116 wm-lh-G_occipital_superior 0 0.000 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 0.000 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 0.000 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 0.000 56 3120 wm-lh-G_orbital 0 0.000 57 3121 wm-lh-G_paracentral 0 0.000 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 0.000 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 0.000 60 3124 wm-lh-G_parietal_superior 0 0.000 61 3125 wm-lh-G_postcentral 0 0.000 62 3126 wm-lh-G_precentral 0 0.000 63 3127 wm-lh-G_precuneus 0 0.000 64 3128 wm-lh-G_rectus 0 0.000 65 3129 wm-lh-G_subcallosal 0 0.000 66 3130 wm-lh-G_subcentral 0 0.000 67 3131 wm-lh-G_temporal_inferior 0 0.000 68 3132 wm-lh-G_temporal_middle 0 0.000 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 0.000 71 3135 wm-lh-G_temp_sup-Planum_polare 0 0.000 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 0.000 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 0.000 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000 76 3140 wm-lh-Lat_Fissure-post_sgt 0 0.000 77 3141 wm-lh-Medial_wall 0 0.000 78 3142 wm-lh-Pole_occipital 0 0.000 79 3143 wm-lh-Pole_temporal 0 0.000 80 3144 wm-lh-S_calcarine 0 0.000 81 3145 wm-lh-S_central 0 0.000 82 3146 wm-lh-S_central_insula 0 0.000 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 0.000 84 3148 wm-lh-S_cingulate-Marginalis_part 0 0.000 85 3149 wm-lh-S_circular_insula_anterior 0 0.000 86 3150 wm-lh-S_circular_insula_inferior 0 0.000 87 3151 wm-lh-S_circular_insula_superior 0 0.000 88 3152 wm-lh-S_collateral_transverse_ant 0 0.000 89 3153 wm-lh-S_collateral_transverse_post 0 0.000 90 3154 wm-lh-S_frontal_inferior 0 0.000 91 3155 wm-lh-S_frontal_middle 0 0.000 92 3156 wm-lh-S_frontal_superior 0 0.000 93 3157 wm-lh-S_frontomarginal 0 0.000 94 3158 wm-lh-S_intermedius_primus-Jensen 0 0.000 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 0.000 96 3160 wm-lh-S_occipital_anterior 0 0.000 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 0.000 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 0.000 99 3163 wm-lh-S_occipito-temporal_lateral 0 0.000 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 0.000 101 3165 wm-lh-S_orbital-H_shapped 0 0.000 102 3166 wm-lh-S_orbital_lateral 0 0.000 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 0.000 104 3168 wm-lh-S_paracentral 0 0.000 105 3169 wm-lh-S_parieto_occipital 0 0.000 106 3170 wm-lh-S_pericallosal 0 0.000 107 3171 wm-lh-S_postcentral 0 0.000 108 3172 wm-lh-S_precentral-Inferior-part 0 0.000 109 3173 wm-lh-S_precentral-Superior-part 0 0.000 110 3174 wm-lh-S_subcentral_ant 0 0.000 111 3175 wm-lh-S_subcentral_post 0 0.000 112 3176 wm-lh-S_suborbital 0 0.000 113 3177 wm-lh-S_subparietal 0 0.000 114 3178 wm-lh-S_supracingulate 0 0.000 115 3179 wm-lh-S_temporal_inferior 0 0.000 116 3180 wm-lh-S_temporal_superior 0 0.000 117 3181 wm-lh-S_temporal_transverse 0 0.000 118 4000 wm-rh-unknown 0 0.000 119 4001 wm-rh-bankssts 2596 2595.795 120 4002 wm-rh-caudalanteriorcingulate 3017 3017.074 121 4003 wm-rh-caudalmiddlefrontal 5195 5194.899 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 1588 1588.360 124 4006 wm-rh-entorhinal 606 606.432 125 4007 wm-rh-fusiform 6949 6948.548 126 4008 wm-rh-inferiorparietal 10527 10527.355 127 4009 wm-rh-inferiortemporal 5132 5131.568 128 4010 wm-rh-isthmuscingulate 3070 3070.067 129 4011 wm-rh-lateraloccipital 7521 7520.850 130 4012 wm-rh-lateralorbitofrontal 6345 6344.756 131 4013 wm-rh-lingual 5076 5075.619 132 4014 wm-rh-medialorbitofrontal 3229 3229.105 133 4015 wm-rh-middletemporal 4762 4761.540 134 4016 wm-rh-parahippocampal 1535 1535.166 135 4017 wm-rh-paracentral 4007 4007.313 136 4018 wm-rh-parsopercularis 3607 3606.822 137 4019 wm-rh-parsorbitalis 1218 1217.623 138 4020 wm-rh-parstriangularis 3051 3050.721 139 4021 wm-rh-pericalcarine 3334 3333.818 140 4022 wm-rh-postcentral 5667 5666.732 141 4023 wm-rh-posteriorcingulate 4097 4097.006 142 4024 wm-rh-precentral 12455 12455.327 143 4025 wm-rh-precuneus 8023 8022.660 144 4026 wm-rh-rostralanteriorcingulate 1792 1791.930 145 4027 wm-rh-rostralmiddlefrontal 10063 10063.224 146 4028 wm-rh-superiorfrontal 14399 14399.007 147 4029 wm-rh-superiorparietal 11331 11330.519 148 4030 wm-rh-superiortemporal 4889 4888.601 149 4031 wm-rh-supramarginal 7315 7315.161 150 4032 wm-rh-frontalpole 208 208.317 151 4033 wm-rh-temporalpole 552 552.410 152 4034 wm-rh-transversetemporal 546 546.043 153 4035 wm-rh-insula 7921 7920.829 154 4100 wm-rh-Unknown 0 0.000 155 4101 wm-rh-Corpus_callosum 0 0.000 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 0.000 157 4103 wm-rh-G_cingulate-Isthmus 0 0.000 158 4104 wm-rh-G_cingulate-Main_part 0 0.000 159 4105 wm-rh-G_cuneus 0 0.000 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 0.000 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 0.000 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 0.000 163 4109 wm-rh-G_frontal_middle 0 0.000 164 4110 wm-rh-G_frontal_superior 0 0.000 165 4111 wm-rh-G_frontomarginal 0 0.000 166 4112 wm-rh-G_insular_long 0 0.000 167 4113 wm-rh-G_insular_short 0 0.000 168 4114 wm-rh-G_and_S_occipital_inferior 0 0.000 169 4115 wm-rh-G_occipital_middle 0 0.000 170 4116 wm-rh-G_occipital_superior 0 0.000 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 0.000 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 0.000 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 0.000 174 4120 wm-rh-G_orbital 0 0.000 175 4121 wm-rh-G_paracentral 0 0.000 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 0.000 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 0.000 178 4124 wm-rh-G_parietal_superior 0 0.000 179 4125 wm-rh-G_postcentral 0 0.000 180 4126 wm-rh-G_precentral 0 0.000 181 4127 wm-rh-G_precuneus 0 0.000 182 4128 wm-rh-G_rectus 0 0.000 183 4129 wm-rh-G_subcallosal 0 0.000 184 4130 wm-rh-G_subcentral 0 0.000 185 4131 wm-rh-G_temporal_inferior 0 0.000 186 4132 wm-rh-G_temporal_middle 0 0.000 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 0.000 189 4135 wm-rh-G_temp_sup-Planum_polare 0 0.000 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 0.000 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 0.000 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000 194 4140 wm-rh-Lat_Fissure-post_sgt 0 0.000 195 4141 wm-rh-Medial_wall 0 0.000 196 4142 wm-rh-Pole_occipital 0 0.000 197 4143 wm-rh-Pole_temporal 0 0.000 198 4144 wm-rh-S_calcarine 0 0.000 199 4145 wm-rh-S_central 0 0.000 200 4146 wm-rh-S_central_insula 0 0.000 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 0.000 202 4148 wm-rh-S_cingulate-Marginalis_part 0 0.000 203 4149 wm-rh-S_circular_insula_anterior 0 0.000 204 4150 wm-rh-S_circular_insula_inferior 0 0.000 205 4151 wm-rh-S_circular_insula_superior 0 0.000 206 4152 wm-rh-S_collateral_transverse_ant 0 0.000 207 4153 wm-rh-S_collateral_transverse_post 0 0.000 208 4154 wm-rh-S_frontal_inferior 0 0.000 209 4155 wm-rh-S_frontal_middle 0 0.000 210 4156 wm-rh-S_frontal_superior 0 0.000 211 4157 wm-rh-S_frontomarginal 0 0.000 212 4158 wm-rh-S_intermedius_primus-Jensen 0 0.000 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 0.000 214 4160 wm-rh-S_occipital_anterior 0 0.000 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 0.000 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 0.000 217 4163 wm-rh-S_occipito-temporal_lateral 0 0.000 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 0.000 219 4165 wm-rh-S_orbital-H_shapped 0 0.000 220 4166 wm-rh-S_orbital_lateral 0 0.000 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 0.000 222 4168 wm-rh-S_paracentral 0 0.000 223 4169 wm-rh-S_parieto_occipital 0 0.000 224 4170 wm-rh-S_pericallosal 0 0.000 225 4171 wm-rh-S_postcentral 0 0.000 226 4172 wm-rh-S_precentral-Inferior-part 0 0.000 227 4173 wm-rh-S_precentral-Superior-part 0 0.000 228 4174 wm-rh-S_subcentral_ant 0 0.000 229 4175 wm-rh-S_subcentral_post 0 0.000 230 4176 wm-rh-S_suborbital 0 0.000 231 4177 wm-rh-S_subparietal 0 0.000 232 4178 wm-rh-S_supracingulate 0 0.000 233 4179 wm-rh-S_temporal_inferior 0 0.000 234 4180 wm-rh-S_temporal_superior 0 0.000 235 4181 wm-rh-S_temporal_transverse 0 0.000 236 5001 Left-UnsegmentedWhiteMatter 23849 23848.785 237 5002 Right-UnsegmentedWhiteMatter 24873 24873.285 238 13100 wm_lh_Unknown 0 0.000 239 13101 wm_lh_G_and_S_frontomargin 0 0.000 240 13102 wm_lh_G_and_S_occipital_inf 0 0.000 241 13103 wm_lh_G_and_S_paracentral 0 0.000 242 13104 wm_lh_G_and_S_subcentral 0 0.000 243 13105 wm_lh_G_and_S_transv_frontopol 0 0.000 244 13106 wm_lh_G_and_S_cingul-Ant 0 0.000 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 0.000 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 0.000 247 13109 wm_lh_G_cingul-Post-dorsal 0 0.000 248 13110 wm_lh_G_cingul-Post-ventral 0 0.000 249 13111 wm_lh_G_cuneus 0 0.000 250 13112 wm_lh_G_front_inf-Opercular 0 0.000 251 13113 wm_lh_G_front_inf-Orbital 0 0.000 252 13114 wm_lh_G_front_inf-Triangul 0 0.000 253 13115 wm_lh_G_front_middle 0 0.000 254 13116 wm_lh_G_front_sup 0 0.000 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 0.000 256 13118 wm_lh_G_insular_short 0 0.000 257 13119 wm_lh_G_occipital_middle 0 0.000 258 13120 wm_lh_G_occipital_sup 0 0.000 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 0.000 260 13122 wm_lh_G_oc-temp_med-Lingual 0 0.000 261 13123 wm_lh_G_oc-temp_med-Parahip 0 0.000 262 13124 wm_lh_G_orbital 0 0.000 263 13125 wm_lh_G_pariet_inf-Angular 0 0.000 264 13126 wm_lh_G_pariet_inf-Supramar 0 0.000 265 13127 wm_lh_G_parietal_sup 0 0.000 266 13128 wm_lh_G_postcentral 0 0.000 267 13129 wm_lh_G_precentral 0 0.000 268 13130 wm_lh_G_precuneus 0 0.000 269 13131 wm_lh_G_rectus 0 0.000 270 13132 wm_lh_G_subcallosal 0 0.000 271 13133 wm_lh_G_temp_sup-G_T_transv 0 0.000 272 13134 wm_lh_G_temp_sup-Lateral 0 0.000 273 13135 wm_lh_G_temp_sup-Plan_polar 0 0.000 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 0.000 275 13137 wm_lh_G_temporal_inf 0 0.000 276 13138 wm_lh_G_temporal_middle 0 0.000 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 0.000 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 0.000 279 13141 wm_lh_Lat_Fis-post 0 0.000 280 13142 wm_lh_Medial_wall 0 0.000 281 13143 wm_lh_Pole_occipital 0 0.000 282 13144 wm_lh_Pole_temporal 0 0.000 283 13145 wm_lh_S_calcarine 0 0.000 284 13146 wm_lh_S_central 0 0.000 285 13147 wm_lh_S_cingul-Marginalis 0 0.000 286 13148 wm_lh_S_circular_insula_ant 0 0.000 287 13149 wm_lh_S_circular_insula_inf 0 0.000 288 13150 wm_lh_S_circular_insula_sup 0 0.000 289 13151 wm_lh_S_collat_transv_ant 0 0.000 290 13152 wm_lh_S_collat_transv_post 0 0.000 291 13153 wm_lh_S_front_inf 0 0.000 292 13154 wm_lh_S_front_middle 0 0.000 293 13155 wm_lh_S_front_sup 0 0.000 294 13156 wm_lh_S_interm_prim-Jensen 0 0.000 295 13157 wm_lh_S_intrapariet_and_P_trans 0 0.000 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 0.000 297 13159 wm_lh_S_oc_sup_and_transversal 0 0.000 298 13160 wm_lh_S_occipital_ant 0 0.000 299 13161 wm_lh_S_oc-temp_lat 0 0.000 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 0.000 301 13163 wm_lh_S_orbital_lateral 0 0.000 302 13164 wm_lh_S_orbital_med-olfact 0 0.000 303 13165 wm_lh_S_orbital-H_Shaped 0 0.000 304 13166 wm_lh_S_parieto_occipital 0 0.000 305 13167 wm_lh_S_pericallosal 0 0.000 306 13168 wm_lh_S_postcentral 0 0.000 307 13169 wm_lh_S_precentral-inf-part 0 0.000 308 13170 wm_lh_S_precentral-sup-part 0 0.000 309 13171 wm_lh_S_suborbital 0 0.000 310 13172 wm_lh_S_subparietal 0 0.000 311 13173 wm_lh_S_temporal_inf 0 0.000 312 13174 wm_lh_S_temporal_sup 0 0.000 313 13175 wm_lh_S_temporal_transverse 0 0.000 314 14100 wm_rh_Unknown 0 0.000 315 14101 wm_rh_G_and_S_frontomargin 0 0.000 316 14102 wm_rh_G_and_S_occipital_inf 0 0.000 317 14103 wm_rh_G_and_S_paracentral 0 0.000 318 14104 wm_rh_G_and_S_subcentral 0 0.000 319 14105 wm_rh_G_and_S_transv_frontopol 0 0.000 320 14106 wm_rh_G_and_S_cingul-Ant 0 0.000 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 0.000 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 0.000 323 14109 wm_rh_G_cingul-Post-dorsal 0 0.000 324 14110 wm_rh_G_cingul-Post-ventral 0 0.000 325 14111 wm_rh_G_cuneus 0 0.000 326 14112 wm_rh_G_front_inf-Opercular 0 0.000 327 14113 wm_rh_G_front_inf-Orbital 0 0.000 328 14114 wm_rh_G_front_inf-Triangul 0 0.000 329 14115 wm_rh_G_front_middle 0 0.000 330 14116 wm_rh_G_front_sup 0 0.000 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 0.000 332 14118 wm_rh_G_insular_short 0 0.000 333 14119 wm_rh_G_occipital_middle 0 0.000 334 14120 wm_rh_G_occipital_sup 0 0.000 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 0.000 336 14122 wm_rh_G_oc-temp_med-Lingual 0 0.000 337 14123 wm_rh_G_oc-temp_med-Parahip 0 0.000 338 14124 wm_rh_G_orbital 0 0.000 339 14125 wm_rh_G_pariet_inf-Angular 0 0.000 340 14126 wm_rh_G_pariet_inf-Supramar 0 0.000 341 14127 wm_rh_G_parietal_sup 0 0.000 342 14128 wm_rh_G_postcentral 0 0.000 343 14129 wm_rh_G_precentral 0 0.000 344 14130 wm_rh_G_precuneus 0 0.000 345 14131 wm_rh_G_rectus 0 0.000 346 14132 wm_rh_G_subcallosal 0 0.000 347 14133 wm_rh_G_temp_sup-G_T_transv 0 0.000 348 14134 wm_rh_G_temp_sup-Lateral 0 0.000 349 14135 wm_rh_G_temp_sup-Plan_polar 0 0.000 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 0.000 351 14137 wm_rh_G_temporal_inf 0 0.000 352 14138 wm_rh_G_temporal_middle 0 0.000 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 0.000 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 0.000 355 14141 wm_rh_Lat_Fis-post 0 0.000 356 14142 wm_rh_Medial_wall 0 0.000 357 14143 wm_rh_Pole_occipital 0 0.000 358 14144 wm_rh_Pole_temporal 0 0.000 359 14145 wm_rh_S_calcarine 0 0.000 360 14146 wm_rh_S_central 0 0.000 361 14147 wm_rh_S_cingul-Marginalis 0 0.000 362 14148 wm_rh_S_circular_insula_ant 0 0.000 363 14149 wm_rh_S_circular_insula_inf 0 0.000 364 14150 wm_rh_S_circular_insula_sup 0 0.000 365 14151 wm_rh_S_collat_transv_ant 0 0.000 366 14152 wm_rh_S_collat_transv_post 0 0.000 367 14153 wm_rh_S_front_inf 0 0.000 368 14154 wm_rh_S_front_middle 0 0.000 369 14155 wm_rh_S_front_sup 0 0.000 370 14156 wm_rh_S_interm_prim-Jensen 0 0.000 371 14157 wm_rh_S_intrapariet_and_P_trans 0 0.000 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 0.000 373 14159 wm_rh_S_oc_sup_and_transversal 0 0.000 374 14160 wm_rh_S_occipital_ant 0 0.000 375 14161 wm_rh_S_oc-temp_lat 0 0.000 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 0.000 377 14163 wm_rh_S_orbital_lateral 0 0.000 378 14164 wm_rh_S_orbital_med-olfact 0 0.000 379 14165 wm_rh_S_orbital-H_Shaped 0 0.000 380 14166 wm_rh_S_parieto_occipital 0 0.000 381 14167 wm_rh_S_pericallosal 0 0.000 382 14168 wm_rh_S_postcentral 0 0.000 383 14169 wm_rh_S_precentral-inf-part 0 0.000 384 14170 wm_rh_S_precentral-sup-part 0 0.000 385 14171 wm_rh_S_suborbital 0 0.000 386 14172 wm_rh_S_subparietal 0 0.000 387 14173 wm_rh_S_temporal_inf 0 0.000 388 14174 wm_rh_S_temporal_sup 0 0.000 389 14175 wm_rh_S_temporal_transverse 0 0.000 Reporting on 70 segmentations mri_segstats done /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/label #-------------------------------------------- #@# BA Labels lh Thu Oct 6 23:34:48 EDT 2016 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /media/jsboucher/C6C84AD8C84AC701/Users/sujets; ln -s /usr/local/freesurfer/subjects/fsaverage; cd - mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA1.label --trgsubject 16945 --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 526 Checking for and removing duplicates Writing label file ./lh.BA1.label 4655 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA2.label --trgsubject 16945 --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.BA2.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 888 Checking for and removing duplicates Writing label file ./lh.BA2.label 8797 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA3a.label --trgsubject 16945 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.BA3a.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 154 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4231 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA3b.label --trgsubject 16945 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.BA3b.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 396 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6379 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA4a.label --trgsubject 16945 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.BA4a.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 381 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6165 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA4p.label --trgsubject 16945 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.BA4p.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 333 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4403 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA6.label --trgsubject 16945 --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.BA6.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 835 Checking for and removing duplicates Writing label file ./lh.BA6.label 14424 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA44.label --trgsubject 16945 --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.BA44.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 841 Checking for and removing duplicates Writing label file ./lh.BA44.label 5022 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA45.label --trgsubject 16945 --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.BA45.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 1405 Checking for and removing duplicates Writing label file ./lh.BA45.label 4827 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.V1.label --trgsubject 16945 --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.V1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 2472 Checking for and removing duplicates Writing label file ./lh.V1.label 7113 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.V2.label --trgsubject 16945 --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.V2.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 4366 Checking for and removing duplicates Writing label file ./lh.V2.label 12480 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.MT.label --trgsubject 16945 --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.MT.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 215 Checking for and removing duplicates Writing label file ./lh.MT.label 2233 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.perirhinal.label --trgsubject 16945 --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.perirhinal.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.perirhinal.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 106 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1305 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA1.thresh.label --trgsubject 16945 --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA1.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.BA1.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 48 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1062 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA2.thresh.label --trgsubject 16945 --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA2.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.BA2.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 413 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2505 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA3a.thresh.label --trgsubject 16945 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA3a.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.BA3a.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 50 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1554 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA3b.thresh.label --trgsubject 16945 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.BA3b.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 193 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2189 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA4a.thresh.label --trgsubject 16945 --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA4a.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.BA4a.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 216 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2535 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA4p.thresh.label --trgsubject 16945 --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA4p.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.BA4p.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 157 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1706 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA6.thresh.label --trgsubject 16945 --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA6.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.BA6.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 360 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 7395 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA44.thresh.label --trgsubject 16945 --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA44.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.BA44.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 517 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2429 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA45.thresh.label --trgsubject 16945 --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.BA45.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.BA45.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 620 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1771 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.V1.thresh.label --trgsubject 16945 --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.V1.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.V1.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 1896 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 5301 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.V2.thresh.label --trgsubject 16945 --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.V2.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.V2.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 1860 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 5194 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.MT.thresh.label --trgsubject 16945 --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/lh.MT.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./lh.MT.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 135267 Number of reverse mapping hits = 53 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 566 mri_label2label: Done mris_label2annot --s 16945 --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/label cmdline mris_label2annot --s 16945 --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname jmlina2 machine x86_64 user jsboucher subject 16945 hemi lh SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT 13 16422433 perirhinal Mapping unhit to unknown Found 91530 unhit vertices Writing annot to /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/label/lh.BA.annot mris_label2annot --s 16945 --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/label cmdline mris_label2annot --s 16945 --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname jmlina2 machine x86_64 user jsboucher subject 16945 hemi lh SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT Mapping unhit to unknown Found 109143 unhit vertices Writing annot to /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab 16945 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/wm.mgz... reading input surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white... reading input pial surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.pial... reading input white surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA.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 1204 745 2085 2.197 0.488 0.176 0.091 39 4.2 BA1 4393 2913 6690 2.238 0.460 0.156 0.066 79 12.0 BA2 921 609 802 1.787 0.363 0.143 0.054 9 2.0 BA3a 2533 1638 3798 1.979 0.613 0.165 0.157 61 8.3 BA3b 1491 847 2595 2.640 0.463 0.150 0.085 48 5.6 BA4a 1403 835 1922 2.455 0.488 0.164 0.101 95 6.4 BA4p 8196 5367 16734 2.724 0.497 0.156 0.087 160 24.3 BA6 2960 1947 5873 2.707 0.419 0.150 0.061 53 7.6 BA44 3857 2567 7293 2.459 0.503 0.168 0.082 97 12.6 BA45 4672 2984 4631 1.579 0.433 0.180 0.114 235 21.1 V1 9595 5996 12460 1.926 0.545 0.186 0.113 489 43.3 V2 1570 1058 2511 2.377 0.386 0.158 0.066 26 3.6 MT 942 634 2370 2.897 0.668 0.155 0.074 22 2.6 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab 16945 lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/wm.mgz... reading input surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white... reading input pial surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.pial... reading input white surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 657 406 1236 2.283 0.489 0.176 0.078 19 1.9 BA1 1911 1256 3052 2.194 0.405 0.161 0.070 42 5.7 BA2 773 519 662 1.793 0.370 0.151 0.060 8 2.0 BA3a 1582 1066 1894 1.653 0.347 0.153 0.065 23 4.5 BA3b 1530 865 2611 2.662 0.484 0.156 0.091 52 6.1 BA4a 1141 669 1484 2.423 0.447 0.159 0.099 89 5.2 BA4p 4548 2922 9083 2.724 0.491 0.161 0.075 79 14.6 BA6 2104 1394 4292 2.713 0.439 0.152 0.057 37 5.1 BA44 1695 1109 3493 2.565 0.510 0.175 0.089 55 5.8 BA45 5013 3177 5043 1.593 0.441 0.182 0.120 185 23.7 V1 4748 2981 5768 1.794 0.501 0.197 0.118 245 23.3 V2 422 277 709 2.503 0.324 0.156 0.055 7 1.0 MT #-------------------------------------------- #@# BA Labels rh Thu Oct 6 23:37:09 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA1.label --trgsubject 16945 --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.BA1.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 272 Checking for and removing duplicates Writing label file ./rh.BA1.label 4234 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA2.label --trgsubject 16945 --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.BA2.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 285 Checking for and removing duplicates Writing label file ./rh.BA2.label 6972 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA3a.label --trgsubject 16945 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.BA3a.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 142 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4122 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA3b.label --trgsubject 16945 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.BA3b.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 244 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4766 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA4a.label --trgsubject 16945 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.BA4a.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 558 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6305 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA4p.label --trgsubject 16945 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.BA4p.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 292 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4765 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA6.label --trgsubject 16945 --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.BA6.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 1188 Checking for and removing duplicates Writing label file ./rh.BA6.label 13444 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA44.label --trgsubject 16945 --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.BA44.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 1424 Checking for and removing duplicates Writing label file ./rh.BA44.label 8336 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA45.label --trgsubject 16945 --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.BA45.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 1672 Checking for and removing duplicates Writing label file ./rh.BA45.label 7027 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.V1.label --trgsubject 16945 --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.V1.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 2808 Checking for and removing duplicates Writing label file ./rh.V1.label 7535 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.V2.label --trgsubject 16945 --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.V2.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 4155 Checking for and removing duplicates Writing label file ./rh.V2.label 12171 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.MT.label --trgsubject 16945 --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.MT.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 304 Checking for and removing duplicates Writing label file ./rh.MT.label 2236 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.perirhinal.label --trgsubject 16945 --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.perirhinal.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.perirhinal.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 82 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 834 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA1.thresh.label --trgsubject 16945 --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA1.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.BA1.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 74 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 950 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA2.thresh.label --trgsubject 16945 --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA2.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.BA2.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 94 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 2782 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA3a.thresh.label --trgsubject 16945 --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA3a.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.BA3a.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 23 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1721 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA3b.thresh.label --trgsubject 16945 --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA3b.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.BA3b.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 174 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2357 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA4a.thresh.label --trgsubject 16945 --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA4a.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.BA4a.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 102 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1490 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA4p.thresh.label --trgsubject 16945 --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA4p.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.BA4p.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 122 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1611 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA6.thresh.label --trgsubject 16945 --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA6.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.BA6.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 767 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 7726 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA44.thresh.label --trgsubject 16945 --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA44.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.BA44.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 351 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1363 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA45.thresh.label --trgsubject 16945 --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.BA45.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.BA45.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 458 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1636 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.V1.thresh.label --trgsubject 16945 --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.V1.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.V1.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 1971 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 5203 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.V2.thresh.label --trgsubject 16945 --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.V2.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.V2.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 2080 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 5517 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.MT.thresh.label --trgsubject 16945 --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface srclabel = /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/label/rh.MT.thresh.label srcsubject = fsaverage trgsubject = 16945 trglabel = ./rh.MT.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white Reading target registration /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 136619 Number of reverse mapping hits = 44 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 312 mri_label2label: Done mris_label2annot --s 16945 --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/label cmdline mris_label2annot --s 16945 --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname jmlina2 machine x86_64 user jsboucher subject 16945 hemi rh SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT 13 16422433 perirhinal Mapping unhit to unknown Found 93536 unhit vertices Writing annot to /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/label/rh.BA.annot mris_label2annot --s 16945 --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/label cmdline mris_label2annot --s 16945 --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname jmlina2 machine x86_64 user jsboucher subject 16945 hemi rh SUBJECTS_DIR /media/jsboucher/C6C84AD8C84AC701/Users/sujets ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT Mapping unhit to unknown Found 111639 unhit vertices Writing annot to /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab 16945 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/wm.mgz... reading input surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white... reading input pial surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.pial... reading input white surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA.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 807 431 1349 2.240 0.528 0.188 0.426 48 5.3 BA1 2807 1823 4078 2.209 0.530 0.156 0.069 94 7.7 BA2 942 641 890 1.801 0.382 0.144 0.056 9 2.2 BA3a 1960 1247 2416 1.723 0.528 0.157 0.100 45 7.3 BA3b 1491 916 2541 2.444 0.452 0.169 0.105 58 6.5 BA4a 1320 822 1755 2.299 0.413 0.165 0.195 81 11.0 BA4p 7918 5046 14920 2.594 0.575 0.169 0.113 281 38.9 BA6 3909 2631 6910 2.408 0.525 0.155 0.061 64 10.4 BA44 4881 3268 9088 2.254 0.583 0.175 0.083 116 16.2 BA45 5077 3163 5768 1.754 0.477 0.183 0.127 157 22.7 V1 9469 5857 12569 2.015 0.542 0.180 0.150 455 46.9 V2 1852 1230 2862 2.278 0.376 0.152 0.063 27 5.0 MT 650 443 1764 3.007 0.964 0.182 0.114 15 3.5 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab 16945 rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/wm.mgz... reading input surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white... reading input pial surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.pial... reading input white surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 576 303 958 2.250 0.509 0.198 0.553 57 3.1 BA1 1604 1056 2371 2.197 0.499 0.144 0.055 22 4.0 BA2 836 569 725 1.766 0.342 0.146 0.054 8 2.0 BA3a 1583 1040 1699 1.562 0.408 0.146 0.064 27 4.6 BA3b 894 509 1562 2.616 0.431 0.148 0.069 36 2.9 BA4a 1058 701 1466 2.302 0.419 0.174 0.225 71 10.0 BA4p 5437 3414 9971 2.570 0.582 0.172 0.117 225 28.5 BA6 1199 824 2567 2.480 0.589 0.179 0.081 30 4.1 BA44 1506 1009 2914 2.319 0.583 0.176 0.081 34 4.9 BA45 4829 3034 5412 1.748 0.478 0.180 0.140 153 27.6 V1 5200 3151 6535 1.891 0.530 0.192 0.197 365 26.7 V2 258 172 434 2.264 0.427 0.186 0.109 5 1.4 MT /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Thu Oct 6 23:39:32 EDT 2016 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject... cd /media/jsboucher/C6C84AD8C84AC701/Users/sujets; ln -s /usr/local/freesurfer/subjects/lh.EC_average; cd - mris_spherical_average -erode 1 -orig white -t 0.4 -o 16945 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject 16945. processing subject lh.EC_average... reading output surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.sphere.reg... eroding label 1 times before writing thresholding label stat at 0.400 before writing only 1 subject - copying statistics... writing label with 957 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label 16945 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/wm.mgz... reading input surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white... reading input pial surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.pial... reading input white surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/lh.white... INFO: assuming MGZ format for volumes. 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 369 236 1177 3.200 0.609 0.159 0.093 12 1.1 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Thu Oct 6 23:39:40 EDT 2016 INFO: rh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to rh.EC_average subject... cd /media/jsboucher/C6C84AD8C84AC701/Users/sujets; ln -s /usr/local/freesurfer/subjects/rh.EC_average; cd - mris_spherical_average -erode 1 -orig white -t 0.4 -o 16945 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject 16945. processing subject rh.EC_average... reading output surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.sphere.reg... eroding label 1 times before writing thresholding label stat at 0.400 before writing only 1 subject - copying statistics... writing label with 837 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label 16945 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/mri/wm.mgz... reading input surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white... reading input pial surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.pial... reading input white surface /media/jsboucher/C6C84AD8C84AC701/Users/sujets/16945/surf/rh.white... INFO: assuming MGZ format for volumes. 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 309 187 999 3.281 0.759 0.145 0.060 4 0.9 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Thu Oct 6 17:16:01 EDT 2016 Ended at Thu Oct 6 23:39:49 EDT 2016 #@#%# recon-all-run-time-hours 6.397 recon-all -s 16945 finished without error at Thu Oct 6 23:39:49 EDT 2016