Fri Dec 13 16:01:42 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2 /usr/local/freesurfer/bin/recon-all -i ../DICOM/ta0313_dicom/MR.1.3.12.2.1107.5.2.32.35071.2010022515350419855176262 -s ta0313_time2 subjid ta0313_time2 setenv SUBJECTS_DIR /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux mani.med.yale.internal 2.6.32-220.17.1.el6.x86_64 #1 SMP Thu Apr 26 13:37:13 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 12121704 9100012 3021692 0 2119132 1481012 -/+ buffers/cache: 5499868 6621836 Swap: 14417912 14016 14403896 ######################################## 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: 2013/12/13-21:01:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 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: 2013/12/13-21:01:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 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: 2013/12/13-21:01:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $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: 2013/12/13-21:01:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $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: 2013/12/13-21:01:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:01:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### 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 ####################################### /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2 mri_convert /mani2/fei_data/Jacobian_maps/DICOM/ta0313_dicom/MR.1.3.12.2.1107.5.2.32.35071.2010022515350419855176262 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/orig/001.mgz mri_convert /mani2/fei_data/Jacobian_maps/DICOM/ta0313_dicom/MR.1.3.12.2.1107.5.2.32.35071.2010022515350419855176262 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /mani2/fei_data/Jacobian_maps/DICOM/ta0313_dicom/MR.1.3.12.2.1107.5.2.32.35071.2010022515350419855176262... Getting Series No INFO: Found 162 files in /mani2/fei_data/Jacobian_maps/DICOM/ta0313_dicom INFO: Scanning for Series Number 12 Scanning Directory INFO: found 160 files in series INFO: loading series header info. RunNo = 11 INFO: sorting. INFO: (256 256 160), 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 /mani2/fei_data/Jacobian_maps/DICOM/ta0313_dicom/MR.1.3.12.2.1107.5.2.32.35071.2010022515350419855176262 Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName face event Date and time StudyDate 20100225 StudyTime 143326.484000 SeriesTime 153506.203000 AcqTime 152528.130000 Acquisition parameters PulseSeq tfl3d1 Protocol T1 MPRAGE sag 1mm PhEncDir ROW EchoNo 1 FlipAngle 15 EchoTime 2.77 InversionTime 700 RepetitionTime 1500 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 11 SeriesNo 12 ImageNo 160 NImageRows 256 NImageCols 256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 80.1614 159.6595 95.3353 VolRes 1.0000 1.0000 1.0000 VolDim 256 256 160 Vc -0.0000 -1.0000 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs -1.0000 -0.0000 0.0000 VolCenter 0.1614 31.6595 -32.6647 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=1500.00, TE=2.77, TI=700.00, flip angle=15.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) writing to /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/orig/001.mgz... #------------------------------------------ Started at Fri Dec 13 16:01:42 EST 2013 Ended at Fri Dec 13 16:02:12 EST 2013 #@#%# recon-all-run-time-hours 0.008 recon-all -s ta0313_time2 finished without error at Fri Dec 13 16:02:12 EST 2013 New invocation of recon-all Fri Dec 13 16:03:10 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2 /usr/local/freesurfer/bin/recon-all -all -openmp 8 -s ta0313_time2 subjid ta0313_time2 setenv SUBJECTS_DIR /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux mani.med.yale.internal 2.6.32-220.17.1.el6.x86_64 #1 SMP Thu Apr 26 13:37:13 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 12121704 8961868 3159836 0 2085352 1571780 -/+ buffers/cache: 5304736 6816968 Swap: 14417912 14016 14403896 ######################################## 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: 2013/12/13-21:03:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 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: 2013/12/13-21:03:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 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: 2013/12/13-21:03:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 8 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $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: 2013/12/13-21:03:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $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: 2013/12/13-21:03:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/13-21:03:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: hblab Machine: mani.med.yale.internal Platform: Linux PlatformVersion: 2.6.32-220.17.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### 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 ####################################### #-------------------------------------------- #@# MotionCor Fri Dec 13 16:03:14 EST 2013 Found 1 runs /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/orig/001.mgz /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/rawavg.mgz /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2 mri_convert /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/rawavg.mgz /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/orig.mgz --conform mri_convert /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/rawavg.mgz /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/rawavg.mgz... TR=1500.00, TE=2.77, TI=700.00, flip angle=15.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) Original Data has (1, 1, 1) mm size and (256, 256, 160) 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/orig.mgz... mri_add_xform_to_header -c /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/transforms/talairach.xfm /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/orig.mgz /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri Dec 13 16:03:29 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 Fri Dec 13 16:05:20 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.8130, pval=0.8469 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/transforms/talairach_avi.log tal_QC_AZS /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/transforms/talairach_avi.log TalAviQA: 0.97621 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Fri Dec 13 16:05:20 EST 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 mani.med.yale.internal 2.6.32-220.17.1.el6.x86_64 #1 SMP Thu Apr 26 13:37:13 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux Fri Dec 13 16:05:20 EST 2013 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.9063 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9063/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9063/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=1500.00, TE=2.77, TI=700.00, flip angle=15.00 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.9063/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Dec 13 16:05:22 EST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.9063/nu0.mnc ./tmp.mri_nu_correct.mni.9063/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9063/0/ [hblab@mani.med.yale.internal:/mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/] [2013-12-13 16:05:22] 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.9063/0/ ./tmp.mri_nu_correct.mni.9063/nu0.mnc ./tmp.mri_nu_correct.mni.9063/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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/usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.9063/nu0.mnc ./tmp.mri_nu_correct.mni.9063/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Fri Dec 13 16:05:57 EST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.9063/nu1.mnc ./tmp.mri_nu_correct.mni.9063/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.9063/1/ [hblab@mani.med.yale.internal:/mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/] [2013-12-13 16:05:57] 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.9063/1/ ./tmp.mri_nu_correct.mni.9063/nu1.mnc ./tmp.mri_nu_correct.mni.9063/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.00105185 [hblab@mani.med.yale.internal:/mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/] [2013-12-13 16:06:31] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.9063/nu1.mnc ./tmp.mri_nu_correct.mni.9063/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.9063/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9063/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.9063/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9063/ones.mgz sysname Linux hostname mani.med.yale.internal machine x86_64 user hblab input ./tmp.mri_nu_correct.mni.9063/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.9063/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.9063/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9063/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9063/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.9063/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9063/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9063/input.mean.dat sysname Linux hostname mani.med.yale.internal machine x86_64 user hblab UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9063/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.9063/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9063/ones.mgz --i ./tmp.mri_nu_correct.mni.9063/nu2.mnc --sum ./tmp.mri_nu_correct.mni.9063/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9063/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.9063/ones.mgz --i ./tmp.mri_nu_correct.mni.9063/nu2.mnc --sum ./tmp.mri_nu_correct.mni.9063/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9063/output.mean.dat sysname Linux hostname mani.med.yale.internal machine x86_64 user hblab UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9063/ones.mgz Loading ./tmp.mri_nu_correct.mni.9063/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.9063/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.9063/nu2.mnc ./tmp.mri_nu_correct.mni.9063/nu2.mnc mul .95118806686818051032 Saving result to './tmp.mri_nu_correct.mni.9063/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.9063/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.9063/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.9063/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 8 seconds. mapping ( 5, 141) to ( 3, 110) Fri Dec 13 16:07:19 EST 2013 mri_nu_correct.mni done mri_add_xform_to_header -c /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Fri Dec 13 16:07:21 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.140 0.028 -0.115 -4.865; 0.002 1.040 0.212 -37.632; 0.106 -0.159 1.229 18.322; 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 = 19 Starting OpenSpline(): npoints = 19 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 109 gm peak at 67 (67), valley at 56 (56) csf peak at 33, setting threshold to 55 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 67 (67), valley at 53 (53) csf peak at 33, setting threshold to 55 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 26 seconds. #-------------------------------------------- #@# Skull Stripping Fri Dec 13 16:09:49 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta ======= NUMBER OF OPENMP THREADS = 8 ======= 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=6.0 skull bounding box = (49, 27, 18) --> (206, 255, 227) using (101, 103, 123) as brain centroid... mean wm in atlas = 126, using box (82,75,97) --> (120, 131,148) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 110, scaling input intensities by 1.145 scaling channel 0 by 1.14545 initial log_p = -4.5 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.466576 @ (9.091, 9.091, -9.091) max log p = -4.335575 @ (-4.545, 4.545, 4.545) max log p = -4.322149 @ (2.273, 2.273, -2.273) max log p = -4.303764 @ (-3.409, -7.955, 1.136) max log p = -4.295465 @ (-0.568, 0.568, 0.568) max log p = -4.287323 @ (-0.284, -0.852, -0.284) Found translation: (2.6, 7.7, -5.4): log p = -4.287 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-4.3 (thresh=-4.3) 1.140 -0.149 -0.020 2.413; 0.161 1.215 0.160 -38.598; 0.000 -0.139 1.055 2.452; 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 =-3.9 (thresh=-3.9) 1.140 -0.149 -0.020 2.413; 0.199 1.502 0.198 -76.330; 0.000 -0.139 1.055 2.452; 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) 1.140 -0.149 -0.020 2.413; 0.199 1.502 0.198 -76.330; 0.000 -0.139 1.055 2.452; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.9 (thresh=-3.9) 1.097 -0.140 -0.052 8.689; 0.188 1.422 0.154 -65.740; 0.043 -0.093 1.039 -7.587; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.097 -0.140 -0.052 8.689; 0.188 1.422 0.154 -65.740; 0.043 -0.093 1.039 -7.587; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** 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) 1.095 -0.128 -0.059 8.386; 0.180 1.429 0.147 -64.976; 0.053 -0.082 1.036 -10.134; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.101 -0.117 -0.050 5.965; 0.170 1.430 0.130 -61.390; 0.047 -0.057 1.040 -11.867; 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 1.10085 -0.11688 -0.05005 5.96510; 0.16956 1.42964 0.12994 -61.39006; 0.04731 -0.05739 1.03979 -11.86661; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.10085 -0.11688 -0.05005 5.96510; 0.16956 1.42964 0.12994 -61.39006; 0.04731 -0.05739 1.03979 -11.86661; 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: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.101 -0.117 -0.050 5.965; 0.170 1.430 0.130 -61.390; 0.047 -0.057 1.040 -11.867; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.8 (old=-4.5) transform before final EM align: 1.101 -0.117 -0.050 5.965; 0.170 1.430 0.130 -61.390; 0.047 -0.057 1.040 -11.867; 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 1.10085 -0.11688 -0.05005 5.96510; 0.16956 1.42964 0.12994 -61.39006; 0.04731 -0.05739 1.03979 -11.86661; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.10085 -0.11688 -0.05005 5.96510; 0.16956 1.42964 0.12994 -61.39006; 0.04731 -0.05739 1.03979 -11.86661; 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: 011: -log(p) = 4.2 tol 0.000000 final transform: 1.101 -0.117 -0.050 5.965; 0.170 1.430 0.130 -61.390; 0.047 -0.057 1.040 -11.867; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 758 minutes and 41 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=95 z=118 r=91 first estimation of the main basin volume: 3213990 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=145, y=88, z=78, 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=20412838185 voxels, voxel volume =1.000 = 20412838185 mmm3 = 20412837.888 cm3 done. PostAnalyze...Basin Prior 3 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=124,y=104, z=110, r=9857 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=71 , nb = 39734 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=45 , nb = -1031022256 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=46 , nb = 1095497056 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=71 , nb = 1081066948 LEFT_BRAIN CSF_MIN=0, CSF_intensity=4, CSF_MAX=97 , nb = 1074021808 OTHER CSF_MIN=3, CSF_intensity=32, CSF_MAX=54 , nb = 1077282972 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 71, 50, 43, 64 after analyzing : 39, 50, 50, 53 RIGHT_CER before analyzing : 45, 46, 47, 62 after analyzing : 45, 46, 47, 50 LEFT_CER before analyzing : 46, 46, 47, 64 after analyzing : 29, 46, 47, 50 RIGHT_BRAIN before analyzing : 71, 48, 39, 64 after analyzing : 38, 48, 48, 52 LEFT_BRAIN before analyzing : 97, 53, 45, 64 after analyzing : 40, 53, 53, 55 OTHER before analyzing : 54, 65, 74, 91 after analyzing : 54, 71, 74, 76 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...70 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.013 curvature mean = 66.714, std = 8.125 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.78, sigma = 4.02 after rotation: sse = 2.78, sigma = 4.02 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.96, its var is 4.09 before Erosion-Dilatation 0.70% 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...45 iterations mri_strip_skull: done peeling brain Brain Size = 1464006 voxels, voxel volume = 1.000 mm3 = 1464006 mmm3 = 1464.006 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sat Dec 14 04:50:29 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta ======= NUMBER OF OPENMP THREADS = 8 ======= 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=29.9 skull bounding box = (63, 45, 35) --> (188, 160, 197) using (105, 83, 116) as brain centroid... mean wm in atlas = 107, using box (90,69,96) --> (120, 97,135) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 initial log_p = -4.3 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.054375 @ (-9.091, 9.091, -9.091) max log p = -3.868742 @ (4.545, 13.636, -4.545) max log p = -3.818662 @ (2.273, -2.273, 2.273) max log p = -3.805067 @ (1.136, -5.682, 1.136) max log p = -3.797352 @ (0.568, 0.568, -1.705) max log p = -3.797352 @ (0.000, 0.000, 0.000) Found translation: (-0.6, 15.3, -11.9): log p = -3.797 **************************************** 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) 1.055 -0.138 -0.016 8.570; 0.161 1.215 0.139 -36.302; 0.000 -0.150 0.991 12.111; 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) 1.055 -0.138 -0.016 8.570; 0.161 1.215 0.139 -36.302; 0.000 -0.150 0.991 12.111; 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=-3.3, old_max_log_p =-3.5 (thresh=-3.5) 1.083 -0.059 -0.007 -3.728; 0.090 1.193 0.170 -30.429; -0.003 -0.196 1.023 11.730; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.079 -0.098 -0.012 1.226; 0.123 1.168 0.167 -31.743; -0.003 -0.199 1.043 9.975; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.079 -0.098 -0.012 1.226; 0.123 1.168 0.167 -31.743; -0.003 -0.199 1.043 9.975; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.079 -0.088 -0.011 0.157; 0.114 1.169 0.150 -29.278; -0.001 -0.180 1.044 7.204; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.3 (thresh=-3.2) 1.083 -0.089 -0.011 -0.289; 0.115 1.173 0.150 -29.800; -0.001 -0.180 1.042 7.434; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.085 -0.089 -0.011 -0.587; 0.115 1.175 0.150 -29.974; -0.001 -0.180 1.040 7.548; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.085 -0.089 -0.011 -0.587; 0.115 1.177 0.151 -30.323; -0.001 -0.180 1.040 7.548; 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 1.08538 -0.08882 -0.01110 -0.58661; 0.11503 1.17747 0.15068 -30.32264; -0.00103 -0.17962 1.04034 7.54847; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.08538 -0.08882 -0.01110 -0.58661; 0.11503 1.17747 0.15068 -30.32264; -0.00103 -0.17962 1.04034 7.54847; 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: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.085 -0.089 -0.011 -0.587; 0.115 1.177 0.151 -30.323; -0.001 -0.180 1.040 7.548; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.2 (old=-4.3) transform before final EM align: 1.085 -0.089 -0.011 -0.587; 0.115 1.177 0.151 -30.323; -0.001 -0.180 1.040 7.548; 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 1.08538 -0.08882 -0.01110 -0.58661; 0.11503 1.17747 0.15068 -30.32264; -0.00103 -0.17962 1.04034 7.54847; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.08538 -0.08882 -0.01110 -0.58661; 0.11503 1.17747 0.15068 -30.32264; -0.00103 -0.17962 1.04034 7.54847; 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: 013: -log(p) = 3.7 tol 0.000000 final transform: 1.085 -0.089 -0.011 -0.587; 0.115 1.177 0.151 -30.323; -0.001 -0.180 1.040 7.548; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 1020 minutes and 17 seconds. #-------------------------------------- #@# CA Normalize Sat Dec 14 21:50:46 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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=29.9 skull bounding box = (63, 45, 35) --> (188, 160, 197) using (105, 83, 116) as brain centroid... mean wm in atlas = 107, using box (90,69,96) --> (120, 97,135) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 using 244171 sample points... INFO: compute sample coordinates transform 1.085 -0.089 -0.011 -0.587; 0.115 1.177 0.151 -30.323; -0.001 -0.180 1.040 7.548; 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 (125, 43, 38) --> (188, 137, 196) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 188.0 1 of 1590 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (66, 47, 37) --> (127, 144, 196) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 188.0 2 of 1188 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 116, 63) --> (175, 152, 114) Left_Cerebellum_White_Matter: limiting intensities to 91.0 --> 188.0 0 of 8 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (87, 116, 61) --> (129, 156, 115) Right_Cerebellum_White_Matter: limiting intensities to 94.0 --> 188.0 0 of 11 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 109, 96) --> (144, 168, 125) Brain_Stem: limiting intensities to 86.0 --> 188.0 0 of 12 (0.0%) samples deleted using 2809 total control points for intensity normalization... bias field = 1.035 +- 0.049 5 of 2806 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (125, 43, 38) --> (188, 137, 196) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 174.0 0 of 1452 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (66, 47, 37) --> (127, 144, 196) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 174.0 0 of 1172 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 116, 63) --> (175, 152, 114) Left_Cerebellum_White_Matter: limiting intensities to 87.0 --> 174.0 15 of 46 (32.6%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (87, 116, 61) --> (129, 156, 115) Right_Cerebellum_White_Matter: limiting intensities to 85.0 --> 174.0 0 of 63 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 109, 96) --> (144, 168, 125) Brain_Stem: limiting intensities to 79.0 --> 174.0 0 of 81 (0.0%) samples deleted using 2814 total control points for intensity normalization... bias field = 1.014 +- 0.041 3 of 2799 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (125, 43, 38) --> (188, 137, 196) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 164.0 0 of 1420 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (66, 47, 37) --> (127, 144, 196) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 164.0 0 of 1191 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 116, 63) --> (175, 152, 114) Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 164.0 7 of 76 (9.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (87, 116, 61) --> (129, 156, 115) Right_Cerebellum_White_Matter: limiting intensities to 79.0 --> 164.0 0 of 70 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 109, 96) --> (144, 168, 125) Brain_Stem: limiting intensities to 71.0 --> 164.0 0 of 147 (0.0%) samples deleted using 2904 total control points for intensity normalization... bias field = 1.012 +- 0.034 9 of 2897 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 7 minutes and 4 seconds. #-------------------------------------- #@# CA Reg Sat Dec 14 21:57:51 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 ======= NUMBER OF OPENMP THREADS = 8 ======= 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=0.754, neg=0, invalid=96777 0001: dt=129.472000, rms=0.691 (8.383%), neg=0, invalid=96777 0002: dt=295.936000, rms=0.664 (3.910%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.656 (1.173%), neg=0, invalid=96777 0004: dt=369.920000, rms=0.649 (1.087%), neg=0, invalid=96777 0005: dt=110.976000, rms=0.644 (0.757%), neg=0, invalid=96777 0006: dt=369.920000, rms=0.641 (0.522%), neg=0, invalid=96777 0007: dt=92.480000, rms=0.638 (0.384%), neg=0, invalid=96777 0008: dt=517.888000, rms=0.634 (0.682%), neg=0, invalid=96777 0009: dt=32.368000, rms=0.633 (0.081%), neg=0, invalid=96777 0010: dt=32.368000, rms=0.633 (0.032%), neg=0, invalid=96777 0011: dt=32.368000, rms=0.633 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.633, neg=0, invalid=96777 0012: dt=73.984000, rms=0.633 (0.037%), neg=0, invalid=96777 0013: dt=517.888000, rms=0.630 (0.380%), neg=0, invalid=96777 0014: dt=129.472000, rms=0.630 (0.124%), neg=0, invalid=96777 0015: dt=129.472000, rms=0.629 (0.081%), neg=0, invalid=96777 0016: dt=129.472000, rms=0.628 (0.149%), neg=0, invalid=96777 0017: dt=129.472000, rms=0.627 (0.200%), neg=0, invalid=96777 0018: dt=129.472000, rms=0.625 (0.239%), neg=0, invalid=96777 0019: dt=129.472000, rms=0.624 (0.217%), neg=0, invalid=96777 0020: dt=129.472000, rms=0.623 (0.203%), neg=0, invalid=96777 0021: dt=129.472000, rms=0.622 (0.210%), neg=0, invalid=96777 0022: dt=129.472000, rms=0.621 (0.153%), neg=0, invalid=96777 0023: dt=129.472000, rms=0.620 (0.153%), neg=0, invalid=96777 0024: dt=129.472000, rms=0.619 (0.171%), neg=0, invalid=96777 0025: dt=129.472000, rms=0.618 (0.165%), neg=0, invalid=96777 0026: dt=129.472000, rms=0.617 (0.130%), neg=0, invalid=96777 0027: dt=129.472000, rms=0.616 (0.123%), neg=0, invalid=96777 0028: dt=129.472000, rms=0.615 (0.121%), neg=0, invalid=96777 0029: dt=443.904000, rms=0.615 (0.065%), neg=0, invalid=96777 0030: dt=443.904000, rms=0.615 (-0.407%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.618, neg=0, invalid=96777 0031: dt=103.680000, rms=0.612 (0.979%), neg=0, invalid=96777 0032: dt=36.288000, rms=0.609 (0.555%), neg=0, invalid=96777 0033: dt=36.288000, rms=0.606 (0.454%), neg=0, invalid=96777 0034: dt=36.288000, rms=0.604 (0.316%), neg=0, invalid=96777 0035: dt=82.944000, rms=0.601 (0.490%), neg=0, invalid=96777 0036: dt=25.920000, rms=0.600 (0.265%), neg=0, invalid=96777 0037: dt=124.416000, rms=0.596 (0.569%), neg=0, invalid=96777 0038: dt=15.552000, rms=0.595 (0.232%), neg=0, invalid=96777 0039: dt=15.552000, rms=0.594 (0.103%), neg=0, invalid=96777 0040: dt=15.552000, rms=0.594 (0.100%), neg=0, invalid=96777 0041: dt=15.552000, rms=0.593 (0.165%), neg=0, invalid=96777 0042: dt=15.552000, rms=0.591 (0.245%), neg=0, invalid=96777 0043: dt=15.552000, rms=0.590 (0.279%), neg=0, invalid=96777 0044: dt=15.552000, rms=0.588 (0.269%), neg=0, invalid=96777 0045: dt=15.552000, rms=0.586 (0.272%), neg=0, invalid=96777 0046: dt=15.552000, rms=0.585 (0.277%), neg=0, invalid=96777 0047: dt=15.552000, rms=0.583 (0.254%), neg=0, invalid=96777 0048: dt=15.552000, rms=0.582 (0.257%), neg=0, invalid=96777 0049: dt=15.552000, rms=0.580 (0.262%), neg=0, invalid=96777 0050: dt=15.552000, rms=0.579 (0.264%), neg=0, invalid=96777 0051: dt=15.552000, rms=0.577 (0.245%), neg=0, invalid=96777 0052: dt=15.552000, rms=0.576 (0.235%), neg=0, invalid=96777 0053: dt=15.552000, rms=0.575 (0.217%), neg=0, invalid=96777 0054: dt=15.552000, rms=0.574 (0.193%), neg=0, invalid=96777 0055: dt=15.552000, rms=0.573 (0.180%), neg=0, invalid=96777 0056: dt=15.552000, rms=0.572 (0.173%), neg=0, invalid=96777 0057: dt=15.552000, rms=0.571 (0.176%), neg=0, invalid=96777 0058: dt=15.552000, rms=0.570 (0.156%), neg=0, invalid=96777 0059: dt=15.552000, rms=0.569 (0.141%), neg=0, invalid=96777 0060: dt=15.552000, rms=0.568 (0.131%), neg=0, invalid=96777 0061: dt=15.552000, rms=0.568 (0.119%), neg=0, invalid=96777 0062: dt=15.552000, rms=0.567 (0.121%), neg=0, invalid=96777 0063: dt=15.552000, rms=0.566 (0.110%), neg=0, invalid=96777 0064: dt=82.944000, rms=0.566 (0.009%), neg=0, invalid=96777 0065: dt=82.944000, rms=0.566 (0.034%), neg=0, invalid=96777 0066: dt=82.944000, rms=0.566 (0.012%), neg=0, invalid=96777 0067: dt=82.944000, rms=0.566 (0.051%), neg=0, invalid=96777 0068: dt=82.944000, rms=0.565 (0.098%), neg=0, invalid=96777 0069: dt=82.944000, rms=0.565 (0.079%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.565, neg=0, invalid=96777 0070: dt=36.288000, rms=0.563 (0.240%), neg=0, invalid=96777 0071: dt=25.920000, rms=0.563 (0.035%), neg=0, invalid=96777 0072: dt=25.920000, rms=0.563 (0.044%), neg=0, invalid=96777 0073: dt=25.920000, rms=0.562 (0.059%), neg=0, invalid=96777 0074: dt=25.920000, rms=0.562 (0.062%), neg=0, invalid=96777 0075: dt=25.920000, rms=0.562 (0.044%), neg=0, invalid=96777 0076: dt=25.920000, rms=0.562 (0.048%), neg=0, invalid=96777 0077: dt=25.920000, rms=0.561 (0.061%), neg=0, invalid=96777 0078: dt=25.920000, rms=0.561 (0.062%), neg=0, invalid=96777 0079: dt=25.920000, rms=0.561 (0.052%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.579, neg=0, invalid=96777 0080: dt=8.260870, rms=0.578 (0.128%), neg=0, invalid=96777 0081: dt=4.800000, rms=0.578 (0.024%), neg=0, invalid=96777 0082: dt=4.800000, rms=0.578 (0.001%), neg=0, invalid=96777 0083: dt=4.800000, rms=0.578 (-0.040%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.578, neg=0, invalid=96777 0084: dt=0.000000, rms=0.578 (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=0.625, neg=0, invalid=96777 0085: dt=5.298701, rms=0.614 (1.660%), neg=0, invalid=96777 0086: dt=0.864000, rms=0.614 (0.003%), neg=0, invalid=96777 0087: dt=0.864000, rms=0.614 (0.000%), neg=0, invalid=96777 0088: dt=0.864000, rms=0.614 (-0.029%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.614, neg=0, invalid=96777 0089: dt=0.000000, rms=0.614 (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=0.668, neg=0, invalid=96777 0090: dt=0.798429, rms=0.666 (0.289%), neg=0, invalid=96777 0091: dt=1.536000, rms=0.663 (0.376%), neg=0, invalid=96777 0092: dt=1.548387, rms=0.662 (0.179%), neg=0, invalid=96777 0093: dt=1.548387, rms=0.662 (0.045%), neg=0, invalid=96777 0094: dt=1.548387, rms=0.662 (-0.138%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.662, neg=0, invalid=96777 0095: dt=0.906832, rms=0.661 (0.156%), neg=0, invalid=96777 0096: dt=0.000078, rms=0.661 (-0.002%), 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=0.619, neg=0, invalid=96777 0097: dt=0.448000, rms=0.607 (1.997%), neg=0, invalid=96777 0098: dt=0.000000, rms=0.607 (0.011%), neg=0, invalid=96777 0099: dt=0.050000, rms=0.607 (-0.198%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.607, neg=0, invalid=96777 0100: dt=0.005000, rms=0.607 (0.001%), neg=0, invalid=96777 0101: dt=0.000020, rms=0.607 (-0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.08267 (54) Left_Lateral_Ventricle (4): linear fit = 1.77 x + 0.0 (1457 voxels, overlap=0.165) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (1457 voxels, peak = 43), gca=36.0 gca peak = 0.14022 (22) mri peak = 0.11372 (54) Right_Lateral_Ventricle (43): linear fit = 2.05 x + 0.0 (1100 voxels, overlap=0.012) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1100 voxels, peak = 45), gca=33.0 gca peak = 0.24234 (100) mri peak = 0.09201 (91) Right_Pallidum (52): linear fit = 0.92 x + 0.0 (409 voxels, overlap=0.441) Right_Pallidum (52): linear fit = 0.92 x + 0.0 (409 voxels, peak = 92), gca=91.5 gca peak = 0.19192 (97) mri peak = 0.06614 (81) Left_Pallidum (13): linear fit = 0.85 x + 0.0 (317 voxels, overlap=0.114) Left_Pallidum (13): linear fit = 0.85 x + 0.0 (317 voxels, peak = 82), gca=82.0 gca peak = 0.24007 (63) mri peak = 0.10663 (67) Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (845 voxels, overlap=1.001) Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (845 voxels, peak = 66), gca=66.5 gca peak = 0.29892 (64) mri peak = 0.09897 (67) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (765 voxels, overlap=0.993) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (765 voxels, peak = 63), gca=63.0 gca peak = 0.12541 (104) mri peak = 0.10444 (108) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (67474 voxels, overlap=0.558) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (67474 voxels, peak = 109), gca=108.7 gca peak = 0.13686 (104) mri peak = 0.09508 (108) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (66870 voxels, overlap=0.583) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (66870 voxels, peak = 108), gca=107.6 gca peak = 0.11691 (63) mri peak = 0.03871 (62) Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (31946 voxels, overlap=0.978) Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (31946 voxels, peak = 61), gca=60.8 gca peak = 0.13270 (63) mri peak = 0.03788 (63) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (34369 voxels, overlap=0.986) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (34369 voxels, peak = 61), gca=60.8 gca peak = 0.15182 (70) mri peak = 0.08246 (76) Right_Caudate (50): linear fit = 1.03 x + 0.0 (527 voxels, overlap=0.951) Right_Caudate (50): linear fit = 1.03 x + 0.0 (527 voxels, peak = 72), gca=72.4 gca peak = 0.14251 (76) mri peak = 0.07504 (76) Left_Caudate (11): linear fit = 0.98 x + 0.0 (721 voxels, overlap=0.968) Left_Caudate (11): linear fit = 0.98 x + 0.0 (721 voxels, peak = 74), gca=74.1 gca peak = 0.12116 (60) mri peak = 0.05204 (65) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (27170 voxels, overlap=0.891) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (27170 voxels, peak = 64), gca=64.5 gca peak = 0.12723 (61) mri peak = 0.04321 (65) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (31498 voxels, overlap=0.940) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (31498 voxels, peak = 66), gca=65.6 gca peak = 0.22684 (88) mri peak = 0.07033 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (8126 voxels, overlap=0.582) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (8126 voxels, peak = 94), gca=93.7 gca peak = 0.21067 (87) mri peak = 0.08819 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (7755 voxels, overlap=0.868) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (7755 voxels, peak = 92), gca=91.8 gca peak = 0.25455 (62) mri peak = 0.13690 (70) Left_Amygdala (18): linear fit = 1.09 x + 0.0 (336 voxels, overlap=0.623) Left_Amygdala (18): linear fit = 1.09 x + 0.0 (336 voxels, peak = 67), gca=67.3 gca peak = 0.39668 (62) mri peak = 0.18438 (68) Right_Amygdala (54): linear fit = 1.08 x + 0.0 (319 voxels, overlap=0.887) Right_Amygdala (54): linear fit = 1.08 x + 0.0 (319 voxels, peak = 67), gca=66.7 gca peak = 0.10129 (93) mri peak = 0.04895 (97) Left_Thalamus_Proper (10): linear fit = 1.04 x + 0.0 (4906 voxels, overlap=0.932) Left_Thalamus_Proper (10): linear fit = 1.04 x + 0.0 (4906 voxels, peak = 97), gca=97.2 gca peak = 0.12071 (89) mri peak = 0.06137 (78) Right_Thalamus_Proper (49): linear fit = 0.96 x + 0.0 (4033 voxels, overlap=0.887) Right_Thalamus_Proper (49): linear fit = 0.96 x + 0.0 (4033 voxels, peak = 86), gca=85.9 gca peak = 0.13716 (82) mri peak = 0.05326 (84) Left_Putamen (12): linear fit = 0.98 x + 0.0 (2432 voxels, overlap=0.876) Left_Putamen (12): linear fit = 0.98 x + 0.0 (2432 voxels, peak = 80), gca=80.0 gca peak = 0.15214 (84) mri peak = 0.07404 (81) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2331 voxels, overlap=0.920) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2331 voxels, peak = 82), gca=81.9 gca peak = 0.08983 (85) mri peak = 0.07938 (88) Brain_Stem (16): linear fit = 1.04 x + 0.0 (10694 voxels, overlap=0.777) Brain_Stem (16): linear fit = 1.04 x + 0.0 (10694 voxels, peak = 89), gca=88.8 gca peak = 0.11809 (92) mri peak = 0.06329 (86) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (958 voxels, overlap=0.772) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (958 voxels, peak = 97), gca=97.1 gca peak = 0.12914 (94) mri peak = 0.06187 (94) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1195 voxels, overlap=0.917) Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1195 voxels, peak = 95), gca=95.4 gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) mri peak = 0.13580 (21) Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (277 voxels, overlap=0.482) Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (277 voxels, peak = 22), gca=22.0 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) 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 1.02 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 1.27 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=0.623, neg=0, invalid=96777 0102: dt=129.472000, rms=0.615 (1.269%), neg=0, invalid=96777 0103: dt=295.936000, rms=0.611 (0.656%), neg=0, invalid=96777 0104: dt=92.480000, rms=0.610 (0.241%), neg=0, invalid=96777 0105: dt=129.472000, rms=0.608 (0.264%), neg=0, invalid=96777 0106: dt=73.984000, rms=0.608 (0.056%), neg=0, invalid=96777 0107: dt=517.888000, rms=0.605 (0.404%), neg=0, invalid=96777 0108: dt=32.368000, rms=0.605 (0.092%), neg=0, invalid=96777 0109: dt=32.368000, rms=0.605 (0.022%), neg=0, invalid=96777 0110: dt=32.368000, rms=0.605 (0.012%), neg=0, invalid=96777 0111: dt=32.368000, rms=0.604 (0.009%), neg=0, invalid=96777 0112: dt=32.368000, rms=0.604 (0.026%), neg=0, invalid=96777 0113: dt=32.368000, rms=0.604 (0.050%), neg=0, invalid=96777 0114: dt=32.368000, rms=0.604 (0.077%), neg=0, invalid=96777 0115: dt=32.368000, rms=0.603 (0.086%), neg=0, invalid=96777 0116: dt=32.368000, rms=0.603 (0.074%), neg=0, invalid=96777 0117: dt=32.368000, rms=0.602 (0.066%), neg=0, invalid=96777 0118: dt=32.368000, rms=0.602 (0.061%), neg=0, invalid=96777 0119: dt=32.368000, rms=0.601 (0.055%), neg=0, invalid=96777 0120: dt=32.368000, rms=0.601 (0.050%), neg=0, invalid=96777 0121: dt=32.368000, rms=0.601 (0.056%), neg=0, invalid=96777 0122: dt=32.368000, rms=0.600 (0.065%), neg=0, invalid=96777 0123: dt=32.368000, rms=0.600 (0.068%), neg=0, invalid=96777 0124: dt=32.368000, rms=0.600 (0.061%), neg=0, invalid=96777 0125: dt=32.368000, rms=0.599 (0.049%), neg=0, invalid=96777 0126: dt=32.368000, rms=0.599 (0.038%), neg=0, invalid=96777 0127: dt=32.368000, rms=0.599 (0.028%), neg=0, invalid=96777 0128: dt=32.368000, rms=0.599 (0.026%), neg=0, invalid=96777 0129: dt=32.368000, rms=0.599 (0.031%), neg=0, invalid=96777 0130: dt=32.368000, rms=0.598 (0.044%), neg=0, invalid=96777 0131: dt=32.368000, rms=0.598 (0.046%), neg=0, invalid=96777 0132: dt=32.368000, rms=0.598 (0.045%), neg=0, invalid=96777 0133: dt=32.368000, rms=0.598 (0.039%), neg=0, invalid=96777 0134: dt=32.368000, rms=0.597 (0.034%), neg=0, invalid=96777 0135: dt=32.368000, rms=0.597 (0.029%), neg=0, invalid=96777 0136: dt=32.368000, rms=0.597 (0.032%), neg=0, invalid=96777 0137: dt=32.368000, rms=0.597 (0.032%), neg=0, invalid=96777 0138: dt=32.368000, rms=0.597 (0.038%), neg=0, invalid=96777 0139: dt=32.368000, rms=0.596 (0.040%), neg=0, invalid=96777 0140: dt=32.368000, rms=0.596 (0.036%), neg=0, invalid=96777 0141: dt=32.368000, rms=0.596 (0.029%), neg=0, invalid=96777 0142: dt=32.368000, rms=0.596 (0.028%), neg=0, invalid=96777 0143: dt=32.368000, rms=0.596 (0.025%), neg=0, invalid=96777 0144: dt=32.368000, rms=0.596 (0.030%), neg=0, invalid=96777 0145: dt=32.368000, rms=0.595 (0.030%), neg=0, invalid=96777 0146: dt=32.368000, rms=0.595 (0.032%), neg=0, invalid=96777 0147: dt=32.368000, rms=0.595 (0.034%), neg=0, invalid=96777 0148: dt=32.368000, rms=0.595 (0.033%), neg=0, invalid=96777 0149: dt=32.368000, rms=0.595 (0.031%), neg=0, invalid=96777 0150: dt=32.368000, rms=0.594 (0.026%), neg=0, invalid=96777 0151: dt=32.368000, rms=0.594 (0.023%), neg=0, invalid=96777 0152: dt=32.368000, rms=0.594 (0.020%), neg=0, invalid=96777 0153: dt=1479.680000, rms=0.593 (0.114%), neg=0, invalid=96777 0154: dt=27.744000, rms=0.593 (0.014%), neg=0, invalid=96777 0155: dt=27.744000, rms=0.593 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.593, neg=0, invalid=96777 0156: dt=73.984000, rms=0.593 (0.036%), neg=0, invalid=96777 0157: dt=221.952000, rms=0.593 (0.094%), neg=0, invalid=96777 0158: dt=110.976000, rms=0.593 (0.015%), neg=0, invalid=96777 0159: dt=110.976000, rms=0.592 (0.052%), neg=0, invalid=96777 0160: dt=110.976000, rms=0.592 (0.048%), neg=0, invalid=96777 0161: dt=110.976000, rms=0.592 (0.030%), neg=0, invalid=96777 0162: dt=110.976000, rms=0.591 (0.048%), neg=0, invalid=96777 0163: dt=110.976000, rms=0.591 (0.078%), neg=0, invalid=96777 0164: dt=110.976000, rms=0.591 (0.052%), neg=0, invalid=96777 0165: dt=110.976000, rms=0.590 (0.039%), neg=0, invalid=96777 0166: dt=110.976000, rms=0.590 (0.040%), neg=0, invalid=96777 0167: dt=110.976000, rms=0.590 (0.067%), neg=0, invalid=96777 0168: dt=110.976000, rms=0.590 (0.053%), neg=0, invalid=96777 0169: dt=110.976000, rms=0.589 (0.043%), neg=0, invalid=96777 0170: dt=110.976000, rms=0.589 (0.038%), neg=0, invalid=96777 0171: dt=110.976000, rms=0.589 (0.051%), neg=0, invalid=96777 0172: dt=110.976000, rms=0.589 (0.039%), neg=0, invalid=96777 0173: dt=110.976000, rms=0.588 (0.029%), neg=0, invalid=96777 0174: dt=110.976000, rms=0.588 (0.040%), neg=0, invalid=96777 0175: dt=110.976000, rms=0.588 (0.049%), neg=0, invalid=96777 0176: dt=110.976000, rms=0.588 (0.039%), neg=0, invalid=96777 0177: dt=110.976000, rms=0.587 (0.033%), neg=0, invalid=96777 0178: dt=110.976000, rms=0.587 (0.031%), neg=0, invalid=96777 0179: dt=110.976000, rms=0.587 (0.036%), neg=0, invalid=96777 0180: dt=110.976000, rms=0.587 (0.030%), neg=0, invalid=96777 0181: dt=110.976000, rms=0.587 (0.029%), neg=0, invalid=96777 0182: dt=110.976000, rms=0.586 (0.032%), neg=0, invalid=96777 0183: dt=110.976000, rms=0.586 (0.033%), neg=0, invalid=96777 0184: dt=110.976000, rms=0.586 (0.027%), neg=0, invalid=96777 0185: dt=110.976000, rms=0.586 (0.027%), neg=0, invalid=96777 0186: dt=110.976000, rms=0.586 (0.036%), neg=0, invalid=96777 0187: dt=110.976000, rms=0.586 (0.032%), neg=0, invalid=96777 0188: dt=110.976000, rms=0.585 (0.027%), neg=0, invalid=96777 0189: dt=110.976000, rms=0.585 (0.031%), neg=0, invalid=96777 0190: dt=110.976000, rms=0.585 (0.030%), neg=0, invalid=96777 0191: dt=110.976000, rms=0.585 (0.026%), neg=0, invalid=96777 0192: dt=110.976000, rms=0.585 (0.029%), neg=0, invalid=96777 0193: dt=110.976000, rms=0.585 (0.030%), neg=0, invalid=96777 0194: dt=110.976000, rms=0.584 (0.024%), neg=0, invalid=96777 0195: dt=110.976000, rms=0.584 (0.017%), neg=0, invalid=96777 0196: dt=369.920000, rms=0.584 (0.017%), neg=0, invalid=96777 0197: dt=27.744000, rms=0.584 (0.000%), neg=0, invalid=96777 0198: dt=27.744000, rms=0.584 (0.001%), neg=0, invalid=96777 0199: dt=27.744000, rms=0.584 (-0.002%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.585, neg=0, invalid=96777 0200: dt=82.944000, rms=0.582 (0.484%), neg=0, invalid=96777 0201: dt=145.152000, rms=0.576 (0.944%), neg=0, invalid=96777 0202: dt=25.920000, rms=0.575 (0.242%), neg=0, invalid=96777 0203: dt=36.288000, rms=0.574 (0.197%), neg=0, invalid=96777 0204: dt=82.944000, rms=0.572 (0.276%), neg=0, invalid=96777 0205: dt=25.920000, rms=0.571 (0.211%), neg=0, invalid=96777 0206: dt=145.152000, rms=0.569 (0.404%), neg=0, invalid=96777 0207: dt=20.736000, rms=0.567 (0.282%), neg=0, invalid=96777 0208: dt=580.608000, rms=0.561 (1.130%), neg=0, invalid=96777 0209: dt=20.736000, rms=0.558 (0.548%), neg=0, invalid=96777 0210: dt=82.944000, rms=0.557 (0.158%), neg=0, invalid=96777 0211: dt=36.288000, rms=0.556 (0.180%), neg=0, invalid=96777 0212: dt=20.736000, rms=0.556 (0.027%), neg=0, invalid=96777 0213: dt=20.736000, rms=0.556 (0.036%), neg=0, invalid=96777 0214: dt=20.736000, rms=0.555 (0.065%), neg=0, invalid=96777 0215: dt=20.736000, rms=0.555 (0.104%), neg=0, invalid=96777 0216: dt=20.736000, rms=0.554 (0.134%), neg=0, invalid=96777 0217: dt=20.736000, rms=0.553 (0.147%), neg=0, invalid=96777 0218: dt=20.736000, rms=0.552 (0.163%), neg=0, invalid=96777 0219: dt=20.736000, rms=0.551 (0.167%), neg=0, invalid=96777 0220: dt=20.736000, rms=0.550 (0.174%), neg=0, invalid=96777 0221: dt=20.736000, rms=0.549 (0.181%), neg=0, invalid=96777 0222: dt=20.736000, rms=0.548 (0.181%), neg=0, invalid=96777 0223: dt=20.736000, rms=0.547 (0.182%), neg=0, invalid=96777 0224: dt=20.736000, rms=0.546 (0.176%), neg=0, invalid=96777 0225: dt=20.736000, rms=0.545 (0.174%), neg=0, invalid=96777 0226: dt=20.736000, rms=0.544 (0.172%), neg=0, invalid=96777 0227: dt=20.736000, rms=0.544 (0.164%), neg=0, invalid=96777 0228: dt=20.736000, rms=0.543 (0.162%), neg=0, invalid=96777 0229: dt=20.736000, rms=0.542 (0.160%), neg=0, invalid=96777 0230: dt=20.736000, rms=0.541 (0.157%), neg=0, invalid=96777 0231: dt=20.736000, rms=0.540 (0.146%), neg=0, invalid=96777 0232: dt=20.736000, rms=0.539 (0.141%), neg=0, invalid=96777 0233: dt=20.736000, rms=0.539 (0.139%), neg=0, invalid=96777 0234: dt=20.736000, rms=0.538 (0.136%), neg=0, invalid=96777 0235: dt=20.736000, rms=0.537 (0.122%), neg=0, invalid=96777 0236: dt=20.736000, rms=0.537 (0.120%), neg=0, invalid=96777 0237: dt=20.736000, rms=0.536 (0.116%), neg=0, invalid=96777 0238: dt=20.736000, rms=0.535 (0.117%), neg=0, invalid=96777 0239: dt=20.736000, rms=0.535 (0.112%), neg=0, invalid=96777 0240: dt=20.736000, rms=0.534 (0.104%), neg=0, invalid=96777 0241: dt=20.736000, rms=0.534 (0.090%), neg=0, invalid=96777 0242: dt=20.736000, rms=0.533 (0.090%), neg=0, invalid=96777 0243: dt=20.736000, rms=0.533 (0.095%), neg=0, invalid=96777 0244: dt=20.736000, rms=0.532 (0.094%), neg=0, invalid=96777 0245: dt=20.736000, rms=0.532 (0.088%), neg=0, invalid=96777 0246: dt=20.736000, rms=0.531 (0.077%), neg=0, invalid=96777 0247: dt=20.736000, rms=0.531 (0.079%), neg=0, invalid=96777 0248: dt=20.736000, rms=0.531 (0.075%), neg=0, invalid=96777 0249: dt=20.736000, rms=0.530 (0.078%), neg=0, invalid=96777 0250: dt=20.736000, rms=0.530 (0.079%), neg=0, invalid=96777 0251: dt=20.736000, rms=0.529 (0.074%), neg=0, invalid=96777 0252: dt=20.736000, rms=0.529 (0.067%), neg=0, invalid=96777 0253: dt=20.736000, rms=0.529 (0.068%), neg=0, invalid=96777 0254: dt=20.736000, rms=0.528 (0.069%), neg=0, invalid=96777 0255: dt=20.736000, rms=0.528 (0.067%), neg=0, invalid=96777 0256: dt=20.736000, rms=0.528 (0.063%), neg=0, invalid=96777 0257: dt=20.736000, rms=0.527 (0.056%), neg=0, invalid=96777 0258: dt=20.736000, rms=0.527 (0.051%), neg=0, invalid=96777 0259: dt=20.736000, rms=0.527 (0.051%), neg=0, invalid=96777 0260: dt=20.736000, rms=0.526 (0.053%), neg=0, invalid=96777 0261: dt=20.736000, rms=0.526 (0.056%), neg=0, invalid=96777 0262: dt=20.736000, rms=0.526 (0.054%), neg=0, invalid=96777 0263: dt=20.736000, rms=0.526 (0.050%), neg=0, invalid=96777 0264: dt=20.736000, rms=0.525 (0.046%), neg=0, invalid=96777 0265: dt=20.736000, rms=0.525 (0.045%), neg=0, invalid=96777 0266: dt=20.736000, rms=0.525 (0.044%), neg=0, invalid=96777 0267: dt=20.736000, rms=0.525 (0.046%), neg=0, invalid=96777 0268: dt=20.736000, rms=0.524 (0.046%), neg=0, invalid=96777 0269: dt=20.736000, rms=0.524 (0.043%), neg=0, invalid=96777 0270: dt=20.736000, rms=0.524 (0.041%), neg=0, invalid=96777 0271: dt=20.736000, rms=0.524 (0.036%), neg=0, invalid=96777 0272: dt=20.736000, rms=0.524 (0.036%), neg=0, invalid=96777 0273: dt=20.736000, rms=0.523 (0.040%), neg=0, invalid=96777 0274: dt=20.736000, rms=0.523 (0.042%), neg=0, invalid=96777 0275: dt=20.736000, rms=0.523 (0.041%), neg=0, invalid=96777 0276: dt=20.736000, rms=0.523 (0.036%), neg=0, invalid=96777 0277: dt=20.736000, rms=0.523 (0.035%), neg=0, invalid=96777 0278: dt=20.736000, rms=0.522 (0.032%), neg=0, invalid=96777 0279: dt=20.736000, rms=0.522 (0.035%), neg=0, invalid=96777 0280: dt=20.736000, rms=0.522 (0.039%), neg=0, invalid=96777 0281: dt=20.736000, rms=0.522 (0.037%), neg=0, invalid=96777 0282: dt=20.736000, rms=0.522 (0.035%), neg=0, invalid=96777 0283: dt=20.736000, rms=0.521 (0.033%), neg=0, invalid=96777 0284: dt=20.736000, rms=0.521 (0.032%), neg=0, invalid=96777 0285: dt=20.736000, rms=0.521 (0.031%), neg=0, invalid=96777 0286: dt=20.736000, rms=0.521 (0.034%), neg=0, invalid=96777 0287: dt=20.736000, rms=0.521 (0.034%), neg=0, invalid=96777 0288: dt=20.736000, rms=0.521 (0.032%), neg=0, invalid=96777 0289: dt=20.736000, rms=0.520 (0.034%), neg=0, invalid=96777 0290: dt=20.736000, rms=0.520 (0.032%), neg=0, invalid=96777 0291: dt=20.736000, rms=0.520 (0.028%), neg=0, invalid=96777 0292: dt=20.736000, rms=0.520 (0.025%), neg=0, invalid=96777 0293: dt=20.736000, rms=0.520 (0.030%), neg=0, invalid=96777 0294: dt=20.736000, rms=0.520 (0.030%), neg=0, invalid=96777 0295: dt=20.736000, rms=0.520 (0.028%), neg=0, invalid=96777 0296: dt=20.736000, rms=0.519 (0.028%), neg=0, invalid=96777 0297: dt=20.736000, rms=0.519 (0.025%), neg=0, invalid=96777 0298: dt=20.736000, rms=0.519 (0.025%), neg=0, invalid=96777 0299: dt=20.736000, rms=0.519 (0.026%), neg=0, invalid=96777 0300: dt=20.736000, rms=0.519 (0.028%), neg=0, invalid=96777 0301: dt=20.736000, rms=0.519 (0.028%), neg=0, invalid=96777 0302: dt=20.736000, rms=0.519 (0.025%), neg=0, invalid=96777 0303: dt=20.736000, rms=0.518 (0.025%), neg=0, invalid=96777 0304: dt=20.736000, rms=0.518 (0.025%), neg=0, invalid=96777 0305: dt=20.736000, rms=0.518 (0.027%), neg=0, invalid=96777 0306: dt=20.736000, rms=0.518 (0.026%), neg=0, invalid=96777 0307: dt=20.736000, rms=0.518 (0.024%), neg=0, invalid=96777 0308: dt=20.736000, rms=0.518 (0.023%), neg=0, invalid=96777 0309: dt=995.328000, rms=0.518 (0.042%), neg=0, invalid=96777 0310: dt=36.288000, rms=0.517 (0.049%), neg=0, invalid=96777 0311: dt=9.072000, rms=0.517 (0.002%), neg=0, invalid=96777 0312: dt=9.072000, rms=0.517 (0.001%), neg=0, invalid=96777 0313: dt=9.072000, rms=0.517 (0.001%), neg=0, invalid=96777 0314: dt=9.072000, rms=0.517 (-0.004%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.517, neg=0, invalid=96777 0315: dt=82.944000, rms=0.516 (0.233%), neg=0, invalid=96777 0316: dt=103.680000, rms=0.515 (0.127%), neg=0, invalid=96777 0317: dt=36.288000, rms=0.515 (0.088%), neg=0, invalid=96777 0318: dt=31.104000, rms=0.515 (0.006%), neg=0, invalid=96777 0319: dt=31.104000, rms=0.515 (0.042%), neg=0, invalid=96777 0320: dt=31.104000, rms=0.515 (0.038%), neg=0, invalid=96777 0321: dt=31.104000, rms=0.514 (0.049%), neg=0, invalid=96777 0322: dt=31.104000, rms=0.514 (0.067%), neg=0, invalid=96777 0323: dt=31.104000, rms=0.514 (0.067%), neg=0, invalid=96777 0324: dt=31.104000, rms=0.513 (0.069%), neg=0, invalid=96777 0325: dt=31.104000, rms=0.513 (0.061%), neg=0, invalid=96777 0326: dt=31.104000, rms=0.513 (0.046%), neg=0, invalid=96777 0327: dt=31.104000, rms=0.512 (0.045%), neg=0, invalid=96777 0328: dt=31.104000, rms=0.512 (0.056%), neg=0, invalid=96777 0329: dt=31.104000, rms=0.512 (0.048%), neg=0, invalid=96777 0330: dt=31.104000, rms=0.512 (0.040%), neg=0, invalid=96777 0331: dt=31.104000, rms=0.512 (0.038%), neg=0, invalid=96777 0332: dt=31.104000, rms=0.511 (0.040%), neg=0, invalid=96777 0333: dt=31.104000, rms=0.511 (0.038%), neg=0, invalid=96777 0334: dt=31.104000, rms=0.511 (0.036%), neg=0, invalid=96777 0335: dt=31.104000, rms=0.511 (0.034%), neg=0, invalid=96777 0336: dt=31.104000, rms=0.511 (0.039%), neg=0, invalid=96777 0337: dt=31.104000, rms=0.510 (0.040%), neg=0, invalid=96777 0338: dt=31.104000, rms=0.510 (0.035%), neg=0, invalid=96777 0339: dt=31.104000, rms=0.510 (0.031%), neg=0, invalid=96777 0340: dt=31.104000, rms=0.510 (0.033%), neg=0, invalid=96777 0341: dt=31.104000, rms=0.510 (0.046%), neg=0, invalid=96777 0342: dt=31.104000, rms=0.509 (0.043%), neg=0, invalid=96777 0343: dt=31.104000, rms=0.509 (0.035%), neg=0, invalid=96777 0344: dt=31.104000, rms=0.509 (0.032%), neg=0, invalid=96777 0345: dt=31.104000, rms=0.509 (0.031%), neg=0, invalid=96777 0346: dt=31.104000, rms=0.509 (0.042%), neg=0, invalid=96777 0347: dt=31.104000, rms=0.509 (0.031%), neg=0, invalid=96777 0348: dt=31.104000, rms=0.508 (0.027%), neg=0, invalid=96777 0349: dt=31.104000, rms=0.508 (0.026%), neg=0, invalid=96777 0350: dt=31.104000, rms=0.508 (0.037%), neg=0, invalid=96777 0351: dt=31.104000, rms=0.508 (0.031%), neg=0, invalid=96777 0352: dt=31.104000, rms=0.508 (0.027%), neg=0, invalid=96777 0353: dt=31.104000, rms=0.508 (0.023%), neg=0, invalid=96777 0354: dt=31.104000, rms=0.508 (0.029%), neg=0, invalid=96777 0355: dt=31.104000, rms=0.507 (0.027%), neg=0, invalid=96777 0356: dt=31.104000, rms=0.507 (0.024%), neg=0, invalid=96777 0357: dt=31.104000, rms=0.507 (0.021%), neg=0, invalid=96777 0358: dt=145.152000, rms=0.507 (0.015%), neg=0, invalid=96777 0359: dt=145.152000, rms=0.507 (-0.323%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.516, neg=0, invalid=96777 0360: dt=25.600000, rms=0.514 (0.321%), neg=0, invalid=96777 0361: dt=11.200000, rms=0.513 (0.264%), neg=0, invalid=96777 0362: dt=32.000000, rms=0.512 (0.265%), neg=0, invalid=96777 0363: dt=8.612766, rms=0.510 (0.292%), neg=0, invalid=96777 0364: dt=19.200000, rms=0.509 (0.198%), neg=0, invalid=96777 0365: dt=11.200000, rms=0.508 (0.206%), neg=0, invalid=96777 0366: dt=11.200000, rms=0.507 (0.149%), neg=0, invalid=96777 0367: dt=11.200000, rms=0.507 (0.157%), neg=0, invalid=96777 0368: dt=25.600000, rms=0.506 (0.154%), neg=0, invalid=96777 0369: dt=8.770370, rms=0.505 (0.192%), neg=0, invalid=96777 0370: dt=19.200000, rms=0.504 (0.175%), neg=0, invalid=96777 0371: dt=9.600000, rms=0.503 (0.125%), neg=0, invalid=96777 0372: dt=11.200000, rms=0.503 (0.124%), neg=0, invalid=96777 0373: dt=11.200000, rms=0.502 (0.102%), neg=0, invalid=96777 0374: dt=25.600000, rms=0.502 (0.135%), neg=0, invalid=96777 0375: dt=8.000000, rms=0.501 (0.134%), neg=0, invalid=96777 0376: dt=25.600000, rms=0.500 (0.166%), neg=0, invalid=96777 0377: dt=8.252632, rms=0.500 (0.105%), neg=0, invalid=96777 0378: dt=19.200000, rms=0.499 (0.131%), neg=0, invalid=96777 0379: dt=9.600000, rms=0.498 (0.087%), neg=0, invalid=96777 0380: dt=11.200000, rms=0.498 (0.096%), neg=0, invalid=96777 0381: dt=11.200000, rms=0.498 (0.079%), neg=0, invalid=96777 0382: dt=25.600000, rms=0.497 (0.107%), neg=0, invalid=96777 0383: dt=7.730337, rms=0.497 (0.088%), neg=0, invalid=96777 0384: dt=25.600000, rms=0.496 (0.131%), neg=0, invalid=96777 0385: dt=8.000000, rms=0.496 (0.071%), neg=0, invalid=96777 0386: dt=25.600000, rms=0.495 (0.120%), neg=0, invalid=96777 0387: dt=8.000000, rms=0.495 (0.071%), neg=0, invalid=96777 0388: dt=25.600000, rms=0.494 (0.103%), neg=0, invalid=96777 0389: dt=8.000000, rms=0.494 (0.069%), neg=0, invalid=96777 0390: dt=25.600000, rms=0.493 (0.100%), neg=0, invalid=96777 0391: dt=8.000000, rms=0.493 (0.062%), neg=0, invalid=96777 0392: dt=25.600000, rms=0.493 (0.088%), neg=0, invalid=96777 0393: dt=8.000000, rms=0.492 (0.065%), neg=0, invalid=96777 0394: dt=19.200000, rms=0.492 (0.082%), neg=0, invalid=96777 0395: dt=9.600000, rms=0.492 (0.048%), neg=0, invalid=96777 0396: dt=9.600000, rms=0.491 (0.050%), neg=0, invalid=96777 0397: dt=9.600000, rms=0.491 (0.070%), neg=0, invalid=96777 0398: dt=9.600000, rms=0.491 (0.100%), neg=0, invalid=96777 0399: dt=9.600000, rms=0.490 (0.048%), neg=0, invalid=96777 0400: dt=9.600000, rms=0.490 (0.064%), neg=0, invalid=96777 0401: dt=9.600000, rms=0.490 (0.091%), neg=0, invalid=96777 0402: dt=9.600000, rms=0.489 (0.110%), neg=0, invalid=96777 0403: dt=9.600000, rms=0.488 (0.132%), neg=0, invalid=96777 0404: dt=9.600000, rms=0.488 (0.141%), neg=0, invalid=96777 0405: dt=9.600000, rms=0.487 (0.149%), neg=0, invalid=96777 0406: dt=9.600000, rms=0.486 (0.153%), neg=0, invalid=96777 0407: dt=9.600000, rms=0.485 (0.163%), neg=0, invalid=96777 0408: dt=9.600000, rms=0.485 (0.156%), neg=0, invalid=96777 0409: dt=9.600000, rms=0.484 (0.155%), neg=0, invalid=96777 0410: dt=9.600000, rms=0.483 (0.150%), neg=0, invalid=96777 0411: dt=9.600000, rms=0.482 (0.146%), neg=0, invalid=96777 0412: dt=9.600000, rms=0.482 (0.145%), neg=0, invalid=96777 0413: dt=9.600000, rms=0.481 (0.138%), neg=0, invalid=96777 0414: dt=9.600000, rms=0.481 (0.126%), neg=0, invalid=96777 0415: dt=9.600000, rms=0.480 (0.121%), neg=0, invalid=96777 0416: dt=9.600000, rms=0.479 (0.116%), neg=0, invalid=96777 0417: dt=9.600000, rms=0.479 (0.106%), neg=0, invalid=96777 0418: dt=9.600000, rms=0.478 (0.098%), neg=0, invalid=96777 0419: dt=9.600000, rms=0.478 (0.093%), neg=0, invalid=96777 0420: dt=9.600000, rms=0.478 (0.091%), neg=0, invalid=96777 0421: dt=9.600000, rms=0.477 (0.085%), neg=0, invalid=96777 0422: dt=9.600000, rms=0.477 (0.078%), neg=0, invalid=96777 0423: dt=9.600000, rms=0.476 (0.073%), neg=0, invalid=96777 0424: dt=9.600000, rms=0.476 (0.067%), neg=0, invalid=96777 0425: dt=9.600000, rms=0.476 (0.062%), neg=0, invalid=96777 0426: dt=9.600000, rms=0.476 (0.056%), neg=0, invalid=96777 0427: dt=9.600000, rms=0.475 (0.054%), neg=0, invalid=96777 0428: dt=9.600000, rms=0.475 (0.050%), neg=0, invalid=96777 0429: dt=9.600000, rms=0.475 (0.051%), neg=0, invalid=96777 0430: dt=9.600000, rms=0.475 (0.041%), neg=0, invalid=96777 0431: dt=9.600000, rms=0.474 (0.041%), neg=0, invalid=96777 0432: dt=9.600000, rms=0.474 (0.044%), neg=0, invalid=96777 0433: dt=9.600000, rms=0.474 (0.039%), neg=0, invalid=96777 0434: dt=9.600000, rms=0.474 (0.038%), neg=0, invalid=96777 0435: dt=9.600000, rms=0.474 (0.033%), neg=0, invalid=96777 0436: dt=9.600000, rms=0.473 (0.036%), neg=0, invalid=96777 0437: dt=9.600000, rms=0.473 (0.028%), neg=0, invalid=96777 0438: dt=9.600000, rms=0.473 (0.031%), neg=0, invalid=96777 0439: dt=9.600000, rms=0.473 (0.031%), neg=0, invalid=96777 0440: dt=9.600000, rms=0.473 (0.029%), neg=0, invalid=96777 0441: dt=9.600000, rms=0.473 (0.029%), neg=0, invalid=96777 0442: dt=9.600000, rms=0.473 (0.035%), neg=0, invalid=96777 0443: dt=9.600000, rms=0.473 (0.025%), neg=0, invalid=96777 0444: dt=9.600000, rms=0.472 (0.025%), neg=0, invalid=96777 0445: dt=9.600000, rms=0.472 (0.032%), neg=0, invalid=96777 0446: dt=9.600000, rms=0.472 (0.036%), neg=0, invalid=96777 0447: dt=9.600000, rms=0.472 (0.019%), neg=0, invalid=96777 0448: dt=9.600000, rms=0.472 (0.015%), neg=0, invalid=96777 0449: dt=32.000000, rms=0.472 (0.025%), neg=0, invalid=96777 0450: dt=0.000000, rms=0.472 (-0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.472, neg=0, invalid=96777 0451: dt=11.200000, rms=0.471 (0.096%), neg=0, invalid=96777 0452: dt=11.200000, rms=0.471 (0.145%), neg=0, invalid=96777 0453: dt=6.400000, rms=0.471 (0.017%), neg=0, invalid=96777 0454: dt=6.400000, rms=0.470 (0.043%), neg=0, invalid=96777 0455: dt=6.400000, rms=0.470 (0.049%), neg=0, invalid=96777 0456: dt=6.400000, rms=0.470 (0.050%), neg=0, invalid=96777 0457: dt=6.400000, rms=0.470 (0.043%), neg=0, invalid=96777 0458: dt=6.400000, rms=0.470 (0.028%), neg=0, invalid=96777 0459: dt=6.400000, rms=0.469 (0.020%), neg=0, invalid=96777 0460: dt=6.400000, rms=0.469 (0.007%), neg=0, invalid=96777 0461: dt=44.800000, rms=0.469 (0.045%), neg=0, invalid=96777 0462: dt=11.200000, rms=0.469 (0.030%), neg=0, invalid=96777 0463: dt=11.200000, rms=0.469 (-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=0.493, neg=0, invalid=96777 0464: dt=0.000000, rms=0.493 (0.000%), neg=0, invalid=96777 0465: dt=0.150000, rms=0.493 (-0.012%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.493, neg=0, invalid=96777 0466: dt=0.000000, rms=0.493 (0.000%), neg=0, invalid=96777 0467: dt=0.150000, rms=0.493 (-0.009%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.540, neg=0, invalid=96777 0468: dt=1.659236, rms=0.533 (1.242%), neg=0, invalid=96777 0469: dt=0.520833, rms=0.533 (0.084%), neg=0, invalid=96777 0470: dt=0.384000, rms=0.533 (0.019%), neg=0, invalid=96777 0471: dt=0.384000, rms=0.533 (-0.009%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.533, neg=0, invalid=96777 0472: dt=1.280000, rms=0.532 (0.176%), neg=0, invalid=96777 0473: dt=0.384000, rms=0.532 (0.008%), neg=0, invalid=96777 0474: dt=0.384000, rms=0.532 (-0.005%), 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=0.494, neg=0, invalid=96777 0475: dt=0.145109, rms=0.490 (0.863%), neg=0, invalid=96777 0476: dt=0.028000, rms=0.489 (0.129%), neg=0, invalid=96777 0477: dt=0.320000, rms=0.483 (1.333%), neg=0, invalid=96777 0478: dt=0.112000, rms=0.482 (0.230%), neg=0, invalid=96777 0479: dt=0.448000, rms=0.478 (0.775%), neg=0, invalid=96777 0480: dt=0.320000, rms=0.477 (0.266%), neg=0, invalid=96777 0481: dt=0.112000, rms=0.476 (0.077%), neg=0, invalid=96777 0482: dt=0.024000, rms=0.476 (0.013%), neg=0, invalid=96777 0483: dt=0.024000, rms=0.476 (0.014%), neg=0, invalid=96777 0484: dt=0.024000, rms=0.476 (0.026%), neg=0, invalid=96777 0485: dt=0.024000, rms=0.476 (0.037%), neg=0, invalid=96777 0486: dt=0.024000, rms=0.476 (0.012%), neg=0, invalid=96777 0487: dt=0.024000, rms=0.476 (0.026%), neg=0, invalid=96777 0488: dt=0.024000, rms=0.475 (0.034%), neg=0, invalid=96777 0489: dt=0.024000, rms=0.475 (0.046%), neg=0, invalid=96777 0490: dt=0.024000, rms=0.475 (0.051%), neg=0, invalid=96777 0491: dt=0.024000, rms=0.475 (0.008%), neg=0, invalid=96777 0492: dt=0.024000, rms=0.475 (0.022%), neg=0, invalid=96777 0493: dt=0.024000, rms=0.475 (0.027%), neg=0, invalid=96777 0494: dt=0.024000, rms=0.474 (0.037%), neg=0, invalid=96777 0495: dt=0.024000, rms=0.474 (0.041%), neg=0, invalid=96777 0496: dt=0.024000, rms=0.474 (0.047%), neg=0, invalid=96777 0497: dt=0.024000, rms=0.474 (0.003%), neg=0, invalid=96777 0498: dt=0.024000, rms=0.474 (0.021%), neg=0, invalid=96777 0499: dt=0.024000, rms=0.474 (0.020%), neg=0, invalid=96777 0500: dt=0.112000, rms=0.474 (0.036%), neg=0, invalid=96777 0501: dt=0.112000, rms=0.474 (0.034%), neg=0, invalid=96777 0502: dt=0.112000, rms=0.473 (0.031%), neg=0, invalid=96777 0503: dt=0.112000, rms=0.473 (0.031%), neg=0, invalid=96777 0504: dt=0.112000, rms=0.473 (0.056%), neg=0, invalid=96777 0505: dt=0.112000, rms=0.473 (0.031%), neg=0, invalid=96777 0506: dt=0.112000, rms=0.473 (0.021%), neg=0, invalid=96777 0507: dt=0.028000, rms=0.473 (0.007%), neg=0, invalid=96777 0508: dt=0.320000, rms=0.472 (0.068%), neg=0, invalid=96777 0509: dt=0.112000, rms=0.472 (0.016%), neg=0, invalid=96777 0510: dt=0.056000, rms=0.472 (0.011%), neg=0, invalid=96777 0511: dt=0.056000, rms=0.472 (0.012%), neg=0, invalid=96777 0512: dt=0.056000, rms=0.472 (0.017%), neg=0, invalid=96777 0513: dt=0.056000, rms=0.472 (0.022%), neg=0, invalid=96777 0514: dt=0.056000, rms=0.472 (0.012%), neg=0, invalid=96777 0515: dt=0.056000, rms=0.472 (0.015%), neg=0, invalid=96777 0516: dt=0.056000, rms=0.472 (0.008%), neg=0, invalid=96777 0517: dt=1.792000, rms=0.471 (0.244%), neg=0, invalid=96777 0518: dt=0.112000, rms=0.471 (0.006%), neg=0, invalid=96777 0519: dt=0.112000, rms=0.471 (0.003%), neg=0, invalid=96777 0520: dt=0.112000, rms=0.471 (0.009%), neg=0, invalid=96777 0521: dt=0.056000, rms=0.471 (0.002%), neg=0, invalid=96777 0522: dt=0.056000, rms=0.471 (0.004%), neg=0, invalid=96777 0523: dt=0.056000, rms=0.471 (0.001%), neg=0, invalid=96777 0524: dt=0.112000, rms=0.471 (0.008%), neg=0, invalid=96777 0525: dt=0.112000, rms=0.470 (0.004%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.470, neg=0, invalid=96777 0526: dt=0.100230, rms=0.470 (0.178%), neg=0, invalid=96777 0527: dt=0.028000, rms=0.469 (0.037%), neg=0, invalid=96777 0528: dt=0.028000, rms=0.469 (0.035%), neg=0, invalid=96777 0529: dt=0.028000, rms=0.469 (0.067%), neg=0, invalid=96777 0530: dt=0.028000, rms=0.469 (0.086%), neg=0, invalid=96777 0531: dt=0.028000, rms=0.468 (0.100%), neg=0, invalid=96777 0532: dt=0.028000, rms=0.468 (0.104%), neg=0, invalid=96777 0533: dt=0.028000, rms=0.468 (0.012%), neg=0, invalid=96777 0534: dt=0.028000, rms=0.467 (0.020%), neg=0, invalid=96777 0535: dt=0.028000, rms=0.467 (0.030%), neg=0, invalid=96777 0536: dt=0.028000, rms=0.467 (0.009%), neg=0, invalid=96777 0537: dt=0.028000, rms=0.467 (0.016%), neg=0, invalid=96777 0538: dt=0.028000, rms=0.467 (0.022%), neg=0, invalid=96777 0539: dt=0.028000, rms=0.467 (0.023%), neg=0, invalid=96777 0540: dt=0.028000, rms=0.467 (0.025%), neg=0, invalid=96777 0541: dt=0.028000, rms=0.467 (0.028%), neg=0, invalid=96777 0542: dt=0.028000, rms=0.467 (0.024%), neg=0, invalid=96777 0543: dt=0.028000, rms=0.467 (0.025%), neg=0, invalid=96777 0544: dt=0.028000, rms=0.466 (0.022%), neg=0, invalid=96777 0545: dt=0.000000, rms=0.466 (0.001%), neg=0, invalid=96777 0546: dt=0.050000, rms=0.466 (-0.002%), 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=0.464, neg=0, invalid=96777 0547: dt=18.496000, rms=0.464 (0.001%), neg=0, invalid=96777 0548: dt=8.092000, rms=0.464 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.464, neg=0, invalid=96777 0549: dt=129.472000, rms=0.464 (0.040%), neg=0, invalid=96777 0550: dt=110.976000, rms=0.464 (0.015%), neg=0, invalid=96777 0551: dt=110.976000, rms=0.464 (0.028%), neg=0, invalid=96777 0552: dt=110.976000, rms=0.464 (0.037%), neg=0, invalid=96777 0553: dt=110.976000, rms=0.464 (0.008%), neg=0, invalid=96777 0554: dt=110.976000, rms=0.463 (0.053%), neg=0, invalid=96777 0555: dt=110.976000, rms=0.463 (0.027%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.463, neg=0, invalid=96777 0556: dt=31.104000, rms=0.463 (0.088%), neg=0, invalid=96777 0557: dt=36.288000, rms=0.463 (0.061%), neg=0, invalid=96777 0558: dt=36.288000, rms=0.462 (0.047%), neg=0, invalid=96777 0559: dt=36.288000, rms=0.462 (0.071%), neg=0, invalid=96777 0560: dt=36.288000, rms=0.462 (0.077%), neg=0, invalid=96777 0561: dt=36.288000, rms=0.461 (0.048%), neg=0, invalid=96777 0562: dt=36.288000, rms=0.461 (0.027%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.461, neg=0, invalid=96777 0563: dt=82.944000, rms=0.459 (0.549%), neg=0, invalid=96777 0564: dt=36.288000, rms=0.458 (0.190%), neg=0, invalid=96777 0565: dt=36.288000, rms=0.457 (0.132%), neg=0, invalid=96777 0566: dt=36.288000, rms=0.457 (0.134%), neg=0, invalid=96777 0567: dt=36.288000, rms=0.456 (0.104%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0568: dt=36.288000, rms=0.456 (0.150%), neg=0, invalid=96777 0569: dt=36.288000, rms=0.455 (0.152%), neg=0, invalid=96777 0570: dt=36.288000, rms=0.454 (0.115%), neg=0, invalid=96777 0571: dt=36.288000, rms=0.454 (0.075%), neg=0, invalid=96777 0572: dt=36.288000, rms=0.454 (0.045%), neg=0, invalid=96777 0573: dt=36.288000, rms=0.454 (-0.005%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.454, neg=0, invalid=96777 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0574: dt=25.600000, rms=0.452 (0.466%), neg=0, invalid=96777 0575: dt=19.200000, rms=0.450 (0.392%), neg=0, invalid=96777 0576: dt=7.154472, rms=0.450 (0.147%), neg=0, invalid=96777 0577: dt=7.154472, rms=0.449 (0.152%), neg=0, invalid=96777 0578: dt=7.154472, rms=0.448 (0.186%), neg=0, invalid=96777 0579: dt=7.154472, rms=0.447 (0.229%), neg=0, invalid=96777 0580: dt=7.154472, rms=0.446 (0.244%), neg=0, invalid=96777 0581: dt=7.154472, rms=0.445 (0.255%), neg=0, invalid=96777 0582: dt=7.154472, rms=0.444 (0.261%), neg=0, invalid=96777 0583: dt=7.154472, rms=0.443 (0.240%), neg=0, invalid=96777 0584: dt=7.154472, rms=0.442 (0.210%), neg=0, invalid=96777 0585: dt=7.154472, rms=0.441 (0.203%), neg=0, invalid=96777 0586: dt=7.154472, rms=0.440 (0.186%), neg=0, invalid=96777 0587: dt=7.154472, rms=0.439 (0.189%), neg=0, invalid=96777 0588: dt=7.154472, rms=0.438 (0.177%), neg=0, invalid=96777 0589: dt=7.154472, rms=0.438 (0.163%), neg=0, invalid=96777 0590: dt=7.154472, rms=0.437 (0.160%), neg=0, invalid=96777 0591: dt=7.154472, rms=0.436 (0.146%), neg=0, invalid=96777 0592: dt=7.154472, rms=0.436 (0.144%), neg=0, invalid=96777 0593: dt=7.154472, rms=0.435 (0.137%), neg=0, invalid=96777 0594: dt=7.154472, rms=0.435 (0.095%), neg=0, invalid=96777 0595: dt=7.154472, rms=0.434 (0.085%), neg=0, invalid=96777 0596: dt=32.000000, rms=0.434 (0.059%), neg=0, invalid=96777 0597: dt=32.000000, rms=0.434 (-0.129%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.434, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0598: dt=25.600000, rms=0.432 (0.387%), neg=0, invalid=96777 0599: dt=9.600000, rms=0.432 (0.177%), neg=0, invalid=96777 0600: dt=9.600000, rms=0.431 (0.111%), neg=0, invalid=96777 0601: dt=9.600000, rms=0.431 (0.120%), neg=0, invalid=96777 0602: dt=9.600000, rms=0.430 (0.212%), neg=0, invalid=96777 0603: dt=9.600000, rms=0.429 (0.165%), neg=0, invalid=96777 0604: dt=9.600000, rms=0.429 (0.116%), neg=0, invalid=96777 0605: dt=9.600000, rms=0.428 (0.060%), neg=0, invalid=96777 0606: dt=9.600000, rms=0.428 (0.072%), neg=0, invalid=96777 0607: dt=2.800000, rms=0.428 (0.010%), neg=0, invalid=96777 0608: dt=2.800000, rms=0.428 (0.014%), neg=0, invalid=96777 0609: dt=2.800000, rms=0.428 (0.007%), neg=0, invalid=96777 0610: dt=2.800000, rms=0.428 (0.002%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.435, neg=0, invalid=96777 0611: dt=2.880000, rms=0.435 (0.039%), neg=0, invalid=96777 0612: dt=1.008000, rms=0.435 (0.015%), neg=0, invalid=96777 0613: dt=1.008000, rms=0.435 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.435, neg=0, invalid=96777 0614: dt=4.526316, rms=0.434 (0.105%), neg=0, invalid=96777 0615: dt=4.032000, rms=0.434 (0.036%), neg=0, invalid=96777 0616: dt=4.032000, rms=0.434 (0.030%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0617: dt=4.032000, rms=0.434 (-0.011%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.442, neg=0, invalid=96777 0618: dt=0.000000, rms=0.442 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.442, neg=0, invalid=96777 0619: dt=0.256000, rms=0.442 (0.005%), neg=0, invalid=96777 0620: dt=0.112000, rms=0.442 (0.003%), neg=0, invalid=96777 0621: dt=0.112000, rms=0.442 (0.003%), neg=0, invalid=96777 0622: dt=0.112000, rms=0.442 (-0.003%), 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=0.429, neg=0, invalid=96777 iter 0, gcam->neg = 524 after 17 iterations, nbhd size=2, neg = 0 0623: dt=1.612999, rms=0.405 (5.629%), neg=0, invalid=96777 0624: dt=0.000375, rms=0.405 (0.005%), neg=0, invalid=96777 0625: dt=0.000375, rms=0.405 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.405, neg=0, invalid=96777 0626: dt=0.000438, rms=0.405 (0.000%), neg=0, invalid=96777 0627: dt=0.000000, rms=0.405 (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=0.395, neg=0, invalid=96777 0628: dt=0.000000, rms=0.396 (-0.273%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.396, neg=0, invalid=96777 0629: dt=73.984000, rms=0.396 (0.011%), neg=0, invalid=96777 0630: dt=92.480000, rms=0.396 (0.002%), neg=0, invalid=96777 0631: dt=92.480000, rms=0.396 (0.003%), neg=0, invalid=96777 0632: dt=92.480000, rms=0.396 (0.003%), neg=0, invalid=96777 0633: dt=92.480000, rms=0.396 (0.002%), neg=0, invalid=96777 0634: dt=92.480000, rms=0.396 (0.002%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.396, neg=0, invalid=96777 0635: dt=1.944000, rms=0.396 (0.000%), neg=0, invalid=96777 0636: dt=0.001582, rms=0.396 (0.000%), neg=0, invalid=96777 0637: dt=0.001582, rms=0.396 (0.000%), neg=0, invalid=96777 0638: dt=0.001582, rms=0.396 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.396, neg=0, invalid=96777 0639: dt=145.152000, rms=0.396 (0.086%), neg=0, invalid=96777 0640: dt=82.944000, rms=0.396 (0.036%), neg=0, invalid=96777 0641: dt=82.944000, rms=0.396 (0.018%), neg=0, invalid=96777 0642: dt=82.944000, rms=0.396 (0.066%), neg=0, invalid=96777 0643: dt=82.944000, rms=0.395 (0.041%), neg=0, invalid=96777 0644: dt=82.944000, rms=0.395 (0.055%), neg=0, invalid=96777 0645: dt=82.944000, rms=0.395 (0.017%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.396, neg=0, invalid=96777 0646: dt=9.600000, rms=0.395 (0.071%), neg=0, invalid=96777 0647: dt=2.800000, rms=0.395 (0.005%), neg=0, invalid=96777 0648: dt=2.800000, rms=0.395 (0.004%), neg=0, invalid=96777 0649: dt=2.800000, rms=0.395 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.395, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0650: dt=38.400000, rms=0.394 (0.344%), neg=0, invalid=96777 0651: dt=19.200000, rms=0.393 (0.230%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0652: dt=19.200000, rms=0.393 (0.053%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 14 iterations, nbhd size=2, neg = 0 0653: dt=19.200000, rms=0.392 (0.109%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0654: dt=19.200000, rms=0.392 (0.212%), neg=0, invalid=96777 0655: dt=19.200000, rms=0.391 (0.231%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0656: dt=19.200000, rms=0.390 (0.224%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 10 iterations, nbhd size=1, neg = 0 0657: dt=19.200000, rms=0.389 (0.184%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0658: dt=19.200000, rms=0.388 (0.179%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0659: dt=19.200000, rms=0.388 (0.171%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0660: dt=19.200000, rms=0.387 (0.158%), neg=0, invalid=96777 iter 0, gcam->neg = 14 after 16 iterations, nbhd size=2, neg = 0 0661: dt=19.200000, rms=0.387 (0.138%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0662: dt=19.200000, rms=0.386 (0.045%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 10 iterations, nbhd size=1, neg = 0 0663: dt=19.200000, rms=0.386 (0.014%), neg=0, invalid=96777 0664: dt=38.400000, rms=0.386 (0.158%), neg=0, invalid=96777 0665: dt=11.200000, rms=0.386 (0.029%), neg=0, invalid=96777 0666: dt=11.200000, rms=0.386 (0.026%), neg=0, invalid=96777 0667: dt=11.200000, rms=0.385 (0.037%), neg=0, invalid=96777 0668: dt=11.200000, rms=0.385 (0.034%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0669: dt=11.200000, rms=0.385 (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=0.389, neg=0, invalid=96777 0670: dt=0.864000, rms=0.389 (0.006%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0671: dt=2.304000, rms=0.389 (0.020%), neg=0, invalid=96777 0672: dt=0.864000, rms=0.389 (0.002%), neg=0, invalid=96777 0673: dt=0.864000, rms=0.389 (-0.001%), 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 = 1 after 0 iterations, nbhd size=0, neg = 0 0674: dt=4.032000, rms=0.388 (0.093%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0675: dt=0.864000, rms=0.388 (0.004%), neg=0, invalid=96777 0676: dt=0.864000, rms=0.388 (0.012%), neg=0, invalid=96777 0677: dt=0.864000, rms=0.388 (0.021%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0678: dt=0.864000, rms=0.388 (0.025%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0679: dt=0.864000, rms=0.388 (0.020%), neg=0, invalid=96777 0680: dt=0.864000, rms=0.388 (0.008%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.393, neg=0, invalid=96777 0681: dt=0.000000, rms=0.393 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.393, neg=0, invalid=96777 0682: dt=0.000000, rms=0.393 (0.000%), neg=0, invalid=96777 0683: dt=0.100000, rms=0.393 (-0.027%), 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=0.384, neg=0, invalid=96777 iter 0, gcam->neg = 306 after 17 iterations, nbhd size=2, neg = 0 0684: dt=0.627315, rms=0.376 (2.094%), neg=0, invalid=96777 0685: dt=0.000094, rms=0.376 (0.003%), neg=0, invalid=96777 0686: dt=0.000094, rms=0.376 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0687: dt=0.000094, rms=0.376 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.376, neg=0, invalid=96777 0688: dt=0.001250, rms=0.376 (0.001%), neg=0, invalid=96777 iter 0, gcam->neg = 20 after 6 iterations, nbhd size=1, neg = 0 0689: dt=0.096000, rms=0.376 (0.053%), neg=0, invalid=96777 0690: dt=0.000063, rms=0.376 (0.001%), neg=0, invalid=96777 0691: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0692: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0693: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0694: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0695: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0696: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0697: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0698: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0699: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0700: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0701: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0702: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0703: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0704: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0705: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0706: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0707: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0708: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0709: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0710: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0711: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0712: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0713: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0714: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0715: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0716: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0717: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0718: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0719: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0720: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0721: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0722: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0723: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0724: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0725: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0726: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0727: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0728: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0729: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0730: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 0731: dt=0.000063, rms=0.376 (0.000%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 5 hours, 11 minutes and 6 seconds. #-------------------------------------- #@# CA Reg Inv Sun Dec 15 03:08:58 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Sun Dec 15 03:14:31 EST 2013 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... 11501222 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 5 minutes and 34 seconds. #-------------------------------------- #@# SkullLTA Sun Dec 15 03:20:06 EST 2013 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 ======= NUMBER OF OPENMP THREADS = 8 ======= 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=6.0 skull bounding box = (48, 26, 15) --> (203, 203, 219) using (100, 85, 117) as brain centroid... mean wm in atlas = 126, using box (81,63,92) --> (119, 106,142) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 109, scaling input intensities by 1.156 scaling channel 0 by 1.15596 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.085 -0.089 -0.011 -0.587; 0.124 1.266 0.162 -41.680; -0.001 -0.180 1.040 7.548; 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 =-3.9 (thresh=-3.8) 1.085 -0.089 -0.011 -0.587; 0.124 1.266 0.162 -41.680; -0.001 -0.180 1.040 7.548; 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 =-3.9 (thresh=-3.8) 1.080 -0.126 -0.048 8.043; 0.159 1.267 0.128 -42.431; 0.039 -0.137 1.024 -0.067; 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) 1.080 -0.126 -0.048 8.043; 0.159 1.267 0.128 -42.431; 0.039 -0.137 1.024 -0.067; 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) 1.086 -0.096 -0.037 3.849; 0.133 1.275 0.129 -38.542; 0.031 -0.135 1.024 1.256; 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) 1.086 -0.096 -0.037 3.849; 0.133 1.275 0.129 -38.542; 0.031 -0.135 1.022 1.501; 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 1.08650 -0.09580 -0.03728 3.84872; 0.13266 1.27458 0.12871 -38.54188; 0.03101 -0.13514 1.02201 1.50128; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.08650 -0.09580 -0.03728 3.84872; 0.13266 1.27458 0.12871 -38.54188; 0.03101 -0.13514 1.02201 1.50128; 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: 1.086 -0.096 -0.037 3.849; 0.133 1.275 0.129 -38.542; 0.031 -0.135 1.022 1.501; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.8 (old=-3.9) transform before final EM align: 1.086 -0.096 -0.037 3.849; 0.133 1.275 0.129 -38.542; 0.031 -0.135 1.022 1.501; 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 1.08650 -0.09580 -0.03728 3.84872; 0.13266 1.27458 0.12871 -38.54188; 0.03101 -0.13514 1.02201 1.50128; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.08650 -0.09580 -0.03728 3.84872; 0.13266 1.27458 0.12871 -38.54188; 0.03101 -0.13514 1.02201 1.50128; 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: 009: -log(p) = 4.2 tol 0.000000 final transform: 1.086 -0.096 -0.037 3.849; 0.133 1.275 0.129 -38.542; 0.031 -0.135 1.022 1.501; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 624 minutes and 26 seconds. #-------------------------------------- #@# SubCort Seg Sun Dec 15 13:44:33 EST 2013 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 mani.med.yale.internal machine x86_64 setenv SUBJECTS_DIR /mani2/fei_data/Jacobian_maps/SUBJECT_DIR cd /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 = 0.08696 (46) Left_Lateral_Ventricle (4): linear fit = 1.68 x + 0.0 (91 voxels, overlap=0.292) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (91 voxels, peak = 45), gca=40.5 gca peak = 0.14982 (20) mri peak = 0.11205 (45) Right_Lateral_Ventricle (43): linear fit = 2.05 x + 0.0 (54 voxels, overlap=0.315) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (54 voxels, peak = 41), gca=30.0 gca peak = 0.28003 (97) mri peak = 0.11714 (94) Right_Pallidum (52): linear fit = 0.93 x + 0.0 (350 voxels, overlap=1.029) Right_Pallidum (52): linear fit = 0.93 x + 0.0 (350 voxels, peak = 90), gca=89.7 gca peak = 0.18160 (96) mri peak = 0.12152 (95) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (377 voxels, overlap=0.624) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (377 voxels, peak = 90), gca=89.8 gca peak = 0.27536 (62) mri peak = 0.11316 (68) Right_Hippocampus (53): linear fit = 1.08 x + 0.0 (689 voxels, overlap=1.007) Right_Hippocampus (53): linear fit = 1.08 x + 0.0 (689 voxels, peak = 67), gca=66.7 gca peak = 0.32745 (63) mri peak = 0.11718 (64) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (726 voxels, overlap=1.005) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (726 voxels, peak = 63), gca=63.0 gca peak = 0.08597 (105) mri peak = 0.11023 (108) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (40844 voxels, overlap=0.558) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (40844 voxels, peak = 109), gca=108.7 gca peak = 0.09209 (106) mri peak = 0.10203 (108) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (40899 voxels, overlap=0.613) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (40899 voxels, peak = 109), gca=108.6 gca peak = 0.07826 (63) mri peak = 0.04268 (65) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (30640 voxels, overlap=0.928) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (30640 voxels, peak = 62), gca=62.1 gca peak = 0.08598 (64) mri peak = 0.04438 (63) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (29460 voxels, overlap=0.873) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (29460 voxels, peak = 62), gca=61.8 gca peak = 0.24164 (71) mri peak = 0.14141 (76) Right_Caudate (50): linear fit = 1.08 x + 0.0 (395 voxels, overlap=0.761) Right_Caudate (50): linear fit = 1.08 x + 0.0 (395 voxels, peak = 76), gca=76.3 gca peak = 0.18227 (75) mri peak = 0.17925 (76) Left_Caudate (11): linear fit = 0.99 x + 0.0 (737 voxels, overlap=0.587) Left_Caudate (11): linear fit = 0.99 x + 0.0 (737 voxels, peak = 74), gca=73.9 gca peak = 0.10629 (62) mri peak = 0.05833 (65) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (27538 voxels, overlap=0.855) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (27538 voxels, peak = 67), gca=66.7 gca peak = 0.11668 (59) mri peak = 0.05423 (65) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (26585 voxels, overlap=0.926) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (26585 voxels, peak = 63), gca=63.4 gca peak = 0.17849 (88) mri peak = 0.10984 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (4812 voxels, overlap=0.722) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (4812 voxels, peak = 93), gca=92.8 gca peak = 0.16819 (86) mri peak = 0.12860 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (4408 voxels, overlap=0.724) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (4408 voxels, peak = 91), gca=90.7 gca peak = 0.41688 (64) mri peak = 0.15588 (70) Left_Amygdala (18): linear fit = 1.09 x + 0.0 (338 voxels, overlap=0.741) Left_Amygdala (18): linear fit = 1.09 x + 0.0 (338 voxels, peak = 69), gca=69.4 gca peak = 0.42394 (62) mri peak = 0.19282 (68) Right_Amygdala (54): linear fit = 1.08 x + 0.0 (260 voxels, overlap=0.466) Right_Amygdala (54): linear fit = 1.08 x + 0.0 (260 voxels, peak = 67), gca=66.7 gca peak = 0.10041 (96) mri peak = 0.07084 (92) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (2910 voxels, overlap=0.965) Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (2910 voxels, peak = 95), gca=94.6 gca peak = 0.13978 (88) mri peak = 0.06588 (87) Right_Thalamus_Proper (49): linear fit = 0.96 x + 0.0 (3202 voxels, overlap=0.887) Right_Thalamus_Proper (49): linear fit = 0.96 x + 0.0 (3202 voxels, peak = 85), gca=84.9 gca peak = 0.08514 (81) mri peak = 0.09593 (83) Left_Putamen (12): linear fit = 0.94 x + 0.0 (1511 voxels, overlap=0.745) Left_Putamen (12): linear fit = 0.94 x + 0.0 (1511 voxels, peak = 77), gca=76.5 gca peak = 0.09624 (82) mri peak = 0.10051 (82) Right_Putamen (51): linear fit = 0.98 x + 0.0 (1649 voxels, overlap=0.830) Right_Putamen (51): linear fit = 0.98 x + 0.0 (1649 voxels, peak = 80), gca=80.0 gca peak = 0.07543 (88) mri peak = 0.08005 (88) Brain_Stem (16): linear fit = 1.01 x + 0.0 (10447 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.01 x + 0.0 (10447 voxels, peak = 89), gca=89.3 gca peak = 0.12757 (95) mri peak = 0.06670 (93) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1073 voxels, overlap=0.851) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1073 voxels, peak = 97), gca=97.4 gca peak = 0.17004 (92) mri peak = 0.05951 (99) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1093 voxels, overlap=0.930) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1093 voxels, peak = 92), gca=91.5 gca peak = 0.21361 (36) mri peak = 1.00000 (54) gca peak = 0.26069 (23) mri peak = 0.15317 (21) Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (123 voxels, overlap=0.651) Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (123 voxels, peak = 20), gca=20.1 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 1.03 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.29 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.12156 (41) mri peak = 0.08696 (46) Left_Lateral_Ventricle (4): linear fit = 1.11 x + 0.0 (91 voxels, overlap=0.495) Left_Lateral_Ventricle (4): linear fit = 1.11 x + 0.0 (91 voxels, peak = 45), gca=45.3 gca peak = 0.12264 (30) mri peak = 0.11205 (45) Right_Lateral_Ventricle (43): linear fit = 1.34 x + 0.0 (54 voxels, overlap=0.499) Right_Lateral_Ventricle (43): linear fit = 1.34 x + 0.0 (54 voxels, peak = 40), gca=40.1 gca peak = 0.31788 (90) mri peak = 0.11714 (94) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (350 voxels, overlap=1.006) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (350 voxels, peak = 91), gca=91.3 gca peak = 0.18463 (90) mri peak = 0.12152 (95) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (377 voxels, overlap=1.003) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (377 voxels, peak = 91), gca=91.3 gca peak = 0.28672 (67) mri peak = 0.11316 (68) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (689 voxels, overlap=1.002) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (689 voxels, peak = 67), gca=67.0 gca peak = 0.31612 (63) mri peak = 0.11718 (64) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (726 voxels, overlap=1.007) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (726 voxels, peak = 63), gca=63.0 gca peak = 0.08285 (109) mri peak = 0.11023 (108) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (40844 voxels, overlap=0.693) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (40844 voxels, peak = 109), gca=109.0 gca peak = 0.08551 (108) mri peak = 0.10203 (108) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (40899 voxels, overlap=0.708) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (40899 voxels, peak = 109), gca=108.5 gca peak = 0.07860 (62) mri peak = 0.04268 (65) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (30640 voxels, overlap=0.960) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (30640 voxels, peak = 64), gca=63.5 gca peak = 0.09133 (62) mri peak = 0.04438 (63) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (29460 voxels, overlap=0.939) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (29460 voxels, peak = 64), gca=63.5 gca peak = 0.27803 (79) mri peak = 0.14141 (76) Right_Caudate (50): linear fit = 1.00 x + 0.0 (395 voxels, overlap=1.005) Right_Caudate (50): linear fit = 1.00 x + 0.0 (395 voxels, peak = 79), gca=79.0 gca peak = 0.17652 (74) mri peak = 0.17925 (76) Left_Caudate (11): linear fit = 1.00 x + 0.0 (737 voxels, overlap=0.698) Left_Caudate (11): linear fit = 1.00 x + 0.0 (737 voxels, peak = 74), gca=74.0 gca peak = 0.09845 (66) mri peak = 0.05833 (65) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (27538 voxels, overlap=0.988) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (27538 voxels, peak = 68), gca=67.7 gca peak = 0.12109 (64) mri peak = 0.05423 (65) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (26585 voxels, overlap=0.997) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (26585 voxels, peak = 63), gca=63.0 gca peak = 0.17033 (92) mri peak = 0.10984 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4812 voxels, overlap=0.971) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4812 voxels, peak = 92), gca=91.5 gca peak = 0.16443 (91) mri peak = 0.12860 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4408 voxels, overlap=0.977) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4408 voxels, peak = 91), gca=90.5 gca peak = 0.30259 (69) mri peak = 0.15588 (70) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (338 voxels, overlap=1.018) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (338 voxels, peak = 68), gca=68.0 gca peak = 0.39634 (67) mri peak = 0.19282 (68) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (260 voxels, overlap=1.007) Right_Amygdala (54): linear fit = 1.01 x + 0.0 (260 voxels, peak = 68), gca=68.0 gca peak = 0.10574 (93) mri peak = 0.07084 (92) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2910 voxels, overlap=0.951) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2910 voxels, peak = 93), gca=92.5 gca peak = 0.13160 (85) mri peak = 0.06588 (87) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3202 voxels, overlap=0.989) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3202 voxels, peak = 83), gca=82.9 gca peak = 0.09203 (76) mri peak = 0.09593 (83) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1511 voxels, overlap=0.830) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1511 voxels, peak = 78), gca=77.9 gca peak = 0.09750 (74) mri peak = 0.10051 (82) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1649 voxels, overlap=0.925) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1649 voxels, peak = 73), gca=72.9 gca peak = 0.07439 (87) mri peak = 0.08005 (88) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10447 voxels, overlap=0.795) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10447 voxels, peak = 87), gca=86.6 gca peak = 0.14204 (97) mri peak = 0.06670 (93) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1073 voxels, overlap=0.872) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1073 voxels, peak = 97), gca=97.5 gca peak = 0.16533 (92) mri peak = 0.05951 (99) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1093 voxels, overlap=0.931) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1093 voxels, peak = 92), gca=91.5 gca peak = 0.16934 (47) mri peak = 1.00000 (54) gca peak = 0.24174 (20) mri peak = 0.15317 (21) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (123 voxels, overlap=0.815) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (123 voxels, peak = 20), gca=20.0 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.16934 (47) gca peak CSF = 0.25444 (50) gca peak Left_Accumbens_area = 0.55262 (69) gca peak Left_undetermined = 0.95107 (47) gca peak Left_vessel = 0.65202 (62) gca peak Left_choroid_plexus = 0.12525 (48) gca peak Right_Inf_Lat_Vent = 0.30889 (34) gca peak Right_Accumbens_area = 0.44203 (77) gca peak Right_vessel = 0.83490 (60) gca peak Right_choroid_plexus = 0.13498 (46) gca peak Fifth_Ventricle = 0.45827 (54) gca peak WM_hypointensities = 0.17769 (84) gca peak non_WM_hypointensities = 0.09425 (54) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.15 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 15194 gm and wm labels changed (%25 to gray, %75 to white out of all changed labels) 387 hippocampal voxels changed. 2 amygdala voxels changed. pass 1: 68528 changed. image ll: -2.124, PF=1.000 pass 2: 11494 changed. image ll: -2.122, PF=1.000 pass 3: 3967 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 27 minutes and 59 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/transforms/cc_up.lta ta0313_time2 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/transforms/cc_up.lta reading aseg from /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/aseg.auto_noCCseg.mgz reading norm from /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/norm.mgz 45242 voxels in left wm, 56015 in right wm, xrange [118, 129] searching rotation angles z=[-2 12], y=[-8 6] 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 searching scale 1 Z rot 9.0 searching scale 1 Z rot 9.3 searching scale 1 Z rot 9.5 searching scale 1 Z rot 9.8 searching scale 1 Z rot 10.0 searching scale 1 Z rot 10.3 searching scale 1 Z rot 10.5 searching scale 1 Z rot 10.8 searching scale 1 Z rot 11.0 searching scale 1 Z rot 11.3 searching scale 1 Z rot 11.5 searching scale 1 Z rot 11.8 global minimum found at slice 123.5, rotations (-1.04, 5.03) final transformation (x=123.5, yr=-1.035, zr=5.029): 0.996 -0.088 -0.018 14.323; 0.088 0.996 -0.002 34.675; 0.018 0.000 1.000 10.787; 0.000 0.000 0.000 1.000; updating x range to be [126, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 150 107 eigenvectors: -0.002 0.010 1.000; -0.011 -1.000 0.010; 1.000 -0.010 0.002; error in mid anterior detected - correcting... writing aseg with callosum to /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/aseg.auto.mgz... corpus callosum matter segmentation took 1.5 minutes #-------------------------------------- #@# Merge ASeg Sun Dec 15 14:14:04 EST 2013 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Sun Dec 15 14:14:04 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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... 2906 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 110 gm peak at 69 (69), valley at 30 (30) csf peak at 34, setting threshold to 57 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 70 (70), valley at 31 (31) csf peak at 35, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 5 minutes and 45 seconds. #-------------------------------------------- #@# Mask BFS Sun Dec 15 14:19:52 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1442840 voxels in mask (pct= 8.60) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sun Dec 15 14:19:56 EST 2013 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 (103.0): 103.2 +- 6.5 [80.0 --> 125.0] GM (74.0) : 72.4 +- 8.8 [30.0 --> 96.0] setting bottom of white matter range to 81.2 setting top of gray matter range to 90.0 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 2974 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3826 filled 1070 bright non-wm voxels segmented. 1621 diagonally connected voxels added... white matter segmentation took 2.7 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 1.05 minutes reading wm segmentation from wm.seg.mgz... 378 voxels added to wm to prevent paths from MTL structures to cortex 1140 additional wm voxels added 0 additional wm voxels added SEG EDIT: 29433 voxels turned on, 39196 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 85 new 85 115,126,128 old 85 new 85 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 19 found - 19 modified | TOTAL: 19 pass 2 (xy+): 0 found - 19 modified | TOTAL: 19 pass 1 (xy-): 23 found - 23 modified | TOTAL: 42 pass 2 (xy-): 0 found - 23 modified | TOTAL: 42 pass 1 (yz+): 43 found - 43 modified | TOTAL: 85 pass 2 (yz+): 0 found - 43 modified | TOTAL: 85 pass 1 (yz-): 24 found - 24 modified | TOTAL: 109 pass 2 (yz-): 0 found - 24 modified | TOTAL: 109 pass 1 (xz+): 20 found - 20 modified | TOTAL: 129 pass 2 (xz+): 0 found - 20 modified | TOTAL: 129 pass 1 (xz-): 20 found - 20 modified | TOTAL: 149 pass 2 (xz-): 0 found - 20 modified | TOTAL: 149 Iteration Number : 1 pass 1 (+++): 17 found - 17 modified | TOTAL: 17 pass 2 (+++): 0 found - 17 modified | TOTAL: 17 pass 1 (+++): 24 found - 24 modified | TOTAL: 41 pass 2 (+++): 0 found - 24 modified | TOTAL: 41 pass 1 (+++): 11 found - 11 modified | TOTAL: 52 pass 2 (+++): 0 found - 11 modified | TOTAL: 52 pass 1 (+++): 17 found - 17 modified | TOTAL: 69 pass 2 (+++): 0 found - 17 modified | TOTAL: 69 Iteration Number : 1 pass 1 (++): 58 found - 58 modified | TOTAL: 58 pass 2 (++): 0 found - 58 modified | TOTAL: 58 pass 1 (+-): 61 found - 61 modified | TOTAL: 119 pass 2 (+-): 0 found - 61 modified | TOTAL: 119 pass 1 (--): 61 found - 61 modified | TOTAL: 180 pass 2 (--): 0 found - 61 modified | TOTAL: 180 pass 1 (-+): 44 found - 44 modified | TOTAL: 224 pass 2 (-+): 0 found - 44 modified | TOTAL: 224 Iteration Number : 2 pass 1 (xy+): 6 found - 6 modified | TOTAL: 6 pass 2 (xy+): 0 found - 6 modified | TOTAL: 6 pass 1 (xy-): 2 found - 2 modified | TOTAL: 8 pass 2 (xy-): 0 found - 2 modified | TOTAL: 8 pass 1 (yz+): 6 found - 6 modified | TOTAL: 14 pass 2 (yz+): 0 found - 6 modified | TOTAL: 14 pass 1 (yz-): 6 found - 6 modified | TOTAL: 20 pass 2 (yz-): 0 found - 6 modified | TOTAL: 20 pass 1 (xz+): 3 found - 3 modified | TOTAL: 23 pass 2 (xz+): 0 found - 3 modified | TOTAL: 23 pass 1 (xz-): 3 found - 3 modified | TOTAL: 26 pass 2 (xz-): 0 found - 3 modified | TOTAL: 26 Iteration Number : 2 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 6 Iteration Number : 2 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 1 found - 1 modified | TOTAL: 4 pass 2 (+-): 0 found - 1 modified | TOTAL: 4 pass 1 (--): 2 found - 2 modified | TOTAL: 6 pass 2 (--): 0 found - 2 modified | TOTAL: 6 pass 1 (-+): 4 found - 4 modified | TOTAL: 10 pass 2 (-+): 0 found - 4 modified | TOTAL: 10 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 2 found - 2 modified | TOTAL: 3 pass 2 (xz+): 0 found - 2 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 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 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 2 found - 2 modified | TOTAL: 3 pass 2 (--): 0 found - 2 modified | TOTAL: 3 pass 1 (-+): 0 found - 0 modified | TOTAL: 3 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 2 found - 2 modified | TOTAL: 2 pass 2 (yz+): 0 found - 2 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 492 (out of 522024: 0.094249) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sun Dec 15 14:23:53 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 1.085 -0.089 -0.011 -0.587; 0.115 1.177 0.151 -30.323; -0.001 -0.180 1.040 7.548; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.085 -0.089 -0.011 -0.587; 0.115 1.177 0.151 -30.323; -0.001 -0.180 1.040 7.548; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1189 (min = 350, max = 1400), aspect = 0.46 (min = 0.10, max = 0.75) no need to search using seed (124, 109, 91), TAL = (4.0, -37.0, 19.0) talairach voxel to voxel transform 0.914 0.069 -0.000 2.627; -0.087 0.824 -0.120 25.853; -0.014 0.142 0.940 -2.790; 0.000 0.000 0.000 1.000; segmentation indicates cc at (124, 109, 91) --> (4.0, -37.0, 19.0) done. writing output to filled.mgz... filling took 1.4 minutes talairach cc position changed to (4.00, -37.00, 19.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(22.00, -37.00, 19.00) SRC: (107.01, 95.48, 96.81) search lh wm seed point around talairach space (-14.00, -37.00, 19.00), SRC: (139.91, 92.33, 96.30) 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 Sun Dec 15 14:25:16 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 4 found - 4 modified | TOTAL: 7 pass 2 (yz+): 0 found - 4 modified | TOTAL: 7 pass 1 (yz-): 2 found - 2 modified | TOTAL: 9 pass 2 (yz-): 0 found - 2 modified | TOTAL: 9 pass 1 (xz+): 2 found - 2 modified | TOTAL: 11 pass 2 (xz+): 0 found - 2 modified | TOTAL: 11 pass 1 (xz-): 0 found - 0 modified | TOTAL: 11 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 13 (out of 250919: 0.005181) 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: 1511 vertices, 1617 faces slice 50: 6450 vertices, 6670 faces slice 60: 14626 vertices, 14936 faces slice 70: 24549 vertices, 24853 faces slice 80: 34909 vertices, 35276 faces slice 90: 44821 vertices, 45178 faces slice 100: 55473 vertices, 55854 faces slice 110: 66136 vertices, 66508 faces slice 120: 76582 vertices, 76977 faces slice 130: 87161 vertices, 87515 faces slice 140: 96931 vertices, 97239 faces slice 150: 104920 vertices, 105207 faces slice 160: 112367 vertices, 112610 faces slice 170: 118859 vertices, 119114 faces slice 180: 124452 vertices, 124668 faces slice 190: 128672 vertices, 128816 faces slice 200: 129800 vertices, 129826 faces slice 210: 129800 vertices, 129826 faces slice 220: 129800 vertices, 129826 faces slice 230: 129800 vertices, 129826 faces slice 240: 129800 vertices, 129826 faces slice 250: 129800 vertices, 129826 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... 129800 voxel in cpt #1: X=-26 [v=129800,e=389478,f=259652] located at (-22.522011, -18.586718, 35.794853) For the whole surface: X=-26 [v=129800,e=389478,f=259652] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sun Dec 15 14:25:27 EST 2013 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 Sun Dec 15 14:25:32 EST 2013 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts avg radius = 45.7 mm, total surface area = 68844 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.8 minutes Not saving sulc step 000: RMS=0.099 (target=0.015) step 005: RMS=0.074 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.031 (target=0.015) step 035: RMS=0.028 (target=0.015) step 040: RMS=0.026 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Sun Dec 15 14:26:23 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 1.01 +- 0.58 (0.00-->7.37) (max @ vno 45585 --> 46590) face area 0.03 +- 0.03 (-0.19-->0.64) scaling brain by 0.309... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.253, avgs=0 005/300: dt: 0.9000, rms radial error=176.993, avgs=0 010/300: dt: 0.9000, rms radial error=176.435, avgs=0 015/300: dt: 0.9000, rms radial error=175.701, avgs=0 020/300: dt: 0.9000, rms radial error=174.867, avgs=0 025/300: dt: 0.9000, rms radial error=173.974, avgs=0 030/300: dt: 0.9000, rms radial error=173.050, avgs=0 035/300: dt: 0.9000, rms radial error=172.109, avgs=0 040/300: dt: 0.9000, rms radial error=171.161, avgs=0 045/300: dt: 0.9000, rms radial error=170.210, avgs=0 050/300: dt: 0.9000, rms radial error=169.260, avgs=0 055/300: dt: 0.9000, rms radial error=168.312, avgs=0 060/300: dt: 0.9000, rms radial error=167.368, avgs=0 065/300: dt: 0.9000, rms radial error=166.429, avgs=0 070/300: dt: 0.9000, rms radial error=165.493, avgs=0 075/300: dt: 0.9000, rms radial error=164.563, avgs=0 080/300: dt: 0.9000, rms radial error=163.638, avgs=0 085/300: dt: 0.9000, rms radial error=162.717, avgs=0 090/300: dt: 0.9000, rms radial error=161.801, avgs=0 095/300: dt: 0.9000, rms radial error=160.891, avgs=0 100/300: dt: 0.9000, rms radial error=159.985, avgs=0 105/300: dt: 0.9000, rms radial error=159.084, avgs=0 110/300: dt: 0.9000, rms radial error=158.188, avgs=0 115/300: dt: 0.9000, rms radial error=157.297, avgs=0 120/300: dt: 0.9000, rms radial error=156.411, avgs=0 125/300: dt: 0.9000, rms radial error=155.530, avgs=0 130/300: dt: 0.9000, rms radial error=154.654, avgs=0 135/300: dt: 0.9000, rms radial error=153.783, avgs=0 140/300: dt: 0.9000, rms radial error=152.916, avgs=0 145/300: dt: 0.9000, rms radial error=152.055, avgs=0 150/300: dt: 0.9000, rms radial error=151.198, avgs=0 155/300: dt: 0.9000, rms radial error=150.346, avgs=0 160/300: dt: 0.9000, rms radial error=149.499, avgs=0 165/300: dt: 0.9000, rms radial error=148.656, avgs=0 170/300: dt: 0.9000, rms radial error=147.819, avgs=0 175/300: dt: 0.9000, rms radial error=146.986, avgs=0 180/300: dt: 0.9000, rms radial error=146.157, avgs=0 185/300: dt: 0.9000, rms radial error=145.334, avgs=0 190/300: dt: 0.9000, rms radial error=144.515, avgs=0 195/300: dt: 0.9000, rms radial error=143.701, avgs=0 200/300: dt: 0.9000, rms radial error=142.891, avgs=0 205/300: dt: 0.9000, rms radial error=142.086, avgs=0 210/300: dt: 0.9000, rms radial error=141.285, avgs=0 215/300: dt: 0.9000, rms radial error=140.489, avgs=0 220/300: dt: 0.9000, rms radial error=139.697, avgs=0 225/300: dt: 0.9000, rms radial error=138.910, avgs=0 230/300: dt: 0.9000, rms radial error=138.127, avgs=0 235/300: dt: 0.9000, rms radial error=137.348, avgs=0 240/300: dt: 0.9000, rms radial error=136.574, avgs=0 245/300: dt: 0.9000, rms radial error=135.804, avgs=0 250/300: dt: 0.9000, rms radial error=135.039, avgs=0 255/300: dt: 0.9000, rms radial error=134.278, avgs=0 260/300: dt: 0.9000, rms radial error=133.521, avgs=0 265/300: dt: 0.9000, rms radial error=132.768, avgs=0 270/300: dt: 0.9000, rms radial error=132.020, avgs=0 275/300: dt: 0.9000, rms radial error=131.275, avgs=0 280/300: dt: 0.9000, rms radial error=130.535, avgs=0 285/300: dt: 0.9000, rms radial error=129.799, avgs=0 290/300: dt: 0.9000, rms radial error=129.067, avgs=0 295/300: dt: 0.9000, rms radial error=128.340, avgs=0 300/300: dt: 0.9000, rms radial error=127.616, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15194.48 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 2 (K=40.0), pass 1, starting sse = 2529.92 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00006 epoch 3 (K=160.0), pass 1, starting sse = 260.17 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/11 = 0.00838 epoch 4 (K=640.0), pass 1, starting sse = 13.86 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/12 = 0.00672 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.11 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Sun Dec 15 14:32:57 EST 2013 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 ta0313_time2 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=-26 (nv=129800, nf=259652, ne=389478, g=14) 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... 2793 ambiguous faces found in tessellation segmenting defects... 20 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 13 into 11 19 defects to be corrected 0 vertices coincident reading input surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1310 (-4.5655) -vertex loglikelihood: -5.9179 (-2.9589) -normal dot loglikelihood: -3.7001 (-3.7001) -quad curv loglikelihood: -6.3781 (-3.1890) Total Loglikelihood : -25.1271 CORRECTING DEFECT 0 (vertices=293, convex hull=152) After retessellation of defect 0, euler #=-17 (128163,383953,255773) : difference with theory (-16) = 1 CORRECTING DEFECT 1 (vertices=25, convex hull=25) After retessellation of defect 1, euler #=-16 (128167,383972,255789) : difference with theory (-15) = 1 CORRECTING DEFECT 2 (vertices=69, convex hull=89) After retessellation of defect 2, euler #=-15 (128206,384127,255906) : difference with theory (-14) = 1 CORRECTING DEFECT 3 (vertices=33, convex hull=56) After retessellation of defect 3, euler #=-14 (128221,384191,255956) : difference with theory (-13) = 1 CORRECTING DEFECT 4 (vertices=5, convex hull=14) After retessellation of defect 4, euler #=-13 (128223,384199,255963) : difference with theory (-12) = 1 CORRECTING DEFECT 5 (vertices=23, convex hull=26) After retessellation of defect 5, euler #=-12 (128224,384212,255976) : difference with theory (-11) = 1 CORRECTING DEFECT 6 (vertices=73, convex hull=37) After retessellation of defect 6, euler #=-11 (128233,384255,256011) : difference with theory (-10) = 1 CORRECTING DEFECT 7 (vertices=128, convex hull=113) After retessellation of defect 7, euler #=-10 (128296,384493,256187) : difference with theory (-9) = 1 CORRECTING DEFECT 8 (vertices=24, convex hull=58) After retessellation of defect 8, euler #=-9 (128305,384542,256228) : difference with theory (-8) = 1 CORRECTING DEFECT 9 (vertices=39, convex hull=105) After retessellation of defect 9, euler #=-8 (128334,384674,256332) : difference with theory (-7) = 1 CORRECTING DEFECT 10 (vertices=75, convex hull=58) After retessellation of defect 10, euler #=-7 (128355,384761,256399) : difference with theory (-6) = 1 CORRECTING DEFECT 11 (vertices=28, convex hull=74) After retessellation of defect 11, euler #=-5 (128369,384833,256459) : difference with theory (-5) = 0 CORRECTING DEFECT 12 (vertices=31, convex hull=36) After retessellation of defect 12, euler #=-4 (128375,384864,256485) : difference with theory (-4) = 0 CORRECTING DEFECT 13 (vertices=36, convex hull=21) After retessellation of defect 13, euler #=-3 (128375,384870,256492) : difference with theory (-3) = 0 CORRECTING DEFECT 14 (vertices=62, convex hull=75) After retessellation of defect 14, euler #=-2 (128387,384937,256548) : difference with theory (-2) = 0 CORRECTING DEFECT 15 (vertices=641, convex hull=287) After retessellation of defect 15, euler #=-1 (128438,385240,256801) : difference with theory (-1) = 0 CORRECTING DEFECT 16 (vertices=51, convex hull=80) After retessellation of defect 16, euler #=0 (128461,385342,256881) : difference with theory (0) = 0 CORRECTING DEFECT 17 (vertices=6, convex hull=24) After retessellation of defect 17, euler #=1 (128462,385352,256891) : difference with theory (1) = 0 CORRECTING DEFECT 18 (vertices=26, convex hull=71) After retessellation of defect 18, euler #=2 (128478,385428,256952) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.08-->8.65) (max @ vno 19817 --> 20911) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.08-->8.65) (max @ vno 19817 --> 20911) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 65 mutations (37.4%), 109 crossovers (62.6%), 234 vertices were eliminated building final representation... 1322 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=128478, nf=256952, ne=385428, g=0) writing corrected surface to /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 20.4 minutes 0 defective edges removing intersecting faces 000: 176 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 128478 - 385428 + 256952 = 2 --> 0 holes F =2V-4: 256952 = 256956-4 (0) 2E=3F: 770856 = 770856 (0) total defect index = 0 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 37 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Sun Dec 15 14:53:28 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/filled.mgz... reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/brain.finalsurfs.mgz... reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/wm.mgz... 8260 bright wm thresholded. 1317 bright non-wm voxels segmented. reading original surface position from /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.orig... computing class statistics... border white: 240773 voxels (1.44%) border gray 270691 voxels (1.61%) WM (94.0): 95.1 +- 7.7 [70.0 --> 110.0] GM (82.0) : 80.6 +- 10.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 60.2 (was 70) setting MAX_BORDER_WHITE to 110.7 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 49.4 (was 40) setting MAX_GRAY to 95.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 38.7 (was 40) repositioning cortical surface to gray/white boundary reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.03-->3.56) (max @ vno 19817 --> 20911) face area 0.28 +- 0.12 (0.00-->1.90) mean absolute distance = 0.68 +- 0.85 3312 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=103, GM=71 mean inside = 94.1, mean outside = 78.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=82.2, 31 (31) missing vertices, mean dist 0.2 [0.6 (%38.1)->0.7 (%61.9))] %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=mani., nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.08-->3.65) (max @ vno 18753 --> 19817) face area 0.28 +- 0.13 (0.00-->1.93) mean absolute distance = 0.32 +- 0.58 2545 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4152864.5, rms=8.83 001: dt: 0.5000, sse=4782896.0, rms=6.165 (0.000%) 002: dt: 0.5000, sse=5152940.5, rms=4.611 (0.000%) 003: dt: 0.5000, sse=5520445.5, rms=3.758 (0.000%) 004: dt: 0.5000, sse=5719000.5, rms=3.266 (0.000%) 005: dt: 0.5000, sse=5922287.0, rms=3.057 (0.000%) 006: dt: 0.5000, sse=5972713.5, rms=2.924 (0.000%) rms = 2.90, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=6065951.0, rms=2.896 (0.000%) 008: dt: 0.2500, sse=3474569.2, rms=1.923 (0.000%) 009: dt: 0.2500, sse=3187620.2, rms=1.726 (0.000%) rms = 1.68, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=3073403.5, rms=1.680 (0.000%) rms = 1.65, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=3023289.5, rms=1.647 (0.000%) positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=84.5, 40 (11) missing vertices, mean dist -0.2 [0.3 (%70.1)->0.3 (%29.9))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=mani., nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.05-->3.69) (max @ vno 101082 --> 101108) face area 0.35 +- 0.16 (0.00-->2.46) mean absolute distance = 0.26 +- 0.41 2679 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3394575.5, rms=3.71 012: dt: 0.5000, sse=3824111.0, rms=2.272 (0.000%) rms = 2.25, time step reduction 1 of 3 to 0.250... 013: dt: 0.5000, sse=4093785.8, rms=2.248 (0.000%) 014: dt: 0.2500, sse=3498397.0, rms=1.463 (0.000%) 015: dt: 0.2500, sse=3380189.8, rms=1.352 (0.000%) rms = 1.34, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=3308073.0, rms=1.337 (0.000%) rms = 1.32, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=3277538.5, rms=1.316 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=86.1, 39 (9) missing vertices, mean dist -0.1 [0.3 (%66.6)->0.2 (%33.4))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=mani., nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.24 (0.06-->3.77) (max @ vno 101082 --> 101108) face area 0.34 +- 0.15 (0.00-->2.48) mean absolute distance = 0.24 +- 0.32 2993 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3378387.8, rms=2.56 018: dt: 0.5000, sse=3810901.0, rms=1.936 (0.000%) rms = 2.10, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=3591600.2, rms=1.475 (0.000%) 020: dt: 0.2500, sse=3486655.8, rms=1.265 (0.000%) rms = 1.23, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=3448609.2, rms=1.225 (0.000%) rms = 1.21, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=3415278.2, rms=1.211 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=86.7, 38 (8) missing vertices, mean dist -0.0 [0.2 (%55.2)->0.2 (%44.8))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=mani., 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3423065.8, rms=1.45 023: dt: 0.5000, sse=4300397.5, rms=1.318 (0.000%) rms = 1.67, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=3941497.0, rms=1.064 (0.000%) 025: dt: 0.2500, sse=3778061.2, rms=1.013 (0.000%) rms = 0.99, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=3824010.2, rms=0.987 (0.000%) rms = 0.99, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3824010.2, rms=0.987 (0.002%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 19 non-cortical segments detected only using segment with 2015 vertices erasing segment 1 (vno[0] = 55943) erasing segment 2 (vno[0] = 59011) erasing segment 3 (vno[0] = 67543) erasing segment 4 (vno[0] = 72868) erasing segment 5 (vno[0] = 75535) erasing segment 6 (vno[0] = 80615) erasing segment 7 (vno[0] = 80905) erasing segment 8 (vno[0] = 82803) erasing segment 9 (vno[0] = 83913) erasing segment 10 (vno[0] = 84226) erasing segment 11 (vno[0] = 85029) erasing segment 12 (vno[0] = 86243) erasing segment 13 (vno[0] = 90814) erasing segment 14 (vno[0] = 90855) erasing segment 15 (vno[0] = 94650) erasing segment 16 (vno[0] = 96987) erasing segment 17 (vno[0] = 101052) erasing segment 18 (vno[0] = 101059) writing cortex label to /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/label/lh.cortex.label... writing curvature file /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.curv writing smoothed area to lh.area writing curvature file /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.area vertex spacing 0.89 +- 0.24 (0.07-->3.90) (max @ vno 101082 --> 101108) face area 0.34 +- 0.15 (0.00-->2.55) refinement took 7.6 minutes #-------------------------------------------- #@# Smooth2 lh Sun Dec 15 15:01:02 EST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 Sun Dec 15 15:01:08 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 45.8 mm, total surface area = 78496 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.113 (target=0.015) step 005: RMS=0.079 (target=0.015) step 010: RMS=0.057 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.026 (target=0.015) step 035: RMS=0.022 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) inflation complete. inflation took 0.7 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 122 vertices thresholded to be in k1 ~ [-0.23 0.42], k2 ~ [-0.14 0.05] total integrated curvature = 0.498*4pi (6.259) --> 1 handles ICI = 1.6, FI = 9.9, variation=170.736 97 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 128 vertices thresholded to be in [-0.15 0.19] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.024 done. #----------------------------------------- #@# Curvature Stats lh Sun Dec 15 15:04:12 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm ta0313_time2 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 [ ta0313_time2/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 [ 226 ] Gb_filter = 0 WARN: S lookup min: -0.248248 WARN: S explicit min: 0.000000 vertex = 9 #-------------------------------------------- #@# Sphere lh Sun Dec 15 15:04:19 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 0.288... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=mani., 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 %20.11 pass 1: epoch 2 of 3 starting distance error %20.07 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/lh.sphere spherical transformation took 1.13 hours #-------------------------------------------- #@# Surf Reg lh Sun Dec 15 16:12:04 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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=mani., 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=mani., 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 = 0.589 curvature mean = 0.033, std = 0.938 curvature mean = 0.016, std = 0.862 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (8.00, 0.00, 8.00) sse = 262611.2, tmin=3.1700 d=16.00 min @ (-4.00, 0.00, -4.00) sse = 240242.6, tmin=4.7105 d=8.00 min @ (0.00, -2.00, 0.00) sse = 239438.4, tmin=6.3056 d=4.00 min @ (0.00, 1.00, 1.00) sse = 237778.4, tmin=7.9075 d=1.00 min @ (0.00, -0.25, -0.25) sse = 237695.2, tmin=11.1020 d=0.50 min @ (0.00, 0.00, 0.12) sse = 237682.6, tmin=12.6369 tol=1.0e+00, sigma=0.5, host=mani., 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 12.64 min curvature mean = 0.005, std = 0.952 curvature mean = 0.006, std = 0.942 curvature mean = 0.005, std = 0.965 curvature mean = 0.003, std = 0.975 curvature mean = 0.004, std = 0.968 curvature mean = 0.001, std = 0.990 2 Reading smoothwm curvature mean = -0.026, std = 0.270 curvature mean = 0.004, std = 0.067 curvature mean = 0.052, std = 0.386 curvature mean = 0.004, std = 0.080 curvature mean = 0.024, std = 0.590 curvature mean = 0.004, std = 0.086 curvature mean = 0.015, std = 0.728 curvature mean = 0.004, std = 0.089 curvature mean = 0.006, std = 0.828 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Sun Dec 15 16:52:41 EST 2013 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 Sun Dec 15 16:52:44 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 Sun Dec 15 16:52:47 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 ta0313_time2 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... 956 labels changed using aseg relabeling using gibbs priors... 000: 2875 changed, 128478 examined... 001: 660 changed, 12334 examined... 002: 177 changed, 3744 examined... 003: 66 changed, 1043 examined... 004: 29 changed, 374 examined... 005: 7 changed, 178 examined... 006: 5 changed, 39 examined... 007: 1 changed, 25 examined... 008: 0 changed, 4 examined... 223 labels changed using aseg 000: 101 total segments, 54 labels (161 vertices) changed 001: 48 total segments, 1 labels (1 vertices) changed 002: 47 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 38 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1414 vertices marked for relabeling... 1414 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 1 minutes and 22 seconds. #-------------------------------------------- #@# Make Pial Surf lh Sun Dec 15 16:54:09 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/filled.mgz... reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/brain.finalsurfs.mgz... reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/wm.mgz... 8260 bright wm thresholded. 1317 bright non-wm voxels segmented. reading original surface position from /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.orig... computing class statistics... border white: 240773 voxels (1.44%) border gray 270691 voxels (1.61%) WM (94.0): 95.1 +- 7.7 [70.0 --> 110.0] GM (82.0) : 80.6 +- 10.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 60.2 (was 70) setting MAX_BORDER_WHITE to 110.7 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 49.4 (was 40) setting MAX_GRAY to 95.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 38.7 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103, GM=71 mean inside = 94.1, mean outside = 78.3 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.03-->3.56) (max @ vno 19817 --> 20911) face area 0.28 +- 0.12 (0.00-->1.90) mean absolute distance = 0.68 +- 0.86 3389 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 6 points - only 0.00% unknown deleting segment 3 with 404 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 7 with 20 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown mean border=82.2, 31 (31) missing vertices, mean dist 0.2 [0.6 (%38.1)->0.7 (%61.9))] %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=mani., nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.08-->3.65) (max @ vno 18753 --> 19817) face area 0.28 +- 0.13 (0.00-->1.93) mean absolute distance = 0.32 +- 0.58 2603 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4163049.0, rms=8.82 001: dt: 0.5000, sse=4802913.0, rms=6.161 (0.000%) 002: dt: 0.5000, sse=5172692.5, rms=4.609 (0.000%) 003: dt: 0.5000, sse=5541572.5, rms=3.758 (0.000%) 004: dt: 0.5000, sse=5741242.0, rms=3.266 (0.000%) 005: dt: 0.5000, sse=5945714.5, rms=3.057 (0.000%) 006: dt: 0.5000, sse=5996699.0, rms=2.924 (0.000%) rms = 2.90, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=6092061.0, rms=2.895 (0.000%) 008: dt: 0.2500, sse=3491652.8, rms=1.925 (0.000%) 009: dt: 0.2500, sse=3203291.2, rms=1.729 (0.000%) rms = 1.68, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=3087891.2, rms=1.683 (0.000%) rms = 1.65, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=3037699.0, rms=1.650 (0.000%) positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 4 with 403 points - only 0.00% unknown deleting segment 6 with 55 points - only 32.73% unknown deleting segment 7 with 14 points - only 0.00% unknown deleting segment 8 with 16 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 11 with 4 points - only 0.00% unknown mean border=84.5, 47 (11) missing vertices, mean dist -0.2 [0.4 (%70.1)->0.3 (%29.9))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=mani., nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.05-->3.78) (max @ vno 87982 --> 87036) face area 0.35 +- 0.15 (0.00-->2.46) mean absolute distance = 0.26 +- 0.41 2756 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3414566.2, rms=3.71 012: dt: 0.5000, sse=3844047.8, rms=2.275 (0.000%) rms = 2.25, time step reduction 1 of 3 to 0.250... 013: dt: 0.5000, sse=4117045.8, rms=2.248 (0.000%) 014: dt: 0.2500, sse=3516604.0, rms=1.465 (0.000%) 015: dt: 0.2500, sse=3398615.5, rms=1.354 (0.000%) rms = 1.34, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=3324492.2, rms=1.338 (0.000%) rms = 1.32, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=3292729.2, rms=1.317 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 2 with 404 points - only 0.00% unknown deleting segment 3 with 80 points - only 52.50% unknown deleting segment 4 with 19 points - only 0.00% unknown deleting segment 5 with 14 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown mean border=86.1, 52 (9) missing vertices, mean dist -0.1 [0.3 (%66.6)->0.2 (%33.4))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=mani., nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.24 (0.06-->4.05) (max @ vno 87982 --> 87036) face area 0.34 +- 0.15 (0.00-->2.48) mean absolute distance = 0.24 +- 0.33 3048 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3398217.2, rms=2.56 018: dt: 0.5000, sse=3835051.8, rms=1.938 (0.000%) rms = 2.10, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=3614290.8, rms=1.479 (0.000%) 020: dt: 0.2500, sse=3510880.2, rms=1.269 (0.000%) rms = 1.23, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=3472937.5, rms=1.229 (0.000%) rms = 1.21, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=3439398.5, rms=1.214 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown deleting segment 1 with 408 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 80 points - only 52.50% unknown deleting segment 4 with 62 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown mean border=86.7, 51 (8) missing vertices, mean dist -0.0 [0.2 (%55.3)->0.2 (%44.7))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=mani., 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=3447624.0, rms=1.45 023: dt: 0.5000, sse=4336260.0, rms=1.320 (0.000%) rms = 1.67, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=3975386.8, rms=1.067 (0.000%) 025: dt: 0.2500, sse=3811517.2, rms=1.017 (0.000%) rms = 0.99, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=3857869.5, rms=0.991 (0.000%) rms = 0.99, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3857869.5, rms=0.991 (0.002%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=61.3, 51 (51) missing vertices, mean dist 1.5 [1.8 (%0.0)->2.7 (%100.0))] %15 local maxima, %37 large gradients and %44 min vals, 2963 gradients ignored tol=1.0e-04, sigma=2.0, host=mani., 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=18810502.0, rms=25.83 001: dt: 0.5000, sse=14455153.0, rms=22.158 (0.000%) 002: dt: 0.5000, sse=11191371.0, rms=18.978 (0.000%) 003: dt: 0.5000, sse=8815640.0, rms=16.272 (0.000%) 004: dt: 0.5000, sse=7214248.0, rms=13.975 (0.000%) 005: dt: 0.5000, sse=6176947.5, rms=12.062 (0.000%) 006: dt: 0.5000, sse=5543144.5, rms=10.521 (0.000%) 007: dt: 0.5000, sse=5209191.0, rms=9.252 (0.000%) 008: dt: 0.5000, sse=5037600.5, rms=8.186 (0.000%) 009: dt: 0.5000, sse=4981718.5, rms=7.298 (0.000%) 010: dt: 0.5000, sse=4977721.0, rms=6.519 (0.000%) 011: dt: 0.5000, sse=5058258.0, rms=5.832 (0.000%) 012: dt: 0.5000, sse=5111020.5, rms=5.199 (0.000%) 013: dt: 0.5000, sse=5237579.5, rms=4.654 (0.000%) 014: dt: 0.5000, sse=5305713.5, rms=4.254 (0.000%) 015: dt: 0.5000, sse=5407209.0, rms=3.956 (0.000%) 016: dt: 0.5000, sse=5492454.0, rms=3.781 (0.000%) 017: dt: 0.5000, sse=5560510.5, rms=3.648 (0.000%) 018: dt: 0.5000, sse=5595311.5, rms=3.571 (0.000%) 019: dt: 0.5000, sse=5627509.0, rms=3.496 (0.000%) rms = 3.46, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=5636697.0, rms=3.456 (0.000%) 021: dt: 0.2500, sse=4286202.5, rms=3.073 (0.000%) 022: dt: 0.2500, sse=4215764.5, rms=2.955 (0.000%) rms = 2.95, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4159747.2, rms=2.951 (0.000%) 024: dt: 0.1250, sse=3991307.2, rms=2.847 (0.000%) rms = 2.82, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3972653.8, rms=2.821 (0.000%) positioning took 4.2 minutes mean border=59.7, 1535 (10) missing vertices, mean dist 0.2 [0.3 (%48.3)->0.8 (%51.7))] %28 local maxima, %30 large gradients and %36 min vals, 1355 gradients ignored tol=1.0e-04, sigma=1.0, host=mani., 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=4478903.5, rms=4.49 026: dt: 0.5000, sse=4658506.5, rms=3.845 (0.000%) 027: dt: 0.5000, sse=5614179.0, rms=3.505 (0.000%) rms = 3.54, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4872086.0, rms=3.099 (0.000%) 029: dt: 0.2500, sse=4555391.0, rms=2.972 (0.000%) rms = 2.95, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4558335.0, rms=2.948 (0.000%) 031: dt: 0.1250, sse=4398037.0, rms=2.798 (0.000%) rms = 2.75, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=4403941.5, rms=2.750 (0.000%) positioning took 1.4 minutes mean border=58.8, 1870 (7) missing vertices, mean dist 0.1 [0.3 (%45.4)->0.5 (%54.6))] %36 local maxima, %22 large gradients and %36 min vals, 1502 gradients ignored tol=1.0e-04, sigma=0.5, host=mani., 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=4499316.0, rms=3.26 rms = 3.40, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=4387561.5, rms=3.035 (0.000%) 034: dt: 0.2500, sse=4452381.0, rms=2.886 (0.000%) rms = 2.91, time step reduction 2 of 3 to 0.125... rms = 2.84, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=4414840.5, rms=2.844 (0.000%) positioning took 0.8 minutes mean border=58.3, 4180 (6) missing vertices, mean dist 0.1 [0.3 (%46.1)->0.5 (%53.9))] %41 local maxima, %17 large gradients and %35 min vals, 1547 gradients ignored tol=1.0e-04, sigma=0.2, host=mani., 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4441387.0, rms=3.02 rms = 3.25, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=4387061.5, rms=2.847 (0.000%) 037: dt: 0.2500, sse=4628851.5, rms=2.749 (0.000%) rms = 2.77, time step reduction 2 of 3 to 0.125... rms = 2.71, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=4589214.0, rms=2.705 (0.000%) positioning took 0.8 minutes writing curvature file /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.area.pial vertex spacing 1.01 +- 0.43 (0.01-->7.51) (max @ vno 86049 --> 86029) face area 0.40 +- 0.31 (0.00-->8.88) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 128478 vertices processed 25000 of 128478 vertices processed 50000 of 128478 vertices processed 75000 of 128478 vertices processed 100000 of 128478 vertices processed 125000 of 128478 vertices processed 0 of 128478 vertices processed 25000 of 128478 vertices processed 50000 of 128478 vertices processed 75000 of 128478 vertices processed 100000 of 128478 vertices processed 125000 of 128478 vertices processed thickness calculation complete, 704:1046 truncations. 26362 vertices at 0 distance 80740 vertices at 1 distance 79937 vertices at 2 distance 37950 vertices at 3 distance 13351 vertices at 4 distance 4555 vertices at 5 distance 1473 vertices at 6 distance 514 vertices at 7 distance 169 vertices at 8 distance 99 vertices at 9 distance 75 vertices at 10 distance 70 vertices at 11 distance 39 vertices at 12 distance 37 vertices at 13 distance 38 vertices at 14 distance 25 vertices at 15 distance 13 vertices at 16 distance 6 vertices at 17 distance 9 vertices at 18 distance 10 vertices at 19 distance 6 vertices at 20 distance writing curvature file /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.thickness positioning took 16.6 minutes #-------------------------------------------- #@# Surf Volume lh Sun Dec 15 17:10:47 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 Sun Dec 15 17:10:48 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts pctsurfcon --s ta0313_time2 --lh-only Log file is /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts/pctsurfcon.log Sun Dec 15 17:10:48 EST 2013 setenv SUBJECTS_DIR /mani2/fei_data/Jacobian_maps/SUBJECT_DIR cd /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux mani.med.yale.internal 2.6.32-220.17.1.el6.x86_64 #1 SMP Thu Apr 26 13:37:13 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/tmp.pctsurfcon.31494/lh.wm.mgh --regheader ta0313_time2 --cortex srcvol = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/orig.mgz as target reference. Loading label /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/label/lh.cortex.label Reading surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 = 71684 Masking with /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/label/lh.cortex.label Writing to /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/tmp.pctsurfcon.31494/lh.wm.mgh Dim: 128478 1 1 mri_vol2surf --mov /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/tmp.pctsurfcon.31494/lh.gm.mgh --projfrac 0.3 --regheader ta0313_time2 --cortex srcvol = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/orig.mgz as target reference. Loading label /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/label/lh.cortex.label Reading surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Done reading source surface Reading thickness /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 = 85651 Masking with /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/label/lh.cortex.label Writing to /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/tmp.pctsurfcon.31494/lh.gm.mgh Dim: 128478 1 1 mri_concat /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/tmp.pctsurfcon.31494/lh.wm.mgh /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/tmp.pctsurfcon.31494/lh.gm.mgh --paired-diff-norm --mul 100 --o /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.w-g.pct.mgh mri_segstats --in /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.w-g.pct.mgh --annot ta0313_time2 lh aparc --sum /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.w-g.pct.mgh --annot ta0313_time2 lh aparc --sum /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/stats/lh.w-g.pct.stats --snr sysname Linux hostname mani.med.yale.internal machine x86_64 user hblab 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.w-g.pct.mgh Vertex Area is 0.66566 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1170 782.164 2 1002 caudalanteriorcingulate 771 496.763 3 1003 caudalmiddlefrontal 3348 2194.169 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2407 1637.677 6 1006 entorhinal 503 343.106 7 1007 fusiform 4201 2794.873 8 1008 inferiorparietal 6588 4430.861 9 1009 inferiortemporal 4887 3269.322 10 1010 isthmuscingulate 1327 878.534 11 1011 lateraloccipital 8511 5581.320 12 1012 lateralorbitofrontal 3771 2534.036 13 1013 lingual 4668 3167.560 14 1014 medialorbitofrontal 2788 1877.034 15 1015 middletemporal 4442 3053.094 16 1016 parahippocampal 1218 767.263 17 1017 paracentral 1764 1158.508 18 1018 parsopercularis 2482 1710.331 19 1019 parsorbitalis 826 543.273 20 1020 parstriangularis 2147 1510.244 21 1021 pericalcarine 2255 1607.131 22 1022 postcentral 5405 3551.804 23 1023 posteriorcingulate 1210 841.011 24 1024 precentral 6993 4675.429 25 1025 precuneus 4922 3290.057 26 1026 rostralanteriorcingulate 1064 691.076 27 1027 rostralmiddlefrontal 6818 4619.646 28 1028 superiorfrontal 10709 7165.557 29 1029 superiorparietal 7979 5235.175 30 1030 superiortemporal 4968 3293.972 31 1031 supramarginal 5281 3571.893 32 1032 frontalpole 324 221.249 33 1033 temporalpole 821 551.661 34 1034 transversetemporal 686 446.922 35 1035 insula 3165 2057.106 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Sun Dec 15 17:11:03 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 ta0313_time2 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/wm.mgz... reading input surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white... reading input pial surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.pial... reading input white surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 1170 782 1800 2.302 0.513 0.112 0.028 10 1.2 bankssts 771 497 1648 3.290 0.648 0.122 0.029 7 0.9 caudalanteriorcingulate 3348 2194 6675 2.768 0.593 0.125 0.049 76 7.0 caudalmiddlefrontal 2407 1638 3255 1.924 0.477 0.166 0.065 37 5.9 cuneus 503 343 1444 3.376 0.650 0.142 0.052 7 1.1 entorhinal 4201 2795 8838 2.665 0.763 0.143 0.072 87 9.3 fusiform 6588 4431 11766 2.412 0.550 0.130 0.046 71 11.9 inferiorparietal 4887 3269 10420 2.595 0.883 0.157 0.068 109 13.5 inferiortemporal 1327 879 2759 2.977 0.804 0.140 0.053 21 2.5 isthmuscingulate 8511 5581 14166 2.305 0.653 0.153 0.053 124 18.1 lateraloccipital 3771 2534 8179 2.953 0.845 0.135 0.049 49 7.5 lateralorbitofrontal 4668 3168 7184 2.015 0.690 0.150 0.057 68 10.8 lingual 2788 1877 5299 2.458 0.751 0.140 0.073 115 8.8 medialorbitofrontal 4442 3053 9445 2.607 0.858 0.140 0.048 66 8.5 middletemporal 1218 767 2040 2.258 0.821 0.102 0.032 8 1.4 parahippocampal 1764 1159 2989 2.361 0.573 0.120 0.036 17 2.6 paracentral 2482 1710 5062 2.581 0.593 0.121 0.036 24 3.4 parsopercularis 826 543 2289 3.444 0.777 0.153 0.053 15 1.7 parsorbitalis 2147 1510 4589 2.600 0.637 0.132 0.044 28 3.3 parstriangularis 2255 1607 2319 1.667 0.489 0.147 0.053 34 4.8 pericalcarine 5405 3552 7500 1.956 0.645 0.132 0.047 71 10.3 postcentral 1210 841 2437 2.709 0.620 0.127 0.042 15 2.0 posteriorcingulate 6993 4675 12531 2.472 0.642 0.128 0.046 98 14.5 precentral 4922 3290 10013 2.718 0.690 0.139 0.049 62 9.5 precuneus 1064 691 2711 3.287 0.617 0.163 0.079 28 3.2 rostralanteriorcingulate 6818 4620 13699 2.530 0.634 0.150 0.056 115 15.4 rostralmiddlefrontal 10709 7166 24891 3.056 0.666 0.137 0.055 166 21.5 superiorfrontal 7979 5235 12504 2.232 0.532 0.132 0.043 88 14.1 superiorparietal 4968 3294 9767 2.638 0.780 0.130 0.044 64 8.8 superiortemporal 5281 3572 9756 2.373 0.621 0.144 0.048 76 10.2 supramarginal 324 221 1058 3.404 0.578 0.215 0.101 11 1.3 frontalpole 821 552 2498 3.449 0.630 0.143 0.056 11 1.8 temporalpole 686 447 1136 2.538 0.437 0.146 0.038 8 1.1 transversetemporal 3165 2057 5954 2.918 0.798 0.130 0.055 42 6.7 insula #----------------------------------------- #@# Cortical Parc 2 lh Sun Dec 15 17:11:25 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 ta0313_time2 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... 128 labels changed using aseg relabeling using gibbs priors... 000: 9053 changed, 128478 examined... 001: 2274 changed, 34442 examined... 002: 689 changed, 11397 examined... 003: 309 changed, 3867 examined... 004: 144 changed, 1725 examined... 005: 83 changed, 747 examined... 006: 39 changed, 432 examined... 007: 21 changed, 226 examined... 008: 17 changed, 126 examined... 009: 12 changed, 94 examined... 010: 3 changed, 58 examined... 011: 1 changed, 19 examined... 012: 1 changed, 7 examined... 013: 2 changed, 7 examined... 014: 1 changed, 12 examined... 015: 1 changed, 5 examined... 016: 4 changed, 11 examined... 017: 1 changed, 16 examined... 018: 2 changed, 7 examined... 019: 0 changed, 7 examined... 52 labels changed using aseg 000: 255 total segments, 174 labels (2001 vertices) changed 001: 88 total segments, 9 labels (26 vertices) changed 002: 79 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 109 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 700 vertices marked for relabeling... 700 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 30 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Sun Dec 15 17:12:55 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 ta0313_time2 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/wm.mgz... reading input surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white... reading input pial surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.pial... reading input white surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 1024 694 1951 2.450 0.647 0.153 0.046 16 1.9 G_and_S_frontomargin 1851 1244 4052 2.728 0.734 0.162 0.052 28 3.9 G_and_S_occipital_inf 1448 932 2508 2.250 0.581 0.135 0.045 17 2.7 G_and_S_paracentral 1206 840 2691 2.701 0.668 0.148 0.049 19 2.4 G_and_S_subcentral 714 467 1841 2.952 0.626 0.218 0.114 27 3.6 G_and_S_transv_frontopol 2177 1473 4744 3.078 0.623 0.137 0.047 32 4.2 G_and_S_cingul-Ant 1760 1165 3516 3.073 0.654 0.123 0.032 17 2.3 G_and_S_cingul-Mid-Ant 1132 805 2119 2.601 0.552 0.116 0.038 11 1.8 G_and_S_cingul-Mid-Post 485 330 1388 3.294 0.533 0.157 0.047 9 0.8 G_cingul-Post-dorsal 308 192 585 2.941 1.153 0.140 0.065 5 0.6 G_cingul-Post-ventral 2247 1535 3073 1.873 0.539 0.169 0.067 37 5.8 G_cuneus 1409 966 3660 2.803 0.589 0.139 0.047 19 2.6 G_front_inf-Opercular 268 179 837 3.135 0.459 0.164 0.089 6 0.7 G_front_inf-Orbital 1366 962 3345 2.725 0.604 0.148 0.049 23 2.5 G_front_inf-Triangul 3762 2480 9092 2.809 0.644 0.152 0.071 107 10.7 G_front_middle 6682 4412 17684 3.179 0.695 0.148 0.069 134 16.1 G_front_sup 513 293 892 2.776 0.807 0.135 0.076 10 1.4 G_Ins_lg_and_S_cent_ins 662 419 1957 3.563 0.722 0.160 0.075 14 2.0 G_insular_short 2189 1458 4538 2.531 0.611 0.157 0.058 37 5.2 G_occipital_middle 1720 1114 3111 2.277 0.674 0.147 0.053 23 3.4 G_occipital_sup 1530 989 3763 2.708 0.600 0.151 0.057 28 3.7 G_oc-temp_lat-fusifor 2952 2019 5160 2.070 0.774 0.169 0.073 54 8.7 G_oc-temp_med-Lingual 1200 764 2712 2.750 0.956 0.127 0.050 16 2.4 G_oc-temp_med-Parahip 2252 1485 6147 3.233 0.864 0.148 0.065 40 6.0 G_orbital 2384 1597 4439 2.330 0.560 0.151 0.066 38 5.9 G_pariet_inf-Angular 2985 2029 6310 2.496 0.655 0.162 0.061 56 7.5 G_pariet_inf-Supramar 3139 2029 5414 2.246 0.530 0.144 0.053 47 7.0 G_parietal_sup 2105 1310 2904 1.864 0.467 0.141 0.059 35 5.4 G_postcentral 2528 1673 4969 2.476 0.709 0.138 0.063 59 7.5 G_precentral 2428 1583 6278 2.923 0.751 0.159 0.064 42 6.3 G_precuneus 1112 747 2606 2.403 0.809 0.193 0.149 103 7.5 G_rectus 462 304 834 2.927 0.680 0.119 0.058 7 0.8 G_subcallosal 509 319 911 2.524 0.334 0.124 0.034 5 0.7 G_temp_sup-G_T_transv 1623 1109 4416 2.924 0.774 0.159 0.063 30 3.7 G_temp_sup-Lateral 691 464 1649 3.245 0.795 0.136 0.061 9 1.8 G_temp_sup-Plan_polar 791 539 1225 1.946 0.530 0.095 0.019 5 0.7 G_temp_sup-Plan_tempo 2952 1965 7430 2.809 0.904 0.174 0.084 84 9.8 G_temporal_inf 2766 1912 6603 2.551 0.876 0.154 0.060 56 6.7 G_temporal_middle 425 289 591 2.162 0.587 0.099 0.019 2 0.3 Lat_Fis-ant-Horizont 288 216 450 2.203 0.411 0.094 0.014 1 0.2 Lat_Fis-ant-Vertical 1123 738 1433 2.324 0.503 0.126 0.039 10 1.8 Lat_Fis-post 2660 1715 3860 2.009 0.588 0.165 0.066 44 6.9 Pole_occipital 2028 1364 6241 3.515 0.647 0.164 0.077 37 6.4 Pole_temporal 2667 1875 2996 1.888 0.655 0.135 0.045 35 4.9 S_calcarine 2798 1924 3105 1.816 0.500 0.122 0.035 20 4.0 S_central 878 589 1274 2.272 0.408 0.098 0.021 5 0.7 S_cingul-Marginalis 510 347 901 2.667 0.730 0.103 0.024 3 0.5 S_circular_insula_ant 1342 890 1931 2.857 0.689 0.100 0.023 7 1.3 S_circular_insula_inf 1811 1226 2734 2.603 0.611 0.111 0.028 12 2.0 S_circular_insula_sup 603 413 964 2.305 0.716 0.111 0.029 4 0.7 S_collat_transv_ant 473 330 621 2.033 0.416 0.147 0.047 6 0.9 S_collat_transv_post 2652 1783 4341 2.378 0.552 0.124 0.038 27 4.1 S_front_inf 1035 704 1600 2.193 0.548 0.111 0.025 7 1.0 S_front_middle 2509 1741 4582 2.793 0.480 0.116 0.031 21 3.2 S_front_sup 187 127 321 2.309 0.485 0.105 0.023 1 0.2 S_interm_prim-Jensen 3088 2050 4463 2.295 0.452 0.104 0.027 18 3.4 S_intrapariet_and_P_trans 1508 1023 1906 2.110 0.428 0.139 0.042 16 2.5 S_oc_middle_and_Lunatus 950 635 1320 2.331 0.513 0.119 0.030 6 1.2 S_oc_sup_and_transversal 1105 737 1695 2.577 0.401 0.121 0.036 12 1.5 S_occipital_ant 621 417 805 2.435 0.715 0.116 0.030 4 0.8 S_oc-temp_lat 2512 1674 3214 2.058 0.570 0.111 0.056 43 2.7 S_oc-temp_med_and_Lingual 415 295 839 2.346 0.744 0.153 0.051 6 0.8 S_orbital_lateral 733 523 1189 2.392 0.757 0.119 0.025 6 0.7 S_orbital_med-olfact 1431 950 2805 3.082 0.779 0.131 0.042 16 2.4 S_orbital-H_Shaped 1790 1216 2488 2.270 0.515 0.121 0.041 14 2.6 S_parieto_occipital 783 475 1121 2.780 0.748 0.135 0.050 14 1.4 S_pericallosal 2820 1870 3570 2.044 0.484 0.130 0.044 32 4.7 S_postcentral 1569 1084 2628 2.569 0.458 0.110 0.027 12 1.8 S_precentral-inf-part 1449 973 2515 2.804 0.501 0.119 0.031 11 2.0 S_precentral-sup-part 482 317 765 2.467 0.809 0.114 0.025 4 0.6 S_suborbital 993 668 1667 2.825 0.573 0.131 0.037 10 1.4 S_subparietal 1461 969 1817 2.172 0.624 0.118 0.032 12 1.8 S_temporal_inf 5063 3379 8066 2.361 0.577 0.114 0.030 39 6.4 S_temporal_sup 325 223 451 2.270 0.577 0.175 0.042 6 0.6 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Sun Dec 15 17:13:19 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 ta0313_time2 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... 1353 labels changed using aseg relabeling using gibbs priors... 000: 2738 changed, 128478 examined... 001: 679 changed, 11516 examined... 002: 183 changed, 3752 examined... 003: 76 changed, 1059 examined... 004: 30 changed, 443 examined... 005: 17 changed, 197 examined... 006: 10 changed, 107 examined... 007: 6 changed, 67 examined... 008: 5 changed, 31 examined... 009: 2 changed, 29 examined... 010: 2 changed, 10 examined... 011: 0 changed, 8 examined... 206 labels changed using aseg 000: 77 total segments, 44 labels (213 vertices) changed 001: 34 total segments, 1 labels (2 vertices) changed 002: 33 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... 409 vertices marked for relabeling... 409 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 1 minutes and 23 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Sun Dec 15 17:14:42 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 ta0313_time2 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/wm.mgz... reading input surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white... reading input pial surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.pial... reading input white surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 1523 973 3466 3.309 0.626 0.132 0.042 18 2.5 caudalanteriorcingulate 3466 2277 6955 2.770 0.592 0.127 0.050 78 7.3 caudalmiddlefrontal 3176 2167 4434 2.008 0.493 0.155 0.058 43 7.0 cuneus 489 334 1384 3.374 0.653 0.144 0.052 7 1.1 entorhinal 3719 2478 7213 2.532 0.696 0.137 0.064 73 6.7 fusiform 6252 4208 11041 2.410 0.550 0.132 0.048 69 11.6 inferiorparietal 4981 3325 11332 2.725 0.904 0.158 0.072 108 14.4 inferiortemporal 1312 867 2725 2.971 0.807 0.141 0.053 21 2.5 isthmuscingulate 8716 5722 14570 2.295 0.656 0.152 0.053 126 18.5 lateraloccipital 3982 2670 8659 2.946 0.842 0.143 0.053 60 8.7 lateralorbitofrontal 4696 3189 7232 2.018 0.691 0.150 0.057 69 10.9 lingual 2364 1611 4885 2.449 0.787 0.148 0.084 112 8.7 medialorbitofrontal 5955 4064 12088 2.557 0.809 0.138 0.047 90 11.4 middletemporal 1219 768 2032 2.250 0.817 0.100 0.031 8 1.3 parahippocampal 2095 1382 3662 2.441 0.586 0.122 0.036 20 3.1 paracentral 2296 1578 4725 2.583 0.600 0.124 0.037 23 3.3 parsopercularis 1037 703 2516 2.927 0.815 0.128 0.044 12 1.7 parsorbitalis 2690 1870 5880 2.640 0.606 0.138 0.047 38 4.8 parstriangularis 2267 1613 2332 1.670 0.494 0.147 0.053 34 4.7 pericalcarine 6027 3961 8349 1.982 0.646 0.132 0.047 77 11.6 postcentral 1483 1020 2946 2.729 0.595 0.127 0.039 19 2.4 posteriorcingulate 6893 4602 12223 2.468 0.645 0.127 0.045 95 14.2 precentral 4771 3179 9893 2.722 0.703 0.142 0.050 63 9.5 precuneus 1352 882 3195 3.271 0.610 0.155 0.069 30 3.5 rostralanteriorcingulate 4544 3079 9235 2.652 0.670 0.143 0.051 67 8.8 rostralmiddlefrontal 11388 7640 25858 2.934 0.722 0.141 0.058 193 24.7 superiorfrontal 6349 4146 9957 2.241 0.520 0.131 0.042 70 10.8 superiorparietal 6757 4486 13883 2.704 0.801 0.131 0.046 85 12.4 superiortemporal 5217 3533 9568 2.374 0.628 0.145 0.048 75 10.3 supramarginal 659 428 1088 2.539 0.441 0.148 0.038 8 1.1 transversetemporal 2744 1795 5296 2.920 0.798 0.125 0.050 34 5.3 insula #-------------------------------------------- #@# Tessellate rh Sun Dec 15 17:15:06 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 2 found - 2 modified | TOTAL: 4 pass 2 (yz-): 0 found - 2 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 4 (out of 250469: 0.001597) 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: 1596 vertices, 1699 faces slice 50: 6740 vertices, 6938 faces slice 60: 14337 vertices, 14620 faces slice 70: 22893 vertices, 23182 faces slice 80: 32357 vertices, 32698 faces slice 90: 41920 vertices, 42202 faces slice 100: 51867 vertices, 52211 faces slice 110: 62352 vertices, 62694 faces slice 120: 72840 vertices, 73203 faces slice 130: 82900 vertices, 83238 faces slice 140: 92280 vertices, 92606 faces slice 150: 100687 vertices, 100966 faces slice 160: 107577 vertices, 107847 faces slice 170: 114288 vertices, 114555 faces slice 180: 120313 vertices, 120538 faces slice 190: 124796 vertices, 124962 faces slice 200: 125972 vertices, 126002 faces slice 210: 125972 vertices, 126002 faces slice 220: 125972 vertices, 126002 faces slice 230: 125972 vertices, 126002 faces slice 240: 125972 vertices, 126002 faces slice 250: 125972 vertices, 126002 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... 125972 voxel in cpt #1: X=-30 [v=125972,e=378006,f=252004] located at (29.402884, -17.313753, 32.011868) For the whole surface: X=-30 [v=125972,e=378006,f=252004] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Sun Dec 15 17:15:16 EST 2013 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 Sun Dec 15 17:15:22 EST 2013 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts avg radius = 46.1 mm, total surface area = 66414 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.7 minutes Not saving sulc step 000: RMS=0.100 (target=0.015) step 005: RMS=0.074 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.044 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.031 (target=0.015) step 035: RMS=0.027 (target=0.015) step 040: RMS=0.025 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.023 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Sun Dec 15 17:16:07 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 1.01 +- 0.58 (0.00-->7.10) (max @ vno 51520 --> 52554) face area 0.03 +- 0.03 (-0.04-->0.61) scaling brain by 0.311... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.146, avgs=0 005/300: dt: 0.9000, rms radial error=176.885, avgs=0 010/300: dt: 0.9000, rms radial error=176.326, avgs=0 015/300: dt: 0.9000, rms radial error=175.594, avgs=0 020/300: dt: 0.9000, rms radial error=174.760, avgs=0 025/300: dt: 0.9000, rms radial error=173.869, avgs=0 030/300: dt: 0.9000, rms radial error=172.946, avgs=0 035/300: dt: 0.9000, rms radial error=172.006, avgs=0 040/300: dt: 0.9000, rms radial error=171.059, avgs=0 045/300: dt: 0.9000, rms radial error=170.109, avgs=0 050/300: dt: 0.9000, rms radial error=169.161, avgs=0 055/300: dt: 0.9000, rms radial error=168.215, avgs=0 060/300: dt: 0.9000, rms radial error=167.273, avgs=0 065/300: dt: 0.9000, rms radial error=166.335, avgs=0 070/300: dt: 0.9000, rms radial error=165.402, avgs=0 075/300: dt: 0.9000, rms radial error=164.474, avgs=0 080/300: dt: 0.9000, rms radial error=163.551, avgs=0 085/300: dt: 0.9000, rms radial error=162.633, avgs=0 090/300: dt: 0.9000, rms radial error=161.720, avgs=0 095/300: dt: 0.9000, rms radial error=160.813, avgs=0 100/300: dt: 0.9000, rms radial error=159.910, avgs=0 105/300: dt: 0.9000, rms radial error=159.012, avgs=0 110/300: dt: 0.9000, rms radial error=158.119, avgs=0 115/300: dt: 0.9000, rms radial error=157.231, avgs=0 120/300: dt: 0.9000, rms radial error=156.348, avgs=0 125/300: dt: 0.9000, rms radial error=155.469, avgs=0 130/300: dt: 0.9000, rms radial error=154.596, avgs=0 135/300: dt: 0.9000, rms radial error=153.727, avgs=0 140/300: dt: 0.9000, rms radial error=152.863, avgs=0 145/300: dt: 0.9000, rms radial error=152.003, avgs=0 150/300: dt: 0.9000, rms radial error=151.148, avgs=0 155/300: dt: 0.9000, rms radial error=150.298, avgs=0 160/300: dt: 0.9000, rms radial error=149.452, avgs=0 165/300: dt: 0.9000, rms radial error=148.611, avgs=0 170/300: dt: 0.9000, rms radial error=147.775, avgs=0 175/300: dt: 0.9000, rms radial error=146.943, avgs=0 180/300: dt: 0.9000, rms radial error=146.116, avgs=0 185/300: dt: 0.9000, rms radial error=145.293, avgs=0 190/300: dt: 0.9000, rms radial error=144.475, avgs=0 195/300: dt: 0.9000, rms radial error=143.661, avgs=0 200/300: dt: 0.9000, rms radial error=142.852, avgs=0 205/300: dt: 0.9000, rms radial error=142.047, avgs=0 210/300: dt: 0.9000, rms radial error=141.247, avgs=0 215/300: dt: 0.9000, rms radial error=140.451, avgs=0 220/300: dt: 0.9000, rms radial error=139.660, avgs=0 225/300: dt: 0.9000, rms radial error=138.873, avgs=0 230/300: dt: 0.9000, rms radial error=138.090, avgs=0 235/300: dt: 0.9000, rms radial error=137.312, avgs=0 240/300: dt: 0.9000, rms radial error=136.538, avgs=0 245/300: dt: 0.9000, rms radial error=135.768, avgs=0 250/300: dt: 0.9000, rms radial error=135.003, avgs=0 255/300: dt: 0.9000, rms radial error=134.242, avgs=0 260/300: dt: 0.9000, rms radial error=133.485, avgs=0 265/300: dt: 0.9000, rms radial error=132.732, avgs=0 270/300: dt: 0.9000, rms radial error=131.984, avgs=0 275/300: dt: 0.9000, rms radial error=131.239, avgs=0 280/300: dt: 0.9000, rms radial error=130.499, avgs=0 285/300: dt: 0.9000, rms radial error=129.763, avgs=0 290/300: dt: 0.9000, rms radial error=129.032, avgs=0 295/300: dt: 0.9000, rms radial error=128.304, avgs=0 300/300: dt: 0.9000, rms radial error=127.580, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14733.66 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00019 epoch 2 (K=40.0), pass 1, starting sse = 2454.26 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 3 (K=160.0), pass 1, starting sse = 256.46 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.14/13 = 0.01072 epoch 4 (K=640.0), pass 1, starting sse = 12.47 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.22/20 = 0.01125 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.12 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Sun Dec 15 17:23:28 EST 2013 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 ta0313_time2 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=-30 (nv=125972, nf=252004, ne=378006, g=16) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 2189 ambiguous faces found in tessellation segmenting defects... 23 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 23 defects to be corrected 0 vertices coincident reading input surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2684 (-4.6342) -vertex loglikelihood: -5.9618 (-2.9809) -normal dot loglikelihood: -3.6788 (-3.6788) -quad curv loglikelihood: -6.3311 (-3.1655) Total Loglikelihood : -25.2402 CORRECTING DEFECT 0 (vertices=40, convex hull=64) After retessellation of defect 0, euler #=-20 (124632,373362,248710) : difference with theory (-20) = 0 CORRECTING DEFECT 1 (vertices=47, convex hull=92) After retessellation of defect 1, euler #=-19 (124646,373442,248777) : difference with theory (-19) = 0 CORRECTING DEFECT 2 (vertices=29, convex hull=78) After retessellation of defect 2, euler #=-18 (124663,373520,248839) : difference with theory (-18) = 0 CORRECTING DEFECT 3 (vertices=44, convex hull=70) After retessellation of defect 3, euler #=-17 (124690,373630,248923) : difference with theory (-17) = 0 CORRECTING DEFECT 4 (vertices=25, convex hull=37) After retessellation of defect 4, euler #=-16 (124695,373657,248946) : difference with theory (-16) = 0 CORRECTING DEFECT 5 (vertices=166, convex hull=71) After retessellation of defect 5, euler #=-15 (124708,373731,249008) : difference with theory (-15) = 0 CORRECTING DEFECT 6 (vertices=202, convex hull=87) After retessellation of defect 6, euler #=-14 (124717,373797,249066) : difference with theory (-14) = 0 CORRECTING DEFECT 7 (vertices=58, convex hull=87) After retessellation of defect 7, euler #=-13 (124749,373929,249167) : difference with theory (-13) = 0 CORRECTING DEFECT 8 (vertices=26, convex hull=70) After retessellation of defect 8, euler #=-12 (124758,373984,249214) : difference with theory (-12) = 0 CORRECTING DEFECT 9 (vertices=67, convex hull=59) After retessellation of defect 9, euler #=-11 (124767,374034,249256) : difference with theory (-11) = 0 CORRECTING DEFECT 10 (vertices=66, convex hull=48) After retessellation of defect 10, euler #=-10 (124796,374145,249339) : difference with theory (-10) = 0 CORRECTING DEFECT 11 (vertices=174, convex hull=65) After retessellation of defect 11, euler #=-9 (124807,374202,249386) : difference with theory (-9) = 0 CORRECTING DEFECT 12 (vertices=7, convex hull=19) After retessellation of defect 12, euler #=-8 (124807,374207,249392) : difference with theory (-8) = 0 CORRECTING DEFECT 13 (vertices=21, convex hull=26) After retessellation of defect 13, euler #=-7 (124810,374223,249406) : difference with theory (-7) = 0 CORRECTING DEFECT 14 (vertices=71, convex hull=88) After retessellation of defect 14, euler #=-6 (124835,374338,249497) : difference with theory (-6) = 0 CORRECTING DEFECT 15 (vertices=8, convex hull=16) After retessellation of defect 15, euler #=-5 (124837,374345,249503) : difference with theory (-5) = 0 CORRECTING DEFECT 16 (vertices=64, convex hull=80) After retessellation of defect 16, euler #=-4 (124867,374470,249599) : difference with theory (-4) = 0 CORRECTING DEFECT 17 (vertices=29, convex hull=62) After retessellation of defect 17, euler #=-3 (124878,374526,249645) : difference with theory (-3) = 0 CORRECTING DEFECT 18 (vertices=36, convex hull=85) After retessellation of defect 18, euler #=-2 (124893,374606,249711) : difference with theory (-2) = 0 CORRECTING DEFECT 19 (vertices=39, convex hull=39) After retessellation of defect 19, euler #=-1 (124900,374644,249743) : difference with theory (-1) = 0 CORRECTING DEFECT 20 (vertices=28, convex hull=54) After retessellation of defect 20, euler #=0 (124913,374702,249789) : difference with theory (0) = 0 CORRECTING DEFECT 21 (vertices=15, convex hull=30) After retessellation of defect 21, euler #=1 (124916,374723,249808) : difference with theory (1) = 0 CORRECTING DEFECT 22 (vertices=92, convex hull=49) After retessellation of defect 22, euler #=2 (124929,374781,249854) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.21 (0.10-->6.10) (max @ vno 31298 --> 34081) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.21 (0.10-->6.10) (max @ vno 31298 --> 34081) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 86 mutations (36.3%), 151 crossovers (63.7%), 78 vertices were eliminated building final representation... 1043 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=124929, nf=249854, ne=374781, g=0) writing corrected surface to /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 17.4 minutes 0 defective edges removing intersecting faces 000: 223 intersecting 001: 2 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 124929 - 374781 + 249854 = 2 --> 0 holes F =2V-4: 249854 = 249858-4 (0) 2E=3F: 749562 = 749562 (0) total defect index = 0 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 20 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Sun Dec 15 17:40:56 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/filled.mgz... reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/brain.finalsurfs.mgz... reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/wm.mgz... 7393 bright wm thresholded. 1314 bright non-wm voxels segmented. reading original surface position from /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.orig... computing class statistics... border white: 240773 voxels (1.44%) border gray 270691 voxels (1.61%) WM (94.0): 95.0 +- 7.5 [70.0 --> 110.0] GM (82.0) : 80.7 +- 11.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.8 (was 70) setting MAX_BORDER_WHITE to 109.5 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.6 (was 40) setting MAX_GRAY to 94.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.4 (was 40) repositioning cortical surface to gray/white boundary reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.03-->2.57) (max @ vno 102770 --> 103546) face area 0.28 +- 0.12 (0.00-->1.60) mean absolute distance = 0.68 +- 0.86 3396 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=102, GM=70 mean inside = 93.7, mean outside = 77.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=81.8, 38 (38) missing vertices, mean dist 0.2 [0.6 (%38.4)->0.8 (%61.6))] %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=mani., 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 0.91 +- 0.25 (0.12-->3.60) (max @ vno 97153 --> 96320) face area 0.28 +- 0.13 (0.00-->1.70) mean absolute distance = 0.32 +- 0.58 2453 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4084421.5, rms=8.93 001: dt: 0.5000, sse=4729967.0, rms=6.264 (0.000%) 002: dt: 0.5000, sse=5110788.5, rms=4.704 (0.000%) 003: dt: 0.5000, sse=5457023.0, rms=3.825 (0.000%) 004: dt: 0.5000, sse=5699531.5, rms=3.326 (0.000%) 005: dt: 0.5000, sse=5877822.0, rms=3.110 (0.000%) 006: dt: 0.5000, sse=5950153.0, rms=2.977 (0.000%) rms = 2.94, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=6007351.5, rms=2.937 (0.000%) 008: dt: 0.2500, sse=3484165.2, rms=1.923 (0.000%) 009: dt: 0.2500, sse=3178982.8, rms=1.707 (0.000%) 010: dt: 0.2500, sse=3064367.5, rms=1.656 (0.000%) rms = 1.63, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=3031679.0, rms=1.627 (0.000%) rms = 1.60, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=2993762.5, rms=1.599 (0.000%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=83.7, 29 (9) missing vertices, mean dist -0.1 [0.3 (%67.9)->0.3 (%32.1))] %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=mani., nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.24 (0.10-->3.63) (max @ vno 97153 --> 96320) face area 0.35 +- 0.15 (0.00-->2.23) mean absolute distance = 0.26 +- 0.41 2927 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3342762.8, rms=3.55 013: dt: 0.5000, sse=3894026.8, rms=2.261 (0.000%) rms = 2.30, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=3597446.5, rms=1.819 (0.000%) 015: dt: 0.2500, sse=3455236.5, rms=1.526 (0.000%) 016: dt: 0.2500, sse=3380786.0, rms=1.427 (0.000%) rms = 1.40, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=3339497.0, rms=1.397 (0.000%) rms = 1.37, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=3309208.8, rms=1.373 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=85.2, 21 (7) missing vertices, mean dist -0.1 [0.3 (%64.8)->0.2 (%35.2))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=mani., nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.24 (0.12-->3.62) (max @ vno 97153 --> 96320) face area 0.34 +- 0.15 (0.00-->2.23) mean absolute distance = 0.24 +- 0.34 3250 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3397461.8, rms=2.44 019: dt: 0.5000, sse=3872706.2, rms=1.914 (0.000%) rms = 2.11, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=3645676.5, rms=1.471 (0.000%) 021: dt: 0.2500, sse=3537185.0, rms=1.283 (0.000%) rms = 1.25, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3494896.8, rms=1.247 (0.000%) rms = 1.23, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=3459156.8, rms=1.231 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=85.8, 22 (6) missing vertices, mean dist -0.0 [0.3 (%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=mani., 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=3468467.0, rms=1.46 024: dt: 0.5000, sse=4408737.0, rms=1.339 (0.000%) rms = 1.72, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=4032055.8, rms=1.074 (0.000%) rms = 1.03, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=3859546.0, rms=1.025 (0.000%) rms = 1.01, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3885431.5, rms=1.006 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group generating cortex label... 17 non-cortical segments detected only using segment with 1959 vertices erasing segment 1 (vno[0] = 54749) erasing segment 2 (vno[0] = 56872) erasing segment 3 (vno[0] = 77230) erasing segment 4 (vno[0] = 78381) erasing segment 5 (vno[0] = 79114) erasing segment 6 (vno[0] = 83979) erasing segment 7 (vno[0] = 87676) erasing segment 8 (vno[0] = 88531) erasing segment 9 (vno[0] = 90268) erasing segment 10 (vno[0] = 91194) erasing segment 11 (vno[0] = 95457) erasing segment 12 (vno[0] = 95496) erasing segment 13 (vno[0] = 97910) erasing segment 14 (vno[0] = 98715) erasing segment 15 (vno[0] = 99463) erasing segment 16 (vno[0] = 99491) writing cortex label to /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/label/rh.cortex.label... writing curvature file /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.curv writing smoothed area to rh.area writing curvature file /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.area vertex spacing 0.90 +- 0.24 (0.08-->3.43) (max @ vno 96320 --> 97153) face area 0.34 +- 0.15 (0.00-->2.20) refinement took 5.0 minutes #-------------------------------------------- #@# Smooth2 rh Sun Dec 15 17:45:55 EST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 Sun Dec 15 17:45:59 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 46.2 mm, total surface area = 76712 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.116 (target=0.015) step 005: RMS=0.079 (target=0.015) step 010: RMS=0.057 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) step 055: RMS=0.015 (target=0.015) inflation complete. inflation took 0.5 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 115 vertices thresholded to be in k1 ~ [-0.35 0.45], k2 ~ [-0.15 0.08] total integrated curvature = 0.629*4pi (7.905) --> 0 handles ICI = 1.5, FI = 7.8, variation=140.297 111 vertices thresholded to be in [-0.04 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 103 vertices thresholded to be in [-0.13 0.20] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.021 done. #----------------------------------------- #@# Curvature Stats rh Sun Dec 15 17:47:59 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm ta0313_time2 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 [ ta0313_time2/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 [ 218 ] Gb_filter = 0 WARN: S lookup min: -0.310656 WARN: S explicit min: 0.000000 vertex = 1372 #-------------------------------------------- #@# Sphere rh Sun Dec 15 17:48:03 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 0.288... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=mani., 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 %20.32 pass 1: epoch 2 of 3 starting distance error %20.30 unfolding complete - removing small folds... starting distance error %20.19 removing remaining folds... final distance error %20.22 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.71 hours #-------------------------------------------- #@# Surf Reg rh Sun Dec 15 18:30:40 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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=mani., 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=mani., 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 = 0.587 curvature mean = 0.038, std = 0.937 curvature mean = 0.014, std = 0.867 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 336841.0, tmin=0.9987 d=32.00 min @ (-8.00, 0.00, 8.00) sse = 302990.8, tmin=2.0096 d=16.00 min @ (4.00, 0.00, -4.00) sse = 291818.9, tmin=3.0574 d=8.00 min @ (-2.00, -2.00, 2.00) sse = 286795.0, tmin=4.1214 d=4.00 min @ (0.00, 1.00, -1.00) sse = 286576.3, tmin=5.1993 d=2.00 min @ (0.50, -0.50, 0.50) sse = 286165.1, tmin=6.2822 d=1.00 min @ (-0.25, 0.25, 0.00) sse = 286093.8, tmin=7.3629 d=0.50 min @ (0.12, -0.12, 0.12) sse = 286082.1, tmin=8.4491 tol=1.0e+00, sigma=0.5, host=mani., nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 8.45 min curvature mean = 0.005, std = 0.933 curvature mean = 0.005, std = 0.940 curvature mean = 0.002, std = 0.944 curvature mean = 0.002, std = 0.972 curvature mean = -0.001, std = 0.942 curvature mean = 0.000, std = 0.986 2 Reading smoothwm curvature mean = -0.027, std = 0.283 curvature mean = 0.006, std = 0.070 curvature mean = 0.049, std = 0.376 curvature mean = 0.005, std = 0.084 curvature mean = 0.028, std = 0.562 curvature mean = 0.006, std = 0.091 curvature mean = 0.015, std = 0.695 curvature mean = 0.006, std = 0.093 curvature mean = 0.005, std = 0.795 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Sun Dec 15 18:57:15 EST 2013 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 Sun Dec 15 18:57:17 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 Sun Dec 15 18:57:18 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 ta0313_time2 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... 1117 labels changed using aseg relabeling using gibbs priors... 000: 2757 changed, 124929 examined... 001: 653 changed, 11781 examined... 002: 145 changed, 3530 examined... 003: 45 changed, 867 examined... 004: 15 changed, 279 examined... 005: 8 changed, 85 examined... 006: 2 changed, 47 examined... 007: 1 changed, 14 examined... 008: 1 changed, 7 examined... 009: 1 changed, 7 examined... 010: 1 changed, 7 examined... 011: 0 changed, 7 examined... 161 labels changed using aseg 000: 95 total segments, 57 labels (356 vertices) changed 001: 41 total segments, 3 labels (10 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 54 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1503 vertices marked for relabeling... 1503 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 53 seconds. #-------------------------------------------- #@# Make Pial Surf rh Sun Dec 15 18:58:12 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/filled.mgz... reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/brain.finalsurfs.mgz... reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/wm.mgz... 7393 bright wm thresholded. 1314 bright non-wm voxels segmented. reading original surface position from /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.orig... computing class statistics... border white: 240773 voxels (1.44%) border gray 270691 voxels (1.61%) WM (94.0): 95.0 +- 7.5 [70.0 --> 110.0] GM (82.0) : 80.7 +- 11.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.8 (was 70) setting MAX_BORDER_WHITE to 109.5 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.6 (was 40) setting MAX_GRAY to 94.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.4 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102, GM=70 mean inside = 93.7, mean outside = 77.7 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.21 (0.03-->2.57) (max @ vno 102770 --> 103546) face area 0.28 +- 0.12 (0.00-->1.60) mean absolute distance = 0.68 +- 0.86 3421 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown deleting segment 4 with 275 points - only 0.00% unknown deleting segment 5 with 16 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 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 10 points - only 0.00% unknown mean border=81.8, 38 (38) missing vertices, mean dist 0.2 [0.6 (%38.3)->0.8 (%61.7))] %76 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=mani., 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 0.91 +- 0.25 (0.12-->3.60) (max @ vno 97153 --> 96320) face area 0.28 +- 0.13 (0.00-->1.69) mean absolute distance = 0.32 +- 0.58 2531 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4090060.8, rms=8.92 001: dt: 0.5000, sse=4736957.0, rms=6.259 (0.000%) 002: dt: 0.5000, sse=5119281.0, rms=4.701 (0.000%) 003: dt: 0.5000, sse=5466555.0, rms=3.822 (0.000%) 004: dt: 0.5000, sse=5709459.5, rms=3.324 (0.000%) 005: dt: 0.5000, sse=5887753.5, rms=3.108 (0.000%) 006: dt: 0.5000, sse=5961071.0, rms=2.975 (0.000%) rms = 2.94, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=6019743.5, rms=2.935 (0.000%) 008: dt: 0.2500, sse=3490667.5, rms=1.922 (0.000%) 009: dt: 0.2500, sse=3184972.8, rms=1.707 (0.000%) 010: dt: 0.2500, sse=3070522.8, rms=1.655 (0.000%) rms = 1.63, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=3037784.2, rms=1.626 (0.000%) rms = 1.60, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=2999911.5, rms=1.599 (0.000%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 227 points - only 0.00% unknown deleting segment 5 with 11 points - only 0.00% unknown deleting segment 7 with 105 points - only 47.62% unknown deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown mean border=83.7, 29 (9) missing vertices, mean dist -0.1 [0.3 (%67.8)->0.3 (%32.2))] %82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=mani., nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.24 (0.10-->3.63) (max @ vno 97153 --> 96320) face area 0.35 +- 0.15 (0.00-->2.23) mean absolute distance = 0.26 +- 0.42 2977 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3356093.2, rms=3.55 013: dt: 0.5000, sse=3907119.5, rms=2.263 (0.000%) rms = 2.30, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=3609941.8, rms=1.822 (0.000%) 015: dt: 0.2500, sse=3467282.0, rms=1.529 (0.000%) 016: dt: 0.2500, sse=3392668.5, rms=1.430 (0.000%) rms = 1.40, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=3351052.8, rms=1.399 (0.000%) rms = 1.37, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=3320706.2, rms=1.375 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 9 points - only 0.00% unknown deleting segment 2 with 232 points - only 0.00% unknown deleting segment 3 with 7 points - only 0.00% unknown deleting segment 5 with 39 points - only 41.03% unknown deleting segment 6 with 10 points - only 0.00% unknown deleting segment 7 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown mean border=85.2, 21 (7) missing vertices, mean dist -0.1 [0.3 (%64.8)->0.2 (%35.2))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=mani., nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.24 (0.12-->3.72) (max @ vno 86735 --> 86761) face area 0.34 +- 0.15 (0.00-->2.23) mean absolute distance = 0.25 +- 0.34 3282 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3408195.0, rms=2.44 019: dt: 0.5000, sse=3884051.5, rms=1.914 (0.000%) rms = 2.11, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=3657106.8, rms=1.472 (0.000%) 021: dt: 0.2500, sse=3548750.8, rms=1.283 (0.000%) rms = 1.25, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3505361.0, rms=1.247 (0.000%) rms = 1.23, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=3470106.8, rms=1.231 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 9 points - only 0.00% unknown deleting segment 1 with 224 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 3 with 79 points - only 34.18% unknown deleting segment 4 with 10 points - only 0.00% unknown deleting segment 5 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown deleting segment 8 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown mean border=85.8, 24 (6) missing vertices, mean dist -0.0 [0.3 (%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=mani., 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=3479334.8, rms=1.46 024: dt: 0.5000, sse=4426492.5, rms=1.338 (0.000%) rms = 1.72, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=4047825.2, rms=1.074 (0.000%) rms = 1.03, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=3875551.5, rms=1.026 (0.000%) rms = 1.01, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3899732.8, rms=1.007 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=60.2, 45 (45) missing vertices, mean dist 1.4 [0.1 (%0.0)->2.7 (%100.0))] %15 local maxima, %37 large gradients and %44 min vals, 2850 gradients ignored tol=1.0e-04, sigma=2.0, host=mani., 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=18611064.0, rms=26.03 001: dt: 0.5000, sse=14319108.0, rms=22.330 (0.000%) 002: dt: 0.5000, sse=11088514.0, rms=19.119 (0.000%) 003: dt: 0.5000, sse=8740631.0, rms=16.389 (0.000%) 004: dt: 0.5000, sse=7179303.5, rms=14.089 (0.000%) 005: dt: 0.5000, sse=6187109.5, rms=12.159 (0.000%) 006: dt: 0.5000, sse=5555874.0, rms=10.601 (0.000%) 007: dt: 0.5000, sse=5202443.5, rms=9.313 (0.000%) 008: dt: 0.5000, sse=5006521.0, rms=8.230 (0.000%) 009: dt: 0.5000, sse=4929545.5, rms=7.299 (0.000%) 010: dt: 0.5000, sse=4934347.5, rms=6.476 (0.000%) 011: dt: 0.5000, sse=4980988.0, rms=5.745 (0.000%) 012: dt: 0.5000, sse=5072064.0, rms=5.120 (0.000%) 013: dt: 0.5000, sse=5152251.0, rms=4.624 (0.000%) 014: dt: 0.5000, sse=5230368.0, rms=4.248 (0.000%) 015: dt: 0.5000, sse=5320799.5, rms=3.962 (0.000%) 016: dt: 0.5000, sse=5406903.5, rms=3.761 (0.000%) 017: dt: 0.5000, sse=5476106.5, rms=3.630 (0.000%) 018: dt: 0.5000, sse=5525603.5, rms=3.540 (0.000%) rms = 3.50, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=5539185.5, rms=3.495 (0.000%) 020: dt: 0.2500, sse=4279722.5, rms=3.140 (0.000%) 021: dt: 0.2500, sse=4203824.0, rms=3.044 (0.000%) rms = 3.04, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=4152770.8, rms=3.038 (0.000%) 023: dt: 0.1250, sse=3979952.5, rms=2.947 (0.000%) rms = 2.92, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3970054.5, rms=2.924 (0.000%) positioning took 2.6 minutes mean border=58.7, 1454 (5) missing vertices, mean dist 0.2 [0.3 (%49.1)->0.9 (%50.9))] %27 local maxima, %30 large gradients and %37 min vals, 1204 gradients ignored tol=1.0e-04, sigma=1.0, host=mani., 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=4467183.5, rms=4.55 025: dt: 0.5000, sse=4648717.5, rms=3.928 (0.000%) 026: dt: 0.5000, sse=5524613.5, rms=3.536 (0.000%) rms = 3.51, time step reduction 1 of 3 to 0.250... 027: dt: 0.5000, sse=5488496.0, rms=3.515 (0.000%) 028: dt: 0.2500, sse=4664250.0, rms=2.985 (0.000%) 029: dt: 0.2500, sse=4627772.5, rms=2.841 (0.000%) rms = 2.88, time step reduction 2 of 3 to 0.125... rms = 2.79, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=4567171.5, rms=2.793 (0.000%) positioning took 0.8 minutes mean border=57.8, 1791 (3) missing vertices, mean dist 0.1 [0.3 (%46.1)->0.6 (%53.9))] %36 local maxima, %21 large gradients and %37 min vals, 1330 gradients ignored tol=1.0e-04, sigma=0.5, host=mani., 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=4670906.0, rms=3.34 rms = 3.38, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=4516419.5, rms=3.061 (0.000%) 032: dt: 0.2500, sse=4529620.5, rms=2.877 (0.000%) rms = 2.83, time step reduction 2 of 3 to 0.125... 033: dt: 0.2500, sse=4661072.5, rms=2.834 (0.000%) 034: dt: 0.1250, sse=4530154.5, rms=2.683 (0.000%) 035: dt: 0.1250, sse=4558441.0, rms=2.631 (0.000%) rms = 2.61, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=4579864.0, rms=2.613 (0.000%) positioning took 0.7 minutes mean border=57.1, 4238 (1) missing vertices, mean dist 0.1 [0.3 (%46.4)->0.5 (%53.6))] %40 local maxima, %16 large gradients and %36 min vals, 1322 gradients ignored tol=1.0e-04, sigma=0.2, host=mani., 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4612421.5, rms=2.85 rms = 3.09, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=4544147.5, rms=2.693 (0.000%) 038: dt: 0.2500, sse=4744039.0, rms=2.611 (0.000%) rms = 2.63, time step reduction 2 of 3 to 0.125... rms = 2.58, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4701041.0, rms=2.576 (0.000%) positioning took 0.5 minutes writing curvature file /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.area.pial vertex spacing 1.02 +- 0.44 (0.08-->6.92) (max @ vno 83010 --> 83011) face area 0.41 +- 0.31 (0.00-->7.43) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 124929 vertices processed 25000 of 124929 vertices processed 50000 of 124929 vertices processed 75000 of 124929 vertices processed 100000 of 124929 vertices processed 0 of 124929 vertices processed 25000 of 124929 vertices processed 50000 of 124929 vertices processed 75000 of 124929 vertices processed 100000 of 124929 vertices processed thickness calculation complete, 675:1212 truncations. 22824 vertices at 0 distance 76978 vertices at 1 distance 79828 vertices at 2 distance 38618 vertices at 3 distance 13475 vertices at 4 distance 4387 vertices at 5 distance 1483 vertices at 6 distance 511 vertices at 7 distance 191 vertices at 8 distance 106 vertices at 9 distance 53 vertices at 10 distance 44 vertices at 11 distance 45 vertices at 12 distance 29 vertices at 13 distance 20 vertices at 14 distance 21 vertices at 15 distance 18 vertices at 16 distance 3 vertices at 17 distance 8 vertices at 18 distance 12 vertices at 19 distance 10 vertices at 20 distance writing curvature file /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.thickness positioning took 10.8 minutes #-------------------------------------------- #@# Surf Volume rh Sun Dec 15 19:08:58 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 Sun Dec 15 19:08:58 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts pctsurfcon --s ta0313_time2 --rh-only Log file is /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts/pctsurfcon.log Sun Dec 15 19:08:58 EST 2013 setenv SUBJECTS_DIR /mani2/fei_data/Jacobian_maps/SUBJECT_DIR cd /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux mani.med.yale.internal 2.6.32-220.17.1.el6.x86_64 #1 SMP Thu Apr 26 13:37:13 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/tmp.pctsurfcon.33723/rh.wm.mgh --regheader ta0313_time2 --cortex srcvol = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/orig.mgz as target reference. Loading label /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/label/rh.cortex.label Reading surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 = 70525 Masking with /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/label/rh.cortex.label Writing to /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/tmp.pctsurfcon.33723/rh.wm.mgh Dim: 124929 1 1 mri_vol2surf --mov /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/tmp.pctsurfcon.33723/rh.gm.mgh --projfrac 0.3 --regheader ta0313_time2 --cortex srcvol = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/orig.mgz as target reference. Loading label /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/label/rh.cortex.label Reading surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Done reading source surface Reading thickness /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 = 83484 Masking with /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/label/rh.cortex.label Writing to /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/tmp.pctsurfcon.33723/rh.gm.mgh Dim: 124929 1 1 mri_concat /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/tmp.pctsurfcon.33723/rh.wm.mgh /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/tmp.pctsurfcon.33723/rh.gm.mgh --paired-diff-norm --mul 100 --o /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.w-g.pct.mgh mri_segstats --in /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.w-g.pct.mgh --annot ta0313_time2 rh aparc --sum /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.w-g.pct.mgh --annot ta0313_time2 rh aparc --sum /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/stats/rh.w-g.pct.stats --snr sysname Linux hostname mani.med.yale.internal machine x86_64 user hblab 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.w-g.pct.mgh Vertex Area is 0.671165 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1243 883.449 2 2002 caudalanteriorcingulate 1265 861.158 3 2003 caudalmiddlefrontal 2379 1616.565 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 1225 851.377 6 2006 entorhinal 339 231.483 7 2007 fusiform 4344 2888.505 8 2008 inferiorparietal 7738 5365.707 9 2009 inferiortemporal 4215 2854.092 10 2010 isthmuscingulate 1833 1190.754 11 2011 lateraloccipital 6160 4102.777 12 2012 lateralorbitofrontal 4340 2897.903 13 2013 lingual 4537 3089.717 14 2014 medialorbitofrontal 2931 1935.341 15 2015 middletemporal 4431 3019.359 16 2016 parahippocampal 1143 710.215 17 2017 paracentral 1982 1310.395 18 2018 parsopercularis 2002 1380.612 19 2019 parsorbitalis 1318 889.206 20 2020 parstriangularis 2746 1885.529 21 2021 pericalcarine 2046 1357.229 22 2022 postcentral 5196 3437.289 23 2023 posteriorcingulate 1543 1051.581 24 2024 precentral 5712 3807.327 25 2025 precuneus 6696 4527.997 26 2026 rostralanteriorcingulate 982 648.901 27 2027 rostralmiddlefrontal 7520 5147.453 28 2028 superiorfrontal 8916 6024.459 29 2029 superiorparietal 9352 6194.345 30 2030 superiortemporal 4661 3148.100 31 2031 supramarginal 4024 2796.339 32 2032 frontalpole 332 223.503 33 2033 temporalpole 580 420.803 34 2034 transversetemporal 367 221.994 35 2035 insula 3112 2084.148 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Sun Dec 15 19:09:07 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 ta0313_time2 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/wm.mgz... reading input surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white... reading input pial surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.pial... reading input white surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 1243 883 1883 2.200 0.468 0.138 0.044 18 2.4 bankssts 1265 861 2849 3.035 0.781 0.143 0.044 21 2.1 caudalanteriorcingulate 2379 1617 5132 2.801 0.665 0.128 0.038 24 3.8 caudalmiddlefrontal 1225 851 1874 1.876 0.721 0.183 0.075 29 3.8 cuneus 339 231 1346 3.952 0.773 0.127 0.040 3 0.6 entorhinal 4344 2889 9101 2.703 0.780 0.135 0.043 53 7.9 fusiform 7738 5366 14982 2.459 0.579 0.142 0.051 108 15.5 inferiorparietal 4215 2854 9947 2.860 0.803 0.151 0.057 71 9.8 inferiortemporal 1833 1191 3629 2.791 0.825 0.143 0.050 27 3.6 isthmuscingulate 6160 4103 10629 2.372 0.672 0.154 0.056 85 13.4 lateraloccipital 4340 2898 9218 2.880 0.922 0.130 0.042 63 7.9 lateralorbitofrontal 4537 3090 7243 2.154 0.709 0.155 0.058 67 10.7 lingual 2931 1935 5655 2.549 0.793 0.131 0.055 45 6.0 medialorbitofrontal 4431 3019 8727 2.354 0.761 0.150 0.063 87 11.2 middletemporal 1143 710 1918 2.290 0.713 0.095 0.029 7 1.3 parahippocampal 1982 1310 3627 2.566 0.705 0.126 0.042 20 3.4 paracentral 2002 1381 4720 2.890 0.623 0.142 0.058 41 4.1 parsopercularis 1318 889 3461 2.939 0.769 0.140 0.120 40 2.2 parsorbitalis 2746 1886 5787 2.441 0.732 0.142 0.046 40 4.9 parstriangularis 2046 1357 1990 1.666 0.430 0.145 0.056 25 4.5 pericalcarine 5196 3437 7289 1.896 0.561 0.132 0.048 66 9.5 postcentral 1543 1052 3014 2.710 0.699 0.145 0.046 23 3.0 posteriorcingulate 5712 3807 10803 2.608 0.577 0.130 0.042 56 10.0 precentral 6696 4528 11796 2.386 0.738 0.134 0.044 72 11.8 precuneus 982 649 2251 3.146 0.695 0.159 0.077 18 2.5 rostralanteriorcingulate 7520 5147 15074 2.567 0.661 0.146 0.049 108 14.9 rostralmiddlefrontal 8916 6024 21204 3.034 0.634 0.141 0.055 132 17.1 superiorfrontal 9352 6194 14668 2.235 0.521 0.144 0.046 118 17.6 superiorparietal 4661 3148 9212 2.515 0.705 0.133 0.048 65 9.2 superiortemporal 4024 2796 7188 2.305 0.642 0.158 0.073 92 11.6 supramarginal 332 224 1022 3.017 0.604 0.187 0.070 8 1.0 frontalpole 580 421 2341 3.900 0.626 0.166 0.063 10 1.4 temporalpole 367 222 542 2.233 0.535 0.142 0.078 43 0.6 transversetemporal 3112 2084 6211 3.089 0.823 0.136 0.078 57 6.5 insula #----------------------------------------- #@# Cortical Parc 2 rh Sun Dec 15 19:09:21 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 ta0313_time2 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... 5 labels changed using aseg relabeling using gibbs priors... 000: 9378 changed, 124929 examined... 001: 2252 changed, 35471 examined... 002: 656 changed, 11400 examined... 003: 287 changed, 3674 examined... 004: 159 changed, 1629 examined... 005: 70 changed, 897 examined... 006: 41 changed, 395 examined... 007: 24 changed, 230 examined... 008: 14 changed, 136 examined... 009: 9 changed, 87 examined... 010: 2 changed, 49 examined... 011: 3 changed, 14 examined... 012: 3 changed, 17 examined... 013: 0 changed, 9 examined... 3 labels changed using aseg 000: 264 total segments, 182 labels (2037 vertices) changed 001: 97 total segments, 16 labels (226 vertices) changed 002: 83 total segments, 2 labels (6 vertices) changed 003: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 139 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 934 vertices marked for relabeling... 934 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 1 minutes and 1 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Sun Dec 15 19:10:23 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 ta0313_time2 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/wm.mgz... reading input surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white... reading input pial surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.pial... reading input white surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 853 568 1946 2.573 0.887 0.164 0.060 17 2.0 G_and_S_frontomargin 1372 940 3174 2.776 0.658 0.147 0.049 17 2.7 G_and_S_occipital_inf 1072 716 2047 2.460 0.644 0.151 0.063 15 2.8 G_and_S_paracentral 1165 820 2311 2.390 0.671 0.161 0.059 22 2.3 G_and_S_subcentral 830 580 1963 2.602 0.687 0.177 0.089 22 2.7 G_and_S_transv_frontopol 2628 1785 5350 2.830 0.610 0.138 0.051 36 4.7 G_and_S_cingul-Ant 1487 1038 3200 2.916 0.624 0.126 0.062 16 2.3 G_and_S_cingul-Mid-Ant 1282 898 2465 2.757 0.583 0.133 0.044 13 2.2 G_and_S_cingul-Mid-Post 717 471 1736 3.128 0.713 0.155 0.050 11 1.5 G_cingul-Post-dorsal 341 222 671 2.339 0.705 0.159 0.074 6 1.1 G_cingul-Post-ventral 1258 870 1749 1.790 0.728 0.189 0.083 30 4.3 G_cuneus 1372 938 3906 3.045 0.590 0.157 0.069 35 3.3 G_front_inf-Opercular 300 214 864 2.907 0.426 0.159 0.044 6 0.6 G_front_inf-Orbital 1603 1115 3967 2.621 0.767 0.169 0.064 33 3.9 G_front_inf-Triangul 3068 2055 7826 2.876 0.641 0.159 0.062 55 7.7 G_front_middle 6164 4077 17033 3.213 0.610 0.152 0.059 113 13.9 G_front_sup 484 327 1123 3.493 0.990 0.144 0.086 9 1.5 G_Ins_lg_and_S_cent_ins 692 443 1898 3.414 0.733 0.149 0.088 15 1.8 G_insular_short 2168 1465 4706 2.594 0.663 0.159 0.059 37 4.8 G_occipital_middle 1673 1095 2769 2.222 0.643 0.161 0.058 26 4.0 G_occipital_sup 1805 1168 4270 2.704 0.785 0.147 0.053 29 4.1 G_oc-temp_lat-fusifor 2766 1859 4673 2.132 0.758 0.163 0.065 48 7.3 G_oc-temp_med-Lingual 1221 753 2780 2.899 1.093 0.114 0.077 12 2.0 G_oc-temp_med-Parahip 2891 1930 7996 3.047 0.950 0.145 0.088 78 6.4 G_orbital 2666 1875 6233 2.586 0.637 0.161 0.064 49 6.6 G_pariet_inf-Angular 2052 1423 4144 2.305 0.617 0.182 0.103 69 8.6 G_pariet_inf-Supramar 3286 2167 5374 2.158 0.502 0.145 0.047 43 6.5 G_parietal_sup 2003 1323 3176 1.917 0.500 0.145 0.057 31 4.4 G_postcentral 2160 1411 5023 2.735 0.593 0.141 0.059 26 5.2 G_precentral 3903 2602 7863 2.421 0.700 0.148 0.054 55 8.4 G_precuneus 802 538 1790 2.376 0.760 0.172 0.094 21 2.7 G_rectus 399 257 817 3.133 1.081 0.133 0.090 20 1.1 G_subcallosal 337 206 624 2.531 0.555 0.122 0.076 41 0.5 G_temp_sup-G_T_transv 1596 1119 3901 2.517 0.797 0.168 0.076 34 5.0 G_temp_sup-Lateral 694 468 1719 3.192 0.819 0.117 0.043 7 1.1 G_temp_sup-Plan_polar 748 525 1283 2.160 0.804 0.136 0.040 9 1.3 G_temp_sup-Plan_tempo 2210 1531 6292 3.008 0.815 0.172 0.071 50 6.5 G_temporal_inf 2768 1894 5780 2.301 0.741 0.173 0.082 73 9.2 G_temporal_middle 446 289 569 1.891 0.518 0.094 0.020 2 0.4 Lat_Fis-ant-Horizont 196 143 308 2.318 0.323 0.101 0.022 1 0.1 Lat_Fis-ant-Vertical 1228 839 1541 2.251 0.519 0.132 0.040 12 2.0 Lat_Fis-post 3133 2084 4757 2.079 0.685 0.163 0.069 47 8.8 Pole_occipital 1682 1176 6054 3.505 0.787 0.159 0.060 29 4.2 Pole_temporal 2279 1583 2524 1.846 0.533 0.132 0.040 21 3.6 S_calcarine 2415 1593 2618 1.855 0.485 0.115 0.029 17 3.0 S_central 1150 762 1526 2.139 0.550 0.096 0.022 5 1.0 S_cingul-Marginalis 746 511 1416 3.242 0.592 0.094 0.021 3 0.7 S_circular_insula_ant 1085 703 1573 2.723 0.732 0.093 0.021 5 1.0 S_circular_insula_inf 1295 880 2059 2.905 0.510 0.111 0.031 7 1.7 S_circular_insula_sup 695 471 1216 3.091 0.589 0.119 0.033 5 0.9 S_collat_transv_ant 629 424 1048 2.313 0.778 0.131 0.034 6 0.9 S_collat_transv_post 2289 1589 4188 2.469 0.593 0.141 0.041 27 4.0 S_front_inf 1605 1116 2611 2.360 0.536 0.117 0.032 10 2.1 S_front_middle 2286 1563 4135 2.835 0.532 0.122 0.034 19 3.1 S_front_sup 202 143 257 1.895 0.435 0.099 0.018 1 0.1 S_interm_prim-Jensen 3815 2575 5369 2.283 0.435 0.131 0.039 40 5.7 S_intrapariet_and_P_trans 434 298 645 2.266 0.382 0.121 0.030 3 0.5 S_oc_middle_and_Lunatus 1650 1071 2477 2.393 0.459 0.143 0.049 19 3.4 S_oc_sup_and_transversal 896 603 1265 2.488 0.352 0.142 0.044 10 1.5 S_occipital_ant 1008 665 1531 2.474 0.479 0.131 0.041 10 1.6 S_oc-temp_lat 2074 1382 2921 2.244 0.520 0.107 0.025 15 2.0 S_oc-temp_med_and_Lingual 533 351 653 2.057 0.442 0.116 0.024 4 0.6 S_orbital_lateral 940 653 1290 2.075 0.766 0.099 0.019 5 0.7 S_orbital_med-olfact 1664 1107 3274 2.905 0.704 0.133 0.039 20 2.7 S_orbital-H_Shaped 893 618 919 1.559 0.452 0.163 0.063 12 2.1 S_parieto_occipital 1671 1078 2340 2.718 0.856 0.142 0.043 29 2.5 S_pericallosal 1961 1290 2338 1.959 0.465 0.123 0.041 19 3.0 S_postcentral 1168 796 1815 2.541 0.551 0.105 0.023 7 1.1 S_precentral-inf-part 993 685 1582 2.729 0.466 0.121 0.029 7 1.1 S_precentral-sup-part 366 245 515 2.214 0.435 0.078 0.014 1 0.2 S_suborbital 2246 1486 4299 2.879 0.635 0.125 0.034 21 3.1 S_subparietal 925 629 1196 2.070 0.635 0.114 0.027 6 1.0 S_temporal_inf 5609 3862 8788 2.329 0.513 0.121 0.036 60 8.0 S_temporal_sup 167 101 278 2.380 0.377 0.146 0.035 3 0.2 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Sun Dec 15 19:10:37 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 ta0313_time2 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... 1198 labels changed using aseg relabeling using gibbs priors... 000: 2477 changed, 124929 examined... 001: 537 changed, 10811 examined... 002: 165 changed, 3036 examined... 003: 64 changed, 925 examined... 004: 37 changed, 335 examined... 005: 24 changed, 197 examined... 006: 10 changed, 135 examined... 007: 4 changed, 63 examined... 008: 6 changed, 27 examined... 009: 3 changed, 36 examined... 010: 0 changed, 17 examined... 172 labels changed using aseg 000: 67 total segments, 34 labels (163 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 54 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 701 vertices marked for relabeling... 701 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 53 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Sun Dec 15 19:11:30 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 ta0313_time2 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/wm.mgz... reading input surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white... reading input pial surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.pial... reading input white surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 1258 853 2820 3.027 0.783 0.145 0.045 21 2.1 caudalanteriorcingulate 2464 1674 5319 2.821 0.664 0.129 0.038 25 4.0 caudalmiddlefrontal 1462 1024 2091 1.819 0.693 0.184 0.078 33 4.5 cuneus 340 230 1309 3.963 0.783 0.130 0.039 3 0.6 entorhinal 3733 2478 7490 2.625 0.732 0.132 0.042 45 6.4 fusiform 7329 5085 14399 2.469 0.581 0.144 0.052 106 15.2 inferiorparietal 4722 3192 11519 2.915 0.827 0.150 0.056 78 10.9 inferiortemporal 1823 1182 3586 2.773 0.824 0.143 0.050 27 3.6 isthmuscingulate 6428 4286 11161 2.378 0.666 0.155 0.056 89 14.1 lateraloccipital 4798 3209 10374 2.836 0.922 0.140 0.058 87 9.6 lateralorbitofrontal 4527 3089 7273 2.157 0.711 0.155 0.058 67 10.7 lingual 2240 1492 4285 2.442 0.860 0.134 0.057 45 4.6 medialorbitofrontal 5439 3725 10165 2.323 0.712 0.149 0.061 104 13.5 middletemporal 1145 714 1896 2.274 0.692 0.096 0.029 7 1.3 parahippocampal 2047 1350 3856 2.594 0.724 0.127 0.042 20 3.6 paracentral 2283 1580 5240 2.830 0.637 0.141 0.056 44 4.5 parsopercularis 1323 893 3301 2.970 0.705 0.120 0.113 31 1.7 parsorbitalis 2836 1954 6021 2.433 0.728 0.146 0.048 43 5.4 parstriangularis 2054 1357 2001 1.676 0.428 0.146 0.053 25 4.5 pericalcarine 5529 3666 7807 1.913 0.555 0.135 0.050 74 10.5 postcentral 1674 1147 3267 2.744 0.694 0.145 0.047 24 3.2 posteriorcingulate 5492 3658 10464 2.596 0.586 0.130 0.043 54 9.8 precentral 6898 4660 12400 2.403 0.745 0.135 0.044 76 12.2 precuneus 1225 808 2705 3.094 0.675 0.149 0.069 20 2.8 rostralanteriorcingulate 5226 3530 10699 2.628 0.656 0.147 0.050 75 10.5 rostralmiddlefrontal 11223 7588 25643 2.935 0.662 0.141 0.054 167 21.8 superiorfrontal 8520 5628 13203 2.227 0.491 0.141 0.045 103 15.5 superiorparietal 5901 4042 12594 2.648 0.808 0.136 0.048 82 11.5 superiortemporal 3969 2749 6957 2.306 0.645 0.155 0.070 86 11.0 supramarginal 394 240 584 2.238 0.555 0.140 0.075 43 0.7 transversetemporal 2908 1973 5904 3.116 0.792 0.129 0.055 35 5.7 insula #-------------------------------------------- #@# Cortical ribbon mask Sun Dec 15 19:11:45 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon ta0313_time2 SUBJECTS_DIR is /mani2/fei_data/Jacobian_maps/SUBJECT_DIR 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 = 110 writing volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Sun Dec 15 19:24:04 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2 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 ta0313_time2 $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 ta0313_time2 sysname Linux hostname mani.med.yale.internal machine x86_64 user hblab UseRobust 0 atlas_icv (eTIV) = 1291098 mm^3 (det: 1.508875 ) Computing euler number orig.nofix lheno = -26, rheno = -30 orig.nofix lhholes = 14, rhholes = 16 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 226077.192 226269.000 diff= -191.8 pctdiff=-0.085 rhCtxGM: 223708.989 223741.000 diff= -32.0 pctdiff=-0.014 lhCtxWM: 222208.480 221985.000 diff= 223.5 pctdiff= 0.101 rhCtxWM: 224716.011 225301.000 diff= -585.0 pctdiff=-0.260 SubCortGMVol 56774.000 SupraTentVol 962349.672 (961053.000) diff=1296.672 pctdiff=0.135 SupraTentVolNotVent 955554.672 (954258.000) diff=1296.672 pctdiff=0.136 BrainSegVol 1099228.000 (1096421.000) diff=2807.000 pctdiff=0.255 BrainSegVolNotVent 1088242.000 (1087441.672) diff=800.328 pctdiff=0.074 BrainSegVolNotVent 1088242.000 CerebellumVol 133769.000 VentChorVol 6795.000 3rd4th5thCSF 4191.000 CSFVol 1384.000, OptChiasmVol 215.000 MaskVol 1460270.000 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 3213 3212.727 4 5 Left-Inf-Lat-Vent 127 127.218 5 7 Left-Cerebellum-White-Matter 13613 13612.682 6 8 Left-Cerebellum-Cortex 55103 55103.102 7 10 Left-Thalamus-Proper 6197 6197.207 8 11 Left-Caudate 3301 3300.542 9 12 Left-Putamen 5618 5618.161 10 13 Left-Pallidum 1781 1781.074 11 14 3rd-Ventricle 1194 1193.951 12 15 4th-Ventricle 1821 1821.114 13 16 Brain-Stem 19799 19799.266 14 17 Left-Hippocampus 4274 4273.943 15 18 Left-Amygdala 1753 1752.610 16 24 CSF 1299 1298.831 17 26 Left-Accumbens-area 764 764.247 18 28 Left-VentralDC 3664 3663.675 19 30 Left-vessel 113 112.981 20 31 Left-choroid-plexus 420 419.513 23 43 Right-Lateral-Ventricle 2882 2881.739 24 44 Right-Inf-Lat-Vent 17 16.742 25 46 Right-Cerebellum-White-Matter 13521 13521.308 26 47 Right-Cerebellum-Cortex 53934 53934.129 27 49 Right-Thalamus-Proper 6409 6408.741 28 50 Right-Caudate 3402 3402.353 29 51 Right-Putamen 5469 5468.763 30 52 Right-Pallidum 1655 1655.391 31 53 Right-Hippocampus 4084 4084.341 32 54 Right-Amygdala 1804 1803.948 33 58 Right-Accumbens-area 792 791.930 34 60 Right-VentralDC 3810 3809.923 35 62 Right-vessel 85 85.373 36 63 Right-choroid-plexus 490 490.204 37 72 5th-Ventricle 6 5.802 38 77 WM-hypointensities 802 801.615 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 0 0.000 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 217 216.984 45 251 CC_Posterior 1114 1113.908 46 252 CC_Mid_Posterior 562 562.225 47 253 CC_Central 638 638.492 48 254 CC_Mid_Anterior 526 526.172 49 255 CC_Anterior 855 855.374 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Sun Dec 15 19:25:17 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2 mri_aparc2aseg --s ta0313_time2 --volmask SUBJECTS_DIR /mani2/fei_data/Jacobian_maps/SUBJECT_DIR subject ta0313_time2 outvol /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading lh pial surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.pial Loading lh annotations from /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading rh pial surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.pial Loading rh annotations from /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 = 448490 Used brute-force search on 0 voxels Writing output aseg to /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/aparc+aseg.mgz /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2 mri_aparc2aseg --s ta0313_time2 --volmask --a2009s SUBJECTS_DIR /mani2/fei_data/Jacobian_maps/SUBJECT_DIR subject ta0313_time2 outvol /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading lh pial surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.pial Loading lh annotations from /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading rh pial surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.pial Loading rh annotations from /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 = 448490 Used brute-force search on 0 voxels Writing output aseg to /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Sun Dec 15 19:28:28 EST 2013 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2 mri_aparc2aseg --s ta0313_time2 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /mani2/fei_data/Jacobian_maps/SUBJECT_DIR subject ta0313_time2 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/aparc+aseg.mgz Reading lh white surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading lh pial surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.pial Loading lh annotations from /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading rh pial surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.pial Loading rh annotations from /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/ribbon.mgz Loading filled from /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/filled.mgz Ripping vertices labeled as unkown Ripped 8059 vertices from left hemi Ripped 7719 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/aseg.mgz Loading Ctx Seg File /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 = 893454 Used brute-force search on 16 voxels Fixing Parahip LH WM Found 10 clusters 0 k 1.000000 1 k 5.000000 2 k 2.000000 3 k 1625.000000 4 k 1.000000 5 k 3.000000 6 k 3.000000 7 k 1.000000 8 k 2.000000 9 k 3.000000 Fixing Parahip RH WM Found 5 clusters 0 k 1.000000 1 k 3.000000 2 k 9.000000 3 k 2.000000 4 k 1712.000000 Writing output aseg to mri/wmparc.mgz /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2 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 ta0313_time2 --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 ta0313_time2 --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname mani.med.yale.internal machine x86_64 user hblab UseRobust 0 atlas_icv (eTIV) = 1291098 mm^3 (det: 1.508875 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 226077.192 226269.000 diff= -191.8 pctdiff=-0.085 rhCtxGM: 223708.989 223741.000 diff= -32.0 pctdiff=-0.014 lhCtxWM: 222208.480 221985.000 diff= 223.5 pctdiff= 0.101 rhCtxWM: 224716.011 225301.000 diff= -585.0 pctdiff=-0.260 SubCortGMVol 56774.000 SupraTentVol 962349.672 (961053.000) diff=1296.672 pctdiff=0.135 SupraTentVolNotVent 955554.672 (954258.000) diff=1296.672 pctdiff=0.136 BrainSegVol 1099228.000 (1096421.000) diff=2807.000 pctdiff=0.255 BrainSegVolNotVent 1088242.000 (1087441.672) diff=800.328 pctdiff=0.074 BrainSegVolNotVent 1088242.000 CerebellumVol 133769.000 VentChorVol 6795.000 3rd4th5thCSF 4191.000 CSFVol 1384.000, OptChiasmVol 215.000 MaskVol 1460270.000 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 1955 1954.696 2 3002 wm-lh-caudalanteriorcingulate 2483 2482.510 3 3003 wm-lh-caudalmiddlefrontal 6231 6231.364 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 3027 3027.115 6 3006 wm-lh-entorhinal 725 724.922 7 3007 wm-lh-fusiform 6059 6058.892 8 3008 wm-lh-inferiorparietal 9343 9342.980 9 3009 wm-lh-inferiortemporal 6153 6153.485 10 3010 wm-lh-isthmuscingulate 3226 3226.270 11 3011 wm-lh-lateraloccipital 12300 12299.990 12 3012 wm-lh-lateralorbitofrontal 6713 6712.691 13 3013 wm-lh-lingual 5946 5945.806 14 3014 wm-lh-medialorbitofrontal 3716 3716.350 15 3015 wm-lh-middletemporal 6228 6228.254 16 3016 wm-lh-parahippocampal 1676 1675.796 17 3017 wm-lh-paracentral 3142 3142.117 18 3018 wm-lh-parsopercularis 3840 3839.939 19 3019 wm-lh-parsorbitalis 872 871.789 20 3020 wm-lh-parstriangularis 3585 3584.770 21 3021 wm-lh-pericalcarine 4276 4276.305 22 3022 wm-lh-postcentral 6568 6568.461 23 3023 wm-lh-posteriorcingulate 3527 3526.624 24 3024 wm-lh-precentral 12922 12922.423 25 3025 wm-lh-precuneus 7941 7940.570 26 3026 wm-lh-rostralanteriorcingulate 2289 2289.417 27 3027 wm-lh-rostralmiddlefrontal 10067 10066.929 28 3028 wm-lh-superiorfrontal 18120 18119.896 29 3029 wm-lh-superiorparietal 13245 13245.069 30 3030 wm-lh-superiortemporal 6501 6501.203 31 3031 wm-lh-supramarginal 7143 7142.814 32 3032 wm-lh-frontalpole 220 220.498 33 3033 wm-lh-temporalpole 855 854.516 34 3034 wm-lh-transversetemporal 1059 1059.245 35 3035 wm-lh-insula 7782 7782.317 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 2621 2620.852 120 4002 wm-rh-caudalanteriorcingulate 3442 3441.556 121 4003 wm-rh-caudalmiddlefrontal 4489 4489.135 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 1155 1155.363 124 4006 wm-rh-entorhinal 440 440.228 125 4007 wm-rh-fusiform 6478 6477.743 126 4008 wm-rh-inferiorparietal 12159 12159.279 127 4009 wm-rh-inferiortemporal 5841 5840.658 128 4010 wm-rh-isthmuscingulate 3710 3710.170 129 4011 wm-rh-lateraloccipital 8583 8582.593 130 4012 wm-rh-lateralorbitofrontal 7561 7560.973 131 4013 wm-rh-lingual 6382 6382.442 132 4014 wm-rh-medialorbitofrontal 3304 3303.678 133 4015 wm-rh-middletemporal 5460 5459.676 134 4016 wm-rh-parahippocampal 1769 1769.247 135 4017 wm-rh-paracentral 4177 4177.127 136 4018 wm-rh-parsopercularis 3188 3187.686 137 4019 wm-rh-parsorbitalis 1399 1399.233 138 4020 wm-rh-parstriangularis 4356 4355.584 139 4021 wm-rh-pericalcarine 3650 3649.968 140 4022 wm-rh-postcentral 6494 6493.893 141 4023 wm-rh-posteriorcingulate 4139 4139.472 142 4024 wm-rh-precentral 11493 11493.195 143 4025 wm-rh-precuneus 10768 10768.241 144 4026 wm-rh-rostralanteriorcingulate 2162 2161.969 145 4027 wm-rh-rostralmiddlefrontal 12414 12413.871 146 4028 wm-rh-superiorfrontal 16270 16270.064 147 4029 wm-rh-superiorparietal 14802 14801.571 148 4030 wm-rh-superiortemporal 5945 5945.182 149 4031 wm-rh-supramarginal 6819 6818.672 150 4032 wm-rh-frontalpole 226 225.530 151 4033 wm-rh-temporalpole 694 693.895 152 4034 wm-rh-transversetemporal 464 464.022 153 4035 wm-rh-insula 7828 7827.817 154 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 29627 29627.232 237 5002 Right-UnsegmentedWhiteMatter 31184 31184.115 238 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/label #-------------------------------------------- #@# BA Labels lh Sun Dec 15 19:35:25 EST 2013 mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA1.label --trgsubject ta0313_time2 --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 192 Checking for and removing duplicates Writing label file ./lh.BA1.label 4321 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA2.label --trgsubject ta0313_time2 --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 344 Checking for and removing duplicates Writing label file ./lh.BA2.label 8253 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA3a.label --trgsubject ta0313_time2 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 113 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4190 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA3b.label --trgsubject ta0313_time2 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 217 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6200 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA4a.label --trgsubject ta0313_time2 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 305 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6089 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA4p.label --trgsubject ta0313_time2 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 135 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4205 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA6.label --trgsubject ta0313_time2 --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 1169 Checking for and removing duplicates Writing label file ./lh.BA6.label 14758 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA44.label --trgsubject ta0313_time2 --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 477 Checking for and removing duplicates Writing label file ./lh.BA44.label 4658 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA45.label --trgsubject ta0313_time2 --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 1126 Checking for and removing duplicates Writing label file ./lh.BA45.label 4548 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.V1.label --trgsubject ta0313_time2 --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 1789 Checking for and removing duplicates Writing label file ./lh.V1.label 6430 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.V2.label --trgsubject ta0313_time2 --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 3671 Checking for and removing duplicates Writing label file ./lh.V2.label 11785 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.MT.label --trgsubject ta0313_time2 --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 553 Checking for and removing duplicates Writing label file ./lh.MT.label 2571 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.perirhinal.label --trgsubject ta0313_time2 --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.perirhinal.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 147 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1346 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA1.thresh.label --trgsubject ta0313_time2 --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA1.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1061 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA2.thresh.label --trgsubject ta0313_time2 --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA2.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 81 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2173 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA3a.thresh.label --trgsubject ta0313_time2 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA3a.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 45 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1549 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA3b.thresh.label --trgsubject ta0313_time2 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 81 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2077 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA4a.thresh.label --trgsubject ta0313_time2 --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA4a.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 110 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2429 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA4p.thresh.label --trgsubject ta0313_time2 --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA4p.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1580 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA6.thresh.label --trgsubject ta0313_time2 --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA6.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 550 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 7585 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA44.thresh.label --trgsubject ta0313_time2 --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA44.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 228 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2140 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA45.thresh.label --trgsubject ta0313_time2 --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.BA45.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 515 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1666 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.V1.thresh.label --trgsubject ta0313_time2 --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.V1.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 1240 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 4645 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.V2.thresh.label --trgsubject ta0313_time2 --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.V2.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 1644 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 4978 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.MT.thresh.label --trgsubject ta0313_time2 --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/lh.MT.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 128478 Number of reverse mapping hits = 120 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 633 mri_label2label: Done mris_label2annot --s ta0313_time2 --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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/label cmdline mris_label2annot --s ta0313_time2 --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 mani.med.yale.internal machine x86_64 user hblab subject ta0313_time2 hemi lh SUBJECTS_DIR /mani2/fei_data/Jacobian_maps/SUBJECT_DIR ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 86877 unhit vertices Writing annot to /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/label/lh.BA.annot mris_label2annot --s ta0313_time2 --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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/label cmdline mris_label2annot --s ta0313_time2 --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 mani.med.yale.internal machine x86_64 user hblab subject ta0313_time2 hemi lh SUBJECTS_DIR /mani2/fei_data/Jacobian_maps/SUBJECT_DIR ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 104528 unhit vertices Writing annot to /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab ta0313_time2 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/wm.mgz... reading input surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white... reading input pial surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.pial... reading input white surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 922 568 1440 1.955 0.432 0.156 0.069 18 2.6 BA1 3492 2285 4751 2.074 0.523 0.130 0.045 40 6.0 BA2 959 614 805 1.803 0.435 0.146 0.048 10 1.8 BA3a 1993 1377 2797 1.738 0.674 0.131 0.044 25 3.5 BA3b 1453 931 2510 2.362 0.537 0.128 0.040 15 2.6 BA4a 1127 802 1529 2.072 0.530 0.125 0.036 9 1.8 BA4p 9162 6064 20089 2.908 0.644 0.131 0.061 202 22.0 BA6 2498 1740 5536 2.698 0.525 0.126 0.037 27 3.8 BA44 3623 2536 7785 2.542 0.643 0.139 0.050 52 6.1 BA45 3954 2798 5033 1.741 0.621 0.151 0.058 58 9.2 V1 9166 6090 13927 2.117 0.650 0.164 0.062 147 22.2 V2 2234 1519 4233 2.640 0.473 0.144 0.044 30 3.9 MT 1018 681 2872 3.187 0.753 0.133 0.051 13 2.2 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab ta0313_time2 lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/wm.mgz... reading input surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white... reading input pial surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.pial... reading input white surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 620 363 876 1.856 0.402 0.172 0.083 13 2.2 BA1 1304 841 1814 2.106 0.539 0.122 0.043 14 2.0 BA2 822 530 681 1.817 0.424 0.152 0.049 9 1.7 BA3a 1307 916 1467 1.453 0.311 0.106 0.026 8 1.3 BA3b 1405 922 2342 2.285 0.546 0.125 0.038 13 2.4 BA4a 940 671 1301 2.093 0.511 0.116 0.035 6 1.3 BA4p 5039 3274 10816 2.863 0.650 0.133 0.053 85 12.3 BA6 1636 1131 3805 2.771 0.483 0.134 0.042 20 2.8 BA44 1567 1094 3440 2.519 0.608 0.152 0.053 26 3.3 BA45 4177 2965 5507 1.764 0.645 0.152 0.057 62 9.9 V1 4555 3026 6209 1.940 0.564 0.168 0.066 77 11.3 V2 578 389 898 2.486 0.388 0.107 0.026 4 0.6 MT #-------------------------------------------- #@# BA Labels rh Sun Dec 15 19:39:18 EST 2013 mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA1.label --trgsubject ta0313_time2 --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 261 Checking for and removing duplicates Writing label file ./rh.BA1.label 4223 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA2.label --trgsubject ta0313_time2 --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 259 Checking for and removing duplicates Writing label file ./rh.BA2.label 6946 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA3a.label --trgsubject ta0313_time2 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 71 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4051 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA3b.label --trgsubject ta0313_time2 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 206 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4728 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA4a.label --trgsubject ta0313_time2 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 205 Checking for and removing duplicates Writing label file ./rh.BA4a.label 5952 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA4p.label --trgsubject ta0313_time2 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 79 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4552 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA6.label --trgsubject ta0313_time2 --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 515 Checking for and removing duplicates Writing label file ./rh.BA6.label 12771 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA44.label --trgsubject ta0313_time2 --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 944 Checking for and removing duplicates Writing label file ./rh.BA44.label 7856 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA45.label --trgsubject ta0313_time2 --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 1439 Checking for and removing duplicates Writing label file ./rh.BA45.label 6794 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.V1.label --trgsubject ta0313_time2 --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 1250 Checking for and removing duplicates Writing label file ./rh.V1.label 5977 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.V2.label --trgsubject ta0313_time2 --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 1935 Checking for and removing duplicates Writing label file ./rh.V2.label 9951 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.MT.label --trgsubject ta0313_time2 --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.perirhinal.label --trgsubject ta0313_time2 --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.perirhinal.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 40 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 792 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA1.thresh.label --trgsubject ta0313_time2 --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA1.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 87 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 963 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA2.thresh.label --trgsubject ta0313_time2 --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA2.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 104 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 2792 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA3a.thresh.label --trgsubject ta0313_time2 --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA3a.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 18 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1716 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA3b.thresh.label --trgsubject ta0313_time2 --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA3b.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 95 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2278 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA4a.thresh.label --trgsubject ta0313_time2 --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA4a.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1458 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA4p.thresh.label --trgsubject ta0313_time2 --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA4p.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 25 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1514 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA6.thresh.label --trgsubject ta0313_time2 --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA6.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 267 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 7226 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA44.thresh.label --trgsubject ta0313_time2 --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA44.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 97 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1109 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA45.thresh.label --trgsubject ta0313_time2 --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.BA45.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 445 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1623 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.V1.thresh.label --trgsubject ta0313_time2 --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.V1.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 884 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 4116 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.V2.thresh.label --trgsubject ta0313_time2 --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.V2.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 991 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 4428 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.MT.thresh.label --trgsubject ta0313_time2 --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface srclabel = /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/label/rh.MT.thresh.label srcsubject = fsaverage trgsubject = ta0313_time2 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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white Reading target registration /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 124929 Number of reverse mapping hits = 13 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 281 mri_label2label: Done mris_label2annot --s ta0313_time2 --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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/label cmdline mris_label2annot --s ta0313_time2 --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 mani.med.yale.internal machine x86_64 user hblab subject ta0313_time2 hemi rh SUBJECTS_DIR /mani2/fei_data/Jacobian_maps/SUBJECT_DIR ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 88971 unhit vertices Writing annot to /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/label/rh.BA.annot mris_label2annot --s ta0313_time2 --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 /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/label cmdline mris_label2annot --s ta0313_time2 --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 mani.med.yale.internal machine x86_64 user hblab subject ta0313_time2 hemi rh SUBJECTS_DIR /mani2/fei_data/Jacobian_maps/SUBJECT_DIR ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 104954 unhit vertices Writing annot to /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab ta0313_time2 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/wm.mgz... reading input surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white... reading input pial surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.pial... reading input white surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 821 523 1510 2.231 0.463 0.165 0.075 15 2.0 BA1 2658 1780 3536 1.941 0.461 0.125 0.043 29 4.4 BA2 875 549 761 1.881 0.451 0.139 0.042 9 1.4 BA3a 1738 1168 2271 1.658 0.492 0.131 0.052 23 3.3 BA3b 1270 812 2645 2.789 0.622 0.121 0.046 11 2.3 BA4a 917 628 1260 2.080 0.433 0.115 0.034 6 1.4 BA4p 6518 4358 14969 2.956 0.585 0.136 0.051 74 12.8 BA6 3064 2138 6934 2.764 0.576 0.135 0.048 48 5.6 BA44 5112 3495 10898 2.545 0.735 0.143 0.066 91 9.0 BA45 3756 2544 4499 1.736 0.552 0.151 0.060 56 9.3 V1 6936 4669 11065 2.197 0.681 0.163 0.062 107 17.3 V2 1733 1184 2947 2.494 0.465 0.146 0.048 22 3.0 MT 560 372 2024 3.501 0.963 0.120 0.041 5 0.9 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab ta0313_time2 rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/wm.mgz... reading input surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white... reading input pial surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.pial... reading input white surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 626 397 1182 2.225 0.501 0.165 0.063 11 1.6 BA1 1605 1040 2010 1.901 0.475 0.104 0.029 11 2.0 BA2 738 462 615 1.943 0.390 0.152 0.045 8 1.3 BA3a 1374 929 1542 1.519 0.370 0.110 0.035 13 1.7 BA3b 812 497 1781 2.999 0.589 0.127 0.053 8 1.6 BA4a 765 538 1050 2.089 0.447 0.116 0.032 5 1.1 BA4p 4146 2771 9272 2.860 0.572 0.139 0.058 48 8.8 BA6 842 594 2273 2.966 0.657 0.144 0.068 20 1.8 BA44 1503 1052 3610 2.649 0.806 0.162 0.056 27 3.3 BA45 3551 2402 4085 1.705 0.521 0.148 0.059 52 8.5 V1 3819 2592 6036 2.167 0.701 0.173 0.070 65 10.9 V2 194 143 348 2.295 0.473 0.124 0.024 1 0.2 MT /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Sun Dec 15 19:43:06 EST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o ta0313_time2 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject ta0313_time2. processing subject lh.EC_average... reading output surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 1022 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label ta0313_time2 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/wm.mgz... reading input surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.white... reading input pial surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/lh.pial... reading input white surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 353 211 1222 3.426 0.774 0.131 0.062 8 0.9 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Sun Dec 15 19:43:20 EST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o ta0313_time2 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject ta0313_time2. processing subject rh.EC_average... reading output surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 703 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label ta0313_time2 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/mri/wm.mgz... reading input surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.white... reading input pial surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/surf/rh.pial... reading input white surface /mani2/fei_data/Jacobian_maps/SUBJECT_DIR/ta0313_time2/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 207 126 796 3.685 0.807 0.109 0.043 2 0.4 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Fri Dec 13 16:03:10 EST 2013 Ended at Sun Dec 15 19:43:35 EST 2013 #@#%# recon-all-run-time-hours 51.674 recon-all -s ta0313_time2 finished without error at Sun Dec 15 19:43:35 EST 2013